analysesPlot.pl

[Sam230685]

Hello

Looking through usage doc. Got everything working except do not know where the plot from using analysesPlot.pl is outputted. Help is appreciated. Thanks.

[abensonca]

It should be output in the same directory as the hdf5 file that you're running the analysesPlot.pl script. If it's not in there it may be that your model did not include any plottable analyses. Were there any messages output by analysesPlot.pl?

[Sam230685]

Output is: logℒ = -2172.84461397124. File would have same name as output file I am using with analysesPlot.pl?

[abensonca]

If you do something like:

./scripts/analysis/analysisPlots.pl path/to/my/file.hdf5

then any plots would be:

path/to/my/<analysis>.pdf

where <analysis> is the name of whatever analysis you had Galacticus do.

If you share your parameter file here I can give now specific answers.

[Sam230685]

Yes ok. Parameter file is here. I am testing the analysis suggested in GalacticusUsage.pdf which is massFunctionStellarBaldry2012GAMA.

<?xml version="1.0" encoding="UTF-8"?>
<!-- Default parameters for Galacticus v0.9.4 -->
<!-- 30-October-2011                          -->
<parameters>
  <formatVersion>2</formatVersion>
  <version>0.9.4</version>

  <!-- Component selection -->
  <componentBasic value="standard"/>
  <componentBlackHole value="standard">
    <massSeed value="100.0"/>
    <heatsHotHalo value="true"/>
    <efficiencyWind value="0.0024"/>
    <efficiencyWindScalesWithEfficiencyRadiative value="true"/>
    <bondiHoyleAccretionEnhancementHotHalo value="6.0"/>
    <bondiHoyleAccretionEnhancementSpheroid value="5.0"/>
    <bondiHoyleAccretionTemperatureSpheroid value="100"/>
    <bondiHoyleAccretionHotModeOnly value="true"/>
  </componentBlackHole>
  <componentDarkMatterProfile value="scale"/>
  <componentDisk value="standard">
    <toleranceAbsoluteMass value="1.0e-6"/>
    <massDistributionDisk value="exponentialDisk">
      <dimensionless value="true"/>
    </massDistributionDisk>
  </componentDisk>
  <componentHotHalo value="standard">
    <fractionLossAngularMomentum value="0.3"/>
    <starveSatellites value="false"/>
    <efficiencyStrippingOutflow value="0.1"/>
    <trackStrippedGas value="true"/>
  </componentHotHalo>
  <componentSatellite value="standard"/>
  <componentSpheroid value="standard">
    <ratioAngularMomentumScaleRadius value="0.5"/>
    <efficiencyEnergeticOutflow value="1.0e-2"/>
    <toleranceAbsoluteMass value="1.0e-6"/>
    <massDistributionSpheroid value="hernquist">
      <dimensionless value="true"/>
    </massDistributionSpheroid>
  </componentSpheroid>
  <componentSpin value="scalar"/>

  <!-- Cosmological parameters and options -->
  <cosmologyFunctions value="matterLambda"/>
  <cosmologyParameters value="simple">
    <HubbleConstant value="70.2"/>
    <OmegaMatter value="0.2725"/>
    <OmegaDarkEnergy value="0.7275"/>
    <OmegaBaryon value="0.0455"/>
    <temperatureCMB value="2.72548"/>
  </cosmologyParameters>
  
  <powerSpectrumNonlinear value="linear"/>

  <!-- Structure formation options -->
  <linearGrowth value="collisionlessMatter"/>
  <haloMassFunction value="tinker2008"/>
  <criticalOverdensity value="sphericalCollapseClsnlssMttrCsmlgclCnstnt"/>
  <virialDensityContrast value="sphericalCollapseClsnlssMttrCsmlgclCnstnt"/>

  <!-- Merger tree building options -->
  <mergerTreeConstructor value="build"/>
  <mergerTreeBuilder value="cole2000">
    <accretionLimit value="0.1"/>
    <mergeProbability value="0.1"/>
  </mergerTreeBuilder>
  <mergerTreeBranchingProbability value="parkinsonColeHelly">
    <G0 value="+0.57"/>
    <gamma1 value="+0.38"/>
    <gamma2 value="-0.01"/>
    <accuracyFirstOrder value="+0.10"/>
  </mergerTreeBranchingProbability>
  <mergerTreeBuildMasses value="sampledDistributionUniform">
    <massTreeMinimum value="1.0e10"/>
    <massTreeMaximum value="1.0e13"/>
    <treesPerDecade value="2"/>
  </mergerTreeBuildMasses>
  <!-- Substructure hierarchy options -->
  <mergerTreeNodeMerger value="singleLevelHierarchy"/>


  <!-- Star formation rate options -->
  <starFormationRateDisks value="intgrtdSurfaceDensity"/>
  <starFormationRateSurfaceDensityDisks value="krumholz2009">
    <frequencyStarFormation value="0.385"/>
    <clumpingFactorMolecularComplex value="5.000"/>
    <molecularFractionFast value="true"/>
  </starFormationRateSurfaceDensityDisks>
  <starFormationRateSpheroids value="timescale">
    <starFormationTimescale value="dynamicalTime">
      <efficiency value="0.04"/>
      <exponentVelocity value="2.0"/>
      <timescaleMinimum value="0.001"/>
    </starFormationTimescale>
  </starFormationRateSpheroids>

  <!-- Stellar populations options -->
  <stellarPopulationProperties value="instantaneous"/>
  <stellarPopulationSpectra value="FSPS"/>
  <stellarPopulationSelector value="fixed"/>

  <initialMassFunction value="chabrier2001"/>
  <stellarPopulation value="standard">
    <recycledFraction value="0.46"/>
    <metalYield value="0.035"/>
  </stellarPopulation>

  <!-- Node evolution and physics -->
  <nodeOperator value="multi">
    <!-- Cosmological epoch -->
    <nodeOperator value="cosmicTime"/>
    <!-- DMO evolution -->
    <nodeOperator value="DMOInterpolate"/>
    <!-- Halo concentrations -->
    <nodeOperator value="darkMatterProfileScaleSet"/>
    <nodeOperator value="darkMatterProfileScaleInterpolate"/>
    <!-- Halo spins -->
    <nodeOperator value="haloAngularMomentumRandom">
      <factorReset value="2.0"/>
    </nodeOperator>
    <nodeOperator value="haloAngularMomentumInterpolate"/>
    <!-- Satellite evolution -->
    <nodeOperator value="satelliteMergingTime"/>
    <nodeOperator value="satelliteMassLoss"/>
    <!-- Star formation -->
    <nodeOperator value="starFormationDisks"/>
    <nodeOperator value="starFormationSpheroids"/>
    <!--Stellar feedback outflows-->
    <nodeOperator value="stellarFeedbackDisks">
      <stellarFeedbackOutflows value="rateLimit">
        <timescaleOutflowFractionalMinimum value="0.001"/>
        <stellarFeedbackOutflows value="powerLaw">
          <velocityCharacteristic value="250.0"/>
          <exponent value="3.5"/>
        </stellarFeedbackOutflows>
      </stellarFeedbackOutflows>
    </nodeOperator>
    <nodeOperator value="stellarFeedbackSpheroids">
      <stellarFeedbackOutflows value="rateLimit">
        <timescaleOutflowFractionalMinimum value="0.001"/>
        <stellarFeedbackOutflows value="powerLaw">
          <velocityCharacteristic value="100.0"/>
          <exponent value="3.5"/>
        </stellarFeedbackOutflows>
      </stellarFeedbackOutflows>
    </nodeOperator>
    <!-- Bar instability in galactic disks -->
    <nodeOperator value="barInstability">
      <galacticDynamicsBarInstability value="efstathiou1982">
	<stabilityThresholdGaseous value="0.7"/>
	<stabilityThresholdStellar value="1.1"/>
      </galacticDynamicsBarInstability>
    </nodeOperator>
  </nodeOperator>

  <!-- Numerical tolerances -->
  <mergerTreeNodeEvolver value="standard">
    <odeToleranceAbsolute value="0.01"/>
    <odeToleranceRelative value="0.01"/>
  </mergerTreeNodeEvolver>

  <mergerTreeEvolver value="standard">
    <timestepHostAbsolute value="1.0"/>
    <timestepHostRelative value="0.1"/>
  </mergerTreeEvolver>
 <!-- Output options -->
  <outputFileName value="test1.hdf5"/>
  <mergerTreeOutputter value="analyzer"/>
  <outputAnalysis value="massFunctionStellarBaldry2012GAMA"/>
  <outputTimes value="list">
	<redshifts value="0.0 0.01 0.02 0.03 0.04 0.05 0.06"/>
  </outputTimes>
 
</parameters>

[abensonca]

Thanks. I ran this exact model myself. Note that there is a bug related to the gravitational lensing calculation which is about to be fixed that affected this model. Once that is fixed the model runs correctly, and output a file test1.hdf5. I then ran the analysis script:

$ ./scripts/analysis/analysesPlot.pl test1.hdf5 
 -> massFunctionStellarBaldry2012GAMA
   -> logℒ = -2983.50061501691
logℒ = -2983.50061501691

which looks good. It created a file massFunctionStellarBaldry2012GAMA.pdf which looks like:

This looks ok (the model is tiny so the results are very noisy).

If you're not getting this it may be that you do not have the necessary tools installed to create the plot. In that case, I just updated the Python-based plotting script to work with this type of analysis. So, if you update your copy of Galacticus, you should be able to now do:

$ ./scripts/analysis/analysesPlot.py test1.hdf5 
-> Generating plots
 -> massFunctionStellarBaldry2012GAMA

and get a plot called massFunctionStellarBaldry2012GAMA.pdf that looks like this:

(assuing that you have Numpy, h5py, and matplotlib installed).

[Sam230685]

Is working now. Thanks. Using the python script did the trick.

[Sam230685]

Hello sir. Looking at this again, I am confused by the x-axis label. If it is in units of solar mass, then would these stars not all be impossibly large? Using the log10(M*/M☉), then a star that is 100M☉ should only be 2 and yet it goes all the way up to 10^11.

[abensonca]

The x-axis is not the mas of an individual star. It is the sum of the masses of all stars in a galaxy.

[Sam230685]

Yes so Galacticus does it possess these abilities to track individual star data, ie number of given type, mass of each.