mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
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updated examples
This commit is contained in:
P.M. Sutter
parent
ad3e5d1577
commit
4494fcdd2f
2 changed files with 108 additions and 242 deletions
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@ -19,18 +19,10 @@
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#+
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#+
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#!/usr/bin/env python
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#!/usr/bin/env python
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# does analysis in real space assuming LCDM cosmology
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import os
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import os
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import numpy as np
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import numpy as np
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from void_python_tools.backend.classes import *
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from void_python_tools.backend.classes import *
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# does full void analysis. Also generates 2d/1d stacked plots and hubble diagram
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# to combine multiple samples:
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# For example, combining dim from 0.0-0.1 and bright from 0.1-0.2:
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# 1) add dim+bright to sampleList - "+" is required to detect combo!
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# if True, will scan log files for last known completed state and run from there
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# if True, will scan log files for last known completed state and run from there
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continueRun = False
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continueRun = False
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@ -38,213 +30,75 @@ continueRun = False
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# 1 : extract redshift slices from data
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# 1 : extract redshift slices from data
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# 2 : void extraction using zobov
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# 2 : void extraction using zobov
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# 3 : removal of small voids and voids near the edge
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# 3 : removal of small voids and voids near the edge
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# 4 : void stacking and combining
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# 5 : 1-d and 2-d profile generation
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# 6 : fitting and plotting stacked voids
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# 7 : determination of error bars (if requested)
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# 8 : hubble diagram generation
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# 9 : liklihood determination
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startCatalogStage = 1
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startCatalogStage = 1
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endCatalogStage = 1
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endCatalogStage = 3
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catalogName = "lcdm"
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# a global name to give
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#catalogName = "lcdm"
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# where main data files are present/will go
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workDir = os.getenv("HOME")+"/workspace/Voids/sdss_dr7LCDM/"
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# directory for input data files
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inputDataDir = os.getenv("HOME")+"/workspace/Voids/catalogs/nyuvagc/"
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inputDataDir = os.getenv("HOME")+"/workspace/Voids/catalogs/nyuvagc/"
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# void catalog output directory
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workDir = os.getenv("HOME")+"/workspace/Voids/sdss_dr7LCDM/"
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# output directory for log files
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logDir = os.getenv("PWD")+"/../logs/sdss_dr7LCDM"
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logDir = os.getenv("PWD")+"/../logs/sdss_dr7LCDM"
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# output directory for figures
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figDir = os.getenv("PWD")+"/../figs/sdss_dr7LCDM"
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figDir = os.getenv("PWD")+"/../figs/sdss_dr7LCDM"
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# you need to set these manually: point to ZOBOV and C_TOOLS in VIDE directory
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ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
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ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
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CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
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CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
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freshStack = True # "no" to continue building onto existing stacked voids
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# if true, convert to comoving space using LCDM cosmology
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useComoving = True
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errorBars = "CALCULATED" # "ESTIMATED" for error bars from multiple null tests
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# optimization: maximum number of parallel threads to use
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#errorBars = "ESTIMATED" # "ESTIMATED" for error bars from multiple null tests
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# "CALCULATED" to use fitting procedure
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numIncoherentRuns = 100
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ranSeed = 101010
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useComoving = True # if true, convert to real space using LCDM cosmology
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# try different portions of data. available options: "all, central, edge"
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dataPortions = ["central", "all"]
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numZobovDivisions = 2
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numZobovThreads = 2
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numZobovThreads = 2
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# optimization: number of subdivisions of the box
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numZobovDivisions = 2
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# don't change this
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dataSampleList = []
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dataSampleList = []
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# define your volume-limited samples
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newSample = Sample(
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# path to galaxy file is inputDataDir+dataFile
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dataFile = "filename.dat"
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newSample = Sample(fullName = "lss.dr72dim1.dat",
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# full name for this sample
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fullName = "lss.dr72dim1.dat",
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# a convenient nickname
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nickName = "dim1",
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nickName = "dim1",
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# don't change this
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dataType = "observation",
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dataType = "observation",
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# HEALpix mask file
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72dim1.dat",
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# max and min redshifts of galaxies in your sample
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zBoundary = (0.0, 0.05),
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zBoundary = (0.0, 0.05),
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# max and min redshifts where you want to find voids
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zRange = (0.0, 0.05),
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zRange = (0.0, 0.05),
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# TODO
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skyFraction = 0.19,
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skyFraction = 0.19,
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minVoidRadius = 3.479,
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fakeDensity = 0.01,
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = True,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.0, 0.1, 8, 12, False, True)
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newSample.addStack(0.0, 0.1, 12, 16, False, True)
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newSample.addStack(0.0, 0.1, 16, 20, False, True)
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newSample.addStack(0.0, 0.1, 20, 28, False, True)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72dim2.dat",
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# leave this at -1 for mean particle separation, or
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nickName = "dim2",
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# specify your own in Mpc/h
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72dim2.dat",
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zBoundary = (0.0, 0.1),
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zRange = (0.05, 0.1),
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skyFraction = 0.19,
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minVoidRadius = 4.723,
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fakeDensity = 0.01,
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = True,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.0, 0.1, 8, 12, False, True)
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newSample.addStack(0.0, 0.1, 12, 16, False, True)
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newSample.addStack(0.0, 0.1, 16, 20, False, True)
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newSample.addStack(0.0, 0.1, 20, 28, False, True)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72dim1+dim2.dat",
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nickName = "dim1+dim2",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72dim.dat",
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zBoundary = (0.0, 0.1),
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zRange = (0.0, 0.1),
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skyFraction = 0.19,
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minVoidRadius = 4.723,
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fakeDensity = 0.01,
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profileBinSize = "auto",
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volumeLimited = True,
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includeInHubble = True,
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partOfCombo = False,
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isCombo = True,
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comboList= ("lss.dr72dim1.dat", "lss.dr72dim2.dat"))
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newSample.addStack(0.0, 0.1, 8, 12, True, False)
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newSample.addStack(0.0, 0.1, 12, 16, True, False)
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newSample.addStack(0.0, 0.1, 16, 20, True, False)
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newSample.addStack(0.0, 0.1, 20, 28, True, False)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72bright1.dat",
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nickName = "bright1",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72bright1.dat",
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zBoundary = (0.0, 0.15),
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zRange = (0.1, 0.15),
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skyFraction = 0.19,
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minVoidRadius = 6.763,
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fakeDensity = 0.01,
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = True,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.1, 0.2, 13, 20, False, True)
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newSample.addStack(0.1, 0.2, 20, 28, False, True)
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newSample.addStack(0.1, 0.2, 28, 36, False, True)
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newSample.addStack(0.1, 0.2, 36, 44, False, True)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72bright2.dat",
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nickName = "bright2",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72bright2.dat",
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zBoundary = (0.0, 0.2),
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zRange = (0.15, 0.2),
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skyFraction = 0.19,
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minVoidRadius = 10.844,
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fakeDensity = 0.001,
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = True,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.1, 0.2, 13, 20, False, True)
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newSample.addStack(0.1, 0.2, 20, 28, False, True)
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newSample.addStack(0.1, 0.2, 28, 36, False, True)
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newSample.addStack(0.1, 0.2, 36, 44, False, True)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72bright1+bright2.dat",
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nickName = "bright1+bright2",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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zBoundary = (0.0, 0.2),
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zRange = (0.1, 0.2),
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skyFraction = 0.19,
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minVoidRadius = -1,
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minVoidRadius = -1,
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fakeDensity = -1,
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profileBinSize = "auto",
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# density of mock particles in cubic Mpc/h
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volumeLimited = True,
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fakeDensity = 0.01,
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includeInHubble = True,
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partOfCombo = False,
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)
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isCombo = True,
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comboList= ("lss.dr72bright1.dat", "lss.dr72bright2.dat"))
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newSample.addStack(0.1, 0.2, 13, 20, True, False)
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newSample.addStack(0.1, 0.2, 20, 28, True, False)
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newSample.addStack(0.1, 0.2, 28, 36, True, False)
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newSample.addStack(0.1, 0.2, 36, 44, True, False)
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dataSampleList.append(newSample)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72lrgdim.dat",
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# repeat the above block for any other samples
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nickName = "lrgdim",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72lrgdim.dat",
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zBoundary = (0.16, 0.36),
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zRange = (0.16, 0.36),
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skyFraction = 0.19,
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minVoidRadius = 24,
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fakeDensity = 0.001,
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profileBinSize = 2, # KEEP
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volumeLimited = True,
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includeInHubble = True,
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partOfCombo = False,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.16, 0.36, 54, 70, True, False, zMinPlot=0.2)
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newSample.addStack(0.16, 0.36, 70, 106, True, False, zMinPlot=0.2)
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dataSampleList.append(newSample)
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newSample = Sample(fullName = "lss.dr72lrgbright.dat",
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nickName = "lrgbright",
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dataType = "observation",
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maskFile = inputDataDir+"/healpix/rast_window_512.fits",
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selFunFile = inputDataDir+"/czselfunc.all.dr72lrgbright.dat",
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zBoundary = (0.36, 0.44),
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zRange = (0.36, 0.44),
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skyFraction = 0.19,
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minVoidRadius = 38,
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fakeDensity = 0.001,
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profileBinSize = "auto",
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volumeLimited = True,
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includeInHubble = False,
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partOfCombo = False,
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isCombo = False,
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comboList= None)
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newSample.addStack(0.36, 0.44, 76, 92, False, False)
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newSample.addStack(0.36, 0.44, 92, 108, False, False)
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dataSampleList.append(newSample)
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@ -23,101 +23,123 @@ import os
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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# CONFIGURATION
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# CONFIGURATION
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startCatalogStage = 0
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# if True, will scan log files for last known completed state and run from there
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endCatalogStage = 0
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continueRun = False
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continueRun = False
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startAPStage = 1
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# stages:
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endAPStage = 2
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# 1 : extract redshift slices from data
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# 2 : void extraction using zobov
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# 3 : removal of small voids and voids near the edge
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startCatalogStage = 1
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endCatalogStage = 3
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# directory for the input simulation/observational particle files
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# directory for the input simulation/observational particle files
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catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/mergertree1024/"
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catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/mergertree1024/"
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# path to HOD code
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# void catalog output directory
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hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
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workDir = os.getenv("HOME")+"/workspace/Voids/sim/"
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# where to put the final void catalog, figures, and output logs
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# output directory for log files
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voidOutputDir = os.getenv("HOME")+"/workspace/Voids/mergertree1024/"
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logDir = os.getenv("PWD")+"/../logs/sim/"
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figDir = os.getenv("PWD")+"/../figs/mergertree1024/"
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logDir = os.getenv("PWD")+"/../logs/mergertree1024/"
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# output directory for figures
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figDir = os.getenv("PWD")+"/../figs/sim/"
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# where to place the pipeline scripts
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# where to place the pipeline scripts
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scriptDir = os.getenv("PWD")+"/mergertree1024/"
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scriptDir = os.getenv("PWD")+"/sim/"
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# simulation or observation?
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# don't change
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dataType = "simulation"
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dataType = "simulation"
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# available formats for simulation: gadget, mergertree
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# available formats for simulation: gadget, sdf, multidark
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dataFormat = "sdf"
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dataFormat = "sdf"
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dataUnit = 1 # as multiple of Mpc/h
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# place particles on the lightcone?
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# units of position in Mpc/h
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dataUnit = 1
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# place particles on the lightcone (z-axis in sims)?
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useLightCone = False
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useLightCone = False
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# also do peculiar velocities?
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# add peculiar velocities?
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doPecVel = False
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doPecVel = False
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# optimization: maximum number of parallel threads to use
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numZobovThreads = 2
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# optimization: number of subdivisions of the box
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numZobovDivisions = 2
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###############################################################################
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# Particles
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# common filename of particle files
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# common filename of particle files
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particleFileBase = "mf_4s_1G_1k_NNNNN"
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particleFileBase = "mf_4s_1G_1k_NNNNN"
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# this flag will be replaced by values in fileNums list below
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particleFileDummy = 'NNNNN'
|
particleFileDummy = 'NNNNN'
|
||||||
|
|
||||||
# list of file numbers for the particle files
|
# list of file numbers for the particle files
|
||||||
# to get particle file name, we take particleFileBase+fileNum
|
|
||||||
fileNums = ["1.000"]
|
fileNums = ["1.000"]
|
||||||
|
|
||||||
# redshift of each file in the above list
|
# redshift of each file in the above fileNums list
|
||||||
redshifts = ["0.0"]
|
redshifts = ["0.0"]
|
||||||
|
|
||||||
# how many independent slices along the z-axis?
|
# how many independent slices along the z-axis?
|
||||||
numSlices = 1
|
numSlices = 1
|
||||||
#numSlices = 4
|
|
||||||
numAPSlices = 1
|
|
||||||
|
|
||||||
# how many subdivisions along the x- and y- axis?
|
# how many subdivisions along the x- and y- axis?
|
||||||
# ( = 2 will make 4 subvolumes for each slice, = 3 will make 9, etc.)
|
# ( = 2 will make 4 subvolumes for each slice, = 3 will make 9, etc.)
|
||||||
numSubvolumes = 1
|
numSubvolumes = 1
|
||||||
|
|
||||||
# prefix to give all outputs
|
# prefix to give all outputs
|
||||||
prefix = "mt_"
|
prefix = "sim_"
|
||||||
|
|
||||||
# list of desired subsamples - these are in unts of h Mpc^-3!
|
# list of desired subsamples - these are in unts of h Mpc^-3!
|
||||||
subSamples = [0.1, 0.05, 0.02, 0.01, 0.004, 0.002, 0.001, 0.0003, 0.0001]
|
subSamples = [1.0, 0.5]
|
||||||
#doSubSampling = False # do the subsampling in preparation script?
|
|
||||||
doSubSampling = True # do the subsampling in preparation script?
|
# if True, do the subsampling in preparation (only for sdf and multidark)
|
||||||
|
doSubSampling = True
|
||||||
|
|
||||||
|
|
||||||
|
###############################################################################
|
||||||
|
# Halos
|
||||||
|
|
||||||
# common filename of halo files, leave blank to ignore halos
|
# common filename of halo files, leave blank to ignore halos
|
||||||
haloFileBase = "mf_4s_1G_1k_bgc2_NNNNN.sdf"
|
haloFileBase = "mf_4s_1G_1k_bgc2_NNNNN.sdf"
|
||||||
|
|
||||||
|
# this flag will be replaced by values in fileNums list above
|
||||||
haloFileDummy = 'NNNNN'
|
haloFileDummy = 'NNNNN'
|
||||||
|
|
||||||
# minimum halo mass cuts to apply for the halo catalog
|
# minimum halo mass cuts to apply for the halo catalog
|
||||||
# use "none" to get all halos
|
# use "none" to get all halos
|
||||||
minHaloMasses = ["none", 1.2e13]
|
minHaloMasses = ["none", 1.2e13]
|
||||||
#minHaloMasses = [7.0e11, 1.2e13]
|
|
||||||
|
|
||||||
# locations of data in the halo catalog
|
# locations of data in the halo catalog
|
||||||
haloFileMCol = 6
|
haloFileMCol = 6 # mass
|
||||||
haloFileXCol = 0
|
haloFileXCol = 0 # x
|
||||||
haloFileYCol = 1
|
haloFileYCol = 1 # y
|
||||||
haloFileZCol = 2
|
haloFileZCol = 2 # z
|
||||||
haloFileVXCol = 3
|
haloFileVXCol = 3 # v_x
|
||||||
haloFileVYCol = 4
|
haloFileVYCol = 4 # v_y
|
||||||
haloFileVZCol = 5
|
haloFileVZCol = 5 # v_z
|
||||||
haloFileColSep = ','
|
haloFileColSep = ',' # separator
|
||||||
haloFileNumComLines = 0
|
haloFileNumComLines = 0 # number of comments before data
|
||||||
|
|
||||||
# adjust these two parameters given the memory contraints on your system:
|
|
||||||
# numZobovDivisions: how many sub-volumes per dimension will zobov process
|
|
||||||
# numZobovThreads: how many sub-volumes to process at once?
|
|
||||||
numZobovDivisions = 4
|
|
||||||
numZobovThreads = 4
|
|
||||||
|
|
||||||
|
###############################################################################
|
||||||
# simulation information
|
# simulation information
|
||||||
|
|
||||||
numPart = 1024*1024*1024
|
numPart = 1024*1024*1024
|
||||||
lbox = 999.983 # Mpc/h
|
lbox = 999.983 # Mpc/h
|
||||||
omegaM = 0.2847979853038958
|
omegaM = 0.2847979853038958
|
||||||
hubble = 0.6962
|
hubble = 0.6962 # h_0
|
||||||
|
|
||||||
#galDens = 0.000225
|
|
||||||
|
###############################################################################
|
||||||
|
# HOD
|
||||||
|
|
||||||
|
# each of the HOD sets will be applied to each halo catalog defined above
|
||||||
hodParmList = [
|
hodParmList = [
|
||||||
{'name' : "LowRes", #BOSS: Manera et al. 2012, eq. 26
|
{'name' : "LowRes", #BOSS: Manera et al. 2012, eq. 26
|
||||||
'Mmin' : 0.0,
|
'Mmin' : 0.0,
|
||||||
|
|
@ -127,16 +149,6 @@ hodParmList = [
|
||||||
'Mcut' : 1.19399e13,
|
'Mcut' : 1.19399e13,
|
||||||
'galDens' : 0.0002,
|
'galDens' : 0.0002,
|
||||||
},
|
},
|
||||||
|
|
||||||
{'name' : "HighRes",
|
|
||||||
'Mmin' : 0.0,
|
|
||||||
#'Mmin' : 1.99525e12,
|
|
||||||
'M1' : 3.80189e13,
|
|
||||||
'sigma_logM' : 0.21,
|
|
||||||
'alpha' : 1.12,
|
|
||||||
'Mcut' : 6.91831e11,
|
|
||||||
'galDens' : 0.02,
|
|
||||||
}
|
|
||||||
]
|
]
|
||||||
|
|
||||||
# END CONFIGURATION
|
# END CONFIGURATION
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue