Merger Tree Importer¶

Class providing functions for importing merger trees. When merger trees are to be read from file, a number of different file formats are supported. This “importer” class is used to read these files and place the contents into internal data structures that Galacticus can then manipulate.

Default implementation: mergerTreeImporterGalacticus

Methods¶

open → void

Opens the merger tree file specified by fileName for reading, initializing any internal state required by the importer before data can be loaded.

type(varying_string), intent(in ) :: fileName

treesHaveSubhalos → integer

Returns a Boolean integer specifying whether or not the trees have subhalos.

massesIncludeSubhalos → logical

Returns a Boolean specifying whether halo masses include the contribution from their subhalos.

angularMomentaIncludeSubhalos → logical

Returns a Boolean specifying whether halo angular momenta (or spins) include the contribution from their subhalos.

treesAreSelfContained → integer

Returns a Boolean integer specifying whether trees are self-contained.

velocitiesIncludeHubbleFlow → integer

Returns a Boolean integer specifying whether velocities include the Hubble flow.

positionsArePeriodic → integer

Returns a Boolean integer specifying whether positions are periodic.

canReadSubsets → logical

Returns true if arbitrary subsets of halos from a forest can be read.

cubeLength → double precision

Returns the comoving side length (in Mpc) of the periodic simulation cube at the given time; used to apply periodic boundary conditions when reading positions.

double precision, intent(in ) :: time
integer , intent( out), optional :: status

treeCount → integer(kind=c_size_t)

Returns a count of the number of trees available.

treeIndex → integer(kind=kind_int8)

Returns the unique integer identifier of the \(i^\mathrm{th}\) tree in the file, used to label the tree in output datasets.

integer, intent(in ) :: i

nodeCount → integer(kind=c_size_t)

Returns the number of nodes in the \(i^\mathrm{th}\) tree.

integer, intent(in ) :: i

treeWeight → double precision

Returns the weight to assign to the \(i^\mathrm{th}\) tree.

integer, intent(in ) :: i

positionsAvailable → logical

Return true if positions and/or velocities are available.

logical, intent(in ) :: positions, velocities

scaleRadiiAvailable → logical

Return true if halo scale radii are available in this merger tree file, so the importer can populate scaleRadius fields when loading nodes.

particleCountAvailable → logical

Return true if particle counts per halo are available in this merger tree file, so the importer can populate particleCount fields when loading nodes.

velocityMaximumAvailable → logical

Return true if rotation curve velocity maxima are available.

velocityDispersionAvailable → logical

Return true if halo velocity dispersions are available.

angularMomentaAvailable → logical

Return true if angular momenta (magnitudes) are available.

angularMomenta3DAvailable → logical

Return true if angular momenta (vectors) are available.

spinAvailable → logical

Return true if spin (magnitudes) are available.

spin3DAvailable → logical

Return true if 3D spin vectors are available in this merger tree file, so the importer can populate spin3D fields when loading nodes.

import → void

Imports all nodes for the \(i^\mathrm{th}\) tree from the open file into the nodes array, reading only those fields requested via the optional arguments.

integer , intent(in ) :: i
class (nodeDataMinimal), intent( out), allocatable, dimension(:) :: nodes
integer(c_size_t ), intent(in ), optional , dimension(:) :: nodeSubset
logical , intent(in ), optional :: requireScaleRadii, requireAngularMomenta, requireAngularMomenta3D, requireSpin, requireSpin3D, requirePositions, structureOnly
type (varying_string ), intent(in ), optional , dimension(:) :: requireNamedReals, requireNamedIntegers

subhaloTrace → void

Supplies epochs, positions, and velocities for traced subhalos.

class (nodeData), intent(in ) :: node
double precision , intent( out), dimension(: ) :: time
double precision , intent( out), dimension(:,:) :: position, velocity

subhaloTraceCount → integer(kind=c_size_t)

Returns the number of snapshot epochs recorded in the subhalo trace for the given node, i.e.the length of the time, position, and velocity arrays to be allocated before calling subhaloTrace.

class(nodeData), intent(in ) :: node

`mergerTreeImporterGalacticus`¶

A merger tree importer class which imports trees from an HDF5 file. HDF5 file should follow the general purpose format described here. To generate HDF5 files in this format from merger tree data produced by a variety of tree builders (e.g.Rockstar/ConsistentTrees), the astrosylva tool (GitHub; PyPI; documentation) can be used.

(Default implementation)

Parameters

[fatalMismatches] (default .true.) — Specifies whether mismatches in cosmological parameter values between Galacticus and the merger tree file should be considered fatal.
[reweightTrees] (default .false.) — Specifies whether merger tree weights should be recomputed from the halo mass function.
[validateData] (default .false.) — If true perform some validation of imported data to identify possible problems.

`mergerTreeImporterSussing`¶

Importer for merger tree files in the “Sussing Merger Trees” format (Srisawat et al., 2013), reading halo properties from N-body simulation snapshots and constructing halo merger histories. Supports spatial subvolume splitting via [subvolumeCount] and [subvolumeIndex], with cosmological parameter mismatch handling controlled by [fatalMismatches].

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 SNe-driven outflow rate equals the star formation rate in disks.
[exponent] (default 3.5d0) — The velocity scaling of the SNe-driven outflow rate in disks.
[fraction] (default 0.01d0) — The normalization \(f\) 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 \((1+z)\) 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 Cole et al. (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 \(V_\mathrm{spheroid}^2\).
[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]\(=\)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 (\(c=r_\mathrm{vir}/r_\mathrm{s}\)) allowed when setting scale radii, \(r_\mathrm{s}\).
[presetScaleRadiiConcentrationMaximum] (default 60.0d0) — The largest concentration (\(c=r_\mathrm{vir}/r_\mathrm{s}\)) allowed when setting scale radii, \(r_\mathrm{s}\).
[presetScaleRadiiMinimumMass] (default 0.0d0) — The minimum halo mass for which scale radii should be preset (if [presetScaleRadii]\(=\)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]\(=\)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]\(=\)read tree construction method.
[fatalMismatches] (default .true.) — Specifies whether mismatches in cosmological parameter values between Galacticus and “Sussing Merger Trees” format (Srisawat et al., 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 (Srisawat et al., 2013).
[subvolumeCount] (default 1) — Specifies the number of subvolumes along each axis into which a “Sussing Merger Trees” format (Srisawat et al., 2013) merger tree files should be split for processing through Galacticus.
[subvolumeBuffer] (default 0.0d0) — Specifies the buffer region (in units of Mpc\(/h\) to follow the format convention) around subvolumes of a “Sussing Merger Trees” format (Srisawat et al., 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 (Srisawat et al., 2013) merger tree file to process. Indices range from 0 to [subvolumeCount]\(-1\).
[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 Cole et al. (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 Cole et al. (2000) method.
[redshiftMaximum] (default 1.0d5) — The highest redshift to which merger trees will be built in the Cole et al. (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 Cole et al. (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 \((\lambda_\mathrm{m}/R,\lambda_\mathrm{m} R\), where \(\lambda_\mathrm{m}\) is the measured spin, and \(R=\)[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 \(\Delta t=\)[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] (6548AA \(+\) 6584AA) 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 \(\Delta t=\)[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\(^{-1}\)) 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 \(\sigma_\mathrm{r}^2(r) \rightarrow \sigma_\mathrm{r}^2(r) - (2/3) \epsilon(r)\), where \(\epsilon(r)\) 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 \(\Delta x\) (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 \(\Delta M\) (in \(\mathrm{M}_\odot\)) 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 \(C\) appearing in the halo concentration algorithm of Ludlow et al. (2016).
[f] (default 0.02d0) — The parameter \(f\) appearing in the halo concentration algorithm of Ludlow et al. (2016).
[timeFormationSeekDelta] (default 0.0d0) — The parameter \(\Delta \log t\) 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 \(\mathrm{M}_\odot\)/Mpc\(^3\)) of the solitonic core at \(r=0\), which sets the overall normalization of the density profile \(\rho(r) = \rho_\mathrm{c} [1+(r/r_c)^2]^{-8}\).
[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 \(f_\mathrm{trans}(r)\).
[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 \(\mathrm{M}_\odot\)) below which halos are excluded from the mass function histogram.
[massMaximum] — The maximum halo mass (in \(\mathrm{M}_\odot\)) 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 \(\log_{10} M_0\) (with \(M_0\) in units of \(\mathrm{M}_\odot\)) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
[logSFR0] (default 9.0d0) — The parameter \(\alpha_0\) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
[logSFR1] (default 0.0d0) — The parameter \(\alpha_1\) appearing in the star formation rate threshold expression for the star formation rate galactic filter class.
[cW] (default 3.78062835d0) — The parameter \(c_\mathrm{W}\) in the Bohr et al. (2021) power spectrum window function.
[beta] (default 3.4638743d0) — The parameter \(\beta\) in the Bohr et al. (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 \(k_\mathrm{max}/f\) to \(k_\mathrm{max}\), where \(f=\)[factorWavenumberSmoothExtrapolation] and \(k_\mathrm{max}\) 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 \(\sigma^2\) 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 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 More et al. (2011).

`mergerTreeImporterSussingASCII`¶

A merger tree importer class for “Sussing Merger Trees” ASCII format merger tree files (Srisawat et al., 2013), along with AHF format halo catalogs. A descriptor file must be specified via the [mergerTreeReadFileName] parameter. This descriptor file should have the following format:

simulation.txt
MergerTree+AHF.txt
snapidzred.txt
AHF/62.5_dm_000.z50.000.AHF_halos
AHF/62.5_dm_001.z30.000.AHF_halos
AHF/62.5_dm_002.z19.916.AHF_halos
.
.
.
AHF/62.5_dm_061.z0.000.AHF_halos

in which each line specifies a file to be read (by default path names are relative to the location of the descriptor file—fully-qualified path names can also be given).

The first line identifies a file which specifies properties of the simulation. This file should look like:

WMAP7 cosmology:
----------------
Omega0          =       0.272
OmegaLambda0    =       0.728
h               =       0.704

simulation:
-----------
B               =       62.5 Mpc/h
N               =       270^3 particles

Currently only the cosmological parameter and box length are read from this file.

The second line identifies the merger tree file which must be in the format specified by Srisawat et al. (2013).

The third line of the descriptor file specifies a snapshot file which should have the following format:

#    snapnum       a             z           t(t0)      t(year)
           0    0.0196080      49.9996   0.00354284  4.87485e+07
           1    0.0322580      30.0001   0.00747572  1.02864e+08
           2    0.0478110      19.9157    0.0134888  1.85602e+08
           3    0.0519650      18.2437    0.0152842  2.10306e+08
           4    0.0564190      16.7245    0.0172905  2.37912e+08
           5    0.0611880      15.3431    0.0195280  2.68700e+08
           6    0.0662870      14.0859    0.0220186  3.02969e+08
             .
             .
             .

This file must contain one line for each snapshot of the simulation, giving the snapshot number, expansion factor, redshift, fractional time (relative to present day), and age of the universe (in years).

Subsequent lines identify the AHF halo files for each snapshot (files can be listed in any order).

Merger tree files of this type can be split into subvolumes before processing. This is useful if the file is too large to read into memory in one go. The number of subvolumes to use (in each of the three dimensions of the simulation cube) is specified by the [subvolumeCount] parameter. The specific subvolume to process is specified by the [subvolumeIndex] parameter, which should give the index (running from \(0\) to [subvolumeCount]\(-1\)) in each dimension (whitespace separated). To ensure that no halos are missed from trees near the edge of the subvolume, a buffer region around the subvolume is also read. The width of this buffer (in units of Mpc\(/h\) to follow the format convention) is specified via the [subvolumeBuffer] parameter.

Methods

initialize — Initialize the object after construction.

Parameters

[convertToBinary] (default .true.) — Specifies whether halo and tree files in the “Sussing” format should be converted to binary the first time they are read and stored to file. This allows rapid re-reading in future.
[binaryFormatOld] (default .false.) — Specifies whether the old binary format is to be used (for reading only).
[forestFile] (default var_str('none')) — Name of file containing data on number of halos in each forest.
[forestFirst] (default 1) — The 1-based index of the first forest in the file to include when reading a subset of forests; forests before this index are skipped.
[forestLast] (default -1) — The 1-based index of the last forest in the file to include when reading a subset of forests; a value of \(-1\) includes all forests through the end of the file.
[forestReverseSnapshotOrder] (default .false.) — If true, the order of forest snapshots will be reversed after being read. This may be necessary to cause them to match the order of snapshot files.

`mergerTreeImporterSussingHDF5`¶

Importer for “Sussing Merger Trees” HDF5 format merger tree files (Srisawat et al., 2013).

Parameters

[fileName] — The name of the file from which to read merger tree masses.
[massIntervalFractional] (default 0.1d0) — The fractional mass interval occupied by the trees. Where the intervals of trees of different mass would overlap this interval will be truncated.

Merger Tree Importer¶

Methods¶

mergerTreeImporterGalacticus¶

mergerTreeImporterSussing¶

mergerTreeImporterSussingASCII¶

mergerTreeImporterSussingHDF5¶

`mergerTreeImporterGalacticus`¶

`mergerTreeImporterSussing`¶

`mergerTreeImporterSussingASCII`¶

`mergerTreeImporterSussingHDF5`¶