.. _physics-nodePropertyExtractor:

Node Property Extractor
=======================

Class providing extraction of scalar, 1D, or multi-D properties from merger tree nodes for output. Property extractors are used by output analysis classes to retrieve galaxy and halo properties (e.g. stellar mass, dark matter halo mass, star formation rate, positions, velocities) and convert them to formats suitable for comparison with observational data or for writing to the Galacticus output file.

**Default implementation:** ``nodePropertyExtractorNodeIndices``

Methods
-------

``type`` → ``type(enumerationOutputAnalysisPropertyTypeType)``
   Return the type of the extracted property.

``quantity`` → ``type(enumerationOutputAnalysisPropertyQuantityType)``
   Return the class of the extracted property.

``addInstances`` → ``void``
   Add multiple instances of this property to a ``multiCounter`` object.

   * ``type(treeNode ), intent(inout) :: node``

   * ``type(multiCounter), intent(inout) :: instance``

.. _physics-nodePropertyExtractorAdiabaticRatioOrbitalDisk:

``nodePropertyExtractorAdiabaticRatioOrbitalDisk``
--------------------------------------------------

A property extractor class for the orbital adiabatic ratio of disks. The orbital adiabatic ratio, :math:`\mathcal{R}`, is defined as:

.. math::

   \mathcal{R} = \frac{r_\mathrm{p} / v_\mathrm{p}}{2 \pi R_\mathrm{d} / v_\mathrm{d}},

where :math:`r_\mathrm{p}` and :math:`v_\mathrm{p}` are the orbital radius and velocity at pericenter respectively, and :math:`R_\mathrm{d}` and :math:`v_\mathrm{d}` are the characteristic radius of the disk and the rotation curve at that radius respectively.

.. _physics-nodePropertyExtractorAgesStellarMassWeighted:

``nodePropertyExtractorAgesStellarMassWeighted``
------------------------------------------------

A node property extractor which extracts stellar mass-weighted ages for disk and spheroid components. Requires the :galacticus-class:`nodeOperatorAgesStellarMassWeighted` node operator to be used to accumulate the relevant integrals for each disk and spheroid.

Specifically, the quantities computed by this class are

.. math::

   \langle t \rangle & = \left. \int_0^t \mathrm{d}t^\prime (t-t^\prime) \dot{\psi}(t^\prime) \right. \int_0^t \mathrm{d}t^\prime \dot{\psi}(t^\prime) \nonumber \\
   & = t - \left. \int_0^t \mathrm{d}t^\prime t^\prime \dot{\psi}(t^\prime) \right. \int_0^t \mathrm{d}t^\prime \dot{\psi}(t^\prime),

where :math:`\dot{\psi}(t^\prime)` is the star formation rate at time :math:`t^\prime` and :math:`t` is the present time..

.. _physics-nodePropertyExtractorAppendSuffix:

``nodePropertyExtractorAppendSuffix``
-------------------------------------

A wrapper property extractor that delegates extraction to one or more child :galacticus-class:`nodePropertyExtractorClass` objects and appends a user-specified ``suffix`` string to all output dataset names. This is useful for disambiguating otherwise identically named properties when, for example, the same extractor is used with different parameter settings, different galaxy components, or at different epochs, and the outputs need to coexist in the same output file.

**Parameters**

* ``[suffix]`` — The suffix to append to parameter names.

.. _physics-nodePropertyExtractorArray:

``nodePropertyExtractorArray``
------------------------------

Abstract base class for extractors that return a fixed-length 2D array of floating-point values per node, defining the interface (including column descriptions, element counts, names, and units) for multi-valued scalar array outputs used in output analysis.

**Methods**

* ``columnDescriptions`` — Return a description of the columns.
* ``size`` — Return the number of elements in the array.
* ``elementCount`` — Return the number of properties in the array.
* ``extract`` — Extract the properties from the given ``node``.
* ``names`` — Return the name of the properties extracted.
* ``descriptions`` — Return a description of the properties extracted.
* ``unitsInSI`` — Return the units of the properties extracted in the SI system.
* ``units`` — Return an object containing units metadata for the properties.
* ``metaData`` — Populate a hash with meta-data for the property.

.. _physics-nodePropertyExtractorBlackHoleFormationChannel:

``nodePropertyExtractorBlackHoleFormationChannel``
--------------------------------------------------

Extracts the formation channel identifier for black hole seeds in each node, enabling classification of black holes by their seeding mechanism (e.g., direct collapse, stellar remnants) for statistical analysis.

.. _physics-nodePropertyExtractorBlackHoleSeedingVergara2023:

``nodePropertyExtractorBlackHoleSeedingVergara2023``
----------------------------------------------------

A property extractor class for the properties of the nuclear star cluster at the moment of the black hole formation.

.. _physics-nodePropertyExtractorBranchMostMassive:

``nodePropertyExtractorBranchMostMassive``
------------------------------------------

A node property extractor class which indicates if a node is on the most massive branch of its tree. The status will be extracted as ``nodeIsOnMostMassiveBranch``, with a value of 1 indicating that the node is on the most massive branch and a value of 0 indicating that it is not.

.. _physics-nodePropertyExtractorCGMCoolingFunction:

``nodePropertyExtractorCGMCoolingFunction``
-------------------------------------------

A property extractor that returns the radiative cooling function :math:`\Lambda(T,n_\mathrm{H},Z)` (in erg cm\ :math:`^3` s\ :math:`^{-1}`) of the circumgalactic medium at a user-specified set of radii in the hot halo, evaluated using the supplied :galacticus-class:`coolingFunctionClass` object with local density, temperature, and metallicity. The ``radiusSpecifiers`` parameter defines the radii; ``includeRadii`` and ``includeDensity`` optionally add the radius (Mpc) and hydrogen number density (cm\ :math:`^{-3}`) columns to the output. The ``label`` suffix distinguishes multiple instances of this extractor.

**Parameters**

* ``[radiusSpecifiers]`` — A list of radius specifiers at which to output the CGM cooling function.
* ``[includeRadii]`` (default ``.false.``) — Specifies whether or not the radii at which density data are output should also be included in the output.
* ``[includeDensity]`` (default ``.false.``) — Specifies whether or not the total hydrogen densities (:math:`n_\mathrm{H}`) at each radius should be included in the output.
* ``[label]`` (default ``var_str('')``) — A label to distinguish this cooling function from others.

.. _physics-nodePropertyExtractorConcentration:

``nodePropertyExtractorConcentration``
--------------------------------------

A property extractor that returns the concentration parameter :math:`c = r_\mathrm{vir}/r_\mathrm{s}` of the dark-matter-only halo profile, where :math:`r_\mathrm{vir}` is defined by the supplied :galacticus-class:`virialDensityContrastClass` object and :math:`r_\mathrm{s}` is the NFW scale radius from the :galacticus-class:`darkMatterProfileDMOClass` object. If ``useLastIsolatedTime`` is ``true``, the virial radius is evaluated using the density contrast at the halo's last isolated time rather than the current time, matching the conventional definition of concentration used in fitting functions.

**Parameters**

* ``[correctForConcentrationDefinition]`` (default ``.false.``) — If true, then when computing dark matter profile scale radii using concentrations, any difference between the current definition of halo scales (i.e. typically virial density contrast definitions) and density profiles and those assumed in measuring the concentrations will be taken into account. If false, the concentration is applied blindly.
* ``[useMeanConcentration]`` (default ``.false.``) — If true, then when computing dark matter profile scale radii using concentrations do not account for any possible scatter in the concentration-mass relation.
* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the concentration using a the virial density definition at the last isolated time of the halo.

.. _physics-nodePropertyExtractorConstrainedStatus:

``nodePropertyExtractorConstrainedStatus``
------------------------------------------

A node property extractor class which extracts the constrained excursion set solution status of each node. The status will be extracted as ``nodeIsConstrained``, with a value of 1 indicating that the node follows the constrained branching rate solution and a value of 0 indicating that it does not.

.. _physics-nodePropertyExtractorCoolingEnergyRadiated:

``nodePropertyExtractorCoolingEnergyRadiated``
----------------------------------------------

Extracts the total energy radiated by the hot halo gas through radiative cooling processes, tracking the cumulative energy loss from the :galacticus-class:`nodeComponentHotHalo` component. This quantity drives the supply of cold gas onto the galactic disk and ultimately powers star formation.

.. _physics-nodePropertyExtractorDarkMatterProfileRadiusInteractionSIDM:

``nodePropertyExtractorDarkMatterProfileRadiusInteractionSIDM``
---------------------------------------------------------------

Extracts the self-interaction radius :math:`r_1` from the dark matter halo density profile under self-interacting dark matter (SIDM) models. This scale marks the boundary within which dark matter particles experience significant scattering, driving core formation and suppressing central density cusps.

.. _physics-nodePropertyExtractorDarkMatterProfileScaleRadius:

``nodePropertyExtractorDarkMatterProfileScaleRadius``
-----------------------------------------------------

Extracts the scale radius of the dark matter halo density profile (e.g., the NFW scale radius :math:`r_\mathrm{s}` where the logarithmic slope equals :math:`-2`), a key structural parameter relating halo mass to its spatial extent and concentration.

.. _physics-nodePropertyExtractorDarkMatterProfileShapeParameter:

``nodePropertyExtractorDarkMatterProfileShapeParameter``
--------------------------------------------------------

Extracts the shape parameter of the dark matter halo density profile (e.g., the Einasto index or inner logarithmic slope), which characterizes the curvature of the profile and distinguishes between different dark matter density models such as NFW, Einasto, or cored profiles.

.. _physics-nodePropertyExtractorDensityContrasts:

``nodePropertyExtractorDensityContrasts``
-----------------------------------------

A property extractor class for the mass and radii of spheres of specified density contrast. A list of density contrasts, :math:`\Delta` (defined in units of the mean density of the Universe), is specified via the ``[densityContrasts]`` parameter. For each specified density contrast, two properties are output for each node: ``nodeRadius``\ :math:`\Delta` and ``nodeMass``\ :math:`\Delta` which give the radius enclosing a mean density contrast of :math:`\Delta` and the mass enclosed within that radius. The parameter ``[darkMatterOnly]`` controls whether density contrasts are measured for total mass (``false``) or dark matter mass only (``true``). In the latter case, density contrasts are defined relative to the mean dark matter density of the Universe.

**Parameters**

* ``[densityContrasts]`` — A list of density contrasts at which to output data.
* ``[densityContrastRelativeTo]`` (default ``var_str('mean')``) — The density (``mean`` or ``critical``) used in defining the density contrast.
* ``[darkMatterOnly]`` (default ``.false.``) — Specifies whether or not density contrast data should be computed using the dark matter component alone.

.. _physics-nodePropertyExtractorDensityContrastVirial:

``nodePropertyExtractorDensityContrastVirial``
----------------------------------------------

Extracts the virial density contrast :math:`\Delta_\mathrm{vir}`, the ratio of mean halo density to the critical (or mean) density of the universe used to define the halo boundary. Evaluated at the time the halo was last isolated, this quantity varies with cosmology and redshift.

.. _physics-nodePropertyExtractorDensityDMOProfile:

``nodePropertyExtractorDensityDMOProfile``
------------------------------------------

A property extractor class for the dark matter only density at a set of radii.

**Parameters**

* ``[radiusSpecifiers]`` — A list of radius specifiers at which to output the density profile.
* ``[includeRadii]`` (default ``.false.``) — Specifies whether or not the radii at which density data are output should also be included in the output file.

.. _physics-nodePropertyExtractorDensityProfile:

``nodePropertyExtractorDensityProfile``
---------------------------------------

A property extractor that returns the mass density profile (in :math:`\mathrm{M}_\odot \, \mathrm{Mpc}^{-3}`) of a galaxy or halo component at a user-specified set of radii. The ``radiusSpecifiers`` parameter provides a list of radius definitions (e.g.\ multiples of the virial radius, disk radius, or half-mass radius), supporting both galactic structural radii and fixed physical radii. If ``includeRadii`` is ``true``, the corresponding radii (in Mpc) are also written to the output file as a second column alongside the density values.

**Parameters**

* ``[radiusSpecifiers]`` — A list of radius specifiers at which to output the density profile.
* ``[includeRadii]`` (default ``.false.``) — Specifies whether or not the radii at which density data are output should also be included in the output file.

.. _physics-nodePropertyExtractorDescendantNode:

``nodePropertyExtractorDescendantNode``
---------------------------------------

A property extractor that traverses the merger tree forward in time from the current node and applies a scalar :galacticus-class:`nodePropertyExtractorClass` to the descendant node found at redshift ``redshiftDescendant``. The descendant is located by walking the main progenitor line until the node whose time matches the target time (converted from ``redshiftDescendant`` via :galacticus-class:`cosmologyFunctionsClass`). This enables comparison of a galaxy's properties at its observed epoch with those of its descendant at a later redshift within a single output dataset.

**Parameters**

* ``[redshiftDescendant]`` — The redshift of the descendant node to which to apply the filter.
* ``[redshiftDescendant]`` — The redshift of the descendant node to which to apply the filter.
* ``[allowSelf]`` — If true, the node itself is considered as a possible descendant, otherwise the node itself is excluded from the descendant node search.

.. _physics-nodePropertyExtractorDescendants:

``nodePropertyExtractorDescendants``
------------------------------------

A node property extractor which extracts the index of the node containing the galaxy to which each current galaxy will belong at the next output time (i.e. the :term:`forward descendant`). To clarify, this will be the index of the node into which the galaxy descends, or the index of a node with which it merges prior to the next output time (and if that node merges with another, the index will be of that node and so on).

Note that, to operate correctly, information about which node a given node may merge with (and when this merger will happen) must be available. This is typically available in merger trees read from file (i.e. using the "``read``" :galacticus-class:`mergerTreeConstructorClass`) providing ``[presetMergerNodes]`` and ``[presetMergerTimes]`` are both set to ``true``. When using randomly assigned satellite orbits and merger times, information on when merging occurs does not exist until a node becomes a satellite. Thus, if the node becomes a satellite after the current output, but before the next output, there is no way to know which node it will belong to at the next output (in such cases, the fallback assumption is no merging).

.. _physics-nodePropertyExtractorExcursion:

``nodePropertyExtractorExcursion``
----------------------------------

Extracts the infimum of the excursion (the minimum value of the random walk trajectory above threshold) corresponding to the mass accretion history for each node in the excursion set formalism.

.. _physics-nodePropertyExtractorFinalDescendant:

``nodePropertyExtractorFinalDescendant``
----------------------------------------

Extracts the index of the final descendant node at the base of the merger tree for each node, enabling identification of the present-day halo into which a given progenitor will ultimately merge. Facilitates comparisons between progenitor states and their final descendants.

.. _physics-nodePropertyExtractorFluxFromLuminosity:

``nodePropertyExtractorFluxFromLuminosity``
-------------------------------------------

Converts intrinsic luminosities to observed fluxes by dividing by :math:`4\pi d_\mathrm{L}^2`, where :math:`d_\mathrm{L}` is the luminosity distance at the output redshift. Enables direct comparison of model predictions to flux-limited observational surveys at :math:`z>0`.

.. _physics-nodePropertyExtractorFractionAccretionHotMode:

``nodePropertyExtractorFractionAccretionHotMode``
-------------------------------------------------

Extracts the fraction of total gas accretion onto a halo that arrives via the hot-mode channel, where infalling gas is shock-heated to the virial temperature rather than streaming in cold. Traces the transition between accretion regimes as a function of halo mass and redshift.

.. _physics-nodePropertyExtractorGalaxyGasMajorMergerTime:

``nodePropertyExtractorGalaxyGasMajorMergerTime``
-------------------------------------------------

Extracts the cosmic times of gas-mass-based major merger events for each galaxy, where merger significance is determined by the gas mass ratio of the merging pair rather than total or stellar mass.

**Parameters**

* ``[countTimesMaximum]`` (default ``huge(0_c_size_t)``) — The maximum number of major merger times to accumulate for each node. Defaults to the maximum possible.
* ``[ratioGasMajorMerger]`` (default ``0.25d0``) — The gas mass ratio threshold defining a major merger.

.. _physics-nodePropertyExtractorGalaxyMajorMergerTime:

``nodePropertyExtractorGalaxyMajorMergerTime``
----------------------------------------------

Extracts the cosmic time of the most recent major merger event for each galaxy, where major mergers are identified by a configurable mass ratio threshold applied to merging halos.

**Parameters**

* ``[countTimesMaximum]`` (default ``huge(0_c_size_t)``) — The maximum number of major merger times to accumulate for each node. Defaults to the maximum possible.

.. _physics-nodePropertyExtractorGalaxyMergers:

``nodePropertyExtractorGalaxyMergers``
--------------------------------------

Extracts combined physical and index properties for galaxy merger events by composing the :galacticus-class:`nodePropertyExtractorGalaxyMergersPhysical` and :galacticus-class:`nodePropertyExtractorGalaxyMergersIndices` extractors, packaging scalar and integer merger information (e.g., mass ratios, progenitor IDs, merger times) into a single output for post-processing analysis.

**Methods**

* ``tabulate`` — Tabulate the virial density contrast as a function of mass and time.
* ``restoreTable`` — Restore a tabulated solution from file.
* ``storeTable`` — Store a tabulated solution to file.

**Parameters**

* ``[velocityCharacteristic]`` (default ``250.0d0``) — The velocity scale at which the :term:`SNe`-driven outflow rate equals the star formation rate in disks.
* ``[exponent]`` (default ``3.5d0``) — The velocity scaling of the :term:`SNe`-driven outflow rate in disks.
* ``[fraction]`` (default ``0.01d0``) — The normalization :math:`f` of the outflow rate relative to the star formation rate at a reference halo velocity of 200 km/s and expansion factor of 1, setting the overall mass-loading amplitude of the halo-scaling feedback model.
* ``[exponentVelocity]`` (default ``-2.0d0``) — The exponent of virial velocity in the outflow rate in disks.
* ``[exponentRedshift]`` (default ``0.0d0``) — The power-law exponent of the cosmological expansion factor :math:`(1+z)` in the halo-scaling outflow rate, allowing the mass-loading factor to evolve with redshift; a value of zero gives no redshift evolution.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[radiusNormalization]`` (default ``3.3d-6``) — The initial value appearing in the radius-mass relation
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the nuclear star cluster is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not nuclear star cluster stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[scaleRelativeMass]`` (default ``1.0d-2``) — The mass scale, relative to the total mass of the node, below which calculations in the delayed very simple hot halo component are allowed to become inaccurate.
* ``[starveSatellites]`` (default ``.false.``) — Specifies whether or not the hot halo should be removed ("starved") when a node becomes a satellite.
* ``[starveSatellitesOutflowed]`` (default ``.false.``) — Specifies whether or not the outflowed hot halo should be removed ("starved") when a node becomes a satellite.
* ``[outflowReturnOnFormation]`` (default ``.false.``) — Specifies whether or not outflowed gas should be returned to the hot reservoir on halo formation events.
* ``[angularMomentumAlwaysGrows]`` (default ``.false.``) — Specifies whether or not negative rates of accretion of angular momentum into the hot halo will be treated as positive for the purposes of computing the hot halo angular momentum.
* ``[fractionBaryonLimitInNodeMerger]`` (default ``.false.``) — Controls whether the hot gas content of nodes should be limited to not exceed the universal baryon fraction at node merger events. If set to ``true``, hot gas (and angular momentum, abundances, and chemicals proportionally) will be removed from the merged halo to the unaccreted gas reservoir to limit the baryonic mass to the universal baryon fraction where possible.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple disk component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[radiusStructureSolver]`` (default ``1.0d0``) — The radius (in units of the standard scale length) to use in solving for the size of the disk.
* ``[structureSolverUseCole2000Method]`` (default ``.false.``) — If true, use the method described in :cite:t:`cole_hierarchical_2000` to correct for difference between thin disk and spherical mass distributions when solving for disk radii.
* ``[diskNegativeAngularMomentumAllowed]`` (default ``.true.``) — Specifies whether or not negative angular momentum is allowed for the disk.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not disk stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumSolverRadius]`` (default ``ratioAngularMomentumSolverRadiusDefault``) — The assumed ratio of the specific angular momentum at the structure solver radius to the mean specific angular momentum of the standard disk component.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple spheroid component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[efficiencyEnergeticOutflow]`` (default ``1.0d-2``) — The proportionality factor relating mass outflow rate from the spheroid to the energy input rate divided by :math:`V_\mathrm{spheroid}^2`.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not spheroid stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumScaleRadius]`` (default ``ratioAngularMomentumScaleRadiusDefault``) — The assumed ratio of the specific angular momentum at the scale radius to the mean specific angular momentum of the standard spheroid component.
* ``[outputMergers]`` (default ``.false.``) — Determines whether or not properties of black hole mergers will be output.
* ``[fileNames]`` — The name of the file(s) from which merger tree data should be read when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[forestSizeMaximum]`` (default ``0_c_size_t``) — The maximum number of nodes allowed in a forest before it will be broken up into trees and processed individually. A value of 0 implies that forests should never be split.
* ``[presetMergerTimes]`` (default ``.true.``) — Specifies whether merging times for subhalos should be preset when reading merger trees from a file.
* ``[presetMergerNodes]`` (default ``.true.``) — Specifies whether the target nodes for mergers should be preset (i.e. determined from descendant nodes). If they are not, merging will be with each satellite's host node.
* ``[presetSubhaloMasses]`` (default ``.true.``) — Specifies whether subhalo mass should be preset when reading merger trees from a file.
* ``[subhaloAngularMomentaMethod]`` (default ``var_str('summation')``) — Specifies how to account for subhalo angular momentum when adding subhalo mass to host halo mass.
* ``[presetSubhaloIndices]`` (default ``.true.``) — Specifies whether subhalo indices should be preset when reading merger trees from a file.
* ``[presetPositions]`` (default ``.true.``) — Specifies whether node positions should be preset when reading merger trees from a file.
* ``[presetScaleRadii]`` (default ``.true.``) — Specifies whether node scale radii should be preset when reading merger trees from a file.
* ``[scaleRadiiFailureIsFatal]`` (default ``.true.``) — Specifies whether failure to set a node scale radii should be regarded as a fatal error. (If not, a fallback method to set scale radius is used in such cases.)
* ``[presetScaleRadiiConcentrationMinimum]`` (default ``3.0d0``) — The lowest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiConcentrationMaximum]`` (default ``60.0d0``) — The largest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiMinimumMass]`` (default ``0.0d0``) — The minimum halo mass for which scale radii should be preset (if ``[presetScaleRadii]``\ :math:`=`\ ``true``).
* ``[presetUnphysicalAngularMomenta]`` (default ``.false.``) — When reading merger trees from file and presetting halo angular momenta, detect unphysical (<=0) angular momenta and preset them using the selected halo spin method.
* ``[presetAngularMomenta]`` (default ``.true.``) — Specifies whether node angular momenta should be preset when reading merger trees from a file.
* ``[presetAngularMomenta3D]`` (default ``.false.``) — Specifies whether node 3-D angular momenta vectors should be preset when reading merger trees from a file.
* ``[presetOrbits]`` (default ``.true.``) — Specifies whether node orbits should be preset when reading merger trees from a file.
* ``[presetOrbitsSetAll]`` (default ``.true.``) — Forces all orbits to be set. If the computed orbit does not cross the virial radius, then select one at random instead.
* ``[presetOrbitsAssertAllSet]`` (default ``.true.``) — Asserts that all virial orbits must be preset. If any can not be set, Galacticus will stop.
* ``[presetOrbitsBoundOnly]`` (default ``.true.``) — Specifies whether only bound node orbits should be set.
* ``[beginAt]`` (default ``-1_kind_int8``) — Specifies the index of the tree to begin at. (Use -1 to always begin with the first tree.)
* ``[outputTimeSnapTolerance]`` (default ``0.0d0``) — The relative tolerance required to "snap" a node time to the closest output time.
* ``[missingHostsAreFatal]`` (default ``.true.``) — Specifies whether nodes with missing host nodes should be considered to be fatal---see the discussion of missing host nodes in the class description above.
* ``[treeIndexToRootNodeIndex]`` (default ``.false.``) — Specifies whether tree indices should always be set to the index of their root node.
* ``[allowBranchJumps]`` (default ``.true.``) — Specifies whether nodes are allowed to jump between branches.
* ``[allowSubhaloPromotions]`` (default ``.true.``) — Specifies whether subhalos are permitted to be promoted to being isolated halos.
* ``[alwaysPromoteMostMassive]`` (default ``.false.``) — If true, the most massive progenitor is always promoted to be the primary progenitor *even if* it is a subhalo. Otherwise, isolated progenitors are given priority over subhalo progenitors, even if they are less massive.
* ``[presetNamedReals]`` — Names of real datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[presetNamedIntegers]`` — Names of integer datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[fatalMismatches]`` (default ``.true.``) — Specifies whether mismatches in cosmological parameter values between Galacticus and "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be considered fatal.
* ``[fatalNonTreeNode]`` (default ``.true.``) — Specifies whether nodes in snapshot files but not in the merger tree file should be considered fatal when importing from the "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013`.
* ``[subvolumeCount]`` (default ``1``) — Specifies the number of subvolumes *along each axis* into which a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be split for processing through Galacticus.
* ``[subvolumeBuffer]`` (default ``0.0d0``) — Specifies the buffer region (in units of Mpc\ :math:`/h` to follow the format convention) around subvolumes of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file which should be read in to ensure that no halos are missed from trees.
* ``[subvolumeIndex]`` (default ``[0,0,0]``) — Specifies the index (in each dimension) of the subvolume of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file to process. Indices range from 0 to ``[subvolumeCount]``\ :math:`-1`.
* ``[badValue]`` (default ``-0.5d0``) — Use for bad value detection in "Sussing" merger trees. Values for scale radius and halo spin which exceed this threshold are assumed to be bad.
* ``[badValueTest]`` (default ``var_str('lessThan')``) — Use for bad value detection in "Sussing" merger trees. Values which exceed the threshold in ths specified direction are assumed to be bad.
* ``[treeSampleRate]`` (default ``1.0d0``) — Specify the probability that any given tree should processed (to permit subsampling).
* ``[massOptions]`` (default ``var_str('default')``) — Mass option for Sussing merger trees.
* ``[mergeProbability]`` (default ``0.1d0``) — The largest probability of branching allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[accretionLimit]`` (default ``0.1d0``) — The largest fractional mass change due to subresolution accretion allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[redshiftMaximum]`` (default ``1.0d5``) — The highest redshift to which merger trees will be built in the :cite:t:`cole_hierarchical_2000` method.
* ``[toleranceTimeEarliest]`` (default ``2.0d-6``) — The fractional tolerance used to judge if a branch is at the earliest allowed time in the tree.
* ``[branchIntervalStep]`` (default ``.true.``) — If ``false`` use the original :cite:t:`cole_hierarchical_2000` method to determine whether branching occurs in a timestep. If ``true`` draw branching intervals from a negative exponential distribution.
* ``[toleranceResolutionSelf]`` (default ``1.0d-6``) — The fractional tolerance in node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[toleranceResolutionParent]`` (default ``1.0d-3``) — The fractional tolerance in parent node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[ignoreNoProgress]`` (default ``.false.``) — If true, failure to make progress on a branch will be ignored (and the branch terminated).
* ``[ignoreWellOrdering]`` (default ``.false.``) — If true, non-well-ordered tree branches are pruned away instead of causing errors..
* ``[redshiftBase]`` (default ``0.0d0``) — The redshift at which to plant the base node when building merger trees.
* ``[timeSnapTolerance]`` (default ``1.0d-6``) — The fractional tolerance within which the tree base time will be snapped to a nearby output time.
* ``[treeBeginAt]`` (default ``0``) — The index (in order of increasing base halo mass) of the tree at which to begin when building merger trees. A value of "0" means to begin with tree number 1 (if processing trees in ascending order), or equal to the number of trees (otherwise).
* ``[processDescending]`` (default ``.true.``) — If true, causes merger trees to be processed in order of decreasing mass.
* ``[splitTrees]`` (default ``.false.``) — If true, prune away any nodes of the tree that are not needed to determine evolution up to the latest time at which a node is present inside the lightcone. This typically leads to a tree splitting into a forest of trees.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[starFormationRates]`` — The star formation rates corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of star formation rate to use when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d10``) — The star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d12``) — The maximum star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[likelihoodBins]`` — Controls which bins in the stellar mass--halo mass relation will be used in computing the likelihood: * *not present*: all bins are included in the likelihood calculation; * *list of integers*: use only the mass bin(s) given in this list in the likelihood calculation; * ``auto``: use only bins which have a non-zero number of halos contributing to them in the likelihood calculation.
* ``[fileNameTarget]`` — The name of the file containing the target data.
* ``[redshiftInterval]`` (default ``1``) — The redshift interval to use.
* ``[likelihoodNormalize]`` (default ``.false.``) — If true, then normalize the likelihood to make it a probability density.
* ``[computeScatter]`` (default ``.false.``) — If true, the scatter in log10(stellar mass) is computed. Otherwise, the mean is computed.
* ``[systematicErrorPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for stellar mass in the stellar vs halo mass relation.
* ``[systematicErrorMassHaloPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for halo mass in the stellar vs halo mass relation.
* ``[errorTolerant]`` (default ``.false.``) — Error tolerance for the N-body spin distribution operator.
* ``[logNormalRange]`` (default ``100.0d0``) — The multiplicative range of the log-normal distribution used to model the distribution of the mass and energy terms in the spin parameter. Specifically, the lognormal distribution is truncated outside the range :math:`(\lambda_\mathrm{m}/R,\lambda_\mathrm{m} R`, where :math:`\lambda_\mathrm{m}` is the measured spin, and :math:`R=`\ ``[logNormalRange]``
* ``[fileName]`` — The name of the file from which to read spin distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the spin distribution function.
* ``[comment]`` — A descriptive comment for the spin distribution function.
* ``[redshift]`` — The redshift at which to compute the spin distribution function.
* ``[massMinimum]`` — Minimum halo mass for the spin distribution function.
* ``[massMaximum]`` — Maximum halo mass for the spin distribution function.
* ``[spinMinimum]`` — Minimum spin for the spin distribution function.
* ``[spinMaximum]`` — Maximum spin for the spin distribution function.
* ``[countSpinsPerDecade]`` — Number of spins per decade at which to compute the spin distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[particleCountMinimum]`` — The minimum particle count to assume when computing N-body errors on spins.
* ``[massParticle]`` — The mass of the particle used in the N-body simulation from which spins were measured.
* ``[energyEstimateParticleCountMaximum]`` — The maximum number of particles used in estimating halo energies when measuring spins from the N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[magnitudesAbsolute]`` — The absolute magnitudes corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[luminosities]`` — The luminosities corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[includeNitrogenII]`` (default ``.false.``) — If true, include contamination by the [NII] (6548\AA :math:`+` 6584\AA) doublet.
* ``[depthOpticalISMCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in the ISM.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[rootVarianceFractionalMinimum]`` (default ``0.0d0``) — The minimum fractional root variance (relative to the target dataset).
* ``[fileName]`` — The name of the file from which to read concentration distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the concentration distribution function.
* ``[comment]`` — A descriptive comment for the concentration distribution function.
* ``[redshift]`` — The redshift at which to compute the concentration distribution function.
* ``[massMinimum]`` — Minimum halo mass for the concentration distribution function.
* ``[massMaximum]`` — Maximum halo mass for the concentration distribution function.
* ``[concentrationMinimum]`` — Minimum concentration for the concentration distribution function.
* ``[concentrationMaximum]`` — Maximum concentration for the concentration distribution function.
* ``[countConcentrationsPerDecade]`` — Number of concentrations per decade at which to compute the concentration distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[massParticle]`` — The particle mass in the source N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[fileName]`` — The name of the file from which to read star forming main sequence function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[separations]`` — The separations corresponding to bin centers.
* ``[massMinima]`` — The minimum mass of each mass sample.
* ``[massMaxima]`` — The maximum mass of each mass sample.
* ``[massHaloBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[wavenumberCount]`` (default ``60_c_size_t``) — The number of bins in wavenumber to use in computing the correlation function.
* ``[wavenumberMinimum]`` (default ``1.0d-3``) — The minimum wavenumber to use when computing the correlation function.
* ``[wavenumberMaximum]`` (default ``1.0d4``) — The maximum wavenumber to use when computing the correlation function.
* ``[integralConstraint]`` — The integral constraint for these correlation functions.
* ``[depthLineOfSight]`` — The line-of-sight depth over which the correlation function was projected.
* ``[halfIntegral]`` — Set to true if the projection integrand should be over line-of-sight depths greater than zero.
* ``[binnedProjectedCorrelationTarget]`` — The target function for likelihood calculations.
* ``[binnedProjectedCorrelationCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[targetLabel]`` (default ``var_str('')``) — A label for the target dataset in a plot of this analysis.
* ``[starFormationRateSpecificQuiescentLogarithmic]`` — The base-10 logarithm specific star formation rate (in units of Gyr\ :math:`^{-1}`) separating quiescent and star-forming galaxies.
* ``[starFormationRateSpecificLogarithmicError]`` — The observational fractional error in specific star formation rate (in units of dex) of galaxies.
* ``[fileName]`` — The name of the file from which to read quiescent fraction function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[radiusFractionalTruncateMinimum]`` (default ``2.0d0``) — The minimum radius (in units of the virial radius) to begin truncating the density profile.
* ``[radiusFractionalTruncateMaximum]`` (default ``4.0d0``) — The maximum radius (in units of the virial radius) to finish truncating the density profile.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[velocityDispersionApproximate]`` (default ``.true.``) — If ``true``, radial velocity dispersion is computed using an approximate method in which we assume that :math:`\sigma_\mathrm{r}^2(r) \rightarrow \sigma_\mathrm{r}^2(r) - (2/3) \epsilon(r)`, where :math:`\epsilon(r)` is the specific heating energy. If ``false`` then radial velocity dispersion is computed by numerically solving the Jeans equation.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[tolerateVelocityDispersionFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the velocity dispersion.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the radius of the maximum circular velocity.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate numerical failures when computing the gravitational potential of a heated dark matter profile, allowing the calculation to continue with a fallback result rather than aborting.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[tolerateVelocityMaximumFailure]`` (default ``.true.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[lengthResolution]`` — The gravitational softening length :math:`\Delta x` (in Mpc) of the N-body simulation, which sets the minimum spatial scale below which the dark matter profile is smoothed to avoid artificial two-body effects.
* ``[massResolution]`` — The mass resolution :math:`\Delta M` (in :math:`\mathrm{M}_\odot`) of the N-body simulation, representing the minimum halo mass that can be resolved; profiles of halos near this limit are softened to account for particle discreteness effects.
* ``[resolutionIsComoving]`` — If true, the resolution length is assumed to be fixed in comoving coordinates, otherwise in physical coordinates.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[C]`` (default ``400.0d0``) — The parameter :math:`C` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[f]`` (default ``0.02d0``) — The parameter :math:`f` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[timeFormationSeekDelta]`` (default ``0.0d0``) — The parameter :math:`\Delta \log t` by which the logarithm of the trial formation time is incremented when stepping through the formation history of a node to find the formation time. If set to zero (or a negative value) the cumulative mass histories of nodes are assumed to be monotonic functions of time, and the formation time is instead found by a root finding algorithm,
* ``[massBoundIsInactive]`` (default ``.false.``) — Specifies whether or not the bound mass of the satellite component is inactive (i.e. does not appear in any ODE being solved).
* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the halo virial radius using a the virial density definition at the last isolated time of the halo.
* ``[filterName]`` — The filter to select.
* ``[filterType]`` — The filter type (rest or observed) to select.
* ``[redshiftBand]`` — The redshift of the band (if not the output redshift).
* ``[postprocessChain]`` — The postprocessing chain to use.
* ``[cloudyTableFileName]`` (default ``var_str('%DATASTATICPATH%/hiiRegions/emissionLineLuminosities_BC2003_highResolution_imfChabrier.hdf5')``) — The file of emission line luminosities to use.
* ``[lineNames]`` — The emission lines to extract.
* ``[component]`` — The component from which to extract star formation rate.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance used in integration over stellar population spectra.
* ``[component]`` — The component from which to extract star formation rate.
* ``[radiusCore]`` — The soliton core radius (in Mpc) characterizing the size of the quantum pressure-supported central core of the fuzzy dark matter halo; the density profile flattens inside this scale.
* ``[densitySolitonCentral]`` — The central density (in :math:`\mathrm{M}_\odot`/Mpc\ :math:`^3`) of the solitonic core at :math:`r=0`, which sets the overall normalization of the density profile :math:`\rho(r) = \rho_\mathrm{c} [1+(r/r_c)^2]^{-8}`.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The relative tolerance used in numerical ODE solutions for the gravitational potential of the solitonic core profile.
* ``[dimensionless]`` (default ``.true.``) — If true the soliton profile is treated as dimensionless (scale-free), allowing its radial and density quantities to be specified in arbitrary units.
* ``[componentType]`` (default ``var_str('unknown')``) — The galactic structure component type (e.g.\ dark matter halo, disk, spheroid) represented by this mass distribution, used for component-specific queries.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type (e.g.\ dark matter, baryonic, total) represented by this mass distribution, used for mass-type-specific queries.
* ``[radiusTransition]`` — The transition radius (in Mpc) at which the density profile smoothly switches from the halo profile to the accretion flow, controlled by the fourth-order transition function :math:`f_\mathrm{trans}(r)`.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[timeAge]`` — The age of the halo (in Gyr) since its formation, determining the total time available for SIDM self-interactions to thermalize the inner halo and produce an isothermal core.
* ``[velocityRelativeMean]`` — Mean relative velocity to calculate self interaction cross section.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the potential.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[lengthResolution]`` — The spatial resolution length scale (in Mpc) below which the underlying density profile is softened to a flat core, mimicking the finite force resolution of an N-body simulation.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[massMinimum]`` — The minimum halo mass (in :math:`\mathrm{M}_\odot`) below which halos are excluded from the mass function histogram.
* ``[massMaximum]`` — The maximum halo mass (in :math:`\mathrm{M}_\odot`) above which halos are excluded from the mass function histogram.
* ``[massCountPerDecade]`` — The number of logarithmic bins per decade of halo mass used when constructing the halo mass function.
* ``[description]`` — A human-readable description of this mass function dataset, stored as metadata in the output file.
* ``[simulationReference]`` — A bibliographic reference for the N-body simulation from which this mass function is derived, stored as metadata.
* ``[simulationURL]`` — A URL pointing to the publicly accessible dataset or documentation for the N-body simulation, stored as metadata.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.
* ``[representativeMinimumCount]`` (default ``10_c_size_t``) — Minimum number of representative particles used to compute the center of a halo.
* ``[tolerance]`` (default ``1.0d-2``) — The tolerance in the summed weight of bound particles which must be attained to declare convergence.
* ``[bootstrapSampleRate]`` (default ``1.0d0``) — The sampling rate for particles.
* ``[representativeFraction]`` (default ``0.05d0``) — Fraction of bound particles used to compute the center of a halo.
* ``[analyzeAllParticles]`` (default ``.true.``) — If true, all particles are assumed to be self-bound at the beginning of the analysis. Unbound particles at previous times are allowed to become bound in the current snapshot. If false and the self-bound information from the previous snapshot is available, only the particles that are self-bound at the previous snapshot are assumed to be bound at the beginning of the analysis.
* ``[useVelocityMostBound]`` (default ``.false.``) — If true, the velocity of the most bound particle in velocity space is used as the representative velocity of the satellite. If false, use the mass weighted mean velocity (center-of-mass velocity) of self-bound particles instead.
* ``[orderRotation]`` (default ``var_str('none')``) — The order in which evaluation of likelihoods should be rotated as a function of process number.
* ``[logLikelihoodAccept]`` (default ``huge(0.0d0)``) — The log-likelihood which should be "accepted"---once the log-likelihood reaches this value (or larger) no further updates to the chain will be made.
* ``[report]`` (default ``.false.``) — If true, report on the log-likelihood obtained.
* ``[means]`` — The mean of the multivariate normal distribution.
* ``[covariance]`` — The covariance matrix for the of the multivariate normal distribution.
* ``[countForestsMaximum]`` (default ``-1_c_size_t``) — If set to a positive number, this is the maximum number of forests that will be evolved.
* ``[walltimeMaximum]`` (default ``-1_kind_int8``) — If set to a positive number, this is the maximum wall time for which forest evolution is allowed to proceed before the task gives up.
* ``[tolerateFailures]`` (default ``.false.``) — If true then failures to evolve a forest are tolerated. The forest is evolved no further, but evolution of other forests continues.
* ``[evolveForestsInParallel]`` (default ``.true.``) — If true then each forest is evolved by a separate OpenMP thread. Otherwise, a single thread evolves all forests.
* ``[suspendToRAM]`` (default ``.true.``) — Specifies whether trees should be suspended to RAM (otherwise they are suspend to file).
* ``[suspendPath]`` — The path to which tree suspension files will be stored.
* ``[timeIntervalCheckpoint]`` (default ``-1_kind_int8``) — If positive, gives the time in seconds between storing of checkpoint files. If zero or negative, no checkpointing is performed..
* ``[fileNameCheckpoint]`` — The path to which checkpoint data will be stored.
* ``[logM0]`` (default ``10.0d0``) — The parameter :math:`\log_{10} M_0` (with :math:`M_0` in units of :math:`\mathrm{M}_\odot`) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR0]`` (default ``9.0d0``) — The parameter :math:`\alpha_0` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR1]`` (default ``0.0d0``) — The parameter :math:`\alpha_1` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[cW]`` (default ``3.78062835d0``) — The parameter :math:`c_\mathrm{W}` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[beta]`` (default ``3.4638743d0``) — The parameter :math:`\beta` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[transferFunctionType]`` (default ``var_str('darkMatter')``) — Specifies whether to use the ``darkMatter`` or ``total`` transfer function.
* ``[fileName]`` — The name of the file from which to read a tabulated transfer function.
* ``[redshift]`` (default ``0.0d0``) — The redshift of the transfer function to read.
* ``[factorWavenumberSmoothExtrapolation]`` (default ``0.0d0``) — If positive, and extrapolation is used at high wavenumbers, the slope for extrapolation will be set by averaging over wavenumbers from :math:`k_\mathrm{max}/f` to :math:`k_\mathrm{max}`, where :math:`f=`\ ``[factorWavenumberSmoothExtrapolation]`` and :math:`k_\mathrm{max}` is the highest wavenumber tabulated. This avoids spurious extrapolation for highly oscillatory transfer functions.
* ``[acceptNegativeValues]`` (default ``.false.``) — If true, negative values in the transfer function are allowed (and the absolute value is taken prior to interpolation). Otherwise, negative values result in an error.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[fileName]`` (default ``var_str('none')``) — The name of the file to/from which tabulations of barrier first crossing probabilities should be written/read. If set to "``none``" tables will not be stored.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[varianceNumberPerUnitProbability]`` (default ``1000``) — The number of points to tabulate per unit variance for first crossing probabilities.
* ``[varianceNumberPerUnit]`` (default ``40``) — The number of tabulation points per unit of :math:`\sigma^2` used when building the rate look-up table for the Farahi excursion-set first-crossing distribution; higher values improve interpolation accuracy at the cost of memory and initialization time.
* ``[varianceNumberPerDecade]`` (default ``400``) — The number of points to tabulate per decade of progenitor variance for first crossing rates.
* ``[varianceNumberPerDecadeNonCrossing]`` (default ``40``) — The number of points to tabulate per decade of progenitor variance for non-crossing rates.
* ``[timeNumberPerDecade]`` (default ``10``) — The number of tabulation points per decade of cosmic time used when building the first-crossing rate look-up table as a function of time; higher values improve temporal interpolation accuracy for rapidly evolving cosmologies.
* ``[varianceIsUnlimited]`` (default ``.false.``) — If true, the variance is assumed to have no upper limit (e.g. as in the case of :term:`CDM`). This allows the tabulated solutions to be extended arbitrarily. Otherwise, tables are extended to encompass just the range of variance requested.
* ``[linkingLength]`` (default ``0.2d0``) — The friends-of-friends linking length to use in computing virial density contrasts with the percolation analysis of :cite:t:`more_overdensity_2011`.

.. _physics-nodePropertyExtractorGalaxyMergersIndices:

``nodePropertyExtractorGalaxyMergersIndices``
---------------------------------------------

Extracts integer index properties of galaxy-galaxy merger events (as distinct from halo mergers), such as node indices of the merging galaxy pair, enabling reconstruction of the galaxy merger history.

.. _physics-nodePropertyExtractorGalaxyMergersPhysical:

``nodePropertyExtractorGalaxyMergersPhysical``
----------------------------------------------

Extracts physical (floating-point) properties of galaxy-galaxy merger events, such as stellar masses, mass ratios, and merger times, providing continuous-valued data for statistical analysis of galaxy merging.

.. _physics-nodePropertyExtractorGalaxyMergerTree:

``nodePropertyExtractorGalaxyMergerTree``
-----------------------------------------

An output extractor property extractor class that combines all extractors needed for building galaxy merger trees.

**Methods**

* ``tabulate`` — Tabulate the virial density contrast as a function of mass and time.
* ``restoreTable`` — Restore a tabulated solution from file.
* ``storeTable`` — Store a tabulated solution to file.

**Parameters**

* ``[velocityCharacteristic]`` (default ``250.0d0``) — The velocity scale at which the :term:`SNe`-driven outflow rate equals the star formation rate in disks.
* ``[exponent]`` (default ``3.5d0``) — The velocity scaling of the :term:`SNe`-driven outflow rate in disks.
* ``[fraction]`` (default ``0.01d0``) — The normalization :math:`f` of the outflow rate relative to the star formation rate at a reference halo velocity of 200 km/s and expansion factor of 1, setting the overall mass-loading amplitude of the halo-scaling feedback model.
* ``[exponentVelocity]`` (default ``-2.0d0``) — The exponent of virial velocity in the outflow rate in disks.
* ``[exponentRedshift]`` (default ``0.0d0``) — The power-law exponent of the cosmological expansion factor :math:`(1+z)` in the halo-scaling outflow rate, allowing the mass-loading factor to evolve with redshift; a value of zero gives no redshift evolution.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[radiusNormalization]`` (default ``3.3d-6``) — The initial value appearing in the radius-mass relation
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the nuclear star cluster is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not nuclear star cluster stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[scaleRelativeMass]`` (default ``1.0d-2``) — The mass scale, relative to the total mass of the node, below which calculations in the delayed very simple hot halo component are allowed to become inaccurate.
* ``[starveSatellites]`` (default ``.false.``) — Specifies whether or not the hot halo should be removed ("starved") when a node becomes a satellite.
* ``[starveSatellitesOutflowed]`` (default ``.false.``) — Specifies whether or not the outflowed hot halo should be removed ("starved") when a node becomes a satellite.
* ``[outflowReturnOnFormation]`` (default ``.false.``) — Specifies whether or not outflowed gas should be returned to the hot reservoir on halo formation events.
* ``[angularMomentumAlwaysGrows]`` (default ``.false.``) — Specifies whether or not negative rates of accretion of angular momentum into the hot halo will be treated as positive for the purposes of computing the hot halo angular momentum.
* ``[fractionBaryonLimitInNodeMerger]`` (default ``.false.``) — Controls whether the hot gas content of nodes should be limited to not exceed the universal baryon fraction at node merger events. If set to ``true``, hot gas (and angular momentum, abundances, and chemicals proportionally) will be removed from the merged halo to the unaccreted gas reservoir to limit the baryonic mass to the universal baryon fraction where possible.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple disk component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[radiusStructureSolver]`` (default ``1.0d0``) — The radius (in units of the standard scale length) to use in solving for the size of the disk.
* ``[structureSolverUseCole2000Method]`` (default ``.false.``) — If true, use the method described in :cite:t:`cole_hierarchical_2000` to correct for difference between thin disk and spherical mass distributions when solving for disk radii.
* ``[diskNegativeAngularMomentumAllowed]`` (default ``.true.``) — Specifies whether or not negative angular momentum is allowed for the disk.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not disk stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumSolverRadius]`` (default ``ratioAngularMomentumSolverRadiusDefault``) — The assumed ratio of the specific angular momentum at the structure solver radius to the mean specific angular momentum of the standard disk component.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple spheroid component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[efficiencyEnergeticOutflow]`` (default ``1.0d-2``) — The proportionality factor relating mass outflow rate from the spheroid to the energy input rate divided by :math:`V_\mathrm{spheroid}^2`.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not spheroid stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumScaleRadius]`` (default ``ratioAngularMomentumScaleRadiusDefault``) — The assumed ratio of the specific angular momentum at the scale radius to the mean specific angular momentum of the standard spheroid component.
* ``[outputMergers]`` (default ``.false.``) — Determines whether or not properties of black hole mergers will be output.
* ``[fileNames]`` — The name of the file(s) from which merger tree data should be read when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[forestSizeMaximum]`` (default ``0_c_size_t``) — The maximum number of nodes allowed in a forest before it will be broken up into trees and processed individually. A value of 0 implies that forests should never be split.
* ``[presetMergerTimes]`` (default ``.true.``) — Specifies whether merging times for subhalos should be preset when reading merger trees from a file.
* ``[presetMergerNodes]`` (default ``.true.``) — Specifies whether the target nodes for mergers should be preset (i.e. determined from descendant nodes). If they are not, merging will be with each satellite's host node.
* ``[presetSubhaloMasses]`` (default ``.true.``) — Specifies whether subhalo mass should be preset when reading merger trees from a file.
* ``[subhaloAngularMomentaMethod]`` (default ``var_str('summation')``) — Specifies how to account for subhalo angular momentum when adding subhalo mass to host halo mass.
* ``[presetSubhaloIndices]`` (default ``.true.``) — Specifies whether subhalo indices should be preset when reading merger trees from a file.
* ``[presetPositions]`` (default ``.true.``) — Specifies whether node positions should be preset when reading merger trees from a file.
* ``[presetScaleRadii]`` (default ``.true.``) — Specifies whether node scale radii should be preset when reading merger trees from a file.
* ``[scaleRadiiFailureIsFatal]`` (default ``.true.``) — Specifies whether failure to set a node scale radii should be regarded as a fatal error. (If not, a fallback method to set scale radius is used in such cases.)
* ``[presetScaleRadiiConcentrationMinimum]`` (default ``3.0d0``) — The lowest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiConcentrationMaximum]`` (default ``60.0d0``) — The largest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiMinimumMass]`` (default ``0.0d0``) — The minimum halo mass for which scale radii should be preset (if ``[presetScaleRadii]``\ :math:`=`\ ``true``).
* ``[presetUnphysicalAngularMomenta]`` (default ``.false.``) — When reading merger trees from file and presetting halo angular momenta, detect unphysical (<=0) angular momenta and preset them using the selected halo spin method.
* ``[presetAngularMomenta]`` (default ``.true.``) — Specifies whether node angular momenta should be preset when reading merger trees from a file.
* ``[presetAngularMomenta3D]`` (default ``.false.``) — Specifies whether node 3-D angular momenta vectors should be preset when reading merger trees from a file.
* ``[presetOrbits]`` (default ``.true.``) — Specifies whether node orbits should be preset when reading merger trees from a file.
* ``[presetOrbitsSetAll]`` (default ``.true.``) — Forces all orbits to be set. If the computed orbit does not cross the virial radius, then select one at random instead.
* ``[presetOrbitsAssertAllSet]`` (default ``.true.``) — Asserts that all virial orbits must be preset. If any can not be set, Galacticus will stop.
* ``[presetOrbitsBoundOnly]`` (default ``.true.``) — Specifies whether only bound node orbits should be set.
* ``[beginAt]`` (default ``-1_kind_int8``) — Specifies the index of the tree to begin at. (Use -1 to always begin with the first tree.)
* ``[outputTimeSnapTolerance]`` (default ``0.0d0``) — The relative tolerance required to "snap" a node time to the closest output time.
* ``[missingHostsAreFatal]`` (default ``.true.``) — Specifies whether nodes with missing host nodes should be considered to be fatal---see the discussion of missing host nodes in the class description above.
* ``[treeIndexToRootNodeIndex]`` (default ``.false.``) — Specifies whether tree indices should always be set to the index of their root node.
* ``[allowBranchJumps]`` (default ``.true.``) — Specifies whether nodes are allowed to jump between branches.
* ``[allowSubhaloPromotions]`` (default ``.true.``) — Specifies whether subhalos are permitted to be promoted to being isolated halos.
* ``[alwaysPromoteMostMassive]`` (default ``.false.``) — If true, the most massive progenitor is always promoted to be the primary progenitor *even if* it is a subhalo. Otherwise, isolated progenitors are given priority over subhalo progenitors, even if they are less massive.
* ``[presetNamedReals]`` — Names of real datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[presetNamedIntegers]`` — Names of integer datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[fatalMismatches]`` (default ``.true.``) — Specifies whether mismatches in cosmological parameter values between Galacticus and "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be considered fatal.
* ``[fatalNonTreeNode]`` (default ``.true.``) — Specifies whether nodes in snapshot files but not in the merger tree file should be considered fatal when importing from the "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013`.
* ``[subvolumeCount]`` (default ``1``) — Specifies the number of subvolumes *along each axis* into which a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be split for processing through Galacticus.
* ``[subvolumeBuffer]`` (default ``0.0d0``) — Specifies the buffer region (in units of Mpc\ :math:`/h` to follow the format convention) around subvolumes of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file which should be read in to ensure that no halos are missed from trees.
* ``[subvolumeIndex]`` (default ``[0,0,0]``) — Specifies the index (in each dimension) of the subvolume of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file to process. Indices range from 0 to ``[subvolumeCount]``\ :math:`-1`.
* ``[badValue]`` (default ``-0.5d0``) — Use for bad value detection in "Sussing" merger trees. Values for scale radius and halo spin which exceed this threshold are assumed to be bad.
* ``[badValueTest]`` (default ``var_str('lessThan')``) — Use for bad value detection in "Sussing" merger trees. Values which exceed the threshold in ths specified direction are assumed to be bad.
* ``[treeSampleRate]`` (default ``1.0d0``) — Specify the probability that any given tree should processed (to permit subsampling).
* ``[massOptions]`` (default ``var_str('default')``) — Mass option for Sussing merger trees.
* ``[mergeProbability]`` (default ``0.1d0``) — The largest probability of branching allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[accretionLimit]`` (default ``0.1d0``) — The largest fractional mass change due to subresolution accretion allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[redshiftMaximum]`` (default ``1.0d5``) — The highest redshift to which merger trees will be built in the :cite:t:`cole_hierarchical_2000` method.
* ``[toleranceTimeEarliest]`` (default ``2.0d-6``) — The fractional tolerance used to judge if a branch is at the earliest allowed time in the tree.
* ``[branchIntervalStep]`` (default ``.true.``) — If ``false`` use the original :cite:t:`cole_hierarchical_2000` method to determine whether branching occurs in a timestep. If ``true`` draw branching intervals from a negative exponential distribution.
* ``[toleranceResolutionSelf]`` (default ``1.0d-6``) — The fractional tolerance in node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[toleranceResolutionParent]`` (default ``1.0d-3``) — The fractional tolerance in parent node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[ignoreNoProgress]`` (default ``.false.``) — If true, failure to make progress on a branch will be ignored (and the branch terminated).
* ``[ignoreWellOrdering]`` (default ``.false.``) — If true, non-well-ordered tree branches are pruned away instead of causing errors..
* ``[redshiftBase]`` (default ``0.0d0``) — The redshift at which to plant the base node when building merger trees.
* ``[timeSnapTolerance]`` (default ``1.0d-6``) — The fractional tolerance within which the tree base time will be snapped to a nearby output time.
* ``[treeBeginAt]`` (default ``0``) — The index (in order of increasing base halo mass) of the tree at which to begin when building merger trees. A value of "0" means to begin with tree number 1 (if processing trees in ascending order), or equal to the number of trees (otherwise).
* ``[processDescending]`` (default ``.true.``) — If true, causes merger trees to be processed in order of decreasing mass.
* ``[splitTrees]`` (default ``.false.``) — If true, prune away any nodes of the tree that are not needed to determine evolution up to the latest time at which a node is present inside the lightcone. This typically leads to a tree splitting into a forest of trees.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[starFormationRates]`` — The star formation rates corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of star formation rate to use when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d10``) — The star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d12``) — The maximum star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[likelihoodBins]`` — Controls which bins in the stellar mass--halo mass relation will be used in computing the likelihood: * *not present*: all bins are included in the likelihood calculation; * *list of integers*: use only the mass bin(s) given in this list in the likelihood calculation; * ``auto``: use only bins which have a non-zero number of halos contributing to them in the likelihood calculation.
* ``[fileNameTarget]`` — The name of the file containing the target data.
* ``[redshiftInterval]`` (default ``1``) — The redshift interval to use.
* ``[likelihoodNormalize]`` (default ``.false.``) — If true, then normalize the likelihood to make it a probability density.
* ``[computeScatter]`` (default ``.false.``) — If true, the scatter in log10(stellar mass) is computed. Otherwise, the mean is computed.
* ``[systematicErrorPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for stellar mass in the stellar vs halo mass relation.
* ``[systematicErrorMassHaloPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for halo mass in the stellar vs halo mass relation.
* ``[errorTolerant]`` (default ``.false.``) — Error tolerance for the N-body spin distribution operator.
* ``[logNormalRange]`` (default ``100.0d0``) — The multiplicative range of the log-normal distribution used to model the distribution of the mass and energy terms in the spin parameter. Specifically, the lognormal distribution is truncated outside the range :math:`(\lambda_\mathrm{m}/R,\lambda_\mathrm{m} R`, where :math:`\lambda_\mathrm{m}` is the measured spin, and :math:`R=`\ ``[logNormalRange]``
* ``[fileName]`` — The name of the file from which to read spin distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the spin distribution function.
* ``[comment]`` — A descriptive comment for the spin distribution function.
* ``[redshift]`` — The redshift at which to compute the spin distribution function.
* ``[massMinimum]`` — Minimum halo mass for the spin distribution function.
* ``[massMaximum]`` — Maximum halo mass for the spin distribution function.
* ``[spinMinimum]`` — Minimum spin for the spin distribution function.
* ``[spinMaximum]`` — Maximum spin for the spin distribution function.
* ``[countSpinsPerDecade]`` — Number of spins per decade at which to compute the spin distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[particleCountMinimum]`` — The minimum particle count to assume when computing N-body errors on spins.
* ``[massParticle]`` — The mass of the particle used in the N-body simulation from which spins were measured.
* ``[energyEstimateParticleCountMaximum]`` — The maximum number of particles used in estimating halo energies when measuring spins from the N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[magnitudesAbsolute]`` — The absolute magnitudes corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[luminosities]`` — The luminosities corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[includeNitrogenII]`` (default ``.false.``) — If true, include contamination by the [NII] (6548\AA :math:`+` 6584\AA) doublet.
* ``[depthOpticalISMCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in the ISM.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[rootVarianceFractionalMinimum]`` (default ``0.0d0``) — The minimum fractional root variance (relative to the target dataset).
* ``[fileName]`` — The name of the file from which to read concentration distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the concentration distribution function.
* ``[comment]`` — A descriptive comment for the concentration distribution function.
* ``[redshift]`` — The redshift at which to compute the concentration distribution function.
* ``[massMinimum]`` — Minimum halo mass for the concentration distribution function.
* ``[massMaximum]`` — Maximum halo mass for the concentration distribution function.
* ``[concentrationMinimum]`` — Minimum concentration for the concentration distribution function.
* ``[concentrationMaximum]`` — Maximum concentration for the concentration distribution function.
* ``[countConcentrationsPerDecade]`` — Number of concentrations per decade at which to compute the concentration distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[massParticle]`` — The particle mass in the source N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[fileName]`` — The name of the file from which to read star forming main sequence function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[separations]`` — The separations corresponding to bin centers.
* ``[massMinima]`` — The minimum mass of each mass sample.
* ``[massMaxima]`` — The maximum mass of each mass sample.
* ``[massHaloBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[wavenumberCount]`` (default ``60_c_size_t``) — The number of bins in wavenumber to use in computing the correlation function.
* ``[wavenumberMinimum]`` (default ``1.0d-3``) — The minimum wavenumber to use when computing the correlation function.
* ``[wavenumberMaximum]`` (default ``1.0d4``) — The maximum wavenumber to use when computing the correlation function.
* ``[integralConstraint]`` — The integral constraint for these correlation functions.
* ``[depthLineOfSight]`` — The line-of-sight depth over which the correlation function was projected.
* ``[halfIntegral]`` — Set to true if the projection integrand should be over line-of-sight depths greater than zero.
* ``[binnedProjectedCorrelationTarget]`` — The target function for likelihood calculations.
* ``[binnedProjectedCorrelationCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[targetLabel]`` (default ``var_str('')``) — A label for the target dataset in a plot of this analysis.
* ``[starFormationRateSpecificQuiescentLogarithmic]`` — The base-10 logarithm specific star formation rate (in units of Gyr\ :math:`^{-1}`) separating quiescent and star-forming galaxies.
* ``[starFormationRateSpecificLogarithmicError]`` — The observational fractional error in specific star formation rate (in units of dex) of galaxies.
* ``[fileName]`` — The name of the file from which to read quiescent fraction function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[radiusFractionalTruncateMinimum]`` (default ``2.0d0``) — The minimum radius (in units of the virial radius) to begin truncating the density profile.
* ``[radiusFractionalTruncateMaximum]`` (default ``4.0d0``) — The maximum radius (in units of the virial radius) to finish truncating the density profile.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[velocityDispersionApproximate]`` (default ``.true.``) — If ``true``, radial velocity dispersion is computed using an approximate method in which we assume that :math:`\sigma_\mathrm{r}^2(r) \rightarrow \sigma_\mathrm{r}^2(r) - (2/3) \epsilon(r)`, where :math:`\epsilon(r)` is the specific heating energy. If ``false`` then radial velocity dispersion is computed by numerically solving the Jeans equation.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[tolerateVelocityDispersionFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the velocity dispersion.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the radius of the maximum circular velocity.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate numerical failures when computing the gravitational potential of a heated dark matter profile, allowing the calculation to continue with a fallback result rather than aborting.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[tolerateVelocityMaximumFailure]`` (default ``.true.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[lengthResolution]`` — The gravitational softening length :math:`\Delta x` (in Mpc) of the N-body simulation, which sets the minimum spatial scale below which the dark matter profile is smoothed to avoid artificial two-body effects.
* ``[massResolution]`` — The mass resolution :math:`\Delta M` (in :math:`\mathrm{M}_\odot`) of the N-body simulation, representing the minimum halo mass that can be resolved; profiles of halos near this limit are softened to account for particle discreteness effects.
* ``[resolutionIsComoving]`` — If true, the resolution length is assumed to be fixed in comoving coordinates, otherwise in physical coordinates.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[C]`` (default ``400.0d0``) — The parameter :math:`C` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[f]`` (default ``0.02d0``) — The parameter :math:`f` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[timeFormationSeekDelta]`` (default ``0.0d0``) — The parameter :math:`\Delta \log t` by which the logarithm of the trial formation time is incremented when stepping through the formation history of a node to find the formation time. If set to zero (or a negative value) the cumulative mass histories of nodes are assumed to be monotonic functions of time, and the formation time is instead found by a root finding algorithm,
* ``[massBoundIsInactive]`` (default ``.false.``) — Specifies whether or not the bound mass of the satellite component is inactive (i.e. does not appear in any ODE being solved).
* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the halo virial radius using a the virial density definition at the last isolated time of the halo.
* ``[filterName]`` — The filter to select.
* ``[filterType]`` — The filter type (rest or observed) to select.
* ``[redshiftBand]`` — The redshift of the band (if not the output redshift).
* ``[postprocessChain]`` — The postprocessing chain to use.
* ``[cloudyTableFileName]`` (default ``var_str('%DATASTATICPATH%/hiiRegions/emissionLineLuminosities_BC2003_highResolution_imfChabrier.hdf5')``) — The file of emission line luminosities to use.
* ``[lineNames]`` — The emission lines to extract.
* ``[component]`` — The component from which to extract star formation rate.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance used in integration over stellar population spectra.
* ``[component]`` — The component from which to extract star formation rate.
* ``[radiusCore]`` — The soliton core radius (in Mpc) characterizing the size of the quantum pressure-supported central core of the fuzzy dark matter halo; the density profile flattens inside this scale.
* ``[densitySolitonCentral]`` — The central density (in :math:`\mathrm{M}_\odot`/Mpc\ :math:`^3`) of the solitonic core at :math:`r=0`, which sets the overall normalization of the density profile :math:`\rho(r) = \rho_\mathrm{c} [1+(r/r_c)^2]^{-8}`.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The relative tolerance used in numerical ODE solutions for the gravitational potential of the solitonic core profile.
* ``[dimensionless]`` (default ``.true.``) — If true the soliton profile is treated as dimensionless (scale-free), allowing its radial and density quantities to be specified in arbitrary units.
* ``[componentType]`` (default ``var_str('unknown')``) — The galactic structure component type (e.g.\ dark matter halo, disk, spheroid) represented by this mass distribution, used for component-specific queries.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type (e.g.\ dark matter, baryonic, total) represented by this mass distribution, used for mass-type-specific queries.
* ``[radiusTransition]`` — The transition radius (in Mpc) at which the density profile smoothly switches from the halo profile to the accretion flow, controlled by the fourth-order transition function :math:`f_\mathrm{trans}(r)`.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[timeAge]`` — The age of the halo (in Gyr) since its formation, determining the total time available for SIDM self-interactions to thermalize the inner halo and produce an isothermal core.
* ``[velocityRelativeMean]`` — Mean relative velocity to calculate self interaction cross section.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the potential.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[lengthResolution]`` — The spatial resolution length scale (in Mpc) below which the underlying density profile is softened to a flat core, mimicking the finite force resolution of an N-body simulation.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[massMinimum]`` — The minimum halo mass (in :math:`\mathrm{M}_\odot`) below which halos are excluded from the mass function histogram.
* ``[massMaximum]`` — The maximum halo mass (in :math:`\mathrm{M}_\odot`) above which halos are excluded from the mass function histogram.
* ``[massCountPerDecade]`` — The number of logarithmic bins per decade of halo mass used when constructing the halo mass function.
* ``[description]`` — A human-readable description of this mass function dataset, stored as metadata in the output file.
* ``[simulationReference]`` — A bibliographic reference for the N-body simulation from which this mass function is derived, stored as metadata.
* ``[simulationURL]`` — A URL pointing to the publicly accessible dataset or documentation for the N-body simulation, stored as metadata.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.
* ``[representativeMinimumCount]`` (default ``10_c_size_t``) — Minimum number of representative particles used to compute the center of a halo.
* ``[tolerance]`` (default ``1.0d-2``) — The tolerance in the summed weight of bound particles which must be attained to declare convergence.
* ``[bootstrapSampleRate]`` (default ``1.0d0``) — The sampling rate for particles.
* ``[representativeFraction]`` (default ``0.05d0``) — Fraction of bound particles used to compute the center of a halo.
* ``[analyzeAllParticles]`` (default ``.true.``) — If true, all particles are assumed to be self-bound at the beginning of the analysis. Unbound particles at previous times are allowed to become bound in the current snapshot. If false and the self-bound information from the previous snapshot is available, only the particles that are self-bound at the previous snapshot are assumed to be bound at the beginning of the analysis.
* ``[useVelocityMostBound]`` (default ``.false.``) — If true, the velocity of the most bound particle in velocity space is used as the representative velocity of the satellite. If false, use the mass weighted mean velocity (center-of-mass velocity) of self-bound particles instead.
* ``[orderRotation]`` (default ``var_str('none')``) — The order in which evaluation of likelihoods should be rotated as a function of process number.
* ``[logLikelihoodAccept]`` (default ``huge(0.0d0)``) — The log-likelihood which should be "accepted"---once the log-likelihood reaches this value (or larger) no further updates to the chain will be made.
* ``[report]`` (default ``.false.``) — If true, report on the log-likelihood obtained.
* ``[means]`` — The mean of the multivariate normal distribution.
* ``[covariance]`` — The covariance matrix for the of the multivariate normal distribution.
* ``[countForestsMaximum]`` (default ``-1_c_size_t``) — If set to a positive number, this is the maximum number of forests that will be evolved.
* ``[walltimeMaximum]`` (default ``-1_kind_int8``) — If set to a positive number, this is the maximum wall time for which forest evolution is allowed to proceed before the task gives up.
* ``[tolerateFailures]`` (default ``.false.``) — If true then failures to evolve a forest are tolerated. The forest is evolved no further, but evolution of other forests continues.
* ``[evolveForestsInParallel]`` (default ``.true.``) — If true then each forest is evolved by a separate OpenMP thread. Otherwise, a single thread evolves all forests.
* ``[suspendToRAM]`` (default ``.true.``) — Specifies whether trees should be suspended to RAM (otherwise they are suspend to file).
* ``[suspendPath]`` — The path to which tree suspension files will be stored.
* ``[timeIntervalCheckpoint]`` (default ``-1_kind_int8``) — If positive, gives the time in seconds between storing of checkpoint files. If zero or negative, no checkpointing is performed..
* ``[fileNameCheckpoint]`` — The path to which checkpoint data will be stored.
* ``[logM0]`` (default ``10.0d0``) — The parameter :math:`\log_{10} M_0` (with :math:`M_0` in units of :math:`\mathrm{M}_\odot`) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR0]`` (default ``9.0d0``) — The parameter :math:`\alpha_0` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR1]`` (default ``0.0d0``) — The parameter :math:`\alpha_1` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[cW]`` (default ``3.78062835d0``) — The parameter :math:`c_\mathrm{W}` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[beta]`` (default ``3.4638743d0``) — The parameter :math:`\beta` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[transferFunctionType]`` (default ``var_str('darkMatter')``) — Specifies whether to use the ``darkMatter`` or ``total`` transfer function.
* ``[fileName]`` — The name of the file from which to read a tabulated transfer function.
* ``[redshift]`` (default ``0.0d0``) — The redshift of the transfer function to read.
* ``[factorWavenumberSmoothExtrapolation]`` (default ``0.0d0``) — If positive, and extrapolation is used at high wavenumbers, the slope for extrapolation will be set by averaging over wavenumbers from :math:`k_\mathrm{max}/f` to :math:`k_\mathrm{max}`, where :math:`f=`\ ``[factorWavenumberSmoothExtrapolation]`` and :math:`k_\mathrm{max}` is the highest wavenumber tabulated. This avoids spurious extrapolation for highly oscillatory transfer functions.
* ``[acceptNegativeValues]`` (default ``.false.``) — If true, negative values in the transfer function are allowed (and the absolute value is taken prior to interpolation). Otherwise, negative values result in an error.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[fileName]`` (default ``var_str('none')``) — The name of the file to/from which tabulations of barrier first crossing probabilities should be written/read. If set to "``none``" tables will not be stored.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[varianceNumberPerUnitProbability]`` (default ``1000``) — The number of points to tabulate per unit variance for first crossing probabilities.
* ``[varianceNumberPerUnit]`` (default ``40``) — The number of tabulation points per unit of :math:`\sigma^2` used when building the rate look-up table for the Farahi excursion-set first-crossing distribution; higher values improve interpolation accuracy at the cost of memory and initialization time.
* ``[varianceNumberPerDecade]`` (default ``400``) — The number of points to tabulate per decade of progenitor variance for first crossing rates.
* ``[varianceNumberPerDecadeNonCrossing]`` (default ``40``) — The number of points to tabulate per decade of progenitor variance for non-crossing rates.
* ``[timeNumberPerDecade]`` (default ``10``) — The number of tabulation points per decade of cosmic time used when building the first-crossing rate look-up table as a function of time; higher values improve temporal interpolation accuracy for rapidly evolving cosmologies.
* ``[varianceIsUnlimited]`` (default ``.false.``) — If true, the variance is assumed to have no upper limit (e.g. as in the case of :term:`CDM`). This allows the tabulated solutions to be extended arbitrarily. Otherwise, tables are extended to encompass just the range of variance requested.
* ``[linkingLength]`` (default ``0.2d0``) — The friends-of-friends linking length to use in computing virial density contrasts with the percolation analysis of :cite:t:`more_overdensity_2011`.

.. _physics-nodePropertyExtractorGalaxyMergerTreeIndices:

``nodePropertyExtractorGalaxyMergerTreeIndices``
------------------------------------------------

Extracts integer index properties (such as tree identifier, node identifier, and host node index) from galaxy merger trees, providing the structural metadata needed for cross-referencing merger tree outputs.

.. _physics-nodePropertyExtractorGalaxyMergerTreeMergerIndices:

``nodePropertyExtractorGalaxyMergerTreeMergerIndices``
------------------------------------------------------

Extracts integer index properties specific to merger events within galaxy merger trees, such as the indices of progenitor nodes involved in each merger, enabling tracking of merger histories.

.. _physics-nodePropertyExtractorGalaxyMergerTreeMergerPhysical:

``nodePropertyExtractorGalaxyMergerTreeMergerPhysical``
-------------------------------------------------------

Extracts physical (floating-point) properties associated with merger events in galaxy merger trees, such as masses, mass ratios, and times of mergers between progenitor galaxies.

.. _physics-nodePropertyExtractorGalaxyMergerTreePhysical:

``nodePropertyExtractorGalaxyMergerTreePhysical``
-------------------------------------------------

Extracts physical (floating-point) properties of nodes within galaxy merger trees, such as halo masses, virial radii, and cosmic times, providing the continuous-valued data needed for merger tree analysis.

.. _physics-nodePropertyExtractorHaloBias:

``nodePropertyExtractorHaloBias``
---------------------------------

A node property extractor which extracts the large scale, linearly theory bias for each node. For satellite nodes, this corresponds to the bias of their host halo.

.. _physics-nodePropertyExtractorHaloCollapseEpoch:

``nodePropertyExtractorHaloCollapseEpoch``
------------------------------------------

A node property extractor which extracts the redshift of collapse, :math:`z_\mathrm{c}`, for a halo using the definition of :cite:t:`schneider_structure_2015`, which is based on the conditional first crossing distribution from excursion set theory:

.. math::

   \delta_\mathrm{c}(z_\mathrm{c}) = \left( {\pi \over 2} \left[ \sigma^2(f M) - \sigma^2(M) \right]
   \right)^{1/2}+\delta_\mathrm{c}(z_0),

where :math:`\delta_\mathrm{c}(z)` is the critical overdensity for collapse at redshift :math:`z`, and :math:`f` is the fraction of a halo's mass assembled at formation time (given by the ``[massFractionFormation]`` parameter.

**Parameters**

* ``[massFractionFormation]`` (default ``0.05d0``) — The fraction of a halo's mass assembled at "formation" in the halo concentration algorithm of :cite:t:`schneider_structure_2015`.

.. _physics-nodePropertyExtractorHaloEnvironment:

``nodePropertyExtractorHaloEnvironment``
----------------------------------------

Extracts environmental metrics for dark matter halos, specifically the linear and non-linear local overdensity, characterizing the large-scale structure environment that influences halo formation rates, assembly bias, and galaxy evolution within the cosmological density field.

.. _physics-nodePropertyExtractorHierarchy:

``nodePropertyExtractorHierarchy``
----------------------------------

Extracts meta-properties describing the structural position of a node within the halo hierarchy, such as its depth level in the subhalo nesting, enabling analysis of multi-level substructure in merger trees.

**Methods**

* ``increment`` — Increment the hierarchy level of a node.
* ``reset`` — Reset the maximum hierarchy level of a node.

**Parameters**

* ``[factorMassReset]`` (default ``1.0d100``) — The factor by which a node's mass must increase before the previous maximum hierarchy level is forgotten.

.. _physics-nodePropertyExtractorHostNode:

``nodePropertyExtractorHostNode``
---------------------------------

An output analysis property extractor class that extracts a property from the host node of the given node.

.. _physics-nodePropertyExtractorICMCoolingPowerInBand:

``nodePropertyExtractorICMCoolingPowerInBand``
----------------------------------------------

A property extractor that returns the fraction of the hot halo (ICM) radiative cooling power emitted within a specified X-ray photon energy band---the ratio of in-band to bolometric cooling luminosity, integrated over the virial radius. The ``energyLow`` and ``energyHigh`` parameters specify the energy band boundaries in keV (e.g.\ 0.5--2.0 keV for soft X-ray). The ``label`` suffix distinguishes multiple instances of this extractor. Requires a :galacticus-class:`coolingFunctionClass` object to evaluate the cooling emissivity at each radius as a function of density, temperature, and metallicity.

**Parameters**

* ``[energyLow]`` — The minimum energy (in units of keV) for the band.
* ``[energyHigh]`` — The maximum energy (in units of keV) for the band.
* ``[label]`` — A label to use as a suffix for this property.

.. _physics-nodePropertyExtractorICMOpticalDepthLymanAlpha:

``nodePropertyExtractorICMOpticalDepthLymanAlpha``
--------------------------------------------------

Extracts the Lyman-:math:`\alpha` optical depth through the intracluster medium, integrating the line-center cross-section against the neutral hydrogen density profile out to the virial radius. Relevant for assessing Lyman-:math:`\alpha` photon escape fractions from galaxies embedded in hot gas environments.

.. _physics-nodePropertyExtractorICMSZ:

``nodePropertyExtractorICMSZ``
------------------------------

An intracluster medium Sunyaev-Zeldovich Compton-:math:`y` parameter property extractor class. Specifically, the quantity extracted is

.. math::

   Y = {\sigma_\mathrm{T} \over \mathrm{m}_\mathrm{e} \mathrm{c}^2} \int_0^{R_\mathrm{outer}} n_\mathrm{e}(R) \mathrm{k}_\mathrm{B} T(r) {4 \pi R^2 \mathrm{d} R \over D_\mathrm{A}^2},

where :math:`D_\mathrm{A}` is the angular diameter distance to the halo, and the result is expressed in units of square arcminutes. The angular diameter distance is, by default, computed from the epoch of the halo. Alternatively, a fixed angular diameter distance can be specified via the ``[distanceAngular]`` parameter. The outer radius, :math:`R_\mathrm{out}`, is either the halo virial radius (by default), or the radius enclosing the density contrast specified by the optional ``[densityContrast]`` parameter. This density contrast is relative to either ``mean`` or ``critical`` density as specified by the ``densityContrastRelativeTo`` parameter.

**Parameters**

* ``[densityContrast]`` — The density contrast within which to compute the Sunyaev-Zeldovich parameter.
* ``[densityContrastRelativeTo]`` (default ``var_str('mean')``) — The density (``mean`` or ``critical``) used in defining the density contrast.
* ``[distanceAngular]`` — The fixed angular diameter distance at which to compute the Sunyaev-Zeldovich parameter.

.. _physics-nodePropertyExtractorICMXRayLuminosity:

``nodePropertyExtractorICMXRayLuminosity``
------------------------------------------

Extracts the X-ray luminosity of the intracluster medium by integrating thermal bremsstrahlung and line emission from hot halo gas out to the virial radius, using a cooling function evaluated at each radial shell. Useful for comparison with X-ray cluster survey observations.

.. _physics-nodePropertyExtractorICMXRayTemperature:

``nodePropertyExtractorICMXRayTemperature``
-------------------------------------------

Extracts the X-ray luminosity-weighted temperature of the intracluster medium, computed as the emission-weighted mean temperature integrated over the hot halo out to the virial radius. This quantity directly corresponds to the spectroscopic temperature observable in X-ray spectroscopy of galaxy clusters.

.. _physics-nodePropertyExtractorIndexBranchTip:

``nodePropertyExtractorIndexBranchTip``
---------------------------------------

Extracts the stored index of the tip node (earliest progenitor) on the same merger tree branch as a given node. Enables identification of the branch origin and facilitates comparisons of progenitor properties along a given merger tree branch across cosmic time.

.. _physics-nodePropertyExtractorIndexLastHost:

``nodePropertyExtractorIndexLastHost``
--------------------------------------

Extracts the stored index of the last host halo node, i.e., the host halo at the time a subhalo most recently became a satellite. Useful for tracking satellite infall histories and computing the elapsed time since infall into the current host environment.

.. _physics-nodePropertyExtractorIndicesHost:

``nodePropertyExtractorIndicesHost``
------------------------------------

A node property extractor which extracts the index of the node which hosts a given node. For unhosted nodes (i.e. nodes which are not subhalos), a value of :math:`-1` is extracted instead.

**Parameters**

* ``[topLevel]`` (default ``.false.``) — If true, output the index of the host at the top level of the hierarchy, otherwise output the index of the direct host.

.. _physics-nodePropertyExtractorIndicesTree:

``nodePropertyExtractorIndicesTree``
------------------------------------

Extracts index identifiers for the merger tree containing each node, including the tree index and node index within that tree, enabling unique identification of nodes across all merger trees in a simulation output for cross-matching and provenance tracking.

.. _physics-nodePropertyExtractorIntegerList:

``nodePropertyExtractorIntegerList``
------------------------------------

Abstract base class for extractors that return a variable-length list of integer values per node, defining the interface (element count, names, descriptions, and units) for extractors that output sequences of integer-valued node properties in output analysis.

**Methods**

* ``elementCount`` — Return a count of the number of properties extracted.
* ``extract`` — Extract the properties from the given ``node``.
* ``names`` — Return the name of the properties extracted.
* ``descriptions`` — Return a description of the properties extracted.
* ``unitsInSI`` — Return the units of the properties extracted in the SI system.
* ``units`` — Return an object containing units metadata for the properties.
* ``metaData`` — Populate a hash with meta-data for the property.

.. _physics-nodePropertyExtractorIntegerScalar:

``nodePropertyExtractorIntegerScalar``
--------------------------------------

Abstract base class for extractors that return a single integer value per node (e.g., node IDs, counts, or boolean flags encoded as integers), defining the interface for all scalar integer property extraction used in output analysis.

**Methods**

* ``extract`` — Extract the property from the given ``node``.
* ``name`` — Return the name of the property extracted.
* ``description`` — Return a description of the property extracted.
* ``unitsInSI`` — Return the units of the property extracted in the SI system.
* ``units`` — Return an object containing units metadata for the property.
* ``metaData`` — Populate a hash with meta-data for the property.

.. _physics-nodePropertyExtractorIntegerTuple:

``nodePropertyExtractorIntegerTuple``
-------------------------------------

Abstract base class for extractors that return a fixed-length tuple of integer values per node, defining the interface (element count, names, descriptions, and units) for multi-valued integer outputs such as combined index arrays used in output analysis.

**Methods**

* ``elementCount`` — Return the number of properties in the tuple.
* ``extract`` — Extract the properties from the given ``node``.
* ``names`` — Return the names of the properties extracted.
* ``descriptions`` — Return descriptions of the properties extracted.
* ``unitsInSI`` — Return the units of the properties extracted in the SI system.
* ``units`` — Return an object containing units metadata for the properties.
* ``metaData`` — Populate a hash with meta-data for the property.

.. _physics-nodePropertyExtractorIsInLightcone:

``nodePropertyExtractorIsInLightcone``
--------------------------------------

Extracts a boolean flag (1 or 0) indicating whether a node falls within the observer's past lightcone geometry, accounting for the node's 3D position and cosmic time via the :galacticus-class:`geometryLightconeClass` interface. Enables construction of mock observational catalogs from simulations.

.. _physics-nodePropertyExtractorIsPhysicallyPlausible:

``nodePropertyExtractorIsPhysicallyPlausible``
----------------------------------------------

Extracts an integer flag indicating whether a node's physical state is considered plausible (e.g., non-negative masses, physical sizes), useful for quality control filtering of output catalogs.

.. _physics-nodePropertyExtractorJetPowerBlackHoles:

``nodePropertyExtractorJetPowerBlackHoles``
-------------------------------------------

Extracts a list of jet power values for all supermassive black holes in a node, enabling output of the mechanical AGN feedback power contributed by each black hole separately.

.. _physics-nodePropertyExtractorKeplerOrbit:

``nodePropertyExtractorKeplerOrbit``
------------------------------------

Abstract base class for extractors of orbital parameters stored in ``keplerOrbit`` objects associated with satellite nodes. Supports extraction of orbital energy, angular momentum, pericenter and apocenter radii, eccentricity, semi-major axis, velocities, and masses of the satellite's orbit within its host halo.

**Methods**

* ``initialize`` — Initialize the properties to be extracted.
* ``extractFromOrbit`` — Extract properties from a ``keplerOrbit`` object.

.. _physics-nodePropertyExtractorLabels:

``nodePropertyExtractorLabels``
-------------------------------

Extracts integer-encoded labels (categorical tags) attached to nodes via the ``Nodes_Labels`` module, such as merger tree branch identifiers or classification flags. Converts each registered label to an integer output for storage and analysis of labeled merger tree populations.

.. _physics-nodePropertyExtractorLightcone:

``nodePropertyExtractorLightcone``
----------------------------------

A lightcone output extractor property extractor class. The position (and velocity and redshift) of a galaxy within a lightcone will be extracted. Specifically, these properties are extracted as:

``lightconePositionX``
   Position of the galaxy (in comoving Mpc) along the radial direction of the lightcone;

``lightconePositionY``
   Position of the galaxy (in comoving Mpc) along the 1\ :math:`^\mathrm{st}` angular direction of the lightcone;

``lightconePositionZ``
   Position of the galaxy (in comoving Mpc) along the 2\ :math:`^\mathrm{nd}` angular direction of the lightcone;

``lightconePositionObservedX``
   Position of the galaxy (in comoving Mpc) along the radial direction of the lightcone, accounting for the effects of line-of-sight peculiar velocity (included only if ``[includeObservedPosition]``\ =\ ``true``);

``lightconePositionObservedY``
   Position of the galaxy (in comoving Mpc) along the 1\ :math:`^\mathrm{st}` angular direction of the lightcone, accounting for the effects of line-of-sight peculiar velocity (included only if ``[includeObservedPosition]``\ =\ ``true``);

``lightconePositionObservedZ``
   Position of the galaxy (in comoving Mpc) along the 2\ :math:`^\mathrm{nd}` angular direction of the lightcone, accounting for the effects of line-of-sight peculiar velocity (included only if ``[includeObservedPosition]``\ =\ ``true``);

``lightconeVelocityX``
   Velocity of the galaxy (in km/s) along the radial direction of the lightcone;

``lightconeVelocityY``
   Velocity of the galaxy (in km/s) along the 1\ :math:`^\mathrm{st}` angular direction of the lightcone;

``lightconeVelocityZ``
   Velocity of the galaxy (in km/s) along the 2\ :math:`^\mathrm{nd}` angular direction of the lightcone;

``lightconeRedshiftCosmological``
   Redshift of the galaxy in the lightcone\footnoteNote that this will not, in general, be precisely the same as the redshift corresponding to the output time.;

``lightconeRedshiftObserved``
   Observed redshift of the galaxy, accounting for the effects of line-of-sight peculiar velocity (included only if ``[includeObservedRedshift]``\ =\ ``true``);

``lightconeAngularTheta``
   Angular distance from pole of coordinate system (i.e. :math:`\theta` in a spherical coordinate system; included only if ``[includeAngularCoordinates]``\ =\ ``true``) [radians]

``lightconeAngularPhi``
   Angular distance around the pole of coordinate system system (i.e. :math:`\phi` in a spherical coordinate system; included only if ``[includeAngularCoordinates]``\ =\ ``true``) [radians]

``angularWeight``
   The mean number density of this galaxy per unit area on the sky (in degrees\ :math:`^{-2}`).

In order to allow this output a lightcone geometry (see :galacticus-class:`geometryLightcone`) must be specified.

**Parameters**

* ``[includeObservedRedshift]`` (default ``.false.``) — If true output the observed redshift (i.e. including the effects of peculiar velocities).
* ``[includeAngularCoordinates]`` (default ``.false.``) — If true output angular coordinates in the lightcone.
* ``[includeObservedPosition]`` (default ``.false.``) — If true output the observed position (i.e. including the effects of peculiar velocities).
* ``[atCrossing]`` (default ``.false.``) — If true output positions/velocities at the time of lightcone crossing. Otherwise, output positions at the output time.
* ``[failIfNotInLightcone]`` (default ``.true.``) — If true, a node that is not in the lightcone will cause a fatal error. Otherwise, such nodes are simply assigned unphysical values for lightcone properties.

.. _physics-nodePropertyExtractorList:

``nodePropertyExtractorList``
-----------------------------

Abstract base class for extractors that return a variable-length list of floating-point values per node, defining the interface (element count, names, descriptions, and units) for extractors that output time series, multi-epoch property histories, or other variable-length sequences in output analysis.

**Methods**

* ``elementCount`` — Return a count of the number of properties extracted.
* ``extract`` — Extract the properties from the given ``node``.
* ``names`` — Return the name of the properties extracted.
* ``descriptions`` — Return a description of the properties extracted.
* ``unitsInSI`` — Return the units of the properties extracted in the SI system.
* ``units`` — Return an object containing units metadata for the properties.
* ``metaData`` — Populate a hash with meta-data for the property.

**Parameters**

* ``[redshifts]`` (default ``[0.0d0]``) — A list of (space-separated) redshifts at which Galacticus results should be output. Redshifts need not be in any particular order.
* ``[times]`` — A list of (space-separated) times at which Galacticus results should be output. Times need not be in any particular order. Negative times are interpreted as look-back times.

.. _physics-nodePropertyExtractorList2D:

``nodePropertyExtractorList2D``
-------------------------------

An abstract base class for node property extractors that provide a 2D list (array of arrays) of floating-point properties, enabling extraction of variable-length per-node data such as merger histories or multi-epoch quantities.

**Methods**

* ``elementCount`` — Return a count of the number of properties extracted.
* ``extract`` — Extract the properties from the given ``node``.
* ``names`` — Return the name of the properties extracted.
* ``descriptions`` — Return a description of the properties extracted.
* ``unitsInSI`` — Return the units of the properties extracted in the SI system.
* ``units`` — Return an object containing units metadata for the properties.
* ``metaData`` — Populate a hash with meta-data for the property.

.. _physics-nodePropertyExtractorLmnstyEmssnLineAGN:

``nodePropertyExtractorLmnstyEmssnLineAGN``
-------------------------------------------

An emission line luminosity property extractor class for AGN narrow line regions. The luminosity of the named emission lines (given by the ``lineNames`` parameter) are computed, largely following the model of :cite:t:`feltre_nuclear_2016`.

**Parameters**

* ``[cloudyTableFileName]`` (default ``var_str('%DATASTATICPATH%/hiiRegions/emissionLineLuminosities_AGN.hdf5')``) — The file of emission line luminosities to use.
* ``[lineNames]`` — The names of the emission lines to extract.
* ``[indexSpectralShortWavelength]`` (default ``-1.7d0``) — The index, :math:`\alpha`, of the power-law spectrum at wavelengths shortward of 0.25\ :math:`\mu`\ m: :math:`S_\nu \propto \nu^\alpha` :cite:p:`feltre_nuclear_2016`.
* ``[factorFillingVolume]`` (default ``0.01d0``) — The volume-filling factor, i.e. the ratio of the volume-averaged hydrogen density to the hydrogen density.
* ``[densityHydrogen]`` (default ``1.0d3``) — Density of hydrogen in narrow line region clouds in units of cm\ :math:`^{-3}`.
* ``[temperature]`` (default ``1.0d4``) — Temperature of narrow line region clouds in units of K.

.. _physics-nodePropertyExtractorLmnstyEmssnLinePanuzzo2003:

``nodePropertyExtractorLmnstyEmssnLinePanuzzo2003``
---------------------------------------------------

An emission line luminosity property extractor class. The luminosity of the named emission line (given by the ``lineNames`` parameter: if multiple lines are named, the sum of their luminosities) is computed. Additional dust attenuation for emission line luminosities can be specified via the ``depthOpticalISMCoefficient`` parameter.

**Parameters**

* ``[lineNames]`` — The emission lines to extract.
* ``[depthOpticalISMCoefficient]`` (default ``0.0d0``) — Multiplicative coefficient for optical depth in the ISM.

.. _physics-nodePropertyExtractorLmnstyStllrCF2000:

``nodePropertyExtractorLmnstyStllrCF2000``
------------------------------------------

A property extractor that returns the dust-attenuated stellar luminosity in a specified broadband ``filterName`` (and ``filterType``) at rest-frame redshift ``redshiftBand``, applying the two-component dust model of :cite:t:`charlot_simple_2000`. In this model, young stars (:math:`\lesssim`\ 10 Myr) are attenuated by both ambient ISM dust and their birth cloud dust, while older stars are attenuated only by ISM dust. The V-band optical depths of each component are set by ``depthOpticalISMCoefficient`` and ``depthOpticalCloudsCoefficient``, with a power-law wavelength dependence controlled by ``wavelengthExponent``. Luminosities are returned in AB zero-point units (i.e.\ :math:`L_\nu` relative to the AB standard source).

**Parameters**

* ``[opacityExponent]`` (default ``0.7d0``) — The power-law exponent of wavelength in the opacity :math:`\tau \propto \lambda^{-n}` in the :cite:t:`charlot_simple_2000` two-component dust attenuation model; a value of 0.7 corresponds to the standard parameterization for interstellar and birth cloud attenuation.
* ``[birthCloudLifetime]`` (default ``1.0d-2``) — The lifetime of stellar birth clouds (in Gyr) in the :cite:t:`charlot_simple_2000` dust model; stars younger than this age are attenuated by both the ISM component and the birth cloud component, while older stars experience only ISM attenuation.
* ``[opticalDepthISM]`` (default ``0.5d0``) — The effective V-band optical depth :math:`\hat{\tau}_\mathrm{V}^\mathrm{ISM}` of the diffuse interstellar medium in the :cite:t:`charlot_simple_2000` dust attenuation model, applied to all stellar populations regardless of age.
* ``[opticalDepthBirthClouds]`` (default ``1.0d0``) — The effective V-band optical depth :math:`\hat{\tau}_\mathrm{V}^\mathrm{BC}` of the stellar birth clouds in the :cite:t:`charlot_simple_2000` dust model, applied only to stellar populations younger than ``birthCloudLifetime``; must exceed ``opticalDepthISM``.
* ``[filterName]`` — The filter to select.
* ``[filterType]`` — The filter type (rest or observed) to select.
* ``[redshiftBand]`` — The redshift of the band (if not the output redshift).
* ``[depthOpticalISMCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in the ISM.
* ``[depthOpticalCloudsCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in birth clouds.
* ``[wavelengthExponent]`` (default ``0.7d0``) — Exponent of wavelength in the optical depth.

.. _physics-nodePropertyExtractorLuminosityEmissionLine:

``nodePropertyExtractorLuminosityEmissionLine``
-----------------------------------------------

An emission line luminosity property extractor class. The luminosities of the named emission lines (given by the ``lineNames`` parameter) are computed.

**Methods**

* ``tabulate`` — Tabulate the virial density contrast as a function of mass and time.
* ``restoreTable`` — Restore a tabulated solution from file.
* ``storeTable`` — Store a tabulated solution to file.

**Parameters**

* ``[velocityCharacteristic]`` (default ``250.0d0``) — The velocity scale at which the :term:`SNe`-driven outflow rate equals the star formation rate in disks.
* ``[exponent]`` (default ``3.5d0``) — The velocity scaling of the :term:`SNe`-driven outflow rate in disks.
* ``[fraction]`` (default ``0.01d0``) — The normalization :math:`f` of the outflow rate relative to the star formation rate at a reference halo velocity of 200 km/s and expansion factor of 1, setting the overall mass-loading amplitude of the halo-scaling feedback model.
* ``[exponentVelocity]`` (default ``-2.0d0``) — The exponent of virial velocity in the outflow rate in disks.
* ``[exponentRedshift]`` (default ``0.0d0``) — The power-law exponent of the cosmological expansion factor :math:`(1+z)` in the halo-scaling outflow rate, allowing the mass-loading factor to evolve with redshift; a value of zero gives no redshift evolution.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[radiusNormalization]`` (default ``3.3d-6``) — The initial value appearing in the radius-mass relation
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the nuclear star cluster is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not nuclear star cluster stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[scaleRelativeMass]`` (default ``1.0d-2``) — The mass scale, relative to the total mass of the node, below which calculations in the delayed very simple hot halo component are allowed to become inaccurate.
* ``[starveSatellites]`` (default ``.false.``) — Specifies whether or not the hot halo should be removed ("starved") when a node becomes a satellite.
* ``[starveSatellitesOutflowed]`` (default ``.false.``) — Specifies whether or not the outflowed hot halo should be removed ("starved") when a node becomes a satellite.
* ``[outflowReturnOnFormation]`` (default ``.false.``) — Specifies whether or not outflowed gas should be returned to the hot reservoir on halo formation events.
* ``[angularMomentumAlwaysGrows]`` (default ``.false.``) — Specifies whether or not negative rates of accretion of angular momentum into the hot halo will be treated as positive for the purposes of computing the hot halo angular momentum.
* ``[fractionBaryonLimitInNodeMerger]`` (default ``.false.``) — Controls whether the hot gas content of nodes should be limited to not exceed the universal baryon fraction at node merger events. If set to ``true``, hot gas (and angular momentum, abundances, and chemicals proportionally) will be removed from the merged halo to the unaccreted gas reservoir to limit the baryonic mass to the universal baryon fraction where possible.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple disk component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[radiusStructureSolver]`` (default ``1.0d0``) — The radius (in units of the standard scale length) to use in solving for the size of the disk.
* ``[structureSolverUseCole2000Method]`` (default ``.false.``) — If true, use the method described in :cite:t:`cole_hierarchical_2000` to correct for difference between thin disk and spherical mass distributions when solving for disk radii.
* ``[diskNegativeAngularMomentumAllowed]`` (default ``.true.``) — Specifies whether or not negative angular momentum is allowed for the disk.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not disk stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumSolverRadius]`` (default ``ratioAngularMomentumSolverRadiusDefault``) — The assumed ratio of the specific angular momentum at the structure solver radius to the mean specific angular momentum of the standard disk component.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple spheroid component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[efficiencyEnergeticOutflow]`` (default ``1.0d-2``) — The proportionality factor relating mass outflow rate from the spheroid to the energy input rate divided by :math:`V_\mathrm{spheroid}^2`.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not spheroid stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumScaleRadius]`` (default ``ratioAngularMomentumScaleRadiusDefault``) — The assumed ratio of the specific angular momentum at the scale radius to the mean specific angular momentum of the standard spheroid component.
* ``[outputMergers]`` (default ``.false.``) — Determines whether or not properties of black hole mergers will be output.
* ``[fileNames]`` — The name of the file(s) from which merger tree data should be read when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[forestSizeMaximum]`` (default ``0_c_size_t``) — The maximum number of nodes allowed in a forest before it will be broken up into trees and processed individually. A value of 0 implies that forests should never be split.
* ``[presetMergerTimes]`` (default ``.true.``) — Specifies whether merging times for subhalos should be preset when reading merger trees from a file.
* ``[presetMergerNodes]`` (default ``.true.``) — Specifies whether the target nodes for mergers should be preset (i.e. determined from descendant nodes). If they are not, merging will be with each satellite's host node.
* ``[presetSubhaloMasses]`` (default ``.true.``) — Specifies whether subhalo mass should be preset when reading merger trees from a file.
* ``[subhaloAngularMomentaMethod]`` (default ``var_str('summation')``) — Specifies how to account for subhalo angular momentum when adding subhalo mass to host halo mass.
* ``[presetSubhaloIndices]`` (default ``.true.``) — Specifies whether subhalo indices should be preset when reading merger trees from a file.
* ``[presetPositions]`` (default ``.true.``) — Specifies whether node positions should be preset when reading merger trees from a file.
* ``[presetScaleRadii]`` (default ``.true.``) — Specifies whether node scale radii should be preset when reading merger trees from a file.
* ``[scaleRadiiFailureIsFatal]`` (default ``.true.``) — Specifies whether failure to set a node scale radii should be regarded as a fatal error. (If not, a fallback method to set scale radius is used in such cases.)
* ``[presetScaleRadiiConcentrationMinimum]`` (default ``3.0d0``) — The lowest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiConcentrationMaximum]`` (default ``60.0d0``) — The largest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiMinimumMass]`` (default ``0.0d0``) — The minimum halo mass for which scale radii should be preset (if ``[presetScaleRadii]``\ :math:`=`\ ``true``).
* ``[presetUnphysicalAngularMomenta]`` (default ``.false.``) — When reading merger trees from file and presetting halo angular momenta, detect unphysical (<=0) angular momenta and preset them using the selected halo spin method.
* ``[presetAngularMomenta]`` (default ``.true.``) — Specifies whether node angular momenta should be preset when reading merger trees from a file.
* ``[presetAngularMomenta3D]`` (default ``.false.``) — Specifies whether node 3-D angular momenta vectors should be preset when reading merger trees from a file.
* ``[presetOrbits]`` (default ``.true.``) — Specifies whether node orbits should be preset when reading merger trees from a file.
* ``[presetOrbitsSetAll]`` (default ``.true.``) — Forces all orbits to be set. If the computed orbit does not cross the virial radius, then select one at random instead.
* ``[presetOrbitsAssertAllSet]`` (default ``.true.``) — Asserts that all virial orbits must be preset. If any can not be set, Galacticus will stop.
* ``[presetOrbitsBoundOnly]`` (default ``.true.``) — Specifies whether only bound node orbits should be set.
* ``[beginAt]`` (default ``-1_kind_int8``) — Specifies the index of the tree to begin at. (Use -1 to always begin with the first tree.)
* ``[outputTimeSnapTolerance]`` (default ``0.0d0``) — The relative tolerance required to "snap" a node time to the closest output time.
* ``[missingHostsAreFatal]`` (default ``.true.``) — Specifies whether nodes with missing host nodes should be considered to be fatal---see the discussion of missing host nodes in the class description above.
* ``[treeIndexToRootNodeIndex]`` (default ``.false.``) — Specifies whether tree indices should always be set to the index of their root node.
* ``[allowBranchJumps]`` (default ``.true.``) — Specifies whether nodes are allowed to jump between branches.
* ``[allowSubhaloPromotions]`` (default ``.true.``) — Specifies whether subhalos are permitted to be promoted to being isolated halos.
* ``[alwaysPromoteMostMassive]`` (default ``.false.``) — If true, the most massive progenitor is always promoted to be the primary progenitor *even if* it is a subhalo. Otherwise, isolated progenitors are given priority over subhalo progenitors, even if they are less massive.
* ``[presetNamedReals]`` — Names of real datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[presetNamedIntegers]`` — Names of integer datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[fatalMismatches]`` (default ``.true.``) — Specifies whether mismatches in cosmological parameter values between Galacticus and "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be considered fatal.
* ``[fatalNonTreeNode]`` (default ``.true.``) — Specifies whether nodes in snapshot files but not in the merger tree file should be considered fatal when importing from the "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013`.
* ``[subvolumeCount]`` (default ``1``) — Specifies the number of subvolumes *along each axis* into which a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be split for processing through Galacticus.
* ``[subvolumeBuffer]`` (default ``0.0d0``) — Specifies the buffer region (in units of Mpc\ :math:`/h` to follow the format convention) around subvolumes of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file which should be read in to ensure that no halos are missed from trees.
* ``[subvolumeIndex]`` (default ``[0,0,0]``) — Specifies the index (in each dimension) of the subvolume of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file to process. Indices range from 0 to ``[subvolumeCount]``\ :math:`-1`.
* ``[badValue]`` (default ``-0.5d0``) — Use for bad value detection in "Sussing" merger trees. Values for scale radius and halo spin which exceed this threshold are assumed to be bad.
* ``[badValueTest]`` (default ``var_str('lessThan')``) — Use for bad value detection in "Sussing" merger trees. Values which exceed the threshold in ths specified direction are assumed to be bad.
* ``[treeSampleRate]`` (default ``1.0d0``) — Specify the probability that any given tree should processed (to permit subsampling).
* ``[massOptions]`` (default ``var_str('default')``) — Mass option for Sussing merger trees.
* ``[mergeProbability]`` (default ``0.1d0``) — The largest probability of branching allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[accretionLimit]`` (default ``0.1d0``) — The largest fractional mass change due to subresolution accretion allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[redshiftMaximum]`` (default ``1.0d5``) — The highest redshift to which merger trees will be built in the :cite:t:`cole_hierarchical_2000` method.
* ``[toleranceTimeEarliest]`` (default ``2.0d-6``) — The fractional tolerance used to judge if a branch is at the earliest allowed time in the tree.
* ``[branchIntervalStep]`` (default ``.true.``) — If ``false`` use the original :cite:t:`cole_hierarchical_2000` method to determine whether branching occurs in a timestep. If ``true`` draw branching intervals from a negative exponential distribution.
* ``[toleranceResolutionSelf]`` (default ``1.0d-6``) — The fractional tolerance in node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[toleranceResolutionParent]`` (default ``1.0d-3``) — The fractional tolerance in parent node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[ignoreNoProgress]`` (default ``.false.``) — If true, failure to make progress on a branch will be ignored (and the branch terminated).
* ``[ignoreWellOrdering]`` (default ``.false.``) — If true, non-well-ordered tree branches are pruned away instead of causing errors..
* ``[redshiftBase]`` (default ``0.0d0``) — The redshift at which to plant the base node when building merger trees.
* ``[timeSnapTolerance]`` (default ``1.0d-6``) — The fractional tolerance within which the tree base time will be snapped to a nearby output time.
* ``[treeBeginAt]`` (default ``0``) — The index (in order of increasing base halo mass) of the tree at which to begin when building merger trees. A value of "0" means to begin with tree number 1 (if processing trees in ascending order), or equal to the number of trees (otherwise).
* ``[processDescending]`` (default ``.true.``) — If true, causes merger trees to be processed in order of decreasing mass.
* ``[splitTrees]`` (default ``.false.``) — If true, prune away any nodes of the tree that are not needed to determine evolution up to the latest time at which a node is present inside the lightcone. This typically leads to a tree splitting into a forest of trees.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[starFormationRates]`` — The star formation rates corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of star formation rate to use when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d10``) — The star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d12``) — The maximum star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[likelihoodBins]`` — Controls which bins in the stellar mass--halo mass relation will be used in computing the likelihood: * *not present*: all bins are included in the likelihood calculation; * *list of integers*: use only the mass bin(s) given in this list in the likelihood calculation; * ``auto``: use only bins which have a non-zero number of halos contributing to them in the likelihood calculation.
* ``[fileNameTarget]`` — The name of the file containing the target data.
* ``[redshiftInterval]`` (default ``1``) — The redshift interval to use.
* ``[likelihoodNormalize]`` (default ``.false.``) — If true, then normalize the likelihood to make it a probability density.
* ``[computeScatter]`` (default ``.false.``) — If true, the scatter in log10(stellar mass) is computed. Otherwise, the mean is computed.
* ``[systematicErrorPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for stellar mass in the stellar vs halo mass relation.
* ``[systematicErrorMassHaloPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for halo mass in the stellar vs halo mass relation.
* ``[errorTolerant]`` (default ``.false.``) — Error tolerance for the N-body spin distribution operator.
* ``[logNormalRange]`` (default ``100.0d0``) — The multiplicative range of the log-normal distribution used to model the distribution of the mass and energy terms in the spin parameter. Specifically, the lognormal distribution is truncated outside the range :math:`(\lambda_\mathrm{m}/R,\lambda_\mathrm{m} R`, where :math:`\lambda_\mathrm{m}` is the measured spin, and :math:`R=`\ ``[logNormalRange]``
* ``[fileName]`` — The name of the file from which to read spin distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the spin distribution function.
* ``[comment]`` — A descriptive comment for the spin distribution function.
* ``[redshift]`` — The redshift at which to compute the spin distribution function.
* ``[massMinimum]`` — Minimum halo mass for the spin distribution function.
* ``[massMaximum]`` — Maximum halo mass for the spin distribution function.
* ``[spinMinimum]`` — Minimum spin for the spin distribution function.
* ``[spinMaximum]`` — Maximum spin for the spin distribution function.
* ``[countSpinsPerDecade]`` — Number of spins per decade at which to compute the spin distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[particleCountMinimum]`` — The minimum particle count to assume when computing N-body errors on spins.
* ``[massParticle]`` — The mass of the particle used in the N-body simulation from which spins were measured.
* ``[energyEstimateParticleCountMaximum]`` — The maximum number of particles used in estimating halo energies when measuring spins from the N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[magnitudesAbsolute]`` — The absolute magnitudes corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[luminosities]`` — The luminosities corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[includeNitrogenII]`` (default ``.false.``) — If true, include contamination by the [NII] (6548\AA :math:`+` 6584\AA) doublet.
* ``[depthOpticalISMCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in the ISM.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[rootVarianceFractionalMinimum]`` (default ``0.0d0``) — The minimum fractional root variance (relative to the target dataset).
* ``[fileName]`` — The name of the file from which to read concentration distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the concentration distribution function.
* ``[comment]`` — A descriptive comment for the concentration distribution function.
* ``[redshift]`` — The redshift at which to compute the concentration distribution function.
* ``[massMinimum]`` — Minimum halo mass for the concentration distribution function.
* ``[massMaximum]`` — Maximum halo mass for the concentration distribution function.
* ``[concentrationMinimum]`` — Minimum concentration for the concentration distribution function.
* ``[concentrationMaximum]`` — Maximum concentration for the concentration distribution function.
* ``[countConcentrationsPerDecade]`` — Number of concentrations per decade at which to compute the concentration distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[massParticle]`` — The particle mass in the source N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[fileName]`` — The name of the file from which to read star forming main sequence function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[separations]`` — The separations corresponding to bin centers.
* ``[massMinima]`` — The minimum mass of each mass sample.
* ``[massMaxima]`` — The maximum mass of each mass sample.
* ``[massHaloBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[wavenumberCount]`` (default ``60_c_size_t``) — The number of bins in wavenumber to use in computing the correlation function.
* ``[wavenumberMinimum]`` (default ``1.0d-3``) — The minimum wavenumber to use when computing the correlation function.
* ``[wavenumberMaximum]`` (default ``1.0d4``) — The maximum wavenumber to use when computing the correlation function.
* ``[integralConstraint]`` — The integral constraint for these correlation functions.
* ``[depthLineOfSight]`` — The line-of-sight depth over which the correlation function was projected.
* ``[halfIntegral]`` — Set to true if the projection integrand should be over line-of-sight depths greater than zero.
* ``[binnedProjectedCorrelationTarget]`` — The target function for likelihood calculations.
* ``[binnedProjectedCorrelationCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[targetLabel]`` (default ``var_str('')``) — A label for the target dataset in a plot of this analysis.
* ``[starFormationRateSpecificQuiescentLogarithmic]`` — The base-10 logarithm specific star formation rate (in units of Gyr\ :math:`^{-1}`) separating quiescent and star-forming galaxies.
* ``[starFormationRateSpecificLogarithmicError]`` — The observational fractional error in specific star formation rate (in units of dex) of galaxies.
* ``[fileName]`` — The name of the file from which to read quiescent fraction function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[radiusFractionalTruncateMinimum]`` (default ``2.0d0``) — The minimum radius (in units of the virial radius) to begin truncating the density profile.
* ``[radiusFractionalTruncateMaximum]`` (default ``4.0d0``) — The maximum radius (in units of the virial radius) to finish truncating the density profile.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[velocityDispersionApproximate]`` (default ``.true.``) — If ``true``, radial velocity dispersion is computed using an approximate method in which we assume that :math:`\sigma_\mathrm{r}^2(r) \rightarrow \sigma_\mathrm{r}^2(r) - (2/3) \epsilon(r)`, where :math:`\epsilon(r)` is the specific heating energy. If ``false`` then radial velocity dispersion is computed by numerically solving the Jeans equation.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[tolerateVelocityDispersionFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the velocity dispersion.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the radius of the maximum circular velocity.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate numerical failures when computing the gravitational potential of a heated dark matter profile, allowing the calculation to continue with a fallback result rather than aborting.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[tolerateVelocityMaximumFailure]`` (default ``.true.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[lengthResolution]`` — The gravitational softening length :math:`\Delta x` (in Mpc) of the N-body simulation, which sets the minimum spatial scale below which the dark matter profile is smoothed to avoid artificial two-body effects.
* ``[massResolution]`` — The mass resolution :math:`\Delta M` (in :math:`\mathrm{M}_\odot`) of the N-body simulation, representing the minimum halo mass that can be resolved; profiles of halos near this limit are softened to account for particle discreteness effects.
* ``[resolutionIsComoving]`` — If true, the resolution length is assumed to be fixed in comoving coordinates, otherwise in physical coordinates.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[C]`` (default ``400.0d0``) — The parameter :math:`C` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[f]`` (default ``0.02d0``) — The parameter :math:`f` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[timeFormationSeekDelta]`` (default ``0.0d0``) — The parameter :math:`\Delta \log t` by which the logarithm of the trial formation time is incremented when stepping through the formation history of a node to find the formation time. If set to zero (or a negative value) the cumulative mass histories of nodes are assumed to be monotonic functions of time, and the formation time is instead found by a root finding algorithm,
* ``[massBoundIsInactive]`` (default ``.false.``) — Specifies whether or not the bound mass of the satellite component is inactive (i.e. does not appear in any ODE being solved).
* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the halo virial radius using a the virial density definition at the last isolated time of the halo.
* ``[filterName]`` — The filter to select.
* ``[filterType]`` — The filter type (rest or observed) to select.
* ``[redshiftBand]`` — The redshift of the band (if not the output redshift).
* ``[postprocessChain]`` — The postprocessing chain to use.
* ``[cloudyTableFileName]`` (default ``var_str('%DATASTATICPATH%/hiiRegions/emissionLineLuminosities_BC2003_highResolution_imfChabrier.hdf5')``) — The file of emission line luminosities to use.
* ``[lineNames]`` — The emission lines to extract.
* ``[component]`` — The component from which to extract star formation rate.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance used in integration over stellar population spectra.
* ``[component]`` — The component from which to extract star formation rate.
* ``[radiusCore]`` — The soliton core radius (in Mpc) characterizing the size of the quantum pressure-supported central core of the fuzzy dark matter halo; the density profile flattens inside this scale.
* ``[densitySolitonCentral]`` — The central density (in :math:`\mathrm{M}_\odot`/Mpc\ :math:`^3`) of the solitonic core at :math:`r=0`, which sets the overall normalization of the density profile :math:`\rho(r) = \rho_\mathrm{c} [1+(r/r_c)^2]^{-8}`.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The relative tolerance used in numerical ODE solutions for the gravitational potential of the solitonic core profile.
* ``[dimensionless]`` (default ``.true.``) — If true the soliton profile is treated as dimensionless (scale-free), allowing its radial and density quantities to be specified in arbitrary units.
* ``[componentType]`` (default ``var_str('unknown')``) — The galactic structure component type (e.g.\ dark matter halo, disk, spheroid) represented by this mass distribution, used for component-specific queries.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type (e.g.\ dark matter, baryonic, total) represented by this mass distribution, used for mass-type-specific queries.
* ``[radiusTransition]`` — The transition radius (in Mpc) at which the density profile smoothly switches from the halo profile to the accretion flow, controlled by the fourth-order transition function :math:`f_\mathrm{trans}(r)`.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[timeAge]`` — The age of the halo (in Gyr) since its formation, determining the total time available for SIDM self-interactions to thermalize the inner halo and produce an isothermal core.
* ``[velocityRelativeMean]`` — Mean relative velocity to calculate self interaction cross section.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the potential.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[lengthResolution]`` — The spatial resolution length scale (in Mpc) below which the underlying density profile is softened to a flat core, mimicking the finite force resolution of an N-body simulation.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[massMinimum]`` — The minimum halo mass (in :math:`\mathrm{M}_\odot`) below which halos are excluded from the mass function histogram.
* ``[massMaximum]`` — The maximum halo mass (in :math:`\mathrm{M}_\odot`) above which halos are excluded from the mass function histogram.
* ``[massCountPerDecade]`` — The number of logarithmic bins per decade of halo mass used when constructing the halo mass function.
* ``[description]`` — A human-readable description of this mass function dataset, stored as metadata in the output file.
* ``[simulationReference]`` — A bibliographic reference for the N-body simulation from which this mass function is derived, stored as metadata.
* ``[simulationURL]`` — A URL pointing to the publicly accessible dataset or documentation for the N-body simulation, stored as metadata.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.
* ``[representativeMinimumCount]`` (default ``10_c_size_t``) — Minimum number of representative particles used to compute the center of a halo.
* ``[tolerance]`` (default ``1.0d-2``) — The tolerance in the summed weight of bound particles which must be attained to declare convergence.
* ``[bootstrapSampleRate]`` (default ``1.0d0``) — The sampling rate for particles.
* ``[representativeFraction]`` (default ``0.05d0``) — Fraction of bound particles used to compute the center of a halo.
* ``[analyzeAllParticles]`` (default ``.true.``) — If true, all particles are assumed to be self-bound at the beginning of the analysis. Unbound particles at previous times are allowed to become bound in the current snapshot. If false and the self-bound information from the previous snapshot is available, only the particles that are self-bound at the previous snapshot are assumed to be bound at the beginning of the analysis.
* ``[useVelocityMostBound]`` (default ``.false.``) — If true, the velocity of the most bound particle in velocity space is used as the representative velocity of the satellite. If false, use the mass weighted mean velocity (center-of-mass velocity) of self-bound particles instead.
* ``[orderRotation]`` (default ``var_str('none')``) — The order in which evaluation of likelihoods should be rotated as a function of process number.
* ``[logLikelihoodAccept]`` (default ``huge(0.0d0)``) — The log-likelihood which should be "accepted"---once the log-likelihood reaches this value (or larger) no further updates to the chain will be made.
* ``[report]`` (default ``.false.``) — If true, report on the log-likelihood obtained.
* ``[means]`` — The mean of the multivariate normal distribution.
* ``[covariance]`` — The covariance matrix for the of the multivariate normal distribution.
* ``[countForestsMaximum]`` (default ``-1_c_size_t``) — If set to a positive number, this is the maximum number of forests that will be evolved.
* ``[walltimeMaximum]`` (default ``-1_kind_int8``) — If set to a positive number, this is the maximum wall time for which forest evolution is allowed to proceed before the task gives up.
* ``[tolerateFailures]`` (default ``.false.``) — If true then failures to evolve a forest are tolerated. The forest is evolved no further, but evolution of other forests continues.
* ``[evolveForestsInParallel]`` (default ``.true.``) — If true then each forest is evolved by a separate OpenMP thread. Otherwise, a single thread evolves all forests.
* ``[suspendToRAM]`` (default ``.true.``) — Specifies whether trees should be suspended to RAM (otherwise they are suspend to file).
* ``[suspendPath]`` — The path to which tree suspension files will be stored.
* ``[timeIntervalCheckpoint]`` (default ``-1_kind_int8``) — If positive, gives the time in seconds between storing of checkpoint files. If zero or negative, no checkpointing is performed..
* ``[fileNameCheckpoint]`` — The path to which checkpoint data will be stored.
* ``[logM0]`` (default ``10.0d0``) — The parameter :math:`\log_{10} M_0` (with :math:`M_0` in units of :math:`\mathrm{M}_\odot`) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR0]`` (default ``9.0d0``) — The parameter :math:`\alpha_0` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR1]`` (default ``0.0d0``) — The parameter :math:`\alpha_1` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[cW]`` (default ``3.78062835d0``) — The parameter :math:`c_\mathrm{W}` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[beta]`` (default ``3.4638743d0``) — The parameter :math:`\beta` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[transferFunctionType]`` (default ``var_str('darkMatter')``) — Specifies whether to use the ``darkMatter`` or ``total`` transfer function.
* ``[fileName]`` — The name of the file from which to read a tabulated transfer function.
* ``[redshift]`` (default ``0.0d0``) — The redshift of the transfer function to read.
* ``[factorWavenumberSmoothExtrapolation]`` (default ``0.0d0``) — If positive, and extrapolation is used at high wavenumbers, the slope for extrapolation will be set by averaging over wavenumbers from :math:`k_\mathrm{max}/f` to :math:`k_\mathrm{max}`, where :math:`f=`\ ``[factorWavenumberSmoothExtrapolation]`` and :math:`k_\mathrm{max}` is the highest wavenumber tabulated. This avoids spurious extrapolation for highly oscillatory transfer functions.
* ``[acceptNegativeValues]`` (default ``.false.``) — If true, negative values in the transfer function are allowed (and the absolute value is taken prior to interpolation). Otherwise, negative values result in an error.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[fileName]`` (default ``var_str('none')``) — The name of the file to/from which tabulations of barrier first crossing probabilities should be written/read. If set to "``none``" tables will not be stored.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[varianceNumberPerUnitProbability]`` (default ``1000``) — The number of points to tabulate per unit variance for first crossing probabilities.
* ``[varianceNumberPerUnit]`` (default ``40``) — The number of tabulation points per unit of :math:`\sigma^2` used when building the rate look-up table for the Farahi excursion-set first-crossing distribution; higher values improve interpolation accuracy at the cost of memory and initialization time.
* ``[varianceNumberPerDecade]`` (default ``400``) — The number of points to tabulate per decade of progenitor variance for first crossing rates.
* ``[varianceNumberPerDecadeNonCrossing]`` (default ``40``) — The number of points to tabulate per decade of progenitor variance for non-crossing rates.
* ``[timeNumberPerDecade]`` (default ``10``) — The number of tabulation points per decade of cosmic time used when building the first-crossing rate look-up table as a function of time; higher values improve temporal interpolation accuracy for rapidly evolving cosmologies.
* ``[varianceIsUnlimited]`` (default ``.false.``) — If true, the variance is assumed to have no upper limit (e.g. as in the case of :term:`CDM`). This allows the tabulated solutions to be extended arbitrarily. Otherwise, tables are extended to encompass just the range of variance requested.
* ``[linkingLength]`` (default ``0.2d0``) — The friends-of-friends linking length to use in computing virial density contrasts with the percolation analysis of :cite:t:`more_overdensity_2011`.

.. _physics-nodePropertyExtractorLuminosityStellar:

``nodePropertyExtractorLuminosityStellar``
------------------------------------------

A property extractor that returns the total stellar luminosity of a node in a specified broadband filter, in units of the AB zero-point. The ``filterName`` and ``filterType`` parameters select the photometric band and whether to use rest-frame or observer-frame luminosities. The optional ``redshiftBand`` shifts the band to a fixed redshift (for K-corrections), and ``postprocessChain`` applies a named spectral postprocessing chain (e.g.\ :term:`IGM` attenuation) before the photometric integration. Luminosity indices are pre-computed per output time for efficiency.

**Methods**

* ``tabulate`` — Tabulate the virial density contrast as a function of mass and time.
* ``restoreTable`` — Restore a tabulated solution from file.
* ``storeTable`` — Store a tabulated solution to file.

**Parameters**

* ``[velocityCharacteristic]`` (default ``250.0d0``) — The velocity scale at which the :term:`SNe`-driven outflow rate equals the star formation rate in disks.
* ``[exponent]`` (default ``3.5d0``) — The velocity scaling of the :term:`SNe`-driven outflow rate in disks.
* ``[fraction]`` (default ``0.01d0``) — The normalization :math:`f` of the outflow rate relative to the star formation rate at a reference halo velocity of 200 km/s and expansion factor of 1, setting the overall mass-loading amplitude of the halo-scaling feedback model.
* ``[exponentVelocity]`` (default ``-2.0d0``) — The exponent of virial velocity in the outflow rate in disks.
* ``[exponentRedshift]`` (default ``0.0d0``) — The power-law exponent of the cosmological expansion factor :math:`(1+z)` in the halo-scaling outflow rate, allowing the mass-loading factor to evolve with redshift; a value of zero gives no redshift evolution.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[radiusNormalization]`` (default ``3.3d-6``) — The initial value appearing in the radius-mass relation
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the nuclear star cluster is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not nuclear star cluster stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[scaleRelativeMass]`` (default ``1.0d-2``) — The mass scale, relative to the total mass of the node, below which calculations in the delayed very simple hot halo component are allowed to become inaccurate.
* ``[starveSatellites]`` (default ``.false.``) — Specifies whether or not the hot halo should be removed ("starved") when a node becomes a satellite.
* ``[starveSatellitesOutflowed]`` (default ``.false.``) — Specifies whether or not the outflowed hot halo should be removed ("starved") when a node becomes a satellite.
* ``[outflowReturnOnFormation]`` (default ``.false.``) — Specifies whether or not outflowed gas should be returned to the hot reservoir on halo formation events.
* ``[angularMomentumAlwaysGrows]`` (default ``.false.``) — Specifies whether or not negative rates of accretion of angular momentum into the hot halo will be treated as positive for the purposes of computing the hot halo angular momentum.
* ``[fractionBaryonLimitInNodeMerger]`` (default ``.false.``) — Controls whether the hot gas content of nodes should be limited to not exceed the universal baryon fraction at node merger events. If set to ``true``, hot gas (and angular momentum, abundances, and chemicals proportionally) will be removed from the merged halo to the unaccreted gas reservoir to limit the baryonic mass to the universal baryon fraction where possible.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple disk component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[radiusStructureSolver]`` (default ``1.0d0``) — The radius (in units of the standard scale length) to use in solving for the size of the disk.
* ``[structureSolverUseCole2000Method]`` (default ``.false.``) — If true, use the method described in :cite:t:`cole_hierarchical_2000` to correct for difference between thin disk and spherical mass distributions when solving for disk radii.
* ``[diskNegativeAngularMomentumAllowed]`` (default ``.true.``) — Specifies whether or not negative angular momentum is allowed for the disk.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not disk stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumSolverRadius]`` (default ``ratioAngularMomentumSolverRadiusDefault``) — The assumed ratio of the specific angular momentum at the structure solver radius to the mean specific angular momentum of the standard disk component.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple spheroid component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[efficiencyEnergeticOutflow]`` (default ``1.0d-2``) — The proportionality factor relating mass outflow rate from the spheroid to the energy input rate divided by :math:`V_\mathrm{spheroid}^2`.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not spheroid stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumScaleRadius]`` (default ``ratioAngularMomentumScaleRadiusDefault``) — The assumed ratio of the specific angular momentum at the scale radius to the mean specific angular momentum of the standard spheroid component.
* ``[outputMergers]`` (default ``.false.``) — Determines whether or not properties of black hole mergers will be output.
* ``[fileNames]`` — The name of the file(s) from which merger tree data should be read when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[forestSizeMaximum]`` (default ``0_c_size_t``) — The maximum number of nodes allowed in a forest before it will be broken up into trees and processed individually. A value of 0 implies that forests should never be split.
* ``[presetMergerTimes]`` (default ``.true.``) — Specifies whether merging times for subhalos should be preset when reading merger trees from a file.
* ``[presetMergerNodes]`` (default ``.true.``) — Specifies whether the target nodes for mergers should be preset (i.e. determined from descendant nodes). If they are not, merging will be with each satellite's host node.
* ``[presetSubhaloMasses]`` (default ``.true.``) — Specifies whether subhalo mass should be preset when reading merger trees from a file.
* ``[subhaloAngularMomentaMethod]`` (default ``var_str('summation')``) — Specifies how to account for subhalo angular momentum when adding subhalo mass to host halo mass.
* ``[presetSubhaloIndices]`` (default ``.true.``) — Specifies whether subhalo indices should be preset when reading merger trees from a file.
* ``[presetPositions]`` (default ``.true.``) — Specifies whether node positions should be preset when reading merger trees from a file.
* ``[presetScaleRadii]`` (default ``.true.``) — Specifies whether node scale radii should be preset when reading merger trees from a file.
* ``[scaleRadiiFailureIsFatal]`` (default ``.true.``) — Specifies whether failure to set a node scale radii should be regarded as a fatal error. (If not, a fallback method to set scale radius is used in such cases.)
* ``[presetScaleRadiiConcentrationMinimum]`` (default ``3.0d0``) — The lowest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiConcentrationMaximum]`` (default ``60.0d0``) — The largest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiMinimumMass]`` (default ``0.0d0``) — The minimum halo mass for which scale radii should be preset (if ``[presetScaleRadii]``\ :math:`=`\ ``true``).
* ``[presetUnphysicalAngularMomenta]`` (default ``.false.``) — When reading merger trees from file and presetting halo angular momenta, detect unphysical (<=0) angular momenta and preset them using the selected halo spin method.
* ``[presetAngularMomenta]`` (default ``.true.``) — Specifies whether node angular momenta should be preset when reading merger trees from a file.
* ``[presetAngularMomenta3D]`` (default ``.false.``) — Specifies whether node 3-D angular momenta vectors should be preset when reading merger trees from a file.
* ``[presetOrbits]`` (default ``.true.``) — Specifies whether node orbits should be preset when reading merger trees from a file.
* ``[presetOrbitsSetAll]`` (default ``.true.``) — Forces all orbits to be set. If the computed orbit does not cross the virial radius, then select one at random instead.
* ``[presetOrbitsAssertAllSet]`` (default ``.true.``) — Asserts that all virial orbits must be preset. If any can not be set, Galacticus will stop.
* ``[presetOrbitsBoundOnly]`` (default ``.true.``) — Specifies whether only bound node orbits should be set.
* ``[beginAt]`` (default ``-1_kind_int8``) — Specifies the index of the tree to begin at. (Use -1 to always begin with the first tree.)
* ``[outputTimeSnapTolerance]`` (default ``0.0d0``) — The relative tolerance required to "snap" a node time to the closest output time.
* ``[missingHostsAreFatal]`` (default ``.true.``) — Specifies whether nodes with missing host nodes should be considered to be fatal---see the discussion of missing host nodes in the class description above.
* ``[treeIndexToRootNodeIndex]`` (default ``.false.``) — Specifies whether tree indices should always be set to the index of their root node.
* ``[allowBranchJumps]`` (default ``.true.``) — Specifies whether nodes are allowed to jump between branches.
* ``[allowSubhaloPromotions]`` (default ``.true.``) — Specifies whether subhalos are permitted to be promoted to being isolated halos.
* ``[alwaysPromoteMostMassive]`` (default ``.false.``) — If true, the most massive progenitor is always promoted to be the primary progenitor *even if* it is a subhalo. Otherwise, isolated progenitors are given priority over subhalo progenitors, even if they are less massive.
* ``[presetNamedReals]`` — Names of real datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[presetNamedIntegers]`` — Names of integer datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[fatalMismatches]`` (default ``.true.``) — Specifies whether mismatches in cosmological parameter values between Galacticus and "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be considered fatal.
* ``[fatalNonTreeNode]`` (default ``.true.``) — Specifies whether nodes in snapshot files but not in the merger tree file should be considered fatal when importing from the "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013`.
* ``[subvolumeCount]`` (default ``1``) — Specifies the number of subvolumes *along each axis* into which a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be split for processing through Galacticus.
* ``[subvolumeBuffer]`` (default ``0.0d0``) — Specifies the buffer region (in units of Mpc\ :math:`/h` to follow the format convention) around subvolumes of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file which should be read in to ensure that no halos are missed from trees.
* ``[subvolumeIndex]`` (default ``[0,0,0]``) — Specifies the index (in each dimension) of the subvolume of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file to process. Indices range from 0 to ``[subvolumeCount]``\ :math:`-1`.
* ``[badValue]`` (default ``-0.5d0``) — Use for bad value detection in "Sussing" merger trees. Values for scale radius and halo spin which exceed this threshold are assumed to be bad.
* ``[badValueTest]`` (default ``var_str('lessThan')``) — Use for bad value detection in "Sussing" merger trees. Values which exceed the threshold in ths specified direction are assumed to be bad.
* ``[treeSampleRate]`` (default ``1.0d0``) — Specify the probability that any given tree should processed (to permit subsampling).
* ``[massOptions]`` (default ``var_str('default')``) — Mass option for Sussing merger trees.
* ``[mergeProbability]`` (default ``0.1d0``) — The largest probability of branching allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[accretionLimit]`` (default ``0.1d0``) — The largest fractional mass change due to subresolution accretion allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[redshiftMaximum]`` (default ``1.0d5``) — The highest redshift to which merger trees will be built in the :cite:t:`cole_hierarchical_2000` method.
* ``[toleranceTimeEarliest]`` (default ``2.0d-6``) — The fractional tolerance used to judge if a branch is at the earliest allowed time in the tree.
* ``[branchIntervalStep]`` (default ``.true.``) — If ``false`` use the original :cite:t:`cole_hierarchical_2000` method to determine whether branching occurs in a timestep. If ``true`` draw branching intervals from a negative exponential distribution.
* ``[toleranceResolutionSelf]`` (default ``1.0d-6``) — The fractional tolerance in node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[toleranceResolutionParent]`` (default ``1.0d-3``) — The fractional tolerance in parent node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[ignoreNoProgress]`` (default ``.false.``) — If true, failure to make progress on a branch will be ignored (and the branch terminated).
* ``[ignoreWellOrdering]`` (default ``.false.``) — If true, non-well-ordered tree branches are pruned away instead of causing errors..
* ``[redshiftBase]`` (default ``0.0d0``) — The redshift at which to plant the base node when building merger trees.
* ``[timeSnapTolerance]`` (default ``1.0d-6``) — The fractional tolerance within which the tree base time will be snapped to a nearby output time.
* ``[treeBeginAt]`` (default ``0``) — The index (in order of increasing base halo mass) of the tree at which to begin when building merger trees. A value of "0" means to begin with tree number 1 (if processing trees in ascending order), or equal to the number of trees (otherwise).
* ``[processDescending]`` (default ``.true.``) — If true, causes merger trees to be processed in order of decreasing mass.
* ``[splitTrees]`` (default ``.false.``) — If true, prune away any nodes of the tree that are not needed to determine evolution up to the latest time at which a node is present inside the lightcone. This typically leads to a tree splitting into a forest of trees.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[starFormationRates]`` — The star formation rates corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of star formation rate to use when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d10``) — The star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d12``) — The maximum star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[likelihoodBins]`` — Controls which bins in the stellar mass--halo mass relation will be used in computing the likelihood: * *not present*: all bins are included in the likelihood calculation; * *list of integers*: use only the mass bin(s) given in this list in the likelihood calculation; * ``auto``: use only bins which have a non-zero number of halos contributing to them in the likelihood calculation.
* ``[fileNameTarget]`` — The name of the file containing the target data.
* ``[redshiftInterval]`` (default ``1``) — The redshift interval to use.
* ``[likelihoodNormalize]`` (default ``.false.``) — If true, then normalize the likelihood to make it a probability density.
* ``[computeScatter]`` (default ``.false.``) — If true, the scatter in log10(stellar mass) is computed. Otherwise, the mean is computed.
* ``[systematicErrorPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for stellar mass in the stellar vs halo mass relation.
* ``[systematicErrorMassHaloPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for halo mass in the stellar vs halo mass relation.
* ``[errorTolerant]`` (default ``.false.``) — Error tolerance for the N-body spin distribution operator.
* ``[logNormalRange]`` (default ``100.0d0``) — The multiplicative range of the log-normal distribution used to model the distribution of the mass and energy terms in the spin parameter. Specifically, the lognormal distribution is truncated outside the range :math:`(\lambda_\mathrm{m}/R,\lambda_\mathrm{m} R`, where :math:`\lambda_\mathrm{m}` is the measured spin, and :math:`R=`\ ``[logNormalRange]``
* ``[fileName]`` — The name of the file from which to read spin distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the spin distribution function.
* ``[comment]`` — A descriptive comment for the spin distribution function.
* ``[redshift]`` — The redshift at which to compute the spin distribution function.
* ``[massMinimum]`` — Minimum halo mass for the spin distribution function.
* ``[massMaximum]`` — Maximum halo mass for the spin distribution function.
* ``[spinMinimum]`` — Minimum spin for the spin distribution function.
* ``[spinMaximum]`` — Maximum spin for the spin distribution function.
* ``[countSpinsPerDecade]`` — Number of spins per decade at which to compute the spin distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[particleCountMinimum]`` — The minimum particle count to assume when computing N-body errors on spins.
* ``[massParticle]`` — The mass of the particle used in the N-body simulation from which spins were measured.
* ``[energyEstimateParticleCountMaximum]`` — The maximum number of particles used in estimating halo energies when measuring spins from the N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[magnitudesAbsolute]`` — The absolute magnitudes corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[luminosities]`` — The luminosities corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[includeNitrogenII]`` (default ``.false.``) — If true, include contamination by the [NII] (6548\AA :math:`+` 6584\AA) doublet.
* ``[depthOpticalISMCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in the ISM.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[rootVarianceFractionalMinimum]`` (default ``0.0d0``) — The minimum fractional root variance (relative to the target dataset).
* ``[fileName]`` — The name of the file from which to read concentration distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the concentration distribution function.
* ``[comment]`` — A descriptive comment for the concentration distribution function.
* ``[redshift]`` — The redshift at which to compute the concentration distribution function.
* ``[massMinimum]`` — Minimum halo mass for the concentration distribution function.
* ``[massMaximum]`` — Maximum halo mass for the concentration distribution function.
* ``[concentrationMinimum]`` — Minimum concentration for the concentration distribution function.
* ``[concentrationMaximum]`` — Maximum concentration for the concentration distribution function.
* ``[countConcentrationsPerDecade]`` — Number of concentrations per decade at which to compute the concentration distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[massParticle]`` — The particle mass in the source N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[fileName]`` — The name of the file from which to read star forming main sequence function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[separations]`` — The separations corresponding to bin centers.
* ``[massMinima]`` — The minimum mass of each mass sample.
* ``[massMaxima]`` — The maximum mass of each mass sample.
* ``[massHaloBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[wavenumberCount]`` (default ``60_c_size_t``) — The number of bins in wavenumber to use in computing the correlation function.
* ``[wavenumberMinimum]`` (default ``1.0d-3``) — The minimum wavenumber to use when computing the correlation function.
* ``[wavenumberMaximum]`` (default ``1.0d4``) — The maximum wavenumber to use when computing the correlation function.
* ``[integralConstraint]`` — The integral constraint for these correlation functions.
* ``[depthLineOfSight]`` — The line-of-sight depth over which the correlation function was projected.
* ``[halfIntegral]`` — Set to true if the projection integrand should be over line-of-sight depths greater than zero.
* ``[binnedProjectedCorrelationTarget]`` — The target function for likelihood calculations.
* ``[binnedProjectedCorrelationCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[targetLabel]`` (default ``var_str('')``) — A label for the target dataset in a plot of this analysis.
* ``[starFormationRateSpecificQuiescentLogarithmic]`` — The base-10 logarithm specific star formation rate (in units of Gyr\ :math:`^{-1}`) separating quiescent and star-forming galaxies.
* ``[starFormationRateSpecificLogarithmicError]`` — The observational fractional error in specific star formation rate (in units of dex) of galaxies.
* ``[fileName]`` — The name of the file from which to read quiescent fraction function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[radiusFractionalTruncateMinimum]`` (default ``2.0d0``) — The minimum radius (in units of the virial radius) to begin truncating the density profile.
* ``[radiusFractionalTruncateMaximum]`` (default ``4.0d0``) — The maximum radius (in units of the virial radius) to finish truncating the density profile.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[velocityDispersionApproximate]`` (default ``.true.``) — If ``true``, radial velocity dispersion is computed using an approximate method in which we assume that :math:`\sigma_\mathrm{r}^2(r) \rightarrow \sigma_\mathrm{r}^2(r) - (2/3) \epsilon(r)`, where :math:`\epsilon(r)` is the specific heating energy. If ``false`` then radial velocity dispersion is computed by numerically solving the Jeans equation.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[tolerateVelocityDispersionFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the velocity dispersion.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the radius of the maximum circular velocity.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate numerical failures when computing the gravitational potential of a heated dark matter profile, allowing the calculation to continue with a fallback result rather than aborting.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[tolerateVelocityMaximumFailure]`` (default ``.true.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[lengthResolution]`` — The gravitational softening length :math:`\Delta x` (in Mpc) of the N-body simulation, which sets the minimum spatial scale below which the dark matter profile is smoothed to avoid artificial two-body effects.
* ``[massResolution]`` — The mass resolution :math:`\Delta M` (in :math:`\mathrm{M}_\odot`) of the N-body simulation, representing the minimum halo mass that can be resolved; profiles of halos near this limit are softened to account for particle discreteness effects.
* ``[resolutionIsComoving]`` — If true, the resolution length is assumed to be fixed in comoving coordinates, otherwise in physical coordinates.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[C]`` (default ``400.0d0``) — The parameter :math:`C` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[f]`` (default ``0.02d0``) — The parameter :math:`f` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[timeFormationSeekDelta]`` (default ``0.0d0``) — The parameter :math:`\Delta \log t` by which the logarithm of the trial formation time is incremented when stepping through the formation history of a node to find the formation time. If set to zero (or a negative value) the cumulative mass histories of nodes are assumed to be monotonic functions of time, and the formation time is instead found by a root finding algorithm,
* ``[massBoundIsInactive]`` (default ``.false.``) — Specifies whether or not the bound mass of the satellite component is inactive (i.e. does not appear in any ODE being solved).
* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the halo virial radius using a the virial density definition at the last isolated time of the halo.
* ``[filterName]`` — The filter to select.
* ``[filterType]`` — The filter type (rest or observed) to select.
* ``[redshiftBand]`` — The redshift of the band (if not the output redshift).
* ``[postprocessChain]`` — The postprocessing chain to use.
* ``[cloudyTableFileName]`` (default ``var_str('%DATASTATICPATH%/hiiRegions/emissionLineLuminosities_BC2003_highResolution_imfChabrier.hdf5')``) — The file of emission line luminosities to use.
* ``[lineNames]`` — The emission lines to extract.
* ``[component]`` — The component from which to extract star formation rate.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance used in integration over stellar population spectra.
* ``[component]`` — The component from which to extract star formation rate.
* ``[radiusCore]`` — The soliton core radius (in Mpc) characterizing the size of the quantum pressure-supported central core of the fuzzy dark matter halo; the density profile flattens inside this scale.
* ``[densitySolitonCentral]`` — The central density (in :math:`\mathrm{M}_\odot`/Mpc\ :math:`^3`) of the solitonic core at :math:`r=0`, which sets the overall normalization of the density profile :math:`\rho(r) = \rho_\mathrm{c} [1+(r/r_c)^2]^{-8}`.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The relative tolerance used in numerical ODE solutions for the gravitational potential of the solitonic core profile.
* ``[dimensionless]`` (default ``.true.``) — If true the soliton profile is treated as dimensionless (scale-free), allowing its radial and density quantities to be specified in arbitrary units.
* ``[componentType]`` (default ``var_str('unknown')``) — The galactic structure component type (e.g.\ dark matter halo, disk, spheroid) represented by this mass distribution, used for component-specific queries.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type (e.g.\ dark matter, baryonic, total) represented by this mass distribution, used for mass-type-specific queries.
* ``[radiusTransition]`` — The transition radius (in Mpc) at which the density profile smoothly switches from the halo profile to the accretion flow, controlled by the fourth-order transition function :math:`f_\mathrm{trans}(r)`.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[timeAge]`` — The age of the halo (in Gyr) since its formation, determining the total time available for SIDM self-interactions to thermalize the inner halo and produce an isothermal core.
* ``[velocityRelativeMean]`` — Mean relative velocity to calculate self interaction cross section.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the potential.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[lengthResolution]`` — The spatial resolution length scale (in Mpc) below which the underlying density profile is softened to a flat core, mimicking the finite force resolution of an N-body simulation.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[massMinimum]`` — The minimum halo mass (in :math:`\mathrm{M}_\odot`) below which halos are excluded from the mass function histogram.
* ``[massMaximum]`` — The maximum halo mass (in :math:`\mathrm{M}_\odot`) above which halos are excluded from the mass function histogram.
* ``[massCountPerDecade]`` — The number of logarithmic bins per decade of halo mass used when constructing the halo mass function.
* ``[description]`` — A human-readable description of this mass function dataset, stored as metadata in the output file.
* ``[simulationReference]`` — A bibliographic reference for the N-body simulation from which this mass function is derived, stored as metadata.
* ``[simulationURL]`` — A URL pointing to the publicly accessible dataset or documentation for the N-body simulation, stored as metadata.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.
* ``[representativeMinimumCount]`` (default ``10_c_size_t``) — Minimum number of representative particles used to compute the center of a halo.
* ``[tolerance]`` (default ``1.0d-2``) — The tolerance in the summed weight of bound particles which must be attained to declare convergence.
* ``[bootstrapSampleRate]`` (default ``1.0d0``) — The sampling rate for particles.
* ``[representativeFraction]`` (default ``0.05d0``) — Fraction of bound particles used to compute the center of a halo.
* ``[analyzeAllParticles]`` (default ``.true.``) — If true, all particles are assumed to be self-bound at the beginning of the analysis. Unbound particles at previous times are allowed to become bound in the current snapshot. If false and the self-bound information from the previous snapshot is available, only the particles that are self-bound at the previous snapshot are assumed to be bound at the beginning of the analysis.
* ``[useVelocityMostBound]`` (default ``.false.``) — If true, the velocity of the most bound particle in velocity space is used as the representative velocity of the satellite. If false, use the mass weighted mean velocity (center-of-mass velocity) of self-bound particles instead.
* ``[orderRotation]`` (default ``var_str('none')``) — The order in which evaluation of likelihoods should be rotated as a function of process number.
* ``[logLikelihoodAccept]`` (default ``huge(0.0d0)``) — The log-likelihood which should be "accepted"---once the log-likelihood reaches this value (or larger) no further updates to the chain will be made.
* ``[report]`` (default ``.false.``) — If true, report on the log-likelihood obtained.
* ``[means]`` — The mean of the multivariate normal distribution.
* ``[covariance]`` — The covariance matrix for the of the multivariate normal distribution.
* ``[countForestsMaximum]`` (default ``-1_c_size_t``) — If set to a positive number, this is the maximum number of forests that will be evolved.
* ``[walltimeMaximum]`` (default ``-1_kind_int8``) — If set to a positive number, this is the maximum wall time for which forest evolution is allowed to proceed before the task gives up.
* ``[tolerateFailures]`` (default ``.false.``) — If true then failures to evolve a forest are tolerated. The forest is evolved no further, but evolution of other forests continues.
* ``[evolveForestsInParallel]`` (default ``.true.``) — If true then each forest is evolved by a separate OpenMP thread. Otherwise, a single thread evolves all forests.
* ``[suspendToRAM]`` (default ``.true.``) — Specifies whether trees should be suspended to RAM (otherwise they are suspend to file).
* ``[suspendPath]`` — The path to which tree suspension files will be stored.
* ``[timeIntervalCheckpoint]`` (default ``-1_kind_int8``) — If positive, gives the time in seconds between storing of checkpoint files. If zero or negative, no checkpointing is performed..
* ``[fileNameCheckpoint]`` — The path to which checkpoint data will be stored.
* ``[logM0]`` (default ``10.0d0``) — The parameter :math:`\log_{10} M_0` (with :math:`M_0` in units of :math:`\mathrm{M}_\odot`) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR0]`` (default ``9.0d0``) — The parameter :math:`\alpha_0` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR1]`` (default ``0.0d0``) — The parameter :math:`\alpha_1` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[cW]`` (default ``3.78062835d0``) — The parameter :math:`c_\mathrm{W}` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[beta]`` (default ``3.4638743d0``) — The parameter :math:`\beta` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[transferFunctionType]`` (default ``var_str('darkMatter')``) — Specifies whether to use the ``darkMatter`` or ``total`` transfer function.
* ``[fileName]`` — The name of the file from which to read a tabulated transfer function.
* ``[redshift]`` (default ``0.0d0``) — The redshift of the transfer function to read.
* ``[factorWavenumberSmoothExtrapolation]`` (default ``0.0d0``) — If positive, and extrapolation is used at high wavenumbers, the slope for extrapolation will be set by averaging over wavenumbers from :math:`k_\mathrm{max}/f` to :math:`k_\mathrm{max}`, where :math:`f=`\ ``[factorWavenumberSmoothExtrapolation]`` and :math:`k_\mathrm{max}` is the highest wavenumber tabulated. This avoids spurious extrapolation for highly oscillatory transfer functions.
* ``[acceptNegativeValues]`` (default ``.false.``) — If true, negative values in the transfer function are allowed (and the absolute value is taken prior to interpolation). Otherwise, negative values result in an error.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[fileName]`` (default ``var_str('none')``) — The name of the file to/from which tabulations of barrier first crossing probabilities should be written/read. If set to "``none``" tables will not be stored.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[varianceNumberPerUnitProbability]`` (default ``1000``) — The number of points to tabulate per unit variance for first crossing probabilities.
* ``[varianceNumberPerUnit]`` (default ``40``) — The number of tabulation points per unit of :math:`\sigma^2` used when building the rate look-up table for the Farahi excursion-set first-crossing distribution; higher values improve interpolation accuracy at the cost of memory and initialization time.
* ``[varianceNumberPerDecade]`` (default ``400``) — The number of points to tabulate per decade of progenitor variance for first crossing rates.
* ``[varianceNumberPerDecadeNonCrossing]`` (default ``40``) — The number of points to tabulate per decade of progenitor variance for non-crossing rates.
* ``[timeNumberPerDecade]`` (default ``10``) — The number of tabulation points per decade of cosmic time used when building the first-crossing rate look-up table as a function of time; higher values improve temporal interpolation accuracy for rapidly evolving cosmologies.
* ``[varianceIsUnlimited]`` (default ``.false.``) — If true, the variance is assumed to have no upper limit (e.g. as in the case of :term:`CDM`). This allows the tabulated solutions to be extended arbitrarily. Otherwise, tables are extended to encompass just the range of variance requested.
* ``[linkingLength]`` (default ``0.2d0``) — The friends-of-friends linking length to use in computing virial density contrasts with the percolation analysis of :cite:t:`more_overdensity_2011`.

.. _physics-nodePropertyExtractorLuminosityStellarFromSED:

``nodePropertyExtractorLuminosityStellarFromSED``
-------------------------------------------------

A property extractor that computes broadband stellar luminosities in AB units by integrating an SED (provided by a :galacticus-class:`nodePropertyExtractorSED` property extractor object) through a set of broadband filter response functions specified by ``filterNames``. For each filter, the filter transmission curve is convolved with the galaxy SED to compute :math:`L_\nu` in the AB zero-point system. This approach allows luminosities to be derived from an already-computed SED without re-running the full stellar population synthesis, making it efficient when many filters are required from a single SED.

**Parameters**

* ``[filterNames]`` — The filters to select.

.. _physics-nodePropertyExtractorMagnitudesAbsolute:

``nodePropertyExtractorMagnitudesAbsolute``
-------------------------------------------

A property extractor that returns stellar absolute magnitudes (AB system) in all broadband filters currently activated in the stellar luminosities structure, for a specified galaxy ``component`` (disk or spheroid). Output datasets are named ``componentMagnitudeAbsoluteStellar:filterName:filterType`` for each active filter and output time. Non-positive luminosities (unresolved or dark galaxies) are returned as the maximum representable double-precision value.

**Parameters**

* ``[component]`` — The component from which to extract star formation rate.

.. _physics-nodePropertyExtractorMagnitudesApparent:

``nodePropertyExtractorMagnitudesApparent``
-------------------------------------------

A property extractor that returns stellar apparent magnitudes (AB system) in all broadband filters currently activated in the stellar luminosities structure, for a specified galaxy ``component`` (disk or spheroid). The distance modulus is computed from the luminosity distance (from :galacticus-class:`cosmologyFunctionsClass`) with a :math:`+2.5\log_{10}(1+z)` K-correction for photon frequency compression. Output dataset names follow the pattern ``componentMagnitudeApparentStellar:filterName:filterType``.

**Parameters**

* ``[component]`` — The component from which to extract star formation rate.

.. _physics-nodePropertyExtractorMainBranchStatus:

``nodePropertyExtractorMainBranchStatus``
-----------------------------------------

A node property extractor class which extracts the status of each node with respect to the main branch of its merger tree. The status will be extracted as ``nodeIsOnMainBranch``, with a value of 1 indicating that the node is a primary progenitor of the final halo (i.e. is on the main branch of the tree) and a value of 0 indicating that it is not.

If ``[includeSubhalos]`` is set to true then subhalos of the main branch halo are also assigned a value of 1 (with subhalos of non-main branch halos assigned a value of 0). Otherwise, all subhalos are assigned a value of 0.

**Parameters**

* ``[massFraction]`` (default ``0.0d0``) — Mass fraction relative to the descendant node on the main branch below which the progenitor branch does not grow any further.
* ``[invertFilter]`` (default ``.false.``) — If true, the filter is inverted to pass only nodes *not* on the main branch.
* ``[includeSubhalos]`` (default ``.false.``) — If set to true then subhalos of the main branch halo are also assigned a value of 1 (with subhalos of non-main branch halos assigned a value of 0). Otherwise, all subhalos are assigned a value of 0.

.. _physics-nodePropertyExtractorMassAccretionHistory:

``nodePropertyExtractorMassAccretionHistory``
---------------------------------------------

Extracts the mass accretion history (a time series of halo mass values) for each node along the main progenitor branch, enabling analysis of halo growth histories across cosmic time.

**Methods**

* ``tabulate`` — Tabulate the virial density contrast as a function of mass and time.
* ``restoreTable`` — Restore a tabulated solution from file.
* ``storeTable`` — Store a tabulated solution to file.

**Parameters**

* ``[velocityCharacteristic]`` (default ``250.0d0``) — The velocity scale at which the :term:`SNe`-driven outflow rate equals the star formation rate in disks.
* ``[exponent]`` (default ``3.5d0``) — The velocity scaling of the :term:`SNe`-driven outflow rate in disks.
* ``[fraction]`` (default ``0.01d0``) — The normalization :math:`f` of the outflow rate relative to the star formation rate at a reference halo velocity of 200 km/s and expansion factor of 1, setting the overall mass-loading amplitude of the halo-scaling feedback model.
* ``[exponentVelocity]`` (default ``-2.0d0``) — The exponent of virial velocity in the outflow rate in disks.
* ``[exponentRedshift]`` (default ``0.0d0``) — The power-law exponent of the cosmological expansion factor :math:`(1+z)` in the halo-scaling outflow rate, allowing the mass-loading factor to evolve with redshift; a value of zero gives no redshift evolution.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[radiusNormalization]`` (default ``3.3d-6``) — The initial value appearing in the radius-mass relation
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the nuclear star cluster is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not nuclear star cluster stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[scaleRelativeMass]`` (default ``1.0d-2``) — The mass scale, relative to the total mass of the node, below which calculations in the delayed very simple hot halo component are allowed to become inaccurate.
* ``[starveSatellites]`` (default ``.false.``) — Specifies whether or not the hot halo should be removed ("starved") when a node becomes a satellite.
* ``[starveSatellitesOutflowed]`` (default ``.false.``) — Specifies whether or not the outflowed hot halo should be removed ("starved") when a node becomes a satellite.
* ``[outflowReturnOnFormation]`` (default ``.false.``) — Specifies whether or not outflowed gas should be returned to the hot reservoir on halo formation events.
* ``[angularMomentumAlwaysGrows]`` (default ``.false.``) — Specifies whether or not negative rates of accretion of angular momentum into the hot halo will be treated as positive for the purposes of computing the hot halo angular momentum.
* ``[fractionBaryonLimitInNodeMerger]`` (default ``.false.``) — Controls whether the hot gas content of nodes should be limited to not exceed the universal baryon fraction at node merger events. If set to ``true``, hot gas (and angular momentum, abundances, and chemicals proportionally) will be removed from the merged halo to the unaccreted gas reservoir to limit the baryonic mass to the universal baryon fraction where possible.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple disk component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[radiusStructureSolver]`` (default ``1.0d0``) — The radius (in units of the standard scale length) to use in solving for the size of the disk.
* ``[structureSolverUseCole2000Method]`` (default ``.false.``) — If true, use the method described in :cite:t:`cole_hierarchical_2000` to correct for difference between thin disk and spherical mass distributions when solving for disk radii.
* ``[diskNegativeAngularMomentumAllowed]`` (default ``.true.``) — Specifies whether or not negative angular momentum is allowed for the disk.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not disk stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumSolverRadius]`` (default ``ratioAngularMomentumSolverRadiusDefault``) — The assumed ratio of the specific angular momentum at the structure solver radius to the mean specific angular momentum of the standard disk component.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple spheroid component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[efficiencyEnergeticOutflow]`` (default ``1.0d-2``) — The proportionality factor relating mass outflow rate from the spheroid to the energy input rate divided by :math:`V_\mathrm{spheroid}^2`.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not spheroid stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumScaleRadius]`` (default ``ratioAngularMomentumScaleRadiusDefault``) — The assumed ratio of the specific angular momentum at the scale radius to the mean specific angular momentum of the standard spheroid component.
* ``[outputMergers]`` (default ``.false.``) — Determines whether or not properties of black hole mergers will be output.
* ``[fileNames]`` — The name of the file(s) from which merger tree data should be read when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[forestSizeMaximum]`` (default ``0_c_size_t``) — The maximum number of nodes allowed in a forest before it will be broken up into trees and processed individually. A value of 0 implies that forests should never be split.
* ``[presetMergerTimes]`` (default ``.true.``) — Specifies whether merging times for subhalos should be preset when reading merger trees from a file.
* ``[presetMergerNodes]`` (default ``.true.``) — Specifies whether the target nodes for mergers should be preset (i.e. determined from descendant nodes). If they are not, merging will be with each satellite's host node.
* ``[presetSubhaloMasses]`` (default ``.true.``) — Specifies whether subhalo mass should be preset when reading merger trees from a file.
* ``[subhaloAngularMomentaMethod]`` (default ``var_str('summation')``) — Specifies how to account for subhalo angular momentum when adding subhalo mass to host halo mass.
* ``[presetSubhaloIndices]`` (default ``.true.``) — Specifies whether subhalo indices should be preset when reading merger trees from a file.
* ``[presetPositions]`` (default ``.true.``) — Specifies whether node positions should be preset when reading merger trees from a file.
* ``[presetScaleRadii]`` (default ``.true.``) — Specifies whether node scale radii should be preset when reading merger trees from a file.
* ``[scaleRadiiFailureIsFatal]`` (default ``.true.``) — Specifies whether failure to set a node scale radii should be regarded as a fatal error. (If not, a fallback method to set scale radius is used in such cases.)
* ``[presetScaleRadiiConcentrationMinimum]`` (default ``3.0d0``) — The lowest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiConcentrationMaximum]`` (default ``60.0d0``) — The largest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiMinimumMass]`` (default ``0.0d0``) — The minimum halo mass for which scale radii should be preset (if ``[presetScaleRadii]``\ :math:`=`\ ``true``).
* ``[presetUnphysicalAngularMomenta]`` (default ``.false.``) — When reading merger trees from file and presetting halo angular momenta, detect unphysical (<=0) angular momenta and preset them using the selected halo spin method.
* ``[presetAngularMomenta]`` (default ``.true.``) — Specifies whether node angular momenta should be preset when reading merger trees from a file.
* ``[presetAngularMomenta3D]`` (default ``.false.``) — Specifies whether node 3-D angular momenta vectors should be preset when reading merger trees from a file.
* ``[presetOrbits]`` (default ``.true.``) — Specifies whether node orbits should be preset when reading merger trees from a file.
* ``[presetOrbitsSetAll]`` (default ``.true.``) — Forces all orbits to be set. If the computed orbit does not cross the virial radius, then select one at random instead.
* ``[presetOrbitsAssertAllSet]`` (default ``.true.``) — Asserts that all virial orbits must be preset. If any can not be set, Galacticus will stop.
* ``[presetOrbitsBoundOnly]`` (default ``.true.``) — Specifies whether only bound node orbits should be set.
* ``[beginAt]`` (default ``-1_kind_int8``) — Specifies the index of the tree to begin at. (Use -1 to always begin with the first tree.)
* ``[outputTimeSnapTolerance]`` (default ``0.0d0``) — The relative tolerance required to "snap" a node time to the closest output time.
* ``[missingHostsAreFatal]`` (default ``.true.``) — Specifies whether nodes with missing host nodes should be considered to be fatal---see the discussion of missing host nodes in the class description above.
* ``[treeIndexToRootNodeIndex]`` (default ``.false.``) — Specifies whether tree indices should always be set to the index of their root node.
* ``[allowBranchJumps]`` (default ``.true.``) — Specifies whether nodes are allowed to jump between branches.
* ``[allowSubhaloPromotions]`` (default ``.true.``) — Specifies whether subhalos are permitted to be promoted to being isolated halos.
* ``[alwaysPromoteMostMassive]`` (default ``.false.``) — If true, the most massive progenitor is always promoted to be the primary progenitor *even if* it is a subhalo. Otherwise, isolated progenitors are given priority over subhalo progenitors, even if they are less massive.
* ``[presetNamedReals]`` — Names of real datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[presetNamedIntegers]`` — Names of integer datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[fatalMismatches]`` (default ``.true.``) — Specifies whether mismatches in cosmological parameter values between Galacticus and "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be considered fatal.
* ``[fatalNonTreeNode]`` (default ``.true.``) — Specifies whether nodes in snapshot files but not in the merger tree file should be considered fatal when importing from the "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013`.
* ``[subvolumeCount]`` (default ``1``) — Specifies the number of subvolumes *along each axis* into which a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be split for processing through Galacticus.
* ``[subvolumeBuffer]`` (default ``0.0d0``) — Specifies the buffer region (in units of Mpc\ :math:`/h` to follow the format convention) around subvolumes of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file which should be read in to ensure that no halos are missed from trees.
* ``[subvolumeIndex]`` (default ``[0,0,0]``) — Specifies the index (in each dimension) of the subvolume of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file to process. Indices range from 0 to ``[subvolumeCount]``\ :math:`-1`.
* ``[badValue]`` (default ``-0.5d0``) — Use for bad value detection in "Sussing" merger trees. Values for scale radius and halo spin which exceed this threshold are assumed to be bad.
* ``[badValueTest]`` (default ``var_str('lessThan')``) — Use for bad value detection in "Sussing" merger trees. Values which exceed the threshold in ths specified direction are assumed to be bad.
* ``[treeSampleRate]`` (default ``1.0d0``) — Specify the probability that any given tree should processed (to permit subsampling).
* ``[massOptions]`` (default ``var_str('default')``) — Mass option for Sussing merger trees.
* ``[mergeProbability]`` (default ``0.1d0``) — The largest probability of branching allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[accretionLimit]`` (default ``0.1d0``) — The largest fractional mass change due to subresolution accretion allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[redshiftMaximum]`` (default ``1.0d5``) — The highest redshift to which merger trees will be built in the :cite:t:`cole_hierarchical_2000` method.
* ``[toleranceTimeEarliest]`` (default ``2.0d-6``) — The fractional tolerance used to judge if a branch is at the earliest allowed time in the tree.
* ``[branchIntervalStep]`` (default ``.true.``) — If ``false`` use the original :cite:t:`cole_hierarchical_2000` method to determine whether branching occurs in a timestep. If ``true`` draw branching intervals from a negative exponential distribution.
* ``[toleranceResolutionSelf]`` (default ``1.0d-6``) — The fractional tolerance in node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[toleranceResolutionParent]`` (default ``1.0d-3``) — The fractional tolerance in parent node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[ignoreNoProgress]`` (default ``.false.``) — If true, failure to make progress on a branch will be ignored (and the branch terminated).
* ``[ignoreWellOrdering]`` (default ``.false.``) — If true, non-well-ordered tree branches are pruned away instead of causing errors..
* ``[redshiftBase]`` (default ``0.0d0``) — The redshift at which to plant the base node when building merger trees.
* ``[timeSnapTolerance]`` (default ``1.0d-6``) — The fractional tolerance within which the tree base time will be snapped to a nearby output time.
* ``[treeBeginAt]`` (default ``0``) — The index (in order of increasing base halo mass) of the tree at which to begin when building merger trees. A value of "0" means to begin with tree number 1 (if processing trees in ascending order), or equal to the number of trees (otherwise).
* ``[processDescending]`` (default ``.true.``) — If true, causes merger trees to be processed in order of decreasing mass.
* ``[splitTrees]`` (default ``.false.``) — If true, prune away any nodes of the tree that are not needed to determine evolution up to the latest time at which a node is present inside the lightcone. This typically leads to a tree splitting into a forest of trees.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[starFormationRates]`` — The star formation rates corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of star formation rate to use when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d10``) — The star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d12``) — The maximum star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[likelihoodBins]`` — Controls which bins in the stellar mass--halo mass relation will be used in computing the likelihood: * *not present*: all bins are included in the likelihood calculation; * *list of integers*: use only the mass bin(s) given in this list in the likelihood calculation; * ``auto``: use only bins which have a non-zero number of halos contributing to them in the likelihood calculation.
* ``[fileNameTarget]`` — The name of the file containing the target data.
* ``[redshiftInterval]`` (default ``1``) — The redshift interval to use.
* ``[likelihoodNormalize]`` (default ``.false.``) — If true, then normalize the likelihood to make it a probability density.
* ``[computeScatter]`` (default ``.false.``) — If true, the scatter in log10(stellar mass) is computed. Otherwise, the mean is computed.
* ``[systematicErrorPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for stellar mass in the stellar vs halo mass relation.
* ``[systematicErrorMassHaloPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for halo mass in the stellar vs halo mass relation.
* ``[errorTolerant]`` (default ``.false.``) — Error tolerance for the N-body spin distribution operator.
* ``[logNormalRange]`` (default ``100.0d0``) — The multiplicative range of the log-normal distribution used to model the distribution of the mass and energy terms in the spin parameter. Specifically, the lognormal distribution is truncated outside the range :math:`(\lambda_\mathrm{m}/R,\lambda_\mathrm{m} R`, where :math:`\lambda_\mathrm{m}` is the measured spin, and :math:`R=`\ ``[logNormalRange]``
* ``[fileName]`` — The name of the file from which to read spin distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the spin distribution function.
* ``[comment]`` — A descriptive comment for the spin distribution function.
* ``[redshift]`` — The redshift at which to compute the spin distribution function.
* ``[massMinimum]`` — Minimum halo mass for the spin distribution function.
* ``[massMaximum]`` — Maximum halo mass for the spin distribution function.
* ``[spinMinimum]`` — Minimum spin for the spin distribution function.
* ``[spinMaximum]`` — Maximum spin for the spin distribution function.
* ``[countSpinsPerDecade]`` — Number of spins per decade at which to compute the spin distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[particleCountMinimum]`` — The minimum particle count to assume when computing N-body errors on spins.
* ``[massParticle]`` — The mass of the particle used in the N-body simulation from which spins were measured.
* ``[energyEstimateParticleCountMaximum]`` — The maximum number of particles used in estimating halo energies when measuring spins from the N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[magnitudesAbsolute]`` — The absolute magnitudes corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[luminosities]`` — The luminosities corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[includeNitrogenII]`` (default ``.false.``) — If true, include contamination by the [NII] (6548\AA :math:`+` 6584\AA) doublet.
* ``[depthOpticalISMCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in the ISM.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[rootVarianceFractionalMinimum]`` (default ``0.0d0``) — The minimum fractional root variance (relative to the target dataset).
* ``[fileName]`` — The name of the file from which to read concentration distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the concentration distribution function.
* ``[comment]`` — A descriptive comment for the concentration distribution function.
* ``[redshift]`` — The redshift at which to compute the concentration distribution function.
* ``[massMinimum]`` — Minimum halo mass for the concentration distribution function.
* ``[massMaximum]`` — Maximum halo mass for the concentration distribution function.
* ``[concentrationMinimum]`` — Minimum concentration for the concentration distribution function.
* ``[concentrationMaximum]`` — Maximum concentration for the concentration distribution function.
* ``[countConcentrationsPerDecade]`` — Number of concentrations per decade at which to compute the concentration distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[massParticle]`` — The particle mass in the source N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[fileName]`` — The name of the file from which to read star forming main sequence function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[separations]`` — The separations corresponding to bin centers.
* ``[massMinima]`` — The minimum mass of each mass sample.
* ``[massMaxima]`` — The maximum mass of each mass sample.
* ``[massHaloBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[wavenumberCount]`` (default ``60_c_size_t``) — The number of bins in wavenumber to use in computing the correlation function.
* ``[wavenumberMinimum]`` (default ``1.0d-3``) — The minimum wavenumber to use when computing the correlation function.
* ``[wavenumberMaximum]`` (default ``1.0d4``) — The maximum wavenumber to use when computing the correlation function.
* ``[integralConstraint]`` — The integral constraint for these correlation functions.
* ``[depthLineOfSight]`` — The line-of-sight depth over which the correlation function was projected.
* ``[halfIntegral]`` — Set to true if the projection integrand should be over line-of-sight depths greater than zero.
* ``[binnedProjectedCorrelationTarget]`` — The target function for likelihood calculations.
* ``[binnedProjectedCorrelationCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[targetLabel]`` (default ``var_str('')``) — A label for the target dataset in a plot of this analysis.
* ``[starFormationRateSpecificQuiescentLogarithmic]`` — The base-10 logarithm specific star formation rate (in units of Gyr\ :math:`^{-1}`) separating quiescent and star-forming galaxies.
* ``[starFormationRateSpecificLogarithmicError]`` — The observational fractional error in specific star formation rate (in units of dex) of galaxies.
* ``[fileName]`` — The name of the file from which to read quiescent fraction function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[radiusFractionalTruncateMinimum]`` (default ``2.0d0``) — The minimum radius (in units of the virial radius) to begin truncating the density profile.
* ``[radiusFractionalTruncateMaximum]`` (default ``4.0d0``) — The maximum radius (in units of the virial radius) to finish truncating the density profile.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[velocityDispersionApproximate]`` (default ``.true.``) — If ``true``, radial velocity dispersion is computed using an approximate method in which we assume that :math:`\sigma_\mathrm{r}^2(r) \rightarrow \sigma_\mathrm{r}^2(r) - (2/3) \epsilon(r)`, where :math:`\epsilon(r)` is the specific heating energy. If ``false`` then radial velocity dispersion is computed by numerically solving the Jeans equation.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[tolerateVelocityDispersionFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the velocity dispersion.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the radius of the maximum circular velocity.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate numerical failures when computing the gravitational potential of a heated dark matter profile, allowing the calculation to continue with a fallback result rather than aborting.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[tolerateVelocityMaximumFailure]`` (default ``.true.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[lengthResolution]`` — The gravitational softening length :math:`\Delta x` (in Mpc) of the N-body simulation, which sets the minimum spatial scale below which the dark matter profile is smoothed to avoid artificial two-body effects.
* ``[massResolution]`` — The mass resolution :math:`\Delta M` (in :math:`\mathrm{M}_\odot`) of the N-body simulation, representing the minimum halo mass that can be resolved; profiles of halos near this limit are softened to account for particle discreteness effects.
* ``[resolutionIsComoving]`` — If true, the resolution length is assumed to be fixed in comoving coordinates, otherwise in physical coordinates.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[C]`` (default ``400.0d0``) — The parameter :math:`C` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[f]`` (default ``0.02d0``) — The parameter :math:`f` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[timeFormationSeekDelta]`` (default ``0.0d0``) — The parameter :math:`\Delta \log t` by which the logarithm of the trial formation time is incremented when stepping through the formation history of a node to find the formation time. If set to zero (or a negative value) the cumulative mass histories of nodes are assumed to be monotonic functions of time, and the formation time is instead found by a root finding algorithm,
* ``[massBoundIsInactive]`` (default ``.false.``) — Specifies whether or not the bound mass of the satellite component is inactive (i.e. does not appear in any ODE being solved).
* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the halo virial radius using a the virial density definition at the last isolated time of the halo.
* ``[filterName]`` — The filter to select.
* ``[filterType]`` — The filter type (rest or observed) to select.
* ``[redshiftBand]`` — The redshift of the band (if not the output redshift).
* ``[postprocessChain]`` — The postprocessing chain to use.
* ``[cloudyTableFileName]`` (default ``var_str('%DATASTATICPATH%/hiiRegions/emissionLineLuminosities_BC2003_highResolution_imfChabrier.hdf5')``) — The file of emission line luminosities to use.
* ``[lineNames]`` — The emission lines to extract.
* ``[component]`` — The component from which to extract star formation rate.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance used in integration over stellar population spectra.
* ``[component]`` — The component from which to extract star formation rate.
* ``[radiusCore]`` — The soliton core radius (in Mpc) characterizing the size of the quantum pressure-supported central core of the fuzzy dark matter halo; the density profile flattens inside this scale.
* ``[densitySolitonCentral]`` — The central density (in :math:`\mathrm{M}_\odot`/Mpc\ :math:`^3`) of the solitonic core at :math:`r=0`, which sets the overall normalization of the density profile :math:`\rho(r) = \rho_\mathrm{c} [1+(r/r_c)^2]^{-8}`.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The relative tolerance used in numerical ODE solutions for the gravitational potential of the solitonic core profile.
* ``[dimensionless]`` (default ``.true.``) — If true the soliton profile is treated as dimensionless (scale-free), allowing its radial and density quantities to be specified in arbitrary units.
* ``[componentType]`` (default ``var_str('unknown')``) — The galactic structure component type (e.g.\ dark matter halo, disk, spheroid) represented by this mass distribution, used for component-specific queries.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type (e.g.\ dark matter, baryonic, total) represented by this mass distribution, used for mass-type-specific queries.
* ``[radiusTransition]`` — The transition radius (in Mpc) at which the density profile smoothly switches from the halo profile to the accretion flow, controlled by the fourth-order transition function :math:`f_\mathrm{trans}(r)`.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[timeAge]`` — The age of the halo (in Gyr) since its formation, determining the total time available for SIDM self-interactions to thermalize the inner halo and produce an isothermal core.
* ``[velocityRelativeMean]`` — Mean relative velocity to calculate self interaction cross section.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the potential.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[lengthResolution]`` — The spatial resolution length scale (in Mpc) below which the underlying density profile is softened to a flat core, mimicking the finite force resolution of an N-body simulation.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[massMinimum]`` — The minimum halo mass (in :math:`\mathrm{M}_\odot`) below which halos are excluded from the mass function histogram.
* ``[massMaximum]`` — The maximum halo mass (in :math:`\mathrm{M}_\odot`) above which halos are excluded from the mass function histogram.
* ``[massCountPerDecade]`` — The number of logarithmic bins per decade of halo mass used when constructing the halo mass function.
* ``[description]`` — A human-readable description of this mass function dataset, stored as metadata in the output file.
* ``[simulationReference]`` — A bibliographic reference for the N-body simulation from which this mass function is derived, stored as metadata.
* ``[simulationURL]`` — A URL pointing to the publicly accessible dataset or documentation for the N-body simulation, stored as metadata.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.
* ``[representativeMinimumCount]`` (default ``10_c_size_t``) — Minimum number of representative particles used to compute the center of a halo.
* ``[tolerance]`` (default ``1.0d-2``) — The tolerance in the summed weight of bound particles which must be attained to declare convergence.
* ``[bootstrapSampleRate]`` (default ``1.0d0``) — The sampling rate for particles.
* ``[representativeFraction]`` (default ``0.05d0``) — Fraction of bound particles used to compute the center of a halo.
* ``[analyzeAllParticles]`` (default ``.true.``) — If true, all particles are assumed to be self-bound at the beginning of the analysis. Unbound particles at previous times are allowed to become bound in the current snapshot. If false and the self-bound information from the previous snapshot is available, only the particles that are self-bound at the previous snapshot are assumed to be bound at the beginning of the analysis.
* ``[useVelocityMostBound]`` (default ``.false.``) — If true, the velocity of the most bound particle in velocity space is used as the representative velocity of the satellite. If false, use the mass weighted mean velocity (center-of-mass velocity) of self-bound particles instead.
* ``[orderRotation]`` (default ``var_str('none')``) — The order in which evaluation of likelihoods should be rotated as a function of process number.
* ``[logLikelihoodAccept]`` (default ``huge(0.0d0)``) — The log-likelihood which should be "accepted"---once the log-likelihood reaches this value (or larger) no further updates to the chain will be made.
* ``[report]`` (default ``.false.``) — If true, report on the log-likelihood obtained.
* ``[means]`` — The mean of the multivariate normal distribution.
* ``[covariance]`` — The covariance matrix for the of the multivariate normal distribution.
* ``[countForestsMaximum]`` (default ``-1_c_size_t``) — If set to a positive number, this is the maximum number of forests that will be evolved.
* ``[walltimeMaximum]`` (default ``-1_kind_int8``) — If set to a positive number, this is the maximum wall time for which forest evolution is allowed to proceed before the task gives up.
* ``[tolerateFailures]`` (default ``.false.``) — If true then failures to evolve a forest are tolerated. The forest is evolved no further, but evolution of other forests continues.
* ``[evolveForestsInParallel]`` (default ``.true.``) — If true then each forest is evolved by a separate OpenMP thread. Otherwise, a single thread evolves all forests.
* ``[suspendToRAM]`` (default ``.true.``) — Specifies whether trees should be suspended to RAM (otherwise they are suspend to file).
* ``[suspendPath]`` — The path to which tree suspension files will be stored.
* ``[timeIntervalCheckpoint]`` (default ``-1_kind_int8``) — If positive, gives the time in seconds between storing of checkpoint files. If zero or negative, no checkpointing is performed..
* ``[fileNameCheckpoint]`` — The path to which checkpoint data will be stored.
* ``[logM0]`` (default ``10.0d0``) — The parameter :math:`\log_{10} M_0` (with :math:`M_0` in units of :math:`\mathrm{M}_\odot`) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR0]`` (default ``9.0d0``) — The parameter :math:`\alpha_0` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR1]`` (default ``0.0d0``) — The parameter :math:`\alpha_1` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[cW]`` (default ``3.78062835d0``) — The parameter :math:`c_\mathrm{W}` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[beta]`` (default ``3.4638743d0``) — The parameter :math:`\beta` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[transferFunctionType]`` (default ``var_str('darkMatter')``) — Specifies whether to use the ``darkMatter`` or ``total`` transfer function.
* ``[fileName]`` — The name of the file from which to read a tabulated transfer function.
* ``[redshift]`` (default ``0.0d0``) — The redshift of the transfer function to read.
* ``[factorWavenumberSmoothExtrapolation]`` (default ``0.0d0``) — If positive, and extrapolation is used at high wavenumbers, the slope for extrapolation will be set by averaging over wavenumbers from :math:`k_\mathrm{max}/f` to :math:`k_\mathrm{max}`, where :math:`f=`\ ``[factorWavenumberSmoothExtrapolation]`` and :math:`k_\mathrm{max}` is the highest wavenumber tabulated. This avoids spurious extrapolation for highly oscillatory transfer functions.
* ``[acceptNegativeValues]`` (default ``.false.``) — If true, negative values in the transfer function are allowed (and the absolute value is taken prior to interpolation). Otherwise, negative values result in an error.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[fileName]`` (default ``var_str('none')``) — The name of the file to/from which tabulations of barrier first crossing probabilities should be written/read. If set to "``none``" tables will not be stored.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[varianceNumberPerUnitProbability]`` (default ``1000``) — The number of points to tabulate per unit variance for first crossing probabilities.
* ``[varianceNumberPerUnit]`` (default ``40``) — The number of tabulation points per unit of :math:`\sigma^2` used when building the rate look-up table for the Farahi excursion-set first-crossing distribution; higher values improve interpolation accuracy at the cost of memory and initialization time.
* ``[varianceNumberPerDecade]`` (default ``400``) — The number of points to tabulate per decade of progenitor variance for first crossing rates.
* ``[varianceNumberPerDecadeNonCrossing]`` (default ``40``) — The number of points to tabulate per decade of progenitor variance for non-crossing rates.
* ``[timeNumberPerDecade]`` (default ``10``) — The number of tabulation points per decade of cosmic time used when building the first-crossing rate look-up table as a function of time; higher values improve temporal interpolation accuracy for rapidly evolving cosmologies.
* ``[varianceIsUnlimited]`` (default ``.false.``) — If true, the variance is assumed to have no upper limit (e.g. as in the case of :term:`CDM`). This allows the tabulated solutions to be extended arbitrarily. Otherwise, tables are extended to encompass just the range of variance requested.
* ``[linkingLength]`` (default ``0.2d0``) — The friends-of-friends linking length to use in computing virial density contrasts with the percolation analysis of :cite:t:`more_overdensity_2011`.

.. _physics-nodePropertyExtractorMassAccretionHistoryHearin2021:

``nodePropertyExtractorMassAccretionHistoryHearin2021``
-------------------------------------------------------

Extracts best-fit parameters of the :cite:t:`hearin_differentiable_2021` differentiable model for halo mass accretion histories, fitting a smooth parametric form to each halo's MAH for use in empirical galaxy-halo connection models.

**Methods**

* ``powerLawIndex`` — Return the power law index at the given time.
* ``powerLawIndexDerivative`` — Return the derivative of the power law index with respect to time.
* ``timeZeroLogarithmic`` — Return the :math:`\log_{10}(t_0)` parameter.
* ``massMaximum`` — Return the maximum mass in the mass accretion history.
* ``sigmoid`` — The sigmoid interpolation function.
* ``powerLawIndexEarly_`` — Return the early-time power law index.
* ``powerLawIndexLate_`` — Return the late-time power law index.
* ``rateRollOver_`` — Return the roll-over rate.
* ``timeMaximum_`` — Return the time of maximum mass.

**Parameters**

* ``[powerLawIndexEarly]`` — The power law index governing halo mass growth at early times in the :cite:t:`hearin_differentiable_2021` rolling power-law MAH model; positive values correspond to a rapidly assembling halo at high redshift.
* ``[powerLawIndexLate]`` — The power law index governing halo mass growth at late times in the :cite:t:`hearin_differentiable_2021` rolling power-law MAH model; negative values correspond to halos that have ceased mass growth or are losing mass via tidal stripping.
* ``[rateRollOver]`` — The roll-over rate parameter :math:`k` in the :cite:t:`hearin_differentiable_2021` MAH model, controlling how rapidly the power law index transitions from its early-time to late-time value; larger :math:`k` gives a sharper transition.
* ``[timeMaximum]`` — The cosmological time (in Gyr) at which the halo reaches its peak mass in the :cite:t:`hearin_differentiable_2021` MAH model, marking the transition between mass assembly and mass loss regimes.

.. _physics-nodePropertyExtractorMassAccretionRateBlackHoles:

``nodePropertyExtractorMassAccretionRateBlackHoles``
----------------------------------------------------

Extracts a list of mass accretion rates for all supermassive black holes in each node, enabling output of per-black-hole accretion activity for analysis of AGN populations and feedback.

.. _physics-nodePropertyExtractorMassBasic:

``nodePropertyExtractorMassBasic``
----------------------------------

Extracts the "basic" mass of a node as defined by the basic component, representing the total dark matter halo mass including all mass associated with the node, suitable for halo mass function and clustering analyses.

.. _physics-nodePropertyExtractorMassBertschinger:

``nodePropertyExtractorMassBertschinger``
-----------------------------------------

Extracts the Bertschinger mass of each halo node, which is the mass enclosed within the secondary infall turnaround radius and provides a measure of the total mass within the halo's influence region.

.. _physics-nodePropertyExtractorMassBlackHole:

``nodePropertyExtractorMassBlackHole``
--------------------------------------

Extracts the mass of the central supermassive black hole in a galaxy node, accounting for growth via gas accretion and black hole mergers, for comparison with :math:`M_\bullet`--:math:`\sigma` and :math:`M_\bullet`--:math:`M_\mathrm{bulge}` scaling relations.

.. _physics-nodePropertyExtractorMassBlackHoles:

``nodePropertyExtractorMassBlackHoles``
---------------------------------------

Extracts a list of masses for all supermassive black holes in each node, providing per-black-hole mass data for analysis of black hole demographics and the black hole mass function.

.. _physics-nodePropertyExtractorMassBound:

``nodePropertyExtractorMassBound``
----------------------------------

Extracts the gravitationally bound mass remaining in a subhalo after tidal stripping, representing the mass retained within the tidal radius as the subhalo orbits in its host potential, relevant to subhalo abundance matching.

.. _physics-nodePropertyExtractorMassBoundMaximum:

``nodePropertyExtractorMassBoundMaximum``
-----------------------------------------

A node property extractor which extracts the maximum bound mass of the node. Requires the :galacticus-class:`nodeOperatorMassBoundMaximum` node operator to be used to track the maximum bound mass.

**Methods**

* ``update`` — Update the maximum bound mass of this node.

.. _physics-nodePropertyExtractorMassCooled:

``nodePropertyExtractorMassCooled``
-----------------------------------

A node property extractor which extracts the mass of gas cooled out of the :term:`CGM`. If the parameter ``[resetAfterExtract]``\ :math:`=`\ ``true`` then the cooled mass is reset to zero after extraction.

**Parameters**

* ``[resetAfterExtract]`` (default ``.false.``) — If true, the mass of gas cooled is reset to zero after being extracted.

.. _physics-nodePropertyExtractorMassHalo:

``nodePropertyExtractorMassHalo``
---------------------------------

A property extractor that returns the dark-matter-only halo mass (in :math:`\mathrm{M}_\odot`) enclosed within a radius defined by a specified virial density contrast. Two density contrast objects must be provided: ``virialDensityContrast`` for the profile interpolation and ``virialDensityContrastDefinition`` for the mass definition. If ``useLastIsolatedTime`` is ``true``, the density contrast is evaluated at the halo's last isolated time rather than the current time, yielding the conventional virial mass definition used by many halo finders.

**Parameters**

* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the halo mass using a the virial density definition at the last isolated time of the halo.

.. _physics-nodePropertyExtractorMassHost:

``nodePropertyExtractorMassHost``
---------------------------------

Extracts the virial mass of the immediate host (parent) halo for satellite nodes, distinguishing the mass of the surrounding host halo from the subhalo mass itself. Returns :math:`-1` for isolated (non-satellite) nodes where no host exists.

.. _physics-nodePropertyExtractorMassHostMaximum:

``nodePropertyExtractorMassHostMaximum``
----------------------------------------

A node property extractor which extracts the mass of the most massive node in which a node has been hosted. Requires the :galacticus-class:`nodeOperatorMassHostMaximum` node operator to be used to track the maximum host mass.

**Methods**

* ``update`` — Update the maximum host mass of this node.

.. _physics-nodePropertyExtractorMassISM:

``nodePropertyExtractorMassISM``
--------------------------------

Extracts the total interstellar medium (ISM) gas mass of a galaxy by summing the gaseous mass distributions of the disk and spheroid components. Provides the combined cold gas reservoir for comparison with observational ISM mass estimates from CO, dust, or HI surveys.

.. _physics-nodePropertyExtractorMassProfile:

``nodePropertyExtractorMassProfile``
------------------------------------

A property extractor that returns the enclosed mass profile (in :math:`\mathrm{M}_\odot`) at a user-specified set of radii, supporting a variety of radius definitions (virial radius multiples, disk/spheroid scale radii, half-mass radii, galactic mass or light fractions, and satellite bound-mass fractions). The ``radiusSpecifiers`` parameter specifies the list of radii; if ``includeRadii`` is ``true``, the actual radii in Mpc are also written to the output. The dark matter fraction from cosmological parameters is used to translate satellite bound mass into a corresponding dark matter radius.

**Parameters**

* ``[radiusSpecifiers]`` — A list of radius specifiers at which to output the enclosed mass profile.
* ``[includeRadii]`` (default ``.false.``) — Specifies whether or not the radii at which enclosed mass data are output should also be included in the output file.

.. _physics-nodePropertyExtractorMassProgenitorMaximum:

``nodePropertyExtractorMassProgenitorMaximum``
----------------------------------------------

A node property extractor which extracts the mass of the most massive progenitor of a node. Requires the :galacticus-class:`nodeOperatorMassProgenitorMaximum` node operator to be used to track the maximum progenitor mass.

.. _physics-nodePropertyExtractorMassStellar:

``nodePropertyExtractorMassStellar``
------------------------------------

Extracts the total stellar mass of a galaxy node by summing the stellar masses of disk and spheroid components, for comparison with stellar mass functions and stellar-to-halo mass relations from photometric surveys.

.. _physics-nodePropertyExtractorMassStellarMorphology:

``nodePropertyExtractorMassStellarMorphology``
----------------------------------------------

Extracts a stellar mass-weighted morphological indicator for a galaxy, quantifying the fractional contribution of disk vs. spheroid components to the total stellar mass as a proxy for Hubble-type morphological classification.

.. _physics-nodePropertyExtractorMassStellarSpheroid:

``nodePropertyExtractorMassStellarSpheroid``
--------------------------------------------

Extracts the stellar mass contained in the spheroid (bulge) component of a galaxy node, used to study bulge growth via mergers and disk instabilities and to calibrate the bulge-to-total mass ratio.

.. _physics-nodePropertyExtractorMergedSubhaloProperties:

``nodePropertyExtractorMergedSubhaloProperties``
------------------------------------------------

Extracts orbital properties (such as orbital energy, angular momentum, and pericentric distance) of subhalos at the time they merged, enabling analysis of merger dynamics and post-merger evolution.

.. _physics-nodePropertyExtractorMetallicityISM:

``nodePropertyExtractorMetallicityISM``
---------------------------------------

A property extractor that returns the gas-phase metallicity of the interstellar medium (ISM), defined as the mass ratio of a specified element to hydrogen, :math:`Z = M_X / M_\mathrm{H}`, summed over disk and spheroid gas components. The ``element`` parameter specifies the atomic symbol (e.g.\ ``Fe``, ``O``, ``Si``) for the element used to define metallicity. Only elements being actively tracked in the abundances structure are valid choices. Returns zero for nodes with no cold gas.

**Parameters**

* ``[element]`` — The atomic symbol for the element to use to define metallicity.

.. _physics-nodePropertyExtractorMetallicityStellar:

``nodePropertyExtractorMetallicityStellar``
-------------------------------------------

A property extractor that returns the stellar metallicity of a node, defined as the mass ratio of a specified element to hydrogen in the stellar component, :math:`Z_\star = M_X / M_\mathrm{H}`, summed over disk and spheroid stars. The ``element`` parameter specifies the atomic symbol (e.g.\ ``Fe``, ``O``) for the metal used in the definition. Only elements tracked by the abundances structure are valid choices. Returns zero for nodes with no stellar mass, and tracks the mass-weighted mean metallicity of all stars formed.

**Parameters**

* ``[element]`` — The atomic symbol for the element to use to define metallicity.

.. _physics-nodePropertyExtractorMostMassiveProgenitor:

``nodePropertyExtractorMostMassiveProgenitor``
----------------------------------------------

A node property extractor class which extracts a value of :math:`1` for the most massive progenitor node in a tree at each output time and :math:`0` for all other nodes.

.. _physics-nodePropertyExtractorMulti:

``nodePropertyExtractorMulti``
------------------------------

Combines multiple individual property extractors into a single extractor, iterating through a list of :galacticus-class:`nodePropertyExtractorClass` objects and collecting their outputs together, enabling extraction of diverse properties in a single pass through the node tree.

**Methods**

* ``columnDescriptions`` — Return a description of the columns.
* ``elementCount`` — Return the number of properties in the tuple.
* ``extractDouble`` — Extract the double properties from the given ``node``.
* ``extractInteger`` — Extract the integer properties from the given ``node``.
* ``names`` — Return the names of the properties extracted.
* ``descriptions`` — Return descriptions of the properties extracted.
* ``unitsInSI`` — Return the units of the properties extracted in the SI system.
* ``units`` — Return an object containing units metadata for the properties.
* ``ranks`` — Return the ranks of the properties extracted.
* ``metaData`` — Populate a hash with meta-data for the property.

.. _physics-nodePropertyExtractorNodeFormationTime:

``nodePropertyExtractorNodeFormationTime``
------------------------------------------

Extracts the cosmic formation time of each node, defined as the time at which the node first exceeded a specified mass threshold, providing a proxy for the assembly epoch of each halo.

.. _physics-nodePropertyExtractorNodeIndices:

``nodePropertyExtractorNodeIndices``
------------------------------------

A node property extract which extracts various indices related to the merger tree structure:

``nodeIndex``
   A unique\footnoteNode indices are typically unique, but there is no actual requirement within Galacticus that this must be the case. A merger tree construction method could create nodes with non-unique indices. (within a tree) integer index identifying the node;

``parentIndex``
   The index of this node's parent node (or :math:`-1` if it has no parent);

``siblingIndex``
   The index of this node's sibling node (or :math:`-1` if it has no sibling);

``satelliteIndex``
   The index of this node's first satellite node (or :math:`-1` if it has no satellites);

``nodeIsIsolated``
   Will be :math:`0` for a node which is a subhalo inside some other node (i.e. a satellite galaxy) or :math:`1` for a node that is an isolated halo (i.e. a central galaxy).

The ``nodeIndex`` property corresponds by default to the index of the node in the original merger tree. This means that as a galaxy evolves through the tree and, in particular, gets promoted into a new halo the index associated with a galaxy will change. This is useful to identify where the galaxy resides in the original (unevolved) tree structure, but does not allow galaxies to be traced from one output to the next using their ``nodeIndex`` value. By use of the node operator ``<nodeOperator value="indexShift"/>`` this behavior can be changed such that the value of ``nodeIndex`` will reflect the index of the earliest progenitor node along the main branch of the current node. As such, this index will remain the same for a given galaxy during its evolution. These two alternative algorithms for propagating node indices are illustrated in Figure :numref:`{number} <fig-NodePromotionIndexAlgorithms>`.

.. figure:: /_figures/NodePromotionIndices.png
   :name: fig-NodePromotionIndexAlgorithms

   Illustration of  options for the propagation  of node indices during  node promotion events.  Two identical trees (top row) are evolved without (left column) and one with (right column) the node operator ``<nodeOperator value="indexShift"/>`` The middle and lower rows indicate the resulting node indices after two stages of tree evolution.

**(Default implementation)**

.. _physics-nodePropertyExtractorNodeMajorMergerRecentCount:

``nodePropertyExtractorNodeMajorMergerRecentCount``
---------------------------------------------------

Extracts the count of major halo merger events that occurred within a configurable lookback time window, enabling statistical analysis of recent merger activity across the halo population.

**Parameters**

* ``[massRatioMajor]`` (default ``0.25d0``) — The mass ratio (:math:`M_2/M_1` where :math:`M_2 < M_1`) of merging halos above which the merger should be considered to be "major".
* ``[intervalRecent]`` (default ``2.0d0``) — The time interval used to define "recent" mergers. This parameter is in units of Gyr if ``[intervalType]``\ :math:`=`\ ``absolute``, or in units of the halo dynamical time if ``[intervalType]``\ :math:`=`\ ``dynamical``.
* ``[intervalType]`` (default ``var_str('dynamical')``) — Specifies the units for the ``[intervalRecent]`` parameter. If set to ``absolute`` then ``[intervalRecent]`` is given in Gyr, while if set to ``dynamical`` ``[intervalRecent]`` is given in units of the halo dynamical time.
* ``[intervalFromInfall]`` (default ``.false.``) — Specifies whether "recent" for satellite galaxies is measured from the current time, or from the time at which they were last isolated.

.. _physics-nodePropertyExtractorNodeMajorMergerTime:

``nodePropertyExtractorNodeMajorMergerTime``
--------------------------------------------

Extracts the cosmic time of the most recent major halo merger event for each node, where major mergers are defined by a configurable mass ratio threshold applied to the merging halo pair.

**Parameters**

* ``[fractionMassMajorMerger]`` (default ``0.25d0``) — The mass ratio (:math:`M_2/M_1` where :math:`M_2 < M_1`) of merging halos above which the merger should be considered to be "major".

.. _physics-nodePropertyExtractorNull:

``nodePropertyExtractorNull``
-----------------------------

A no-op property extractor that returns no output, used as a placeholder or default when no property extraction is required, primarily useful in testing or when an extractor slot must be filled without producing output.

**Parameters**

* ``[dimensionless]`` (default ``.true.``) — If true the null profile is considered to be dimensionless.

.. _physics-nodePropertyExtractorOutputSelector:

``nodePropertyExtractorOutputSelector``
---------------------------------------

A wrapper property extractor that delegates extraction to one or more child :galacticus-class:`nodePropertyExtractorClass` objects but restricts output to a user-specified subset of output times. At each output time, the extractor checks whether that time matches one of the allowed output times (within a relative tolerance set by ``toleranceRelative``); non-matching times return zero-size datasets. This is useful when different properties need to be extracted at different output epochs without running separate simulations.

**Methods**

* ``initialize`` — Initialize the object after construction.
* ``timeMatches`` — Return true if the current time matches a time for which we should extract properties.

**Parameters**

* ``[toleranceRelative]`` (default ``0.0d0``) — The relative tolerance to accept when comparing times.

.. _physics-nodePropertyExtractorPeakHeight:

``nodePropertyExtractorPeakHeight``
-----------------------------------

Extracts the peak height :math:`\nu = \delta_c / \sigma(M)` of a dark matter halo, the ratio of the linear collapse threshold to the mass-variance, which parametrizes halo formation probability and is used in excursion-set and bias analyses.

.. _physics-nodePropertyExtractorPositionOrbital:

``nodePropertyExtractorPositionOrbital``
----------------------------------------

An orbital position output analysis property extractor class. Specifically, the orbital position is defined relative to the top-level halo in any sub-halo hierarchy. That is, relative to the host halo which is itself not a sub-halo of any other halo. If the position of a (sub)\ :math:`^i`-halo with respect to the center of its (sub)\ :math:`^{i-1}`-halo host is :math:`\mathbf{x}_i` then the orbital position computed by this class is

.. math::

   \mathbf{x} = sum_{i=1}^N \mathbf{x}_i,

where :math:`N` is the depth of the node in the sub-halo hierarchy.

.. _physics-nodePropertyExtractorPresetNamedIntegers:

``nodePropertyExtractorPresetNamedIntegers``
--------------------------------------------

A node property extractor which extracts "preset" named integer quantities. These are typically used to provide additional quantities read from N-body merger trees.

**Parameters**

* ``[presetNames]`` — The names of preset properties to extract.

.. _physics-nodePropertyExtractorPresetNamedReals:

``nodePropertyExtractorPresetNamedReals``
-----------------------------------------

A node property extractor which extracts "preset" named real quantities. These are typically used to provide additional quantities read from N-body merger trees.

**Parameters**

* ``[presetNames]`` — The names of preset properties to extract.

.. _physics-nodePropertyExtractorProjectedDensity:

``nodePropertyExtractorProjectedDensity``
-----------------------------------------

A property extractor class for the projected density at a set of radii. The radii and types of projected density to output is specified by the ``radiusSpecifiers`` parameter. This parameter's value can contain multiple entries, each of which should be a valid :ref:`radius specifier <manual-sec-radiusspecifiers>`.

**Parameters**

* ``[radiusSpecifiers]`` — A list of radius specifiers at which to output the projected density profile.
* ``[includeRadii]`` (default ``.false.``) — Specifies whether or not the radii at which projected density data are output should also be included in the output file.
* ``[tolerateIntegrationFailures]`` (default ``.false.``) — Specifies whether or not failures in integration of the projected density should be tolerated.

.. _physics-nodePropertyExtractorProjectedMass:

``nodePropertyExtractorProjectedMass``
--------------------------------------

A property extractor class for the projected mass at a set of radii. The radii and types of projected mass to output is specified by the ``radiusSpecifiers`` parameter. This parameter's value can contain multiple entries, each of which should be a valid :ref:`radius specifier <manual-sec-radiusspecifiers>`.

**Parameters**

* ``[radiusSpecifiers]`` — A list of radius specifiers at which to output the projected mass profile.
* ``[includeRadii]`` (default ``.false.``) — Specifies whether or not the radii at which projected mass data are output should also be included in the output file.

.. _physics-nodePropertyExtractorPromptCusps:

``nodePropertyExtractorPromptCusps``
------------------------------------

A property extractor class for the properties of the nuclear star cluster at the moment of the black hole formation.

.. _physics-nodePropertyExtractorRadiativeEfficiencyBlackHoles:

``nodePropertyExtractorRadiativeEfficiencyBlackHoles``
------------------------------------------------------

Extracts a list of radiative efficiencies for all supermassive black holes in each node, providing the fraction of accreted mass-energy radiated as electromagnetic radiation for each black hole.

.. _physics-nodePropertyExtractorRadiiHalfLightProperties:

``nodePropertyExtractorRadiiHalfLightProperties``
-------------------------------------------------

A node property extractor which extracts half-light radii and the masses enclosed within them. The half-light radius in each specified luminosity band is extracted as ``[halfLightRadius{luminosityID}]`` (in Mpc), where ``{luminosityID}`` is the usual luminosity identifier suffix, and the total (dark + baryonic) mass within that radius is extracted as ``[halfLightMass{luminosityID}]`` (in :math:`\mathrm{M}_\odot`).

.. _physics-nodePropertyExtractorRadiusBlackHoles:

``nodePropertyExtractorRadiusBlackHoles``
-----------------------------------------

Extracts a list of radial positions and radial migration rates for all supermassive black holes in each node, enabling analysis of black hole orbital evolution within their host galaxies.

.. _physics-nodePropertyExtractorRadiusBoundMass:

``nodePropertyExtractorRadiusBoundMass``
----------------------------------------

Extracts the radius enclosing the currently gravitationally bound mass of a node, providing a measure of the physical extent of bound material as a halo undergoes tidal stripping or mass loss.

.. _physics-nodePropertyExtractorRadiusCooling:

``nodePropertyExtractorRadiusCooling``
--------------------------------------

A cooling radius property extractor class. Extracts the characteristic cooling radius in the halo in Mpc.

.. _physics-nodePropertyExtractorRadiusEffectiveStellar:

``nodePropertyExtractorRadiusEffectiveStellar``
-----------------------------------------------

Extracts the stellar mass-weighted effective (half-mass) radius of a galaxy, combining disk and spheroid contributions to compute the projected radius enclosing half the total stellar mass, for comparison to observed size--mass relations.

.. _physics-nodePropertyExtractorRadiusEinstein:

``nodePropertyExtractorRadiusEinstein``
---------------------------------------

A property extractor that computes the Einstein radius (in arcseconds) of the dark matter halo for gravitational lensing, given a background source at redshift ``redshiftSource``. The Einstein radius is determined numerically by finding the projected impact parameter at which the mean projected surface mass density enclosed within that radius equals the critical surface density :math:`\Sigma_\mathrm{cr} = \mathrm{c}^2 D_\mathrm{s} / (4\pi \mathrm{G} D_\mathrm{l} D_\mathrm{ls})`, where :math:`D_\mathrm{s}`, :math:`D_\mathrm{l}`, and :math:`D_\mathrm{ls}` are the angular diameter distances to the source, lens, and from lens to source, respectively. Numerical integration over the line-of-sight and impact parameter is performed using the halo mass distribution from :galacticus-class:`massDistributionClass`.

**Parameters**

* ``[redshiftSource]`` — The source redshift to using in Einstein radius calculations.

.. _physics-nodePropertyExtractorRadiusHalfMassGalactic:

``nodePropertyExtractorRadiusHalfMassGalactic``
-----------------------------------------------

Extracts the half-galactic-mass radius, the 3D radius enclosing half of the total galactic mass (stars plus gas) in both disk and spheroid components, used to characterize the physical extent of galaxies across cosmic time.

.. _physics-nodePropertyExtractorRadiusHalfMassStellar:

``nodePropertyExtractorRadiusHalfMassStellar``
----------------------------------------------

Extracts the projected half-stellar-mass radius (effective radius), the radius enclosing half the total stellar luminosity or stellar mass of a galaxy, a fundamental size observable used in galaxy structural studies.

.. _physics-nodePropertyExtractorRadiusOrbital:

``nodePropertyExtractorRadiusOrbital``
--------------------------------------

Extracts the current 3D orbital radius of a satellite node from the center of its host halo, tracking the satellite's position along its orbit for use in analyses of satellite radial distributions and orbital evolution.

.. _physics-nodePropertyExtractorRadiusOrbitalProjected:

``nodePropertyExtractorRadiusOrbitalProjected``
-----------------------------------------------

Extracts the projected orbital radius of a satellite node on the plane of the sky (projected along the :math:`z`-axis), providing the 2D projected separation from the host halo center for comparison with observational satellite radial profiles.

.. _physics-nodePropertyExtractorRadiusTidal:

``nodePropertyExtractorRadiusTidal``
------------------------------------

Extracts the tidal radius of each halo in Mpc, defined as the radius at which the tidal forces from the host halo equal the self-gravity of the subhalo, beyond which mass is susceptible to stripping.

.. _physics-nodePropertyExtractorRadiusVelocityMaximum:

``nodePropertyExtractorRadiusVelocityMaximum``
----------------------------------------------

Extracts the radius at which the circular velocity reaches its maximum value in the dark matter-only density profile of each halo, a key structural parameter that characterizes halo concentration and mass distribution.

**Parameters**

* ``[propertyName]`` (default ``var_str('RadiusVelocityMaximum')``) — Name of the property.

.. _physics-nodePropertyExtractorRadiusVirial:

``nodePropertyExtractorRadiusVirial``
-------------------------------------

A property extractor that returns the virial radius (in Mpc) of the dark-matter-only halo---the radius enclosing the density contrast specified by the ``virialDensityContrastDefinition`` object, with the profile computed using :galacticus-class:`darkMatterProfileDMOClass`. Two density contrast objects must be provided: one for the profile interpolation and one for the mass definition. If ``useLastIsolatedTime`` is ``true``, the density contrast is evaluated at the halo's last isolated time rather than the current time, yielding the conventionally-defined virial radius.

**Methods**

* ``tabulate`` — Tabulate the virial density contrast as a function of mass and time.
* ``restoreTable`` — Restore a tabulated solution from file.
* ``storeTable`` — Store a tabulated solution to file.

**Parameters**

* ``[velocityCharacteristic]`` (default ``250.0d0``) — The velocity scale at which the :term:`SNe`-driven outflow rate equals the star formation rate in disks.
* ``[exponent]`` (default ``3.5d0``) — The velocity scaling of the :term:`SNe`-driven outflow rate in disks.
* ``[fraction]`` (default ``0.01d0``) — The normalization :math:`f` of the outflow rate relative to the star formation rate at a reference halo velocity of 200 km/s and expansion factor of 1, setting the overall mass-loading amplitude of the halo-scaling feedback model.
* ``[exponentVelocity]`` (default ``-2.0d0``) — The exponent of virial velocity in the outflow rate in disks.
* ``[exponentRedshift]`` (default ``0.0d0``) — The power-law exponent of the cosmological expansion factor :math:`(1+z)` in the halo-scaling outflow rate, allowing the mass-loading factor to evolve with redshift; a value of zero gives no redshift evolution.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[radiusNormalization]`` (default ``3.3d-6``) — The initial value appearing in the radius-mass relation
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the nuclear star cluster is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not nuclear star cluster stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[scaleRelativeMass]`` (default ``1.0d-2``) — The mass scale, relative to the total mass of the node, below which calculations in the delayed very simple hot halo component are allowed to become inaccurate.
* ``[starveSatellites]`` (default ``.false.``) — Specifies whether or not the hot halo should be removed ("starved") when a node becomes a satellite.
* ``[starveSatellitesOutflowed]`` (default ``.false.``) — Specifies whether or not the outflowed hot halo should be removed ("starved") when a node becomes a satellite.
* ``[outflowReturnOnFormation]`` (default ``.false.``) — Specifies whether or not outflowed gas should be returned to the hot reservoir on halo formation events.
* ``[angularMomentumAlwaysGrows]`` (default ``.false.``) — Specifies whether or not negative rates of accretion of angular momentum into the hot halo will be treated as positive for the purposes of computing the hot halo angular momentum.
* ``[fractionBaryonLimitInNodeMerger]`` (default ``.false.``) — Controls whether the hot gas content of nodes should be limited to not exceed the universal baryon fraction at node merger events. If set to ``true``, hot gas (and angular momentum, abundances, and chemicals proportionally) will be removed from the merged halo to the unaccreted gas reservoir to limit the baryonic mass to the universal baryon fraction where possible.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple disk component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[radiusStructureSolver]`` (default ``1.0d0``) — The radius (in units of the standard scale length) to use in solving for the size of the disk.
* ``[structureSolverUseCole2000Method]`` (default ``.false.``) — If true, use the method described in :cite:t:`cole_hierarchical_2000` to correct for difference between thin disk and spherical mass distributions when solving for disk radii.
* ``[diskNegativeAngularMomentumAllowed]`` (default ``.true.``) — Specifies whether or not negative angular momentum is allowed for the disk.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not disk stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumSolverRadius]`` (default ``ratioAngularMomentumSolverRadiusDefault``) — The assumed ratio of the specific angular momentum at the structure solver radius to the mean specific angular momentum of the standard disk component.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple spheroid component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[efficiencyEnergeticOutflow]`` (default ``1.0d-2``) — The proportionality factor relating mass outflow rate from the spheroid to the energy input rate divided by :math:`V_\mathrm{spheroid}^2`.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not spheroid stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumScaleRadius]`` (default ``ratioAngularMomentumScaleRadiusDefault``) — The assumed ratio of the specific angular momentum at the scale radius to the mean specific angular momentum of the standard spheroid component.
* ``[outputMergers]`` (default ``.false.``) — Determines whether or not properties of black hole mergers will be output.
* ``[fileNames]`` — The name of the file(s) from which merger tree data should be read when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[forestSizeMaximum]`` (default ``0_c_size_t``) — The maximum number of nodes allowed in a forest before it will be broken up into trees and processed individually. A value of 0 implies that forests should never be split.
* ``[presetMergerTimes]`` (default ``.true.``) — Specifies whether merging times for subhalos should be preset when reading merger trees from a file.
* ``[presetMergerNodes]`` (default ``.true.``) — Specifies whether the target nodes for mergers should be preset (i.e. determined from descendant nodes). If they are not, merging will be with each satellite's host node.
* ``[presetSubhaloMasses]`` (default ``.true.``) — Specifies whether subhalo mass should be preset when reading merger trees from a file.
* ``[subhaloAngularMomentaMethod]`` (default ``var_str('summation')``) — Specifies how to account for subhalo angular momentum when adding subhalo mass to host halo mass.
* ``[presetSubhaloIndices]`` (default ``.true.``) — Specifies whether subhalo indices should be preset when reading merger trees from a file.
* ``[presetPositions]`` (default ``.true.``) — Specifies whether node positions should be preset when reading merger trees from a file.
* ``[presetScaleRadii]`` (default ``.true.``) — Specifies whether node scale radii should be preset when reading merger trees from a file.
* ``[scaleRadiiFailureIsFatal]`` (default ``.true.``) — Specifies whether failure to set a node scale radii should be regarded as a fatal error. (If not, a fallback method to set scale radius is used in such cases.)
* ``[presetScaleRadiiConcentrationMinimum]`` (default ``3.0d0``) — The lowest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiConcentrationMaximum]`` (default ``60.0d0``) — The largest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiMinimumMass]`` (default ``0.0d0``) — The minimum halo mass for which scale radii should be preset (if ``[presetScaleRadii]``\ :math:`=`\ ``true``).
* ``[presetUnphysicalAngularMomenta]`` (default ``.false.``) — When reading merger trees from file and presetting halo angular momenta, detect unphysical (<=0) angular momenta and preset them using the selected halo spin method.
* ``[presetAngularMomenta]`` (default ``.true.``) — Specifies whether node angular momenta should be preset when reading merger trees from a file.
* ``[presetAngularMomenta3D]`` (default ``.false.``) — Specifies whether node 3-D angular momenta vectors should be preset when reading merger trees from a file.
* ``[presetOrbits]`` (default ``.true.``) — Specifies whether node orbits should be preset when reading merger trees from a file.
* ``[presetOrbitsSetAll]`` (default ``.true.``) — Forces all orbits to be set. If the computed orbit does not cross the virial radius, then select one at random instead.
* ``[presetOrbitsAssertAllSet]`` (default ``.true.``) — Asserts that all virial orbits must be preset. If any can not be set, Galacticus will stop.
* ``[presetOrbitsBoundOnly]`` (default ``.true.``) — Specifies whether only bound node orbits should be set.
* ``[beginAt]`` (default ``-1_kind_int8``) — Specifies the index of the tree to begin at. (Use -1 to always begin with the first tree.)
* ``[outputTimeSnapTolerance]`` (default ``0.0d0``) — The relative tolerance required to "snap" a node time to the closest output time.
* ``[missingHostsAreFatal]`` (default ``.true.``) — Specifies whether nodes with missing host nodes should be considered to be fatal---see the discussion of missing host nodes in the class description above.
* ``[treeIndexToRootNodeIndex]`` (default ``.false.``) — Specifies whether tree indices should always be set to the index of their root node.
* ``[allowBranchJumps]`` (default ``.true.``) — Specifies whether nodes are allowed to jump between branches.
* ``[allowSubhaloPromotions]`` (default ``.true.``) — Specifies whether subhalos are permitted to be promoted to being isolated halos.
* ``[alwaysPromoteMostMassive]`` (default ``.false.``) — If true, the most massive progenitor is always promoted to be the primary progenitor *even if* it is a subhalo. Otherwise, isolated progenitors are given priority over subhalo progenitors, even if they are less massive.
* ``[presetNamedReals]`` — Names of real datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[presetNamedIntegers]`` — Names of integer datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[fatalMismatches]`` (default ``.true.``) — Specifies whether mismatches in cosmological parameter values between Galacticus and "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be considered fatal.
* ``[fatalNonTreeNode]`` (default ``.true.``) — Specifies whether nodes in snapshot files but not in the merger tree file should be considered fatal when importing from the "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013`.
* ``[subvolumeCount]`` (default ``1``) — Specifies the number of subvolumes *along each axis* into which a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be split for processing through Galacticus.
* ``[subvolumeBuffer]`` (default ``0.0d0``) — Specifies the buffer region (in units of Mpc\ :math:`/h` to follow the format convention) around subvolumes of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file which should be read in to ensure that no halos are missed from trees.
* ``[subvolumeIndex]`` (default ``[0,0,0]``) — Specifies the index (in each dimension) of the subvolume of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file to process. Indices range from 0 to ``[subvolumeCount]``\ :math:`-1`.
* ``[badValue]`` (default ``-0.5d0``) — Use for bad value detection in "Sussing" merger trees. Values for scale radius and halo spin which exceed this threshold are assumed to be bad.
* ``[badValueTest]`` (default ``var_str('lessThan')``) — Use for bad value detection in "Sussing" merger trees. Values which exceed the threshold in ths specified direction are assumed to be bad.
* ``[treeSampleRate]`` (default ``1.0d0``) — Specify the probability that any given tree should processed (to permit subsampling).
* ``[massOptions]`` (default ``var_str('default')``) — Mass option for Sussing merger trees.
* ``[mergeProbability]`` (default ``0.1d0``) — The largest probability of branching allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[accretionLimit]`` (default ``0.1d0``) — The largest fractional mass change due to subresolution accretion allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[redshiftMaximum]`` (default ``1.0d5``) — The highest redshift to which merger trees will be built in the :cite:t:`cole_hierarchical_2000` method.
* ``[toleranceTimeEarliest]`` (default ``2.0d-6``) — The fractional tolerance used to judge if a branch is at the earliest allowed time in the tree.
* ``[branchIntervalStep]`` (default ``.true.``) — If ``false`` use the original :cite:t:`cole_hierarchical_2000` method to determine whether branching occurs in a timestep. If ``true`` draw branching intervals from a negative exponential distribution.
* ``[toleranceResolutionSelf]`` (default ``1.0d-6``) — The fractional tolerance in node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[toleranceResolutionParent]`` (default ``1.0d-3``) — The fractional tolerance in parent node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[ignoreNoProgress]`` (default ``.false.``) — If true, failure to make progress on a branch will be ignored (and the branch terminated).
* ``[ignoreWellOrdering]`` (default ``.false.``) — If true, non-well-ordered tree branches are pruned away instead of causing errors..
* ``[redshiftBase]`` (default ``0.0d0``) — The redshift at which to plant the base node when building merger trees.
* ``[timeSnapTolerance]`` (default ``1.0d-6``) — The fractional tolerance within which the tree base time will be snapped to a nearby output time.
* ``[treeBeginAt]`` (default ``0``) — The index (in order of increasing base halo mass) of the tree at which to begin when building merger trees. A value of "0" means to begin with tree number 1 (if processing trees in ascending order), or equal to the number of trees (otherwise).
* ``[processDescending]`` (default ``.true.``) — If true, causes merger trees to be processed in order of decreasing mass.
* ``[splitTrees]`` (default ``.false.``) — If true, prune away any nodes of the tree that are not needed to determine evolution up to the latest time at which a node is present inside the lightcone. This typically leads to a tree splitting into a forest of trees.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[starFormationRates]`` — The star formation rates corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of star formation rate to use when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d10``) — The star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d12``) — The maximum star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[likelihoodBins]`` — Controls which bins in the stellar mass--halo mass relation will be used in computing the likelihood: * *not present*: all bins are included in the likelihood calculation; * *list of integers*: use only the mass bin(s) given in this list in the likelihood calculation; * ``auto``: use only bins which have a non-zero number of halos contributing to them in the likelihood calculation.
* ``[fileNameTarget]`` — The name of the file containing the target data.
* ``[redshiftInterval]`` (default ``1``) — The redshift interval to use.
* ``[likelihoodNormalize]`` (default ``.false.``) — If true, then normalize the likelihood to make it a probability density.
* ``[computeScatter]`` (default ``.false.``) — If true, the scatter in log10(stellar mass) is computed. Otherwise, the mean is computed.
* ``[systematicErrorPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for stellar mass in the stellar vs halo mass relation.
* ``[systematicErrorMassHaloPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for halo mass in the stellar vs halo mass relation.
* ``[errorTolerant]`` (default ``.false.``) — Error tolerance for the N-body spin distribution operator.
* ``[logNormalRange]`` (default ``100.0d0``) — The multiplicative range of the log-normal distribution used to model the distribution of the mass and energy terms in the spin parameter. Specifically, the lognormal distribution is truncated outside the range :math:`(\lambda_\mathrm{m}/R,\lambda_\mathrm{m} R`, where :math:`\lambda_\mathrm{m}` is the measured spin, and :math:`R=`\ ``[logNormalRange]``
* ``[fileName]`` — The name of the file from which to read spin distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the spin distribution function.
* ``[comment]`` — A descriptive comment for the spin distribution function.
* ``[redshift]`` — The redshift at which to compute the spin distribution function.
* ``[massMinimum]`` — Minimum halo mass for the spin distribution function.
* ``[massMaximum]`` — Maximum halo mass for the spin distribution function.
* ``[spinMinimum]`` — Minimum spin for the spin distribution function.
* ``[spinMaximum]`` — Maximum spin for the spin distribution function.
* ``[countSpinsPerDecade]`` — Number of spins per decade at which to compute the spin distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[particleCountMinimum]`` — The minimum particle count to assume when computing N-body errors on spins.
* ``[massParticle]`` — The mass of the particle used in the N-body simulation from which spins were measured.
* ``[energyEstimateParticleCountMaximum]`` — The maximum number of particles used in estimating halo energies when measuring spins from the N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[magnitudesAbsolute]`` — The absolute magnitudes corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[luminosities]`` — The luminosities corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[includeNitrogenII]`` (default ``.false.``) — If true, include contamination by the [NII] (6548\AA :math:`+` 6584\AA) doublet.
* ``[depthOpticalISMCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in the ISM.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[rootVarianceFractionalMinimum]`` (default ``0.0d0``) — The minimum fractional root variance (relative to the target dataset).
* ``[fileName]`` — The name of the file from which to read concentration distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the concentration distribution function.
* ``[comment]`` — A descriptive comment for the concentration distribution function.
* ``[redshift]`` — The redshift at which to compute the concentration distribution function.
* ``[massMinimum]`` — Minimum halo mass for the concentration distribution function.
* ``[massMaximum]`` — Maximum halo mass for the concentration distribution function.
* ``[concentrationMinimum]`` — Minimum concentration for the concentration distribution function.
* ``[concentrationMaximum]`` — Maximum concentration for the concentration distribution function.
* ``[countConcentrationsPerDecade]`` — Number of concentrations per decade at which to compute the concentration distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[massParticle]`` — The particle mass in the source N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[fileName]`` — The name of the file from which to read star forming main sequence function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[separations]`` — The separations corresponding to bin centers.
* ``[massMinima]`` — The minimum mass of each mass sample.
* ``[massMaxima]`` — The maximum mass of each mass sample.
* ``[massHaloBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[wavenumberCount]`` (default ``60_c_size_t``) — The number of bins in wavenumber to use in computing the correlation function.
* ``[wavenumberMinimum]`` (default ``1.0d-3``) — The minimum wavenumber to use when computing the correlation function.
* ``[wavenumberMaximum]`` (default ``1.0d4``) — The maximum wavenumber to use when computing the correlation function.
* ``[integralConstraint]`` — The integral constraint for these correlation functions.
* ``[depthLineOfSight]`` — The line-of-sight depth over which the correlation function was projected.
* ``[halfIntegral]`` — Set to true if the projection integrand should be over line-of-sight depths greater than zero.
* ``[binnedProjectedCorrelationTarget]`` — The target function for likelihood calculations.
* ``[binnedProjectedCorrelationCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[targetLabel]`` (default ``var_str('')``) — A label for the target dataset in a plot of this analysis.
* ``[starFormationRateSpecificQuiescentLogarithmic]`` — The base-10 logarithm specific star formation rate (in units of Gyr\ :math:`^{-1}`) separating quiescent and star-forming galaxies.
* ``[starFormationRateSpecificLogarithmicError]`` — The observational fractional error in specific star formation rate (in units of dex) of galaxies.
* ``[fileName]`` — The name of the file from which to read quiescent fraction function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[radiusFractionalTruncateMinimum]`` (default ``2.0d0``) — The minimum radius (in units of the virial radius) to begin truncating the density profile.
* ``[radiusFractionalTruncateMaximum]`` (default ``4.0d0``) — The maximum radius (in units of the virial radius) to finish truncating the density profile.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[velocityDispersionApproximate]`` (default ``.true.``) — If ``true``, radial velocity dispersion is computed using an approximate method in which we assume that :math:`\sigma_\mathrm{r}^2(r) \rightarrow \sigma_\mathrm{r}^2(r) - (2/3) \epsilon(r)`, where :math:`\epsilon(r)` is the specific heating energy. If ``false`` then radial velocity dispersion is computed by numerically solving the Jeans equation.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[tolerateVelocityDispersionFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the velocity dispersion.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the radius of the maximum circular velocity.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate numerical failures when computing the gravitational potential of a heated dark matter profile, allowing the calculation to continue with a fallback result rather than aborting.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[tolerateVelocityMaximumFailure]`` (default ``.true.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[lengthResolution]`` — The gravitational softening length :math:`\Delta x` (in Mpc) of the N-body simulation, which sets the minimum spatial scale below which the dark matter profile is smoothed to avoid artificial two-body effects.
* ``[massResolution]`` — The mass resolution :math:`\Delta M` (in :math:`\mathrm{M}_\odot`) of the N-body simulation, representing the minimum halo mass that can be resolved; profiles of halos near this limit are softened to account for particle discreteness effects.
* ``[resolutionIsComoving]`` — If true, the resolution length is assumed to be fixed in comoving coordinates, otherwise in physical coordinates.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[C]`` (default ``400.0d0``) — The parameter :math:`C` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[f]`` (default ``0.02d0``) — The parameter :math:`f` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[timeFormationSeekDelta]`` (default ``0.0d0``) — The parameter :math:`\Delta \log t` by which the logarithm of the trial formation time is incremented when stepping through the formation history of a node to find the formation time. If set to zero (or a negative value) the cumulative mass histories of nodes are assumed to be monotonic functions of time, and the formation time is instead found by a root finding algorithm,
* ``[massBoundIsInactive]`` (default ``.false.``) — Specifies whether or not the bound mass of the satellite component is inactive (i.e. does not appear in any ODE being solved).
* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the halo virial radius using a the virial density definition at the last isolated time of the halo.
* ``[filterName]`` — The filter to select.
* ``[filterType]`` — The filter type (rest or observed) to select.
* ``[redshiftBand]`` — The redshift of the band (if not the output redshift).
* ``[postprocessChain]`` — The postprocessing chain to use.
* ``[cloudyTableFileName]`` (default ``var_str('%DATASTATICPATH%/hiiRegions/emissionLineLuminosities_BC2003_highResolution_imfChabrier.hdf5')``) — The file of emission line luminosities to use.
* ``[lineNames]`` — The emission lines to extract.
* ``[component]`` — The component from which to extract star formation rate.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance used in integration over stellar population spectra.
* ``[component]`` — The component from which to extract star formation rate.
* ``[radiusCore]`` — The soliton core radius (in Mpc) characterizing the size of the quantum pressure-supported central core of the fuzzy dark matter halo; the density profile flattens inside this scale.
* ``[densitySolitonCentral]`` — The central density (in :math:`\mathrm{M}_\odot`/Mpc\ :math:`^3`) of the solitonic core at :math:`r=0`, which sets the overall normalization of the density profile :math:`\rho(r) = \rho_\mathrm{c} [1+(r/r_c)^2]^{-8}`.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The relative tolerance used in numerical ODE solutions for the gravitational potential of the solitonic core profile.
* ``[dimensionless]`` (default ``.true.``) — If true the soliton profile is treated as dimensionless (scale-free), allowing its radial and density quantities to be specified in arbitrary units.
* ``[componentType]`` (default ``var_str('unknown')``) — The galactic structure component type (e.g.\ dark matter halo, disk, spheroid) represented by this mass distribution, used for component-specific queries.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type (e.g.\ dark matter, baryonic, total) represented by this mass distribution, used for mass-type-specific queries.
* ``[radiusTransition]`` — The transition radius (in Mpc) at which the density profile smoothly switches from the halo profile to the accretion flow, controlled by the fourth-order transition function :math:`f_\mathrm{trans}(r)`.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[timeAge]`` — The age of the halo (in Gyr) since its formation, determining the total time available for SIDM self-interactions to thermalize the inner halo and produce an isothermal core.
* ``[velocityRelativeMean]`` — Mean relative velocity to calculate self interaction cross section.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the potential.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[lengthResolution]`` — The spatial resolution length scale (in Mpc) below which the underlying density profile is softened to a flat core, mimicking the finite force resolution of an N-body simulation.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[massMinimum]`` — The minimum halo mass (in :math:`\mathrm{M}_\odot`) below which halos are excluded from the mass function histogram.
* ``[massMaximum]`` — The maximum halo mass (in :math:`\mathrm{M}_\odot`) above which halos are excluded from the mass function histogram.
* ``[massCountPerDecade]`` — The number of logarithmic bins per decade of halo mass used when constructing the halo mass function.
* ``[description]`` — A human-readable description of this mass function dataset, stored as metadata in the output file.
* ``[simulationReference]`` — A bibliographic reference for the N-body simulation from which this mass function is derived, stored as metadata.
* ``[simulationURL]`` — A URL pointing to the publicly accessible dataset or documentation for the N-body simulation, stored as metadata.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.
* ``[representativeMinimumCount]`` (default ``10_c_size_t``) — Minimum number of representative particles used to compute the center of a halo.
* ``[tolerance]`` (default ``1.0d-2``) — The tolerance in the summed weight of bound particles which must be attained to declare convergence.
* ``[bootstrapSampleRate]`` (default ``1.0d0``) — The sampling rate for particles.
* ``[representativeFraction]`` (default ``0.05d0``) — Fraction of bound particles used to compute the center of a halo.
* ``[analyzeAllParticles]`` (default ``.true.``) — If true, all particles are assumed to be self-bound at the beginning of the analysis. Unbound particles at previous times are allowed to become bound in the current snapshot. If false and the self-bound information from the previous snapshot is available, only the particles that are self-bound at the previous snapshot are assumed to be bound at the beginning of the analysis.
* ``[useVelocityMostBound]`` (default ``.false.``) — If true, the velocity of the most bound particle in velocity space is used as the representative velocity of the satellite. If false, use the mass weighted mean velocity (center-of-mass velocity) of self-bound particles instead.
* ``[orderRotation]`` (default ``var_str('none')``) — The order in which evaluation of likelihoods should be rotated as a function of process number.
* ``[logLikelihoodAccept]`` (default ``huge(0.0d0)``) — The log-likelihood which should be "accepted"---once the log-likelihood reaches this value (or larger) no further updates to the chain will be made.
* ``[report]`` (default ``.false.``) — If true, report on the log-likelihood obtained.
* ``[means]`` — The mean of the multivariate normal distribution.
* ``[covariance]`` — The covariance matrix for the of the multivariate normal distribution.
* ``[countForestsMaximum]`` (default ``-1_c_size_t``) — If set to a positive number, this is the maximum number of forests that will be evolved.
* ``[walltimeMaximum]`` (default ``-1_kind_int8``) — If set to a positive number, this is the maximum wall time for which forest evolution is allowed to proceed before the task gives up.
* ``[tolerateFailures]`` (default ``.false.``) — If true then failures to evolve a forest are tolerated. The forest is evolved no further, but evolution of other forests continues.
* ``[evolveForestsInParallel]`` (default ``.true.``) — If true then each forest is evolved by a separate OpenMP thread. Otherwise, a single thread evolves all forests.
* ``[suspendToRAM]`` (default ``.true.``) — Specifies whether trees should be suspended to RAM (otherwise they are suspend to file).
* ``[suspendPath]`` — The path to which tree suspension files will be stored.
* ``[timeIntervalCheckpoint]`` (default ``-1_kind_int8``) — If positive, gives the time in seconds between storing of checkpoint files. If zero or negative, no checkpointing is performed..
* ``[fileNameCheckpoint]`` — The path to which checkpoint data will be stored.
* ``[logM0]`` (default ``10.0d0``) — The parameter :math:`\log_{10} M_0` (with :math:`M_0` in units of :math:`\mathrm{M}_\odot`) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR0]`` (default ``9.0d0``) — The parameter :math:`\alpha_0` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR1]`` (default ``0.0d0``) — The parameter :math:`\alpha_1` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[cW]`` (default ``3.78062835d0``) — The parameter :math:`c_\mathrm{W}` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[beta]`` (default ``3.4638743d0``) — The parameter :math:`\beta` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[transferFunctionType]`` (default ``var_str('darkMatter')``) — Specifies whether to use the ``darkMatter`` or ``total`` transfer function.
* ``[fileName]`` — The name of the file from which to read a tabulated transfer function.
* ``[redshift]`` (default ``0.0d0``) — The redshift of the transfer function to read.
* ``[factorWavenumberSmoothExtrapolation]`` (default ``0.0d0``) — If positive, and extrapolation is used at high wavenumbers, the slope for extrapolation will be set by averaging over wavenumbers from :math:`k_\mathrm{max}/f` to :math:`k_\mathrm{max}`, where :math:`f=`\ ``[factorWavenumberSmoothExtrapolation]`` and :math:`k_\mathrm{max}` is the highest wavenumber tabulated. This avoids spurious extrapolation for highly oscillatory transfer functions.
* ``[acceptNegativeValues]`` (default ``.false.``) — If true, negative values in the transfer function are allowed (and the absolute value is taken prior to interpolation). Otherwise, negative values result in an error.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[fileName]`` (default ``var_str('none')``) — The name of the file to/from which tabulations of barrier first crossing probabilities should be written/read. If set to "``none``" tables will not be stored.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[varianceNumberPerUnitProbability]`` (default ``1000``) — The number of points to tabulate per unit variance for first crossing probabilities.
* ``[varianceNumberPerUnit]`` (default ``40``) — The number of tabulation points per unit of :math:`\sigma^2` used when building the rate look-up table for the Farahi excursion-set first-crossing distribution; higher values improve interpolation accuracy at the cost of memory and initialization time.
* ``[varianceNumberPerDecade]`` (default ``400``) — The number of points to tabulate per decade of progenitor variance for first crossing rates.
* ``[varianceNumberPerDecadeNonCrossing]`` (default ``40``) — The number of points to tabulate per decade of progenitor variance for non-crossing rates.
* ``[timeNumberPerDecade]`` (default ``10``) — The number of tabulation points per decade of cosmic time used when building the first-crossing rate look-up table as a function of time; higher values improve temporal interpolation accuracy for rapidly evolving cosmologies.
* ``[varianceIsUnlimited]`` (default ``.false.``) — If true, the variance is assumed to have no upper limit (e.g. as in the case of :term:`CDM`). This allows the tabulated solutions to be extended arbitrarily. Otherwise, tables are extended to encompass just the range of variance requested.
* ``[linkingLength]`` (default ``0.2d0``) — The friends-of-friends linking length to use in computing virial density contrasts with the percolation analysis of :cite:t:`more_overdensity_2011`.

.. _physics-nodePropertyExtractorRadiusVirialLastDefined:

``nodePropertyExtractorRadiusVirialLastDefined``
------------------------------------------------

Extracts the most recently computed virial radius of a halo, retaining the last well-defined value even after a node becomes a subhalo and its own virial radius is no longer physically meaningful.

.. _physics-nodePropertyExtractorRateCooling:

``nodePropertyExtractorRateCooling``
------------------------------------

A cooling rate property extractor class. Extracts the rate at which gas is cooling from the halo (assuming no sources of heating) in :math:`\mathrm{M}_\odot` Gyr\ :math:`^{-1}`.

.. _physics-nodePropertyExtractorRateInfallColdMode:

``nodePropertyExtractorRateInfallColdMode``
-------------------------------------------

Extracts the infall rate of cold-mode gas accreting onto a galaxy, capturing the filamentary cold-stream accretion channel that bypasses virial shock heating and directly feeds star formation. Particularly relevant for high-redshift galaxies in massive halos.

.. _physics-nodePropertyExtractorRatio:

``nodePropertyExtractorRatio``
------------------------------

A property extractor that returns the ratio of two scalar node properties---the value extracted by ``nodePropertyExtractorNumerator`` divided by that extracted by ``nodePropertyExtractorDenominator``. The output dataset ``name`` and ``description`` are specified directly as parameters, allowing arbitrary dimensionless ratios (e.g.\ disk-to-total stellar mass, gas fraction, size ratio) to be computed on-the-fly at output time without defining a dedicated extractor class for each combination.

**Parameters**

* ``[name]`` — The name of this property.
* ``[description]`` — A description of this property.

.. _physics-nodePropertyExtractorRedshift:

``nodePropertyExtractorRedshift``
---------------------------------

Extracts the current cosmological redshift at which a node exists, computed from the node's cosmic time, and outputs it as the scalar property named "``redshift``".

.. _physics-nodePropertyExtractorRedshiftLastIsolated:

``nodePropertyExtractorRedshiftLastIsolated``
---------------------------------------------

Extracts the cosmological redshift at which a node was last an isolated (field) halo before becoming a satellite, providing a proxy for the epoch of environmental quenching onset, output as "``redshiftLastIsolated``".

.. _physics-nodePropertyExtractorRotationCurve:

``nodePropertyExtractorRotationCurve``
--------------------------------------

A property extractor class for the rotation curve at a set of radii. The radii and types of rotation curve to output are specified by the ``radiusSpecifiers`` parameter. This parameter's value can contain multiple entries, each of which should be a valid :ref:`radius specifier <manual-sec-radiusspecifiers>`.

**Parameters**

* ``[radiusSpecifiers]`` — A list of radius specifiers at which to output the rotation curve.
* ``[includeRadii]`` (default ``.false.``) — Specifies whether or not the radii at which rotation curve data are output should also be included in the output file.
* ``[selfBoundParticlesOnly]`` — If true, the mean position and velocity are computed only for self-bound particles.
* ``[radius]`` — An array of galactocentric radii (in the same units as particle positions) at which the circular velocity rotation curve will be evaluated.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.

.. _physics-nodePropertyExtractorSatelliteDynamicalTime:

``nodePropertyExtractorSatelliteDynamicalTime``
-----------------------------------------------

A satellite dynamical time extractor class. Extracts the satellite dynamical time in units of Gyr, following the definition from :cite:t:`binney_galactic_2008`:

.. math::

   \tau_\mathrm{dyn} = \sqrt{\frac{3 \pi}{16 \mathrm{G} \rho_\mathrm{tidal}}} = \sqrt{\frac{\pi^2 r_\mathrm{tidal}^3}{4 \mathrm{G} M_\mathrm{tidal}}},

with :math:`\rho_\mathrm{tidal}` being the density within the tidal radius, :math:`r_\mathrm{tidal}`, of the satellite which encloses a mass :math:`M_\mathrm{tidal}`.

**Parameters**

* ``[efficiency]`` (default ``0.01d0``) — The efficiency of star formation for the dynamical time method.
* ``[exponentVelocity]`` (default ``-1.50d0``) — The velocity exponent for star formation for the dynamical time method.
* ``[timescaleMinimum]`` (default ``1.0d-3``) — The minimum allowed timescale for star formation (in Gyr) in the dynamical time prescription, preventing unphysically short formation timescales in high-density or high-velocity systems.
* ``[dynamicalRateFraction]`` (default ``2.0d0``) — The fraction of the inverse dynamical time to use as the rate for infall of the cold mode component.

.. _physics-nodePropertyExtractorSatelliteMinimumDistance:

``nodePropertyExtractorSatelliteMinimumDistance``
-------------------------------------------------

Extracts the minimum pericentric distance ever reached by a satellite node within its current host halo, recording the closest approach to the halo center as an indicator of tidal stripping history.

**Methods**

* ``distanceRelative`` — Compute the distance to the center of the relevant host halo.

**Parameters**

* ``[relativeTo]`` (default ``var_str('immediateHost')``) — Specifies to which host halo the minimum distance should be referenced. "``immediateHost``" computes the minimum distance to the first host (so, for a sub-subhalo, this would be the subhalo in which it is orbiting). "``isolatedHost``" computes the minimum distance to the final (isolated halo) host.

.. _physics-nodePropertyExtractorSatelliteOrbitalExtrema:

``nodePropertyExtractorSatelliteOrbitalExtrema``
------------------------------------------------

A node property extractor which extracts the radii of a satellite's orbital extrema (i.e. pericenter and apocenter) as ``satellitePericenterRadius`` and ``satellitePericenterVelocity``.

**Parameters**

* ``[extractPericenter]`` (default ``.false.``) — Specifies whether or not satellite orbital pericenter data (radius, velocity) should be extracted.
* ``[extractApocenter]`` (default ``.false.``) — Specifies whether or not satellite orbital apocenter data (radius, velocity) should be extracted.

.. _physics-nodePropertyExtractorSatelliteStatus:

``nodePropertyExtractorSatelliteStatus``
----------------------------------------

A property extractor that returns an integer satellite status flag for each node: 0 for central (non-satellite) halos, 1 for satellites that still have a resolved dark matter subhalo, and 2 for orphaned satellites that have lost their subhalo below the resolution limit. The ``discriminator`` parameter (default: ``boundMass``) controls whether orphan status is determined from the bound mass history of the satellite component or the position history of the position component, allowing flexibility in how subhalo disruption is identified.

**Parameters**

* ``[discriminator]`` (default ``var_str('boundMass')``) — Specifies whether bound mass or position history will be used to determine satellite orphan status.

.. _physics-nodePropertyExtractorSatelliteVirialOrbit:

``nodePropertyExtractorSatelliteVirialOrbit``
---------------------------------------------

A property extractor that outputs selected orbital elements of the virial orbit of satellite nodes---the Keplerian orbit at the time the satellite first crosses the host virial radius. The ``properties`` parameter specifies the list of orbital quantities to extract (e.g.\ radial velocity, tangential velocity, specific energy, angular momentum), returning one output column per selected property per satellite. This is used to characterize the infall conditions of satellite galaxies and dark matter subhalos.

**Parameters**

* ``[properties]`` — The set of properties of the orbit to output.

.. _physics-nodePropertyExtractorScalar:

``nodePropertyExtractorScalar``
-------------------------------

Abstract base class for all extractors that return a single floating-point scalar value per node (e.g., mass, radius, temperature), defining the common interface implemented by the large majority of node property extractors.

**Methods**

* ``extract`` — Extract the property from the given ``node``.
* ``name`` — Return the name of the property extracted.
* ``description`` — Return a description of the property extracted.
* ``unitsInSI`` — Return the units of the property extracted in the SI system.
* ``units`` — Return an object containing units metadata for the properties.
* ``metaData`` — Populate a hash with meta-data for the property.

.. _physics-nodePropertyExtractorScalarizer:

``nodePropertyExtractorScalarizer``
-----------------------------------

A property extractor that wraps an array or tuple :galacticus-class:`nodePropertyExtractorClass` and returns a single scalar value by selecting one entry from the array. The ``element`` parameter specifies which element index to extract; for tuple extractors an additional ``item`` parameter selects the item (row) within the tuple. This allows individual components of compound property arrays (e.g.\ a single radial bin from a density profile, or one filter band from a magnitude tuple) to be extracted as independent scalar output datasets.

**Parameters**

* ``[element]`` — The element to scalarize from the array.
* ``[item]`` — The item to scalarize from the array.

.. _physics-nodePropertyExtractorSED:

``nodePropertyExtractorSED``
----------------------------

A property extractor that returns the spectral energy distribution (SED) of a galaxy component (disk, spheroid, or total) at a grid of wavelengths, computed by convolving the star formation history with stellar population spectral templates. Parameters include ``component`` (the galaxy component), ``frame`` (``rest`` or ``observed``), ``wavelengthMinimum`` and ``wavelengthMaximum`` (in \AA), ``resolution`` (:math:`\lambda/\Delta\lambda`; negative for full template resolution), and ``toleranceRelative`` for the spectral integration. The SED is returned as a 2D array over wavelength and output time.

**Methods**

* ``indexTemplateTime`` — Return the index of the template SEDs to use.
* ``indexTemplateNode`` — Return the index of the template SEDs to use.
* ``luminosityMean`` — Compute the mean luminosity of the stellar population in the given bin of the star formation history.
* ``historyHashedDescriptor`` — Return a hashed descriptor of the object which incorporates the time and metallicity binning of the star formation history.
* ``wavelengths`` — Return an array of the wavelengths at which the SED is computed.

**Parameters**

* ``[component]`` — The component from which to extract star formation rate.
* ``[frame]`` (default ``var_str('rest')``) — The frame (``rest`` or ``observed``) for which to compute the SED.
* ``[wavelengthMinimum]`` (default ``0.0d0``) — The minimum wavelength at which to compute the SED.
* ``[wavelengthMaximum]`` (default ``huge(0.0d0)``) — The maximum wavelength at which to compute the SED.
* ``[resolution]`` (default ``-1.0d0``) — The resolution, :math:`\lambda/\Delta\lambda`, at which to compute the SED. If a negative value is given the SED will be computed at the full resolution provided by the stellar population spectra class.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance used in integration over stellar population spectra.

.. _physics-nodePropertyExtractorSEDAGN:

``nodePropertyExtractorSEDAGN``
-------------------------------

A property extractor class for the SED of the AGN. The spectrum is computed using the provided :galacticus-class:`accretionDiskSpectraClass` object, and will be output between wavelengths ``[wavelengthMinimum]`` and ``[wavelengthMaximum]``. If ``[resolution]`` is set to a positive value then this specifies the resolution, :math:`\lambda/\Delta\lambda`, at which to compute the SED. If ``[resolution]`` is non-positive then the SED will be output at the full native resolution provided by the :galacticus-class:`accretionDiskSpectraClass` object. The frame for the SED, ``rest`` or ``observed``, is specified by ``[frame]``. Note that using ``observed`` merely means that the extracted spectrum is evaluated at wavelength :math:`\lambda_\mathrm{r} = \lambda_\mathrm{o} / (1+z)` where :math:`\lambda_\mathrm{o}` is the observed wavelength (and is the wavelength returned by the `columnDescriptions` method), :math:`\lambda_\mathrm{r}` is the rest-frame wavelength, and :math:`z` is redshift---*no adjustment* is made for the boost in observed flux due to the :math:`\mathrm{d}\lambda_\mathrm{o}/\mathrm{d}\lambda_\mathrm{r}` term which appears when computing observed-frame fluxes.

**Methods**

* ``wavelengths`` — Return an array of the wavelengths at which the SED is computed.

**Parameters**

* ``[frame]`` (default ``var_str('rest')``) — The frame (``rest`` or ``observed``) for which to compute the SED.
* ``[wavelengthMinimum]`` (default ``0.0d0``) — The minimum wavelength at which to compute the SED.
* ``[wavelengthMaximum]`` (default ``huge(0.0d0)``) — The maximum wavelength at which to compute the SED.
* ``[resolution]`` (default ``-1.0d0``) — The resolution, :math:`\lambda/\Delta\lambda`, at which to compute the SED. If a negative value is given the SED will be computed at the full resolution provided by the :galacticus-class:`accretionDiskSpectraClass` object.

.. _physics-nodePropertyExtractorSIDMParametric:

``nodePropertyExtractorSIDMParametric``
---------------------------------------

A node property extractor which extracts dark matter profile properties for the SIDM parametric model.

**Parameters**

* ``[beta]`` (default ``4.0d0``) — The value :math:`\beta` in a SIDMParametric-model mass distribution.
* ``[alpha]`` (default ``2.0d0``) — The coefficient :math:`\alpha` of the halo mass-growth term in the gravothermal :math:`\tau` evolution, :math:`\dot\tau = 1/t_\mathrm{c} - \alpha \, (\dot{M}/M) \, \tau`. The default value of :math:`2.0` is the best-fit value found by :cite:t:`raut_extended_2026`.
* ``[C]`` (default ``0.75d0``) — The calibration constant :math:`C` relating the gravothermal collapse timescale :math:`t_\mathrm{c}` to the relaxation time (eqn. 2.2 of :cite:t:`yang_parametric_2024`). The default value of :math:`0.75` is the best-fit value found by :cite:t:`raut_extended_2026`.

.. _physics-nodePropertyExtractorSoliton:

``nodePropertyExtractorSoliton``
--------------------------------

Extracts physical properties of the fuzzy dark matter (:term:`FDM`) soliton core (such as core radius and core mass) associated with each halo node, enabling analysis of quantum pressure effects in FDM models.

**Methods**

* ``radiusMerge`` — Compute the radius at which the satellite will be merged in FDM models.

**Parameters**

* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[recordMergedSubhaloProperties]`` (default ``.false.``) — If true, record the orbital properties of subhalo that merge.
* ``[recordFirstLevelOnly]`` (default ``.false.``) — If true, record only mergers with first-level subhalos relative to the host.

.. _physics-nodePropertyExtractorSpeedOrbital:

``nodePropertyExtractorSpeedOrbital``
-------------------------------------

Extracts the current orbital speed of a satellite node as it moves through its host halo potential, computed from the satellite's velocity vector, for use in orbital energy analyses and comparison with observed satellite velocity distributions.

.. _physics-nodePropertyExtractorSpin:

``nodePropertyExtractorSpin``
-----------------------------

Extracts the dimensionless spin parameter :math:`\lambda` of a dark matter halo, characterizing its angular momentum content relative to gravitational and kinetic energy, a key parameter linking halo properties to disk galaxy sizes in semi-analytic models.

.. _physics-nodePropertyExtractorSpinBlackHoles:

``nodePropertyExtractorSpinBlackHoles``
---------------------------------------

Extracts a list of dimensionless spin parameters for all supermassive black holes in each node, providing per-black-hole angular momentum data for studies of black hole spin evolution and jet production efficiency.

.. _physics-nodePropertyExtractorSpinBullock:

``nodePropertyExtractorSpinBullock``
------------------------------------

Extracts the :cite:t:`bullock_profiles_2001` spin parameter :math:`\lambda' = J / (\sqrt{2} M V r)` of dark matter halos, an alternative dimensionless spin measure that is more easily computed from halo catalogs than the classical Peebles spin parameter.

.. _physics-nodePropertyExtractorStarFormationHistory:

``nodePropertyExtractorStarFormationHistory``
---------------------------------------------

A composite property extractor that combines both the stellar mass formed in each age--metallicity bin and the corresponding time bin boundaries of the star formation history for a specified galaxy ``component`` (disk, spheroid, nuclearStarCluster, or all). It bundles together the outputs of :galacticus-class:`nodePropertyExtractorStarFormationHistoryMass` and :galacticus-class:`nodePropertyExtractorStarFormationHistoryTimes` for convenient simultaneous extraction, providing the full information needed to reconstruct the star formation history from output datasets.

**Parameters**

* ``[component]`` — The component from which to extract star formation history.

.. _physics-nodePropertyExtractorStarFormationHistoryMass:

``nodePropertyExtractorStarFormationHistoryMass``
-------------------------------------------------

A property extractor that returns the stellar mass formed in each age and metallicity bin of the star formation history for a specified galaxy component (disk, spheroid, nuclearStarCluster, or all combined), as a 2D array (time :math:`\times` metallicity) in units of :math:`\mathrm{M}_\odot \, \mathrm{Gyr}^{-1}`. The ``component`` parameter selects which component's history to extract. Metallicity bin boundaries and, when the age grid is fixed per output, the time array are written as metadata to allow reconstruction of the full star formation history from the output dataset.

**Parameters**

* ``[component]`` — The component from which to extract star formation history.

.. _physics-nodePropertyExtractorStarFormationHistoryTimes:

``nodePropertyExtractorStarFormationHistoryTimes``
--------------------------------------------------

A property extractor that returns the lookback-time bin boundaries (in Gyr) used to tabulate the star formation history for a specified galaxy ``component`` (disk, spheroid, or nuclearStarCluster). These time values define the age axis of the star formation history grid and are needed to reconstruct the full star formation history from the mass array returned by :galacticus-class:`nodePropertyExtractorStarFormationHistoryMass`. The number of returned times depends on the specific :galacticus-class:`starFormationHistoryClass` implementation.

**Parameters**

* ``[component]`` — The component from which to extract star formation history.

.. _physics-nodePropertyExtractorStarFormationRate:

``nodePropertyExtractorStarFormationRate``
------------------------------------------

A node property extractor which extracts the star formation rate in a galaxy. The type of star formation rate is controlled by the ``[component]`` parameter, which can be either "``disk``", "``spheroid``", "``nsc``" or "``total``". The corresponding star formation rate is extracted as ``<component>StarFormationRate`` in units of :math:`\mathrm{M}_\odot`/Gyr.

**Methods**

* ``tabulate`` — Tabulate the virial density contrast as a function of mass and time.
* ``restoreTable`` — Restore a tabulated solution from file.
* ``storeTable`` — Store a tabulated solution to file.

**Parameters**

* ``[velocityCharacteristic]`` (default ``250.0d0``) — The velocity scale at which the :term:`SNe`-driven outflow rate equals the star formation rate in disks.
* ``[exponent]`` (default ``3.5d0``) — The velocity scaling of the :term:`SNe`-driven outflow rate in disks.
* ``[fraction]`` (default ``0.01d0``) — The normalization :math:`f` of the outflow rate relative to the star formation rate at a reference halo velocity of 200 km/s and expansion factor of 1, setting the overall mass-loading amplitude of the halo-scaling feedback model.
* ``[exponentVelocity]`` (default ``-2.0d0``) — The exponent of virial velocity in the outflow rate in disks.
* ``[exponentRedshift]`` (default ``0.0d0``) — The power-law exponent of the cosmological expansion factor :math:`(1+z)` in the halo-scaling outflow rate, allowing the mass-loading factor to evolve with redshift; a value of zero gives no redshift evolution.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[radiusNormalization]`` (default ``3.3d-6``) — The initial value appearing in the radius-mass relation
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the nuclear star cluster is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not nuclear star cluster stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[scaleRelativeMass]`` (default ``1.0d-2``) — The mass scale, relative to the total mass of the node, below which calculations in the delayed very simple hot halo component are allowed to become inaccurate.
* ``[starveSatellites]`` (default ``.false.``) — Specifies whether or not the hot halo should be removed ("starved") when a node becomes a satellite.
* ``[starveSatellitesOutflowed]`` (default ``.false.``) — Specifies whether or not the outflowed hot halo should be removed ("starved") when a node becomes a satellite.
* ``[outflowReturnOnFormation]`` (default ``.false.``) — Specifies whether or not outflowed gas should be returned to the hot reservoir on halo formation events.
* ``[angularMomentumAlwaysGrows]`` (default ``.false.``) — Specifies whether or not negative rates of accretion of angular momentum into the hot halo will be treated as positive for the purposes of computing the hot halo angular momentum.
* ``[fractionBaryonLimitInNodeMerger]`` (default ``.false.``) — Controls whether the hot gas content of nodes should be limited to not exceed the universal baryon fraction at node merger events. If set to ``true``, hot gas (and angular momentum, abundances, and chemicals proportionally) will be removed from the merged halo to the unaccreted gas reservoir to limit the baryonic mass to the universal baryon fraction where possible.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple disk component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the disk is physically plausible.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[radiusStructureSolver]`` (default ``1.0d0``) — The radius (in units of the standard scale length) to use in solving for the size of the disk.
* ``[structureSolverUseCole2000Method]`` (default ``.false.``) — If true, use the method described in :cite:t:`cole_hierarchical_2000` to correct for difference between thin disk and spherical mass distributions when solving for disk radii.
* ``[diskNegativeAngularMomentumAllowed]`` (default ``.true.``) — Specifies whether or not negative angular momentum is allowed for the disk.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not disk stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumSolverRadius]`` (default ``ratioAngularMomentumSolverRadiusDefault``) — The assumed ratio of the specific angular momentum at the structure solver radius to the mean specific angular momentum of the standard disk component.
* ``[scaleAbsoluteMass]`` (default ``100.0d0``) — The absolute mass scale below which calculations in the very simple spheroid component are allowed to become inaccurate.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[efficiencyEnergeticOutflow]`` (default ``1.0d-2``) — The proportionality factor relating mass outflow rate from the spheroid to the energy input rate divided by :math:`V_\mathrm{spheroid}^2`.
* ``[toleranceRelativeMetallicity]`` (default ``1.0d-4``) — The metallicity tolerance for ODE solution.
* ``[toleranceAbsoluteMass]`` (default ``1.0d-6``) — The mass tolerance used to judge whether the spheroid is physically plausible.
* ``[inactiveLuminositiesStellar]`` (default ``.false.``) — Specifies whether or not spheroid stellar luminosities are inactive properties (i.e. do not appear in any ODE being solved).
* ``[postStepZeroNegativeMasses]`` (default ``.true.``) — If true, negative masses will be zeroed after each ODE step. Note that this can lead to non-conservation of mass.
* ``[ratioAngularMomentumScaleRadius]`` (default ``ratioAngularMomentumScaleRadiusDefault``) — The assumed ratio of the specific angular momentum at the scale radius to the mean specific angular momentum of the standard spheroid component.
* ``[outputMergers]`` (default ``.false.``) — Determines whether or not properties of black hole mergers will be output.
* ``[fileNames]`` — The name of the file(s) from which merger tree data should be read when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[forestSizeMaximum]`` (default ``0_c_size_t``) — The maximum number of nodes allowed in a forest before it will be broken up into trees and processed individually. A value of 0 implies that forests should never be split.
* ``[presetMergerTimes]`` (default ``.true.``) — Specifies whether merging times for subhalos should be preset when reading merger trees from a file.
* ``[presetMergerNodes]`` (default ``.true.``) — Specifies whether the target nodes for mergers should be preset (i.e. determined from descendant nodes). If they are not, merging will be with each satellite's host node.
* ``[presetSubhaloMasses]`` (default ``.true.``) — Specifies whether subhalo mass should be preset when reading merger trees from a file.
* ``[subhaloAngularMomentaMethod]`` (default ``var_str('summation')``) — Specifies how to account for subhalo angular momentum when adding subhalo mass to host halo mass.
* ``[presetSubhaloIndices]`` (default ``.true.``) — Specifies whether subhalo indices should be preset when reading merger trees from a file.
* ``[presetPositions]`` (default ``.true.``) — Specifies whether node positions should be preset when reading merger trees from a file.
* ``[presetScaleRadii]`` (default ``.true.``) — Specifies whether node scale radii should be preset when reading merger trees from a file.
* ``[scaleRadiiFailureIsFatal]`` (default ``.true.``) — Specifies whether failure to set a node scale radii should be regarded as a fatal error. (If not, a fallback method to set scale radius is used in such cases.)
* ``[presetScaleRadiiConcentrationMinimum]`` (default ``3.0d0``) — The lowest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiConcentrationMaximum]`` (default ``60.0d0``) — The largest concentration (:math:`c=r_\mathrm{vir}/r_\mathrm{s}`) allowed when setting scale radii, :math:`r_\mathrm{s}`.
* ``[presetScaleRadiiMinimumMass]`` (default ``0.0d0``) — The minimum halo mass for which scale radii should be preset (if ``[presetScaleRadii]``\ :math:`=`\ ``true``).
* ``[presetUnphysicalAngularMomenta]`` (default ``.false.``) — When reading merger trees from file and presetting halo angular momenta, detect unphysical (<=0) angular momenta and preset them using the selected halo spin method.
* ``[presetAngularMomenta]`` (default ``.true.``) — Specifies whether node angular momenta should be preset when reading merger trees from a file.
* ``[presetAngularMomenta3D]`` (default ``.false.``) — Specifies whether node 3-D angular momenta vectors should be preset when reading merger trees from a file.
* ``[presetOrbits]`` (default ``.true.``) — Specifies whether node orbits should be preset when reading merger trees from a file.
* ``[presetOrbitsSetAll]`` (default ``.true.``) — Forces all orbits to be set. If the computed orbit does not cross the virial radius, then select one at random instead.
* ``[presetOrbitsAssertAllSet]`` (default ``.true.``) — Asserts that all virial orbits must be preset. If any can not be set, Galacticus will stop.
* ``[presetOrbitsBoundOnly]`` (default ``.true.``) — Specifies whether only bound node orbits should be set.
* ``[beginAt]`` (default ``-1_kind_int8``) — Specifies the index of the tree to begin at. (Use -1 to always begin with the first tree.)
* ``[outputTimeSnapTolerance]`` (default ``0.0d0``) — The relative tolerance required to "snap" a node time to the closest output time.
* ``[missingHostsAreFatal]`` (default ``.true.``) — Specifies whether nodes with missing host nodes should be considered to be fatal---see the discussion of missing host nodes in the class description above.
* ``[treeIndexToRootNodeIndex]`` (default ``.false.``) — Specifies whether tree indices should always be set to the index of their root node.
* ``[allowBranchJumps]`` (default ``.true.``) — Specifies whether nodes are allowed to jump between branches.
* ``[allowSubhaloPromotions]`` (default ``.true.``) — Specifies whether subhalos are permitted to be promoted to being isolated halos.
* ``[alwaysPromoteMostMassive]`` (default ``.false.``) — If true, the most massive progenitor is always promoted to be the primary progenitor *even if* it is a subhalo. Otherwise, isolated progenitors are given priority over subhalo progenitors, even if they are less massive.
* ``[presetNamedReals]`` — Names of real datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[presetNamedIntegers]`` — Names of integer datasets to be additionally read and stored in the nodes of the merger tree when using the ``[mergerTreeConstruct]``\ :math:`=`\ ``read`` tree construction method.
* ``[fatalMismatches]`` (default ``.true.``) — Specifies whether mismatches in cosmological parameter values between Galacticus and "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be considered fatal.
* ``[fatalNonTreeNode]`` (default ``.true.``) — Specifies whether nodes in snapshot files but not in the merger tree file should be considered fatal when importing from the "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013`.
* ``[subvolumeCount]`` (default ``1``) — Specifies the number of subvolumes *along each axis* into which a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree files should be split for processing through Galacticus.
* ``[subvolumeBuffer]`` (default ``0.0d0``) — Specifies the buffer region (in units of Mpc\ :math:`/h` to follow the format convention) around subvolumes of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file which should be read in to ensure that no halos are missed from trees.
* ``[subvolumeIndex]`` (default ``[0,0,0]``) — Specifies the index (in each dimension) of the subvolume of a "Sussing Merger Trees" format :cite:p:`srisawat_sussing_2013` merger tree file to process. Indices range from 0 to ``[subvolumeCount]``\ :math:`-1`.
* ``[badValue]`` (default ``-0.5d0``) — Use for bad value detection in "Sussing" merger trees. Values for scale radius and halo spin which exceed this threshold are assumed to be bad.
* ``[badValueTest]`` (default ``var_str('lessThan')``) — Use for bad value detection in "Sussing" merger trees. Values which exceed the threshold in ths specified direction are assumed to be bad.
* ``[treeSampleRate]`` (default ``1.0d0``) — Specify the probability that any given tree should processed (to permit subsampling).
* ``[massOptions]`` (default ``var_str('default')``) — Mass option for Sussing merger trees.
* ``[mergeProbability]`` (default ``0.1d0``) — The largest probability of branching allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[accretionLimit]`` (default ``0.1d0``) — The largest fractional mass change due to subresolution accretion allowed in a timestep in merger trees built by the :cite:t:`cole_hierarchical_2000` method.
* ``[redshiftMaximum]`` (default ``1.0d5``) — The highest redshift to which merger trees will be built in the :cite:t:`cole_hierarchical_2000` method.
* ``[toleranceTimeEarliest]`` (default ``2.0d-6``) — The fractional tolerance used to judge if a branch is at the earliest allowed time in the tree.
* ``[branchIntervalStep]`` (default ``.true.``) — If ``false`` use the original :cite:t:`cole_hierarchical_2000` method to determine whether branching occurs in a timestep. If ``true`` draw branching intervals from a negative exponential distribution.
* ``[toleranceResolutionSelf]`` (default ``1.0d-6``) — The fractional tolerance in node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[toleranceResolutionParent]`` (default ``1.0d-3``) — The fractional tolerance in parent node mass at the resolution limit below which branch mis-orderings will be ignored.
* ``[ignoreNoProgress]`` (default ``.false.``) — If true, failure to make progress on a branch will be ignored (and the branch terminated).
* ``[ignoreWellOrdering]`` (default ``.false.``) — If true, non-well-ordered tree branches are pruned away instead of causing errors..
* ``[redshiftBase]`` (default ``0.0d0``) — The redshift at which to plant the base node when building merger trees.
* ``[timeSnapTolerance]`` (default ``1.0d-6``) — The fractional tolerance within which the tree base time will be snapped to a nearby output time.
* ``[treeBeginAt]`` (default ``0``) — The index (in order of increasing base halo mass) of the tree at which to begin when building merger trees. A value of "0" means to begin with tree number 1 (if processing trees in ascending order), or equal to the number of trees (otherwise).
* ``[processDescending]`` (default ``.true.``) — If true, causes merger trees to be processed in order of decreasing mass.
* ``[splitTrees]`` (default ``.false.``) — If true, prune away any nodes of the tree that are not needed to determine evolution up to the latest time at which a node is present inside the lightcone. This typically leads to a tree splitting into a forest of trees.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[starFormationRates]`` — The star formation rates corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of star formation rate to use when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d10``) — The star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d12``) — The maximum star formation rate to consider when constructing star formation rate function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[likelihoodBins]`` — Controls which bins in the stellar mass--halo mass relation will be used in computing the likelihood: * *not present*: all bins are included in the likelihood calculation; * *list of integers*: use only the mass bin(s) given in this list in the likelihood calculation; * ``auto``: use only bins which have a non-zero number of halos contributing to them in the likelihood calculation.
* ``[fileNameTarget]`` — The name of the file containing the target data.
* ``[redshiftInterval]`` (default ``1``) — The redshift interval to use.
* ``[likelihoodNormalize]`` (default ``.false.``) — If true, then normalize the likelihood to make it a probability density.
* ``[computeScatter]`` (default ``.false.``) — If true, the scatter in log10(stellar mass) is computed. Otherwise, the mean is computed.
* ``[systematicErrorPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for stellar mass in the stellar vs halo mass relation.
* ``[systematicErrorMassHaloPolynomialCoefficient]`` (default ``[0.0d0]``) — The coefficients of the systematic error polynomial for halo mass in the stellar vs halo mass relation.
* ``[errorTolerant]`` (default ``.false.``) — Error tolerance for the N-body spin distribution operator.
* ``[logNormalRange]`` (default ``100.0d0``) — The multiplicative range of the log-normal distribution used to model the distribution of the mass and energy terms in the spin parameter. Specifically, the lognormal distribution is truncated outside the range :math:`(\lambda_\mathrm{m}/R,\lambda_\mathrm{m} R`, where :math:`\lambda_\mathrm{m}` is the measured spin, and :math:`R=`\ ``[logNormalRange]``
* ``[fileName]`` — The name of the file from which to read spin distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the spin distribution function.
* ``[comment]`` — A descriptive comment for the spin distribution function.
* ``[redshift]`` — The redshift at which to compute the spin distribution function.
* ``[massMinimum]`` — Minimum halo mass for the spin distribution function.
* ``[massMaximum]`` — Maximum halo mass for the spin distribution function.
* ``[spinMinimum]`` — Minimum spin for the spin distribution function.
* ``[spinMaximum]`` — Maximum spin for the spin distribution function.
* ``[countSpinsPerDecade]`` — Number of spins per decade at which to compute the spin distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[particleCountMinimum]`` — The minimum particle count to assume when computing N-body errors on spins.
* ``[massParticle]`` — The mass of the particle used in the N-body simulation from which spins were measured.
* ``[energyEstimateParticleCountMaximum]`` — The maximum number of particles used in estimating halo energies when measuring spins from the N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing HI mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[magnitudesAbsolute]`` — The absolute magnitudes corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the luminosity function.
* ``[comment]`` — A descriptive comment for the luminosity function.
* ``[luminosities]`` — The luminosities corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing luminosity function covariance matrices for main branch galaxies.
* ``[includeNitrogenII]`` (default ``.false.``) — If true, include contamination by the [NII] (6548\AA :math:`+` 6584\AA) doublet.
* ``[depthOpticalISMCoefficient]`` (default ``1.0d0``) — Multiplicative coefficient for optical depth in the ISM.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[masses]`` — The masses corresponding to bin centers.
* ``[covarianceBinomialBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[covarianceBinomialMassHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing stellar mass function covariance matrices for main branch galaxies.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[rootVarianceFractionalMinimum]`` (default ``0.0d0``) — The minimum fractional root variance (relative to the target dataset).
* ``[fileName]`` — The name of the file from which to read concentration distribution function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the concentration distribution function.
* ``[comment]`` — A descriptive comment for the concentration distribution function.
* ``[redshift]`` — The redshift at which to compute the concentration distribution function.
* ``[massMinimum]`` — Minimum halo mass for the concentration distribution function.
* ``[massMaximum]`` — Maximum halo mass for the concentration distribution function.
* ``[concentrationMinimum]`` — Minimum concentration for the concentration distribution function.
* ``[concentrationMaximum]`` — Maximum concentration for the concentration distribution function.
* ``[countConcentrationsPerDecade]`` — Number of concentrations per decade at which to compute the concentration distribution function.
* ``[timeRecent]`` — Halos which experienced a major node merger within a time :math:`\Delta t=`\ ``[timeRecent]`` of the analysis time will be excluded from the analysis.
* ``[massParticle]`` — The particle mass in the source N-body simulation.
* ``[targetLabel]`` — Label for the target dataset.
* ``[functionValueTarget]`` — The target function for likelihood calculations.
* ``[functionCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[fileName]`` — The name of the file from which to read star forming main sequence function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[label]`` — A label for the mass function.
* ``[comment]`` — A descriptive comment for the mass function.
* ``[separations]`` — The separations corresponding to bin centers.
* ``[massMinima]`` — The minimum mass of each mass sample.
* ``[massMaxima]`` — The maximum mass of each mass sample.
* ``[massHaloBinsPerDecade]`` (default ``10``) — The number of bins per decade of halo mass to use when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMinimum]`` (default ``1.0d8``) — The minimum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[massHaloMaximum]`` (default ``1.0d16``) — The maximum halo mass to consider when constructing the mass function covariance matrix for main branch galaxies.
* ``[wavenumberCount]`` (default ``60_c_size_t``) — The number of bins in wavenumber to use in computing the correlation function.
* ``[wavenumberMinimum]`` (default ``1.0d-3``) — The minimum wavenumber to use when computing the correlation function.
* ``[wavenumberMaximum]`` (default ``1.0d4``) — The maximum wavenumber to use when computing the correlation function.
* ``[integralConstraint]`` — The integral constraint for these correlation functions.
* ``[depthLineOfSight]`` — The line-of-sight depth over which the correlation function was projected.
* ``[halfIntegral]`` — Set to true if the projection integrand should be over line-of-sight depths greater than zero.
* ``[binnedProjectedCorrelationTarget]`` — The target function for likelihood calculations.
* ``[binnedProjectedCorrelationCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[targetLabel]`` (default ``var_str('')``) — A label for the target dataset in a plot of this analysis.
* ``[starFormationRateSpecificQuiescentLogarithmic]`` — The base-10 logarithm specific star formation rate (in units of Gyr\ :math:`^{-1}`) separating quiescent and star-forming galaxies.
* ``[starFormationRateSpecificLogarithmicError]`` — The observational fractional error in specific star formation rate (in units of dex) of galaxies.
* ``[fileName]`` — The name of the file from which to read quiescent fraction function parameters.
* ``[comment]`` — A comment describing this analysis.
* ``[label]`` — A label for this analysis.
* ``[label]`` — A label for the star forming main sequence function.
* ``[comment]`` — A descriptive comment for the star forming main sequence function.
* ``[massMinimum]`` — Minimum stellar mass for the star forming main sequence function.
* ``[massMaximum]`` — Maximum stellar mass for the star forming main sequence function.
* ``[countMassesPerDecade]`` — Number of masses per decade at which to compute the star forming main sequence function.
* ``[targetLabel]`` — Label for the target dataset.
* ``[meanValueTarget]`` — The target function for likelihood calculations.
* ``[meanCovarianceTarget]`` — The target function covariance for likelihood calculations.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[radiusFractionalTruncateMinimum]`` (default ``2.0d0``) — The minimum radius (in units of the virial radius) to begin truncating the density profile.
* ``[radiusFractionalTruncateMaximum]`` (default ``4.0d0``) — The maximum radius (in units of the virial radius) to finish truncating the density profile.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[velocityDispersionApproximate]`` (default ``.true.``) — If ``true``, radial velocity dispersion is computed using an approximate method in which we assume that :math:`\sigma_\mathrm{r}^2(r) \rightarrow \sigma_\mathrm{r}^2(r) - (2/3) \epsilon(r)`, where :math:`\epsilon(r)` is the specific heating energy. If ``false`` then radial velocity dispersion is computed by numerically solving the Jeans equation.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[tolerateVelocityDispersionFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the velocity dispersion.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the radius of the maximum circular velocity.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate numerical failures when computing the gravitational potential of a heated dark matter profile, allowing the calculation to continue with a fallback result rather than aborting.
* ``[toleranceRelativeVelocityDispersion]`` (default ``1.0d-6``) — The relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[toleranceRelativeVelocityDispersionMaximum]`` (default ``1.0d-3``) — The maximum relative tolerance to use in numerical solutions for the velocity dispersion in dark-matter-only density profiles.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[tolerateVelocityMaximumFailure]`` (default ``.true.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[lengthResolution]`` — The gravitational softening length :math:`\Delta x` (in Mpc) of the N-body simulation, which sets the minimum spatial scale below which the dark matter profile is smoothed to avoid artificial two-body effects.
* ``[massResolution]`` — The mass resolution :math:`\Delta M` (in :math:`\mathrm{M}_\odot`) of the N-body simulation, representing the minimum halo mass that can be resolved; profiles of halos near this limit are softened to account for particle discreteness effects.
* ``[resolutionIsComoving]`` — If true, the resolution length is assumed to be fixed in comoving coordinates, otherwise in physical coordinates.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[C]`` (default ``400.0d0``) — The parameter :math:`C` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[f]`` (default ``0.02d0``) — The parameter :math:`f` appearing in the halo concentration algorithm of :cite:t:`ludlow_mass-concentration-redshift_2016`.
* ``[timeFormationSeekDelta]`` (default ``0.0d0``) — The parameter :math:`\Delta \log t` by which the logarithm of the trial formation time is incremented when stepping through the formation history of a node to find the formation time. If set to zero (or a negative value) the cumulative mass histories of nodes are assumed to be monotonic functions of time, and the formation time is instead found by a root finding algorithm,
* ``[massBoundIsInactive]`` (default ``.false.``) — Specifies whether or not the bound mass of the satellite component is inactive (i.e. does not appear in any ODE being solved).
* ``[useLastIsolatedTime]`` (default ``.false.``) — If true, evaluate the halo virial radius using a the virial density definition at the last isolated time of the halo.
* ``[filterName]`` — The filter to select.
* ``[filterType]`` — The filter type (rest or observed) to select.
* ``[redshiftBand]`` — The redshift of the band (if not the output redshift).
* ``[postprocessChain]`` — The postprocessing chain to use.
* ``[cloudyTableFileName]`` (default ``var_str('%DATASTATICPATH%/hiiRegions/emissionLineLuminosities_BC2003_highResolution_imfChabrier.hdf5')``) — The file of emission line luminosities to use.
* ``[lineNames]`` — The emission lines to extract.
* ``[component]`` — The component from which to extract star formation rate.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance used in integration over stellar population spectra.
* ``[component]`` — The component from which to extract star formation rate.
* ``[radiusCore]`` — The soliton core radius (in Mpc) characterizing the size of the quantum pressure-supported central core of the fuzzy dark matter halo; the density profile flattens inside this scale.
* ``[densitySolitonCentral]`` — The central density (in :math:`\mathrm{M}_\odot`/Mpc\ :math:`^3`) of the solitonic core at :math:`r=0`, which sets the overall normalization of the density profile :math:`\rho(r) = \rho_\mathrm{c} [1+(r/r_c)^2]^{-8}`.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The relative tolerance used in numerical ODE solutions for the gravitational potential of the solitonic core profile.
* ``[dimensionless]`` (default ``.true.``) — If true the soliton profile is treated as dimensionless (scale-free), allowing its radial and density quantities to be specified in arbitrary units.
* ``[componentType]`` (default ``var_str('unknown')``) — The galactic structure component type (e.g.\ dark matter halo, disk, spheroid) represented by this mass distribution, used for component-specific queries.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type (e.g.\ dark matter, baryonic, total) represented by this mass distribution, used for mass-type-specific queries.
* ``[radiusTransition]`` — The transition radius (in Mpc) at which the density profile smoothly switches from the halo profile to the accretion flow, controlled by the fourth-order transition function :math:`f_\mathrm{trans}(r)`.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[timeAge]`` — The age of the halo (in Gyr) since its formation, determining the total time available for SIDM self-interactions to thermalize the inner halo and produce an isothermal core.
* ``[velocityRelativeMean]`` — Mean relative velocity to calculate self interaction cross section.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[tolerateVelocityMaximumFailure]`` (default ``.false.``) — If true, tolerate failures to find the radius of the peak in the rotation curve.
* ``[tolerateEnclosedMassIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to find the mass enclosed as a function of radius.
* ``[toleratePotentialIntegrationFailure]`` (default ``.false.``) — If ``true``, tolerate failures to compute the potential.
* ``[fractionRadiusFinalSmall]`` (default ``1.0d-3``) — The initial radius is limited to be no smaller than this fraction of the final radius. This can help avoid problems in profiles that are extremely close to being disrupted.
* ``[toleranceRelativePotential]`` (default ``1.0d-3``) — The maximum allowed relative tolerance to use in numerical solutions for the gravitational potential in dark-matter-only density profiles before aborting.
* ``[lengthResolution]`` — The spatial resolution length scale (in Mpc) below which the underlying density profile is softened to a flat core, mimicking the finite force resolution of an N-body simulation.
* ``[nonAnalyticSolver]`` (default ``var_str('fallThrough')``) — Selects how solutions are computed when no analytic solution is available. If set to "``fallThrough``" then the solution ignoring heating is used, while if set to "``numerical``" then numerical solvers are used to find solutions.
* ``[componentType]`` (default ``var_str('unknown')``) — The component type that this mass distribution represents.
* ``[massType]`` (default ``var_str('unknown')``) — The mass type that this mass distribution represents.
* ``[massMinimum]`` — The minimum halo mass (in :math:`\mathrm{M}_\odot`) below which halos are excluded from the mass function histogram.
* ``[massMaximum]`` — The maximum halo mass (in :math:`\mathrm{M}_\odot`) above which halos are excluded from the mass function histogram.
* ``[massCountPerDecade]`` — The number of logarithmic bins per decade of halo mass used when constructing the halo mass function.
* ``[description]`` — A human-readable description of this mass function dataset, stored as metadata in the output file.
* ``[simulationReference]`` — A bibliographic reference for the N-body simulation from which this mass function is derived, stored as metadata.
* ``[simulationURL]`` — A URL pointing to the publicly accessible dataset or documentation for the N-body simulation, stored as metadata.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.
* ``[representativeMinimumCount]`` (default ``10_c_size_t``) — Minimum number of representative particles used to compute the center of a halo.
* ``[tolerance]`` (default ``1.0d-2``) — The tolerance in the summed weight of bound particles which must be attained to declare convergence.
* ``[bootstrapSampleRate]`` (default ``1.0d0``) — The sampling rate for particles.
* ``[representativeFraction]`` (default ``0.05d0``) — Fraction of bound particles used to compute the center of a halo.
* ``[analyzeAllParticles]`` (default ``.true.``) — If true, all particles are assumed to be self-bound at the beginning of the analysis. Unbound particles at previous times are allowed to become bound in the current snapshot. If false and the self-bound information from the previous snapshot is available, only the particles that are self-bound at the previous snapshot are assumed to be bound at the beginning of the analysis.
* ``[useVelocityMostBound]`` (default ``.false.``) — If true, the velocity of the most bound particle in velocity space is used as the representative velocity of the satellite. If false, use the mass weighted mean velocity (center-of-mass velocity) of self-bound particles instead.
* ``[orderRotation]`` (default ``var_str('none')``) — The order in which evaluation of likelihoods should be rotated as a function of process number.
* ``[logLikelihoodAccept]`` (default ``huge(0.0d0)``) — The log-likelihood which should be "accepted"---once the log-likelihood reaches this value (or larger) no further updates to the chain will be made.
* ``[report]`` (default ``.false.``) — If true, report on the log-likelihood obtained.
* ``[means]`` — The mean of the multivariate normal distribution.
* ``[covariance]`` — The covariance matrix for the of the multivariate normal distribution.
* ``[countForestsMaximum]`` (default ``-1_c_size_t``) — If set to a positive number, this is the maximum number of forests that will be evolved.
* ``[walltimeMaximum]`` (default ``-1_kind_int8``) — If set to a positive number, this is the maximum wall time for which forest evolution is allowed to proceed before the task gives up.
* ``[tolerateFailures]`` (default ``.false.``) — If true then failures to evolve a forest are tolerated. The forest is evolved no further, but evolution of other forests continues.
* ``[evolveForestsInParallel]`` (default ``.true.``) — If true then each forest is evolved by a separate OpenMP thread. Otherwise, a single thread evolves all forests.
* ``[suspendToRAM]`` (default ``.true.``) — Specifies whether trees should be suspended to RAM (otherwise they are suspend to file).
* ``[suspendPath]`` — The path to which tree suspension files will be stored.
* ``[timeIntervalCheckpoint]`` (default ``-1_kind_int8``) — If positive, gives the time in seconds between storing of checkpoint files. If zero or negative, no checkpointing is performed..
* ``[fileNameCheckpoint]`` — The path to which checkpoint data will be stored.
* ``[logM0]`` (default ``10.0d0``) — The parameter :math:`\log_{10} M_0` (with :math:`M_0` in units of :math:`\mathrm{M}_\odot`) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR0]`` (default ``9.0d0``) — The parameter :math:`\alpha_0` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[logSFR1]`` (default ``0.0d0``) — The parameter :math:`\alpha_1` appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
* ``[cW]`` (default ``3.78062835d0``) — The parameter :math:`c_\mathrm{W}` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[beta]`` (default ``3.4638743d0``) — The parameter :math:`\beta` in the :cite:t:`bohr_halo_2021` power spectrum window function.
* ``[transferFunctionType]`` (default ``var_str('darkMatter')``) — Specifies whether to use the ``darkMatter`` or ``total`` transfer function.
* ``[fileName]`` — The name of the file from which to read a tabulated transfer function.
* ``[redshift]`` (default ``0.0d0``) — The redshift of the transfer function to read.
* ``[factorWavenumberSmoothExtrapolation]`` (default ``0.0d0``) — If positive, and extrapolation is used at high wavenumbers, the slope for extrapolation will be set by averaging over wavenumbers from :math:`k_\mathrm{max}/f` to :math:`k_\mathrm{max}`, where :math:`f=`\ ``[factorWavenumberSmoothExtrapolation]`` and :math:`k_\mathrm{max}` is the highest wavenumber tabulated. This avoids spurious extrapolation for highly oscillatory transfer functions.
* ``[acceptNegativeValues]`` (default ``.false.``) — If true, negative values in the transfer function are allowed (and the absolute value is taken prior to interpolation). Otherwise, negative values result in an error.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[fileName]`` (default ``var_str('none')``) — The name of the file to/from which tabulations of barrier first crossing probabilities should be written/read. If set to "``none``" tables will not be stored.
* ``[fractionalTimeStep]`` (default ``0.01d0``) — The fractional time step used when computing barrier crossing rates (i.e. the step used in finite difference calculations).
* ``[varianceNumberPerUnitProbability]`` (default ``1000``) — The number of points to tabulate per unit variance for first crossing probabilities.
* ``[varianceNumberPerUnit]`` (default ``40``) — The number of tabulation points per unit of :math:`\sigma^2` used when building the rate look-up table for the Farahi excursion-set first-crossing distribution; higher values improve interpolation accuracy at the cost of memory and initialization time.
* ``[varianceNumberPerDecade]`` (default ``400``) — The number of points to tabulate per decade of progenitor variance for first crossing rates.
* ``[varianceNumberPerDecadeNonCrossing]`` (default ``40``) — The number of points to tabulate per decade of progenitor variance for non-crossing rates.
* ``[timeNumberPerDecade]`` (default ``10``) — The number of tabulation points per decade of cosmic time used when building the first-crossing rate look-up table as a function of time; higher values improve temporal interpolation accuracy for rapidly evolving cosmologies.
* ``[varianceIsUnlimited]`` (default ``.false.``) — If true, the variance is assumed to have no upper limit (e.g. as in the case of :term:`CDM`). This allows the tabulated solutions to be extended arbitrarily. Otherwise, tables are extended to encompass just the range of variance requested.
* ``[linkingLength]`` (default ``0.2d0``) — The friends-of-friends linking length to use in computing virial density contrasts with the percolation analysis of :cite:t:`more_overdensity_2011`.

.. _physics-nodePropertyExtractorStarFormationRateInterOutput:

``nodePropertyExtractorStarFormationRateInterOutput``
-----------------------------------------------------

A node property extractor which extracts the mean star formation rate between successive outputs. Intended to be paired with the :galacticus-class:`nodeOperatorStarFormationRateInterOutput` node operator class to compute those rates.

.. _physics-nodePropertyExtractorStellarFeedbackOutflowRate:

``nodePropertyExtractorStellarFeedbackOutflowRate``
---------------------------------------------------

A node property extractor which extracts the stellar feedback-driven mass outflow rate from a galaxy. The type of mass outflow rate is controlled by the ``[component]`` parameter, which can be either "``disk``", "``spheroid``", or "``total``". The corresponding mass outflow rate is extracted as ``<component>StellarFeedbackOutflowRate`` in units of :math:`\mathrm{M}_\odot`/Gyr.

**Parameters**

* ``[component]`` — The component from which to extract star formation rate.

.. _physics-nodePropertyExtractorTidalField:

``nodePropertyExtractorTidalField``
-----------------------------------

A property extractor class which extracts the radial component of the tidal tensor in units of :math:`\mathrm{Gyr^{-2}}`.

.. _physics-nodePropertyExtractorTidallyTruncatedNFWFit:

``nodePropertyExtractorTidallyTruncatedNFWFit``
-----------------------------------------------

Fits a tidally truncated NFW profile to the dark matter halo, extracting the best-fit tidal truncation radius and associated structural parameters, useful for characterizing the degree of tidal stripping experienced by satellite subhalos.

.. _physics-nodePropertyExtractorTime:

``nodePropertyExtractorTime``
-----------------------------

Extracts the cosmic time (age of the universe) at the epoch of each output snapshot, providing the absolute time coordinate for each node and enabling time-based analysis of galaxy formation histories across cosmic epochs.

**Methods**

* ``timeMergingSet`` — Set the time of merging for a satellite node.

**Parameters**

* ``[resetOnHaloFormation]`` (default ``.false.``) — Specifies whether satellite virial orbital parameters should be reset on halo formation events.

.. _physics-nodePropertyExtractorTimeFirstInfall:

``nodePropertyExtractorTimeFirstInfall``
----------------------------------------

Extracts the cosmic time at which a satellite node first crossed the virial radius of its host halo (first infall), a key epoch for quantifying how long satellites have been processed by environmental effects such as ram pressure stripping and tidal forces.

.. _physics-nodePropertyExtractorTimescaleBarInstability:

``nodePropertyExtractorTimescaleBarInstability``
------------------------------------------------

Extracts the bar instability timescale for disk galaxies, which governs how quickly a stellar bar can form via gravitational instability in the disk component. Used to diagnose the onset of secular evolution and the transfer of angular momentum from disk to spheroid.

.. _physics-nodePropertyExtractorTrackOutflowedMass:

``nodePropertyExtractorTrackOutflowedMass``
-------------------------------------------

Extracts the cumulative mass and metal mass of gas that has been outflowed to the circumgalactic medium (:term:`CGM`) via stellar and AGN feedback, as tracked by the :galacticus-class:`nodeOperatorTrackOutflowedMass` operator.

.. _physics-nodePropertyExtractorTreeWeight:

``nodePropertyExtractorTreeWeight``
-----------------------------------

Extracts the statistical weight assigned to each merger tree, representing the number density of halos of that mass in the target cosmology, used when combining results across trees sampled at discrete mass points to recover volume-averaged statistics.

.. _physics-nodePropertyExtractorTuple:

``nodePropertyExtractorTuple``
------------------------------

Abstract base class for extractors that return a fixed-length tuple of floating-point values per node (e.g., 3D position or velocity vectors), defining the interface for multi-component vector property extraction used in output analysis.

**Methods**

* ``elementCount`` — Return the number of properties in the tuple.
* ``extract`` — Extract the properties from the given ``node``.
* ``names`` — Return the names of the properties extracted.
* ``descriptions`` — Return descriptions of the properties extracted.
* ``unitsInSI`` — Return the units of the properties extracted in the SI system.
* ``units`` — Return an object containing units metadata for the properties.
* ``metaData`` — Populate a hash with meta-data for the property.

.. _physics-nodePropertyExtractorUniqueIDBranchTip:

``nodePropertyExtractorUniqueIDBranchTip``
------------------------------------------

Extracts the unique global identifier of the tip (earliest progenitor) node on the current merger tree branch, providing a persistent cross-snapshot identifier that enables tracking of branch origins across different output times and tree realizations.

.. _physics-nodePropertyExtractorVelocityDispersion:

``nodePropertyExtractorVelocityDispersion``
-------------------------------------------

A property extractor class for the velocity dispersion at a set of radii. The radii and types of projected density to output is specified by the ``radiusSpecifiers`` parameter. This parameter's value can contain multiple entries, each of which should be a valid :ref:`radius specifier <manual-sec-radiusspecifiers>`, but with an additional, colon-separated, value at the end indicating the direction in which the velocity dispersion should be computed. This direction should be one of ``radial`` (computes the radial component of velocity dispersion), ``lineOfSight{<luminosity>}`` (computes the line-of-sight velocity dispersion), ``lineOfSightInteriorAverage{<luminosity>}`` (computes the line-of-sight velocity dispersion averaged interior to the given radius), or ``lambdaR{<luminosity>}`` (computes the :math:`\lambda_\mathrm{R}` statistic of :cite:author:`cappellari_sauron_2007` :cite:year:`cappellari_sauron_2007`)---in the latter three cases ``{<luminosity>}`` specifies which band should be used to weight the velocity dispersion, alternatively setting ``{<luminosity>}``\ :math:`=`\ ``mass`` (or just leaving off this specifier entirely) will use mass weighting instead.

**Parameters**

* ``[radiusSpecifiers]`` — A list of radius specifiers at which to output the velocity dispersion.
* ``[includeRadii]`` (default ``.false.``) — Specifies whether or not the radii at which velocity dispersion data are output should also be included in the output file.
* ``[integrationFailureIsFatal]`` (default ``.true.``) — If true, failure of line-of-sight integrals is fatal. Otherwise, such errors are tolerated.
* ``[toleranceRelative]`` (default ``1.0d-3``) — The relative tolerance to use in integrals.
* ``[selfBoundParticlesOnly]`` — If true, the velocity dispersion is computed only for self-bound particles.
* ``[radiusInner]`` — Inner radii of spherical shells within which the velocity dispersion should be computed.
* ``[radiusOuter]`` — Outer radii of spherical shells within which the velocity dispersion should be computed.
* ``[bootstrapSampleCount]`` (default ``30_c_size_t``) — The number of bootstrap resamples of the particles that should be used.

.. _physics-nodePropertyExtractorVelocityMaximum:

``nodePropertyExtractorVelocityMaximum``
----------------------------------------

A property extractor that returns the maximum circular velocity (in km s\ :math:`^{-1}`) of the dark-matter-only halo profile, :math:`V_\mathrm{max} = \max_r \sqrt{GM(< r)/r}`, computed from the supplied :galacticus-class:`darkMatterProfileDMOClass` object. The output dataset is named ``darkMatterProfileDMO``\ ``propertyName``, where ``propertyName`` (default: ``VelocityMaximum``) can be set to distinguish multiple instances of this extractor.

**Parameters**

* ``[mu]`` (default ``0.4d0``) — The parameter :math:`\mu` in the :cite:t:`penarrubia_impact_2010` tidal track fitting function.
* ``[eta]`` (default ``0.3d0``) — The parameter :math:`\eta` in the :cite:t:`penarrubia_impact_2010` tidal track fitting function.
* ``[propertyName]`` (default ``var_str('VelocityMaximum')``) — Name of the property.

.. _physics-nodePropertyExtractorVelocityOrbital:

``nodePropertyExtractorVelocityOrbital``
----------------------------------------

An orbital velocity output analysis property extractor class. Specifically, the orbital velocity is defined relative to the top-level halo in any sub-halo hierarchy. That is, relative to the host halo which is itself not a sub-halo of any other halo. If the velocity of a (sub)\ :math:`^i`-halo with respect to the center of its (sub)\ :math:`^{i-1}`-halo host is :math:`\mathbf{v}_i` then the orbital velocity computed by this class is

.. math::

   \mathbf{v} = sum_{i=1}^N \mathbf{v}_i,

where :math:`N` is the depth of the node in the sub-halo hierarchy.

.. _physics-nodePropertyExtractorVirialProperties:

``nodePropertyExtractorVirialProperties``
-----------------------------------------

A node property extractor which extracts the following quantities related to the virialized region of each node:

``nodeVirialRadius``
   The virial radius (following whatever definition of virial overdensity is specified by the virial density contrast (see :galacticus-class:`virialDensityContrast`)) in units of Mpc;

``nodeVirialVelocity``
   The circular velocity at the virial radius (in km/s).