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Merge pull request #686 from cgannonucm/UniverseMachine-fix
fix spheroidRadiusPowerLaw nodeOperator
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,168 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!--Parameters for testing univerMachine nodeOperator --> | ||
| <parameters> | ||
| <formatVersion>2</formatVersion> | ||
| <version>0.9.4</version> | ||
| <randomNumberGenerator value="GSL"> | ||
| <seed value="153" /> | ||
| </randomNumberGenerator> | ||
|
|
||
| <!-- Specify tasks to perform --> | ||
| <task value="evolveForests"/> | ||
|
|
||
| <!-- Component selection --> | ||
| <componentBasic value="standard"/> | ||
| <componentBlackHole value="null"/> | ||
| <componentDarkMatterProfile value="scale"/> | ||
| <componentDisk value="standard"/> | ||
| <componentHotHalo value="null"/> | ||
| <componentSatellite value="standard"/> | ||
| <componentSpheroid value="standard"/> | ||
| <componentSpin value="null"/> | ||
|
|
||
| <!-- Cosmological parameters and options --> | ||
| <cosmologyFunctions value="matterLambda"/> | ||
| <cosmologyParameters value="simple"> | ||
| <HubbleConstant value="70.20000"/> | ||
| <OmegaMatter value=" 0.27250"/> | ||
| <OmegaDarkEnergy value=" 0.72750"/> | ||
| <OmegaBaryon value=" 0.00000"/> | ||
| <temperatureCMB value=" 2.72548"/> | ||
| </cosmologyParameters> | ||
|
|
||
| <!-- Power spectrum options --> | ||
| <transferFunction value="eisensteinHu1999"> | ||
| <neutrinoNumberEffective value="3.046"/> | ||
| <neutrinoMassSummed value="0.000"/> | ||
| <cosmologyParameters value="simple"> | ||
| <HubbleConstant value="70.20000"/> | ||
| <OmegaMatter value=" 0.27250"/> | ||
| <OmegaDarkEnergy value=" 0.72750"/> | ||
| <OmegaBaryon value=" 0.04550"/> | ||
| <temperatureCMB value=" 2.72548"/> | ||
| </cosmologyParameters> | ||
| </transferFunction> | ||
| <powerSpectrumPrimordial value="powerLaw"> | ||
| <index value="0.961"/> | ||
| <wavenumberReference value="1.000"/> | ||
| <running value="0.000"/> | ||
| </powerSpectrumPrimordial> | ||
| <powerSpectrumPrimordialTransferred value="simple"/> | ||
| <cosmologicalMassVariance value="filteredPower"> | ||
| <sigma_8 value="0.807"/> | ||
| </cosmologicalMassVariance> | ||
|
|
||
| <!-- Structure formation options --> | ||
| <linearGrowth value="collisionlessMatter"/> | ||
| <haloMassFunction value="tinker2008"/> | ||
| <criticalOverdensity value="sphericalCollapseClsnlssMttrCsmlgclCnstnt"/> | ||
| <virialDensityContrast value="sphericalCollapseClsnlssMttrCsmlgclCnstnt"/> | ||
|
|
||
| <!-- Merger tree building options --> | ||
| <mergerTreeConstructor value="build"> | ||
| <redshiftBase value="0.0" /> | ||
| </mergerTreeConstructor> | ||
| <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="readXML"> | ||
| <fileName value="testSuite/parameters/UniverseMachine-treemass.xml" /> | ||
| </mergerTreeBuildMasses> | ||
|
|
||
| <mergerTreeMassResolution value="scaled"> | ||
| <massResolutionFractional value="1.0e-1"/> | ||
| </mergerTreeMassResolution> | ||
|
|
||
|
|
||
| <!-- Substructure hierarchy options --> | ||
| <mergerTreeNodeMerger value="singleLevelHierarchy"/> | ||
|
|
||
| <!-- Dark matter halo structure options --> | ||
| <darkMatterProfileDMO value="NFW"/> | ||
| <darkMatterProfileConcentration value="gao2008"/> | ||
| <darkMatterProfileScaleRadius value="concentrationLimiter"> | ||
| <concentrationMinimum value=" 4.0"/> | ||
| <concentrationMaximum value="100.0"/> | ||
| <darkMatterProfileScaleRadius value="concentration"/> | ||
| </darkMatterProfileScaleRadius> | ||
|
|
||
| <!-- Switch off baryonic physics --> | ||
| <hotHaloMassDistribution value="null"/> | ||
|
|
||
| <!-- Tree evolution --> | ||
| <mergerTreeNodeEvolver value="standard"> | ||
| <odeToleranceAbsolute value="0.001"/> | ||
| <odeToleranceRelative value="0.001"/> | ||
| </mergerTreeNodeEvolver> | ||
| <mergerTreeEvolver value="standard"> | ||
| <timestepHostAbsolute value="0.01"/> | ||
| <timestepHostRelative value="0.01"/> | ||
| </mergerTreeEvolver> | ||
|
|
||
| <!-- Output options --> | ||
| <outputFileName value="testSuite/outputs/test-spheroid-power-law/test-spheroid-power-law.hdf5"/> | ||
| <outputTimes value="list"> | ||
| <redshifts value="0.0"/> | ||
| </outputTimes> | ||
| <mergerTreeOutputter value="standard"> | ||
| <outputReferences value="false"/> | ||
| </mergerTreeOutputter> | ||
| <nodePropertyExtractor value="multi"> | ||
| <nodePropertyExtractor value="massHalo"> | ||
| <virialDensityContrastDefinition value="bryanNorman1998" /> | ||
| </nodePropertyExtractor> | ||
| <nodePropertyExtractor value="nodeIndices" /> | ||
| <nodePropertyExtractor value="redshiftLastIsolated" /> | ||
| </nodePropertyExtractor> | ||
|
|
||
| <!-- Node physics --> | ||
| <nodeOperator value="multi"> | ||
| <!-- Cosmological epoch --> | ||
| <nodeOperator value="cosmicTime"/> | ||
| <!-- DMO evolution --> | ||
| <nodeOperator value="DMOInterpolate"/> | ||
| <!-- Halo concentrations --> | ||
| <nodeOperator value="darkMatterProfileScaleSet" /> | ||
| <nodeOperator value="darkMatterProfileScaleInterpolate"/> | ||
| <!-- Satellite evolution --> | ||
| <nodeOperator value="satelliteMergingTime"/> | ||
| <nodeOperator value="satelliteMassLoss" /> | ||
| <nodeOperator value="empiricalGalaxyUniverseMachine"> | ||
| <massStellarFinal value="-1.0d0" /> | ||
| <fractionMassSpheroid value="1.0d0" /> | ||
| <fractionMassDisk value="0.0d0" /> | ||
| <epsilon_0 value="-1.435" /> | ||
| <epsilon_a value= "+1.831" /> | ||
| <epsilon_lna value= "+1.368"/> | ||
| <epsilon_z value= "-0.217"/> | ||
| <M_0 value="+12.035"/> | ||
| <M_a value="+4.556"/> | ||
| <M_lna value="+4.417"/> | ||
| <M_z value="-0.731"/> | ||
| <alpha_0 value="+1.963"/> | ||
| <alpha_a value="-2.316"/> | ||
| <alpha_lna value="-1.733"/> | ||
| <alpha_z value="+0.178"/> | ||
| <beta_0 value= "+0.482"/> | ||
| <beta_a value = "-0.841"/> | ||
| <beta_z value= "-0.471"/> | ||
| <delta_0 value="+0.411"/> | ||
| <gamma_0 value="-1.034"/> | ||
| <gamma_a value="-3.10"/> | ||
| <gamma_z value="-1.055"/> | ||
| </nodeOperator> | ||
| <nodeOperator value="spheroidRadiusPowerLaw"> | ||
| <alpha value="0.56" /> | ||
| <beta value="1.19E-9"/> | ||
| </nodeOperator> | ||
| </nodeOperator> | ||
|
|
||
| </parameters> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| #!/usr/bin/env python3 | ||
| import subprocess | ||
| import os | ||
| import sys | ||
| import h5py | ||
| import numpy as np | ||
| import xml.etree.ElementTree as ET | ||
|
|
||
| # Test spheroidRadiusPowerLaw nodeOperator. | ||
| # Charles Gannon (31-August-2024) | ||
| path_in_param = os.path.abspath(f"parameters/test-spheroid-power-law.xml" ) | ||
| path_out_dir = os.path.abspath(f"outputs/test-spheroid-power-law" ) | ||
| path_out_log = os.path.abspath(f"outputs/test-spheroid-power-law/test-spheroid-power-law.log" ) | ||
| path_out_hdf = os.path.abspath(f"outputs/test-spheroid-power-law/test-spheroid-power-law.hdf5" ) | ||
|
|
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| status = subprocess.run(f"mkdir -p {path_out_dir}",shell=True) | ||
|
|
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| # Run the model and check for completion | ||
| print("Running model...") | ||
|
|
||
| log = open(path_out_log,"w") | ||
| status = subprocess.run(f"cd ..; ./Galacticus.exe {path_in_param}",stdout=log,stderr=log,shell=True) | ||
| log.close() | ||
|
|
||
| print("...done ("+str(status)+")") | ||
|
|
||
| if status.returncode != 0: | ||
| print("FAILED: model run:") | ||
| subprocess.run(f"cat {path_out_log}",shell=True) | ||
| sys.exit() | ||
| print("Checking for errors...") | ||
| status = subprocess.run(f"grep -q -i -e fatal -e aborted -e \"Galacticus experienced an error in the GSL library\" {path_out_log}",shell=True) | ||
| print("...done ("+str(status)+")") | ||
| if status.returncode == 0: | ||
| print("FAILED: model run (errors):") | ||
| subprocess.run(f"cat {path_out_log}",shell=True) | ||
| sys.exit() | ||
| print("SUCCESS: model run") | ||
|
|
||
| # Open the model and extract the recycled fraction. | ||
| model = h5py.File(path_out_hdf,'r') | ||
| massStellar = model["Outputs/Output1/nodeData/spheroidMassStellar" ][:] | ||
| radiusStellar = model["Outputs/Output1/nodeData/spheroidRadius" ] | ||
| isIsolated = model["Outputs/Output1/nodeData/nodeIsIsolated" ][:].astype(bool) | ||
|
|
||
| massStellarHost, radiusStellarHost = massStellar[isIsolated], radiusStellar[isIsolated] | ||
|
|
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| alpha = 0.56 | ||
| beta = 1.19E-9 | ||
|
|
||
| radiusStellarHostPython = ( | ||
| +beta | ||
| *massStellarHost**alpha | ||
| ) | ||
| if np.allclose(np.log10(radiusStellarHost), np.log10(radiusStellarHostPython), rtol=1e-6): | ||
| print(f"SUCCESS: results do agree" ) | ||
| else: | ||
| print(f"FAILED: results do not agree") |