Tutorial: Dark matter subhalo evolution - galacticusorg/galacticus GitHub Wiki
In this tutorial we'll use Galacticus to evolve populations of subhalos within a dark matter halo merger tree and output their properties. No baryonic physics (well, almost no baryonic physics) is included in this model.
If you haven't already installed Galacticus, you can find the installation instructions here.
For this tutorial we'll use the parameters/tutorials/darkMatterOnlySubHalos.xml parameter file:
$ ./Galacticus.exe parameters/tutorials/darkMatterOnlySubHalos.xml
If everything is working you should see output which looks something like:
##
#### # #
# # # #
# ### # ### ### ### ## ### ## ## ##
# # # # # # # # # # # # # # #
# ### ### # ### # # # # # # #
# # # # # # # # # # # # # #
#### #### ### #### ### ## ### ### #### ##
© 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016,
2017, 2018, 2019, 2020, 2021
- Andrew Benson
M: Memory: code + nodes + misc = total
M: 22.246Mib + 1.000 b + 9.000 b = 22.246Mib
M: -> Begin multiple tasks
.
.
.
and a file darkMatterOnlySubHalos.hdf5 will have been created. Typically this model will take around 30s to run, but it may be (much) slower the first time you run it as various power spectra and linear growth tables are computed and stored.
You can look at the entire parameter file for this tutorial here. Below we'll explore sections of the file to understand what they do. (Sections that have been explored in previous tutorials, e.g. cosmological parameters, will not be re-examined here.)
<!-- Task -->
<task value="multi" >
<task value="powerSpectra" >
<wavenumberMinimum value="1.0e-3"/>
<wavenumberMaximum value="1.0e+2"/>
<pointsPerDecade value="10" />
</task>
<task value="haloMassFunction" >
<haloMassMinimum value="1.0e06"/>
<haloMassMaximum value="1.0e15"/>
<pointsPerDecade value="10" />
</task>
<task value="evolveForests" />
</task>
<evolveForestsWorkShare value="cyclic"/>
This block tells Galacticus what task we want it to perform - here we're just asking it to compute the power spectrum, the halo mass function, and then to evolve merger tree forests.
<!-- Structure formation options -->
<linearGrowth value="baryonsDarkMatter" />
<criticalOverdensity value="sphericalCollapseBrynsDrkMttrDrkEnrgy"/>
<virialDensityContrast value="sphericalCollapseBrynsDrkMttrDrkEnrgy"/>
<haloMassFunction value="shethTormen" >
<a value="0.791"/> <!-- Best fit values from Benson, Ludlow, & Cole (2019). -->
<normalization value="0.302"/>
<p value="0.218"/>
</haloMassFunction>
<excursionSetBarrier value="remapScale" >
<!-- Remap the barrier height by a constant factor to account for the difference in sigma(M) on large scales introduced by our
choice of using a sharp-in-k-space filter on the power spectrum. -->
<factor value="1.1965" />
<applyTo value="nonRates" />
<!-- Remap the barrier height according to the parameterization of Sheth, Mo, & Tormen (2001) to account for ellipsoidal
collapse. -->
<excursionSetBarrier value="remapShethMoTormen" >
<a value="0.707" />
<b value="0.500" />
<c value="0.600" />
<applyTo value="nonRates" />
<!-- Use the critical overdensity as the barrier height in the excursion set problem. -->
<excursionSetBarrier value="criticalOverdensity"/>
</excursionSetBarrier>
</excursionSetBarrier>
<excursionSetFirstCrossing value="linearBarrier"/>
This block specifies various options related to large scale structure growth. The linear growth function is set to the baryonsDarkMatter model of Benson (2020), in which the suppression of growth of large wavenumber modes due to baryon pressure is accounted for. Options for solving the excursion set problem are also included here, even though it is not used with the Sheth & Tormen (2002) mass function which we select. It is included since it is required if the mass function is switched to the [Press & Schechter (1974)[http://adsabs.harvard.edu/abs/1974ApJ...187..425P] form used for some non-CDM dark matter models.
<intergalacticMediumState value="instantReionization">
<reionizationRedshift value="8.0e0" />
<reionizationTemperature value="1.5e4" />
<presentDayTemperature value="1.0e3" />
<intergalacticMediumState value="recFast"/>
</intergalacticMediumState>
Here we select a simple model of the evolution of the IGM. The thermal history of the IGM is needed to solve for the growth of large wavenumber modes where baryon pressure delays the growth of structure. This IGM model assumes instant reionization at z=8, heating to a temperature of 15,000K, and cooling to 1,000K by the present day. Prior to reionization the IGM state is computed using the RecFast code.
<!-- Dark matter halo structure options -->
<darkMatterProfileDMO value="heated" >
<darkMatterProfileDMO value="NFW" />
<nonAnalyticSolver value="numerical"/>
</darkMatterProfileDMO>
<darkMatterProfileHeating value="tidal" />
<darkMatterProfileScaleRadius value="ludlow2016" >
<C value="700.27000" /> <!-- Best fit values from Johnson, Benson, & Grin (2020). -->
<f value=" 0.07534" />
<timeFormationSeekDelta value=" 0.00000" />
<darkMatterProfileScaleRadius value="concentration" >
<correctForConcentrationDefinition value="true" />
<darkMatterProfileConcentration value="diemerKravtsov2014" >
<alpha value="1.12"/>
<beta value="1.69"/>
<eta0 value="6.82"/>
<eta1 value="1.42"/>
<kappa value="0.69"/>
<phi0 value="6.58"/>
<phi1 value="1.37"/>
<scatter value="0.00"/>
</darkMatterProfileConcentration>
</darkMatterProfileScaleRadius>
</darkMatterProfileScaleRadius>
<darkMatterProfileMinimumConcentration value=" 4.0"/>
<darkMatterProfileMaximumConcentration value="100.0"/>
<!-- Concentration model -->
<darkMatterProfileScaleVirialTheoremUnresolvedEnergy value="0.5500"/> <!-- Best fit value from Johnson, Benson, & Grin (2020) -->
<darkMatterProfileScaleVirialTheoremMassExponent value="1.5552"/>
<darkMatterProfileScaleVirialTheoremEnergyBoost value="0.6773"/>
Here we select our model for dark matter halo profiles - we use an NFW profile but allowing for "heating" of the profile as described in Pullen et al. (2016). We also define parameters of the concentration model. In this model scale radii of halos are computed using the random walk approach of Johnson, Benson & Grin (2021). The parameters of that model are given here, along with the parameters of the "fallback" model used for nodes in the merger tree for which the random walk model can not be applied.
<!-- Dark matter halo spin -->
<haloSpinDistribution value="bett2007"> <!-- Values from Benson (2017) -->
<alpha value="1.7091800"/>
<lambda0 value="0.0420190"/>
</haloSpinDistribution>
<spinVitvitskaMassExponent value="0.10475"/> <!-- Best fit value from Benson, Behrens, & Lu (2020) -->
Halo spin parameters are also modeled using a random walk approach Benson, Behrens & Lu (2020) - here we specify the parameters of that random walk model and a "fallback" spin distribution to be used for halos for which the random walk model can not be applied.
<!-- Halo accretion options -->
<accretionHalo value="zero"/>
<!-- Hot halo gas model options -->
<hotHaloMassDistribution value="null" />
<!-- Galactic structure solver options -->
<galacticStructureSolver value="null" />
<darkMatterProfile value="darkMatterOnly"/>
<!-- Galaxy mergers -->
<mergerRemnantSize value="null"/>
The preceeding block acts to switch off various baryonic physics which we want to exclude from this model.
<!-- Satellite orbit options -->
<virialOrbit value="spinCorrelated">
<alpha value="0.47263" /> <!-- Best fit value from Benson, Behrens, & Lu (2020) -->
<virialOrbit value="jiang2014" >
<!-- Best fit value from Benson, Behrens, & Lu (2020) -->
<bRatioHigh value="+2.88333 +4.06371 +3.86726"/>
<bRatioIntermediate value="+1.05361 +1.56868 +2.89027"/>
<bRatioLow value="+0.07432 +0.54554 +1.04721"/>
<gammaRatioHigh value="+0.07124 +0.04737 -0.01913"/>
<gammaRatioIntermediate value="+0.10069 +0.07821 +0.04231"/>
<gammaRatioLow value="+0.10866 +0.11260 +0.11698"/>
<muRatioHigh value="+1.10168 +1.09639 +1.09819"/>
<muRatioIntermediate value="+1.18205 +1.19573 +1.24581"/>
<muRatioLow value="+1.22053 +1.22992 +1.25528"/>
<sigmaRatioHigh value="+0.09244 +0.14335 +0.21079"/>
<sigmaRatioIntermediate value="+0.07397 +0.09590 +0.10941"/>
<sigmaRatioLow value="+0.07458 +0.09040 +0.06981"/>
</virialOrbit>
</virialOrbit>
<satelliteOrbitStoreOrbitalParameters value="true"/>
When halos first become subhalos they are assigned orbital parameters. The above defines the distribution of those parameters, using the Jiang et al. (2015) model for the distribution of radial and tangential velocities, plus the model of Benson, Behrens & Lu (2020) for the anisotropy of the distribution of orbits.
<!-- Orbiting model of satellites -->
<!-- Values taken from Yang et al. (2020) for their gamma=0 case using the Caterpillar simulations as calibration target -->
<satelliteDynamicalFriction value="chandrasekhar1943">
<logarithmCoulomb value="1.53"/>
</satelliteDynamicalFriction>
<satelliteTidalHeatingRate value="gnedin1999" >
<epsilon value="0.33"/>
<gamma value="0.00"/>
</satelliteTidalHeatingRate>
<satelliteTidalStripping value="zentner2005" >
<efficiency value="2.86"/>
</satelliteTidalStripping>
Here we define parameters of the various physics models applied to the evolution of subhalos, as outlined in Yang et al. (2020).
<!-- Node evolution and physics -->
<nodeOperator value="multi">
<!-- Subhalo hierarchy -->
<nodeOperator value="subsubhaloPromotion" />
<!-- Subhalo orbits -->
<nodeOperator value="satelliteOrbit" />
<nodeOperator value="satelliteDynamicalFriction" />
<nodeOperator value="satelliteTidalMassLoss" />
<nodeOperator value="satelliteTidalHeating" />
<nodeOperator value="satelliteMergingRadiusTrigger" >
<radiusVirialFraction value="0.01"/>
</nodeOperator>
<nodeOperator value="satelliteDestructionMassThreshold" >
<massDestruction value="=[mergerTreeMassResolution::massResolution]"/>
<massDestructionFractional value="0.0e0"/>
</nodeOperator>
</nodeOperator>
This block applies various physical processes to subhalos.
<!-- Output options -->
<galacticusOutputFileName value="darkMatterOnlySubHalos.hdf5"/>
<mergerTreeOutputter value="multi">
<mergerTreeOutputter value="standard">
<outputReferences value="false"/>
</mergerTreeOutputter>
<mergerTreeOutputter value="analyzer"/>
</mergerTreeOutputter>
<outputTimes value="list">
<redshifts value="0.5"/>
</outputTimes>
<nodePropertyExtractor value="multi">
<nodePropertyExtractor value="nodeIndices" />
<nodePropertyExtractor value="indicesTree" />
<nodePropertyExtractor value="redshiftLastIsolated" />
<nodePropertyExtractor value="radiusTidal" />
<nodePropertyExtractor value="radiusBoundMass" />
<nodePropertyExtractor value="virialProperties" />
<nodePropertyExtractor value="radiusVelocityMaximum"/>
<nodePropertyExtractor value="velocityMaximum" />
<nodePropertyExtractor value="positionOrbital" />
<nodePropertyExtractor value="densityProfile" >
<includeRadii value="true" />
<radiusSpecifiers value="darkMatterScaleRadius:all:all:0.3 darkMatterScaleRadius:all:all:1.0 darkMatterScaleRadius:all:all:3.0 virialRadius:all:all:0.1 virialRadius:all:all:0.3 virialRadius:all:all:1.0"/>
</nodePropertyExtractor>
<nodePropertyExtractor value="projectedDensity" >
<includeRadii value="true" />
<radiusSpecifiers value="darkMatterScaleRadius:all:all:0.3 darkMatterScaleRadius:all:all:1.0 darkMatterScaleRadius:all:all:3.0 virialRadius:all:all:0.1 virialRadius:all:all:0.3 virialRadius:all:all:1.0"/>
</nodePropertyExtractor>
</nodePropertyExtractor>
<outputAnalysis value="multi">
<outputAnalysis value="subhaloMassFunction">
<fileName value="%DATASTATICPATH%/darkMatter/subhaloDistributionsCaterpillar.hdf5"/>
<negativeBinomialScatterFractional value="0.18" /> <!-- Boylan-Kolchin et al. (2010) -->
<virialDensityContrast value="bryanNorman1998" />
<redshift value="0.0" />
</outputAnalysis>
<outputAnalysis value="subhaloRadialDistribution">
<fileName value="%DATASTATICPATH%/darkMatter/subhaloDistributionsCaterpillar.hdf5"/>
<negativeBinomialScatterFractional value="0.18" /> <!-- Boylan-Kolchin et al. (2010) -->
<virialDensityContrast value="bryanNorman1998" />
<redshift value="0.0" />
</outputAnalysis>
<outputAnalysis value="subhaloVMaxVsMass">
<fileName value="%DATASTATICPATH%/darkMatter/subhaloDistributionsCaterpillar.hdf5"/>
<virialDensityContrast value="bryanNorman1998" />
<redshift value="0.0" />
</outputAnalysis>
</outputAnalysis>
Finally we specify the outputs that we want. Here we request a number of additional properties to be output, and also request thee summary analyses (subhalo mass function, Vmax function, and radial distribution - each compared to results from the Caterpillar simulations) to be computed and output.
The main output follows the general form described in the tutorial on dark matter only merger trees, but with some additional properties (subhalo orbital positions, tidal radii, etc.)
In addition, there is now an analyses group:
$ h5ls galacticus.hdf5/analyses
subhaloMassFunction Group
subhaloRadialDistribution Group
subhaloVelocityMaximumMean Group
Each group contains the results of one summary analysis. For example:
$ h5ls darkMatterOnlySubHalos.hdf5/analyses/subhaloMassFunction
massFunction Dataset {20}
massFunctionCovariance Dataset {20, 20}
massFunctionCovarianceTarget Dataset {20, 20}
massFunctionTarget Dataset {20}
massRatio Dataset {20}
gives the results of a subhalo mass function analysis. The mass function is given by the massFunction dataset in bins of subhalo-to-host-halo mass ratio as given by the massRatio dataset. Additionally the covariance of the mass function is given in the massFunctionCovariance dataset. For comparison the subhalo mass function and its covariance from a target dataset (in this case the Caterpillar simulations) are included also.