.. _physics-mergerTreeConstructor: Merger Tree Constructors ======================== Class providing merger tree constructors---any process by which a representation of a dark matter halo merger tree is created and made available within Galacticus for subsequent galaxy formation calculations. Implementations include stochastic Monte Carlo tree building algorithms (which generate trees on-the-fly from excursion set merger rates), reading pre-computed trees from N-body simulations stored in HDF5 or other formats, and analytic approximations. The ``construct`` method returns a :galacticus-class:`mergerTree` pointer for the given tree index, and signals completion once all trees in the set have been constructed. **Default implementation:** ``mergerTreeConstructorBuild`` Methods ------- ``construct`` → ``type(mergerTree), pointer`` Construct the merger tree corresponding to the given ``treeNumber``. * ``integer(c_size_t), intent(in ) :: treeNumber`` * ``logical , intent( out) :: finished`` ``randomSequenceNonDeterministicWarn`` → ``void`` Display a warning if the merger tree random number generator sequence is non-deterministic. * ``type(mergerTree), intent(inout) :: tree`` .. _physics-mergerTreeConstructorBuild: ``mergerTreeConstructorBuild`` ------------------------------ A merger tree constructor class which builds merger trees. This class first creates a distribution of tree root halo masses and then builds a merger tree from each root halo. **(Default implementation)** **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-mergerTreeConstructorFilter: ``mergerTreeConstructorFilter`` ------------------------------- A merger tree constructor class filters trees from another constructor. Trees which do not pass the filter are dropped. Those that do pass the filter are returned. .. _physics-mergerTreeConstructorFullySpecified: ``mergerTreeConstructorFullySpecified`` --------------------------------------- A merger tree constructor class which constructs a merger tree given a full specification in XML. This class will construct a merger tree, and set properties of components in each node, using a description read from an XML document. The document is specified via the ``[fileName]`` input parameter. The tree specification document looks as follows: .. code-block:: none 2 1 -1 -1 1.0 1.0e12 7.9365079e9 0.1 1.0e10 1.0e10 1.0e9 1.0e9 1 -1 2 -1 13.8 1.1e12 7.8125e9 1.23 6.31 3.59 The document consists of a set of ``node`` elements, each of which defines a single node in the merger tree. Each ``node`` element must specify the ``index`` of the node, along with the index of the node's ``parent``, ``firstChild``, and ``sibling``. Each ``node`` element may contain elements which specify the properties of a component in the node. For example, a ``basic`` element will specify properties of the "basic" component. If multiple elements for a given component type are present, then multiple instances of that component will be created in the node. Within a component definition element scalar properties are set using an element with the same name as that property (e.g. ``mass`` in the ``basic`` components in the above example). Rank-1 properties are set using a list of elements with the same name as the property (e.g. ``position`` in the ``position`` component in the above example). For composite properties (e.g. abundances), the specification element should contain sub-elements that specify each property of the composite. Currently only the ``abundances`` object supports specification in this way, as detailed below: ``abundances`` (See ``abundancesGas`` in the above example.) The total metal content is specified via a ``metals`` element. If other elements are being tracked, their content is specified via an element with the short-name of the element (e.g. ``Fe`` for iron). The parameter ``[countRealizations]`` (defaulting to 1) controls how many merger tree realizations are simulated for each input tree. **Parameters** * ``[fileName]`` — The name of the file containing the merger tree specification. * ``[countRealizations]`` (default ``1_c_size_t``) — The number of realizations of each tree to generate. .. _physics-mergerTreeConstructorRead: ``mergerTreeConstructorRead`` ----------------------------- A merger tree constructor class from data imported from a file and processed into a form suitable for Galacticus to evolve. Merger trees are inherently complex structures, particularly when the possibility of subhalos are considered. Galacticus is currently designed to work with single descendant merger trees, i.e. ones in which the tree structure is entirely defined by specifying which :term:`node` a given :term:`node` is physically associated with at a later time. Additionally, Galacticus expects the merger tree file to contain information on the host :term:`node`, i.e. the node within which a given node is physically located. In the following, these two properties are labeled ``descendantNode`` and ``hostNode``. Galacticus assumes that nodes for which ``descendantNode``\ :math:`=`\ ``hostNode`` are isolated halos (i.e. they are their own hosts) while other nodes are subhalos (i.e. they are hosted by some other node). An example of a simple tree structure is shown in Fig. :numref:`{number} `. The particular structure would be represented by the following list of nodes and node properties (a :math:`-1` indicates that no descendant node exists): .. list-table:: :header-rows: 1 * - ``node`` - ``descendantNode`` - ``hostNode`` * - 1 - -1 - 1 * - 2 - 1 - 2 * - 3 - 2 - 3 * - 4 - 1 - 4 * - 5 - 4 - 5 * - 6 - -1 - 1 * - 7 - 6 - 4 * - 8 - 7 - 8 .. figure:: /_figures/MergerTreeSimple.png :name: fig-MergerTreeSimple An example of a simple merger tree structure. Colored circles represent nodes in the merger tree. Each node has a unique index indicated by the number inside each circle. Black arrows link each node to its descendant node (as specified by the ``descendantNode`` property). Where a node is not its own host node it is placed inside its host node. The following should be noted when constructing merger tree files: * Note that Galacticus does not require that nodes be placed on a uniform grid of times/redshifts, nor that mass be conserved along a branch of the tree. After processing the tree in this way, Galacticus builds additional links which identify the child node of each halo and any sibling nodes. These are not required to specify the tree structure but are computationally convenient. * It is acceptable for a node to begin its existence as a subhalo (i.e. to have never had an isolated node progenitor). Such nodes will be created as satellites in the merger tree and, providing the selected node components (see :ref:`here `) initialize their properties appropriately, will be evolved correctly. * It is acceptable for an isolated node to have progenitors, none of which are a primary progenitor. This can happen if all progenitors descend into subhalos in the isolated node. In such cases, Galacticus will create a clone of the isolated node at a very slightly earlier time to act as the primary progenitor. This is necessary to allow the tree to be processed correctly, but does not affect the evolution of the tree. * Normally, cases where a node's host node cannot be found in the :term:`forest` will cause Galacticus to exit with an error. Setting ``[missingHostsAreFatal]``\ :math:`=`\ ``false`` will instead circumvent this issue by making any such nodes self-hosting (i.e. they become isolated nodes rather than subhalos). Note that this behavior is not a physically correct way to treat such cases---it is intended only to allow trees to be processed in cases where the full :term:`forest` is not available. * It is acceptable for nodes to jump between branches in a tree, or even to jump between branches in different trees. In the latter case, all trees linked by jumping nodes (a so-called ":term:`forest`" of connected trees) must be stored as a single forest (with multiple root-nodes) in the merger tree file. Galacticus will process this :term:`forest` of trees simultaneously, allowing to nodes to move between their branches. * It is acceptable for a subhalo to later become an isolated halo (as can happen due to three-body interactions; see :cite:author:`sales_cosmic_2007` :cite:year:`sales_cosmic_2007`). If ``[allowSubhaloPromotions]``\ :math:`=`\ ``true`` then such cases will be handled correctly (i.e. the subhalo will be promoted back to being an isolated halo). If the parameter ``[alwaysPromoteMostMassive]``\ :math:`=`\ ``true`` then the most massive progenitor is treated as the primary progenitor, even if that progenitor is a subhalo. Alternatively, if ``[alwaysPromoteMostMassive]``\ :math:`=`\ ``false`` then a most massive progenitor that is a subhalo is only treated as the primary progenitor *if* no isolated progenitors exist (otherwise, the most massive of the isolated progenitors is treated as the primary progenitor). If ``[allowSubhaloPromotions]``\ :math:`=`\ ``false`` then subhalos are not permitted to become isolated halos. In this case, the following logic will be applied to remove all such cases from the tree: * For any branch in a tree which at some point is a subhalo: * Beginning from the earliest node in the branch that is a subhalo, repeatedly step to the next descendant node; * If that descendant is *not* a subhalo then: * If there is not currently any non-subhalo node which has the present node as its descendant then current node is only descendant of a subhalo. Therefore, try to make this node a subhalo, and propose the descendant of the host node of the previous node visited in the branch as the new host: * If the proposed host exists: * If the mass of the current node is less than that of the proposed host: * If the proposed hosts exists before the current node, repeatedly step to its descendants until one is found which exists at or after the time of the current node. This is the new proposed host. * If the proposed host is a subhalo, make it an isolated node. * The current node is made a subhalo within the proposed host. * Otherwise: * The current node remains an isolated node, while the proposed host is instead made a subhalo within the current node. * Otherwise: * The proposed host does not exists, which implies the end of a branch has been reached. Therefore, flag the current node as being a subhalo with a host identical to that of the node from which it descended. **Requirements for Galacticus Input Parameters:** The following requirements must be met for the input parameters to Galacticus when using merger trees read from file: * The cosmological parameters (:math:`\Omega_\mathrm{M}`, :math:`\Omega_\Lambda`, :math:`\Omega_\mathrm{b}`, :math:`H_0`, :math:`\sigma_8`), if defined in the file, must be set identically in the Galacticus input file unless you set ``[mismatchIsFatal]``\ :math:`=`\ ``false`` in which case you'll just be warned about any mismatch; * Galacticus assumes by default that all merger trees exist at the final output time---if this is not the case set ``[allTreesExistAtFinalTime]``\ :math:`=`\ ``false``. **Dark Matter Scale Radii**: If ``[presetScaleRadii]``\ :math:`=`\ ``true`` and the ``halfMassRadius`` dataset is available within the ``haloTrees`` group (see `here `_) then the half-mass radii of nodes will be used to compute the corresponding scale length of the dark matter halo profile\footnoteThe scale radius is found by seeking a value which gives the correct half mass radius. It is therefore important that the definition of halo mass (specifically the virial overdensity) in Galacticus be the same as was used in computing the input half mass radii.. This requires a dark matter profile scale component which supports setting of the scale length (see :ref:`here `). **Satellite Merger Times:** If ``[presetMergerTimes]``\ :math:`=`\ ``true`` then merger times for satellites will be computed directly from the merger tree data read from file. When a subhalo has an isolated halo as a descendant it is assumed to undergo a merger with that isolated halo at that time. Note that this requires a satellite orbit component method which supports setting of merger times (e.g. ``[componentSatellite]``\ :math:`=`\ ``preset``). **Dark Matter Halo Angular Momenta:** If ``[presetAngularMomenta]``\ :math:`=`\ ``true`` and the ``angularMomentum`` dataset is available within the ``haloTrees`` group (see `here `_) then the angular momenta of nodes will be computed and set. This requires a dark matter halo spin component which supports setting of the angular momentum (see :ref:`here `). **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-mergerTreeConstructorStateRestored: ``mergerTreeConstructorStateRestored`` -------------------------------------- A merger tree constructor class which will restore a merger tree whose complete internal state was written to file. It is intended primarily for debugging purposes to allow a tree to begin processing just prior to the point of failure. To use this method, the following procedure should be followed: #. Identify a point in the evolution of the tree suitably close to, but before, the point of failure; #. Insert appropriate code into Galacticus to have it call the function to store the state of the file and then stop, e.g.: .. code-block:: none use :: Merger_Tree_Construction, only : mergerTreeStateStore . . . if () then call mergerTreeStateStore(tree,'storedTree.dat') stop 'tree internal state was stored' end if #. Run the model ensuring that ``[stateFileRoot]`` is set to a suitable file root name to allow the internal state of Galacticus to be stored; #. Remove the code inserted above and recompile; #. Run Galacticus with an input parameter file identical to the one used previously except with ``[mergerTreeConstruct]``\ :math:`=`\ ``stateRestore``, ``[stateFileRoot]`` removed, ``[stateRetrieveFileRoot]`` set to the value previously used for ``[stateFileRoot]`` and ``[fileName]``\ :math:`=`\ ``storedTree.dat``. This should restore the tree and the internal state of Galacticus precisely from the point where they were saved and produce the same subsequent evolution. Note that currently this method does not support storing and restoring of trees which contain components that have more than one instance. **Parameters** * ``[fileName]`` (default ``var_str('storedTree.dat')``) — The name of the file containing the stored merger tree.