mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 23:31:12 +00:00
fixed bug in gadget generation script; prepareGadget now uses separate parameter files; support for random catalogs now enabled
This commit is contained in:
P.M. Sutter
parent
292afacaf5
commit
443b4bdeec
4 changed files with 91 additions and 342 deletions
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@ -113,10 +113,10 @@ if (startCatalogStage <= 4) and (endCatalogStage >= 4):
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for thisDataPortion in dataPortions:
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plotRedshiftDistribution(workDir, dataSampleList, figDir, showPlot=False,
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dataPortion=thisDataPortion, setName=catalogName)
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dataPortion=thisDataPortion, setName=setName)
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plotSizeDistribution(workDir, dataSampleList, figDir, showPlot=False,
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dataPortion=thisDataPortion, setName=catalogName)
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dataPortion=thisDataPortion, setName=setName)
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plotNumberDistribution(workDir, dataSampleList, figDir, showPlot=False,
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dataPortion=thisDataPortion, setName=catalogName)
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dataPortion=thisDataPortion, setName=setName)
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print "\n Done!"
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@ -9,66 +9,17 @@ import os
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import sys
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import void_python_tools as vp
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import argparse
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import imp
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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# CONFIGURATION
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# ------------------------------------------------------------------------------
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# directory for the input simulation/observational particle files
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catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/multidark/"
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def my_import(name):
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mod = __import__(name)
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components = name.split('.')
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for comp in components[1:]:
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mod = getattr(mod, comp)
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return mod
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# path to HOD code
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hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
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# where to put the final void catalog, figures, and output logs
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voidOutputDir = os.getenv("HOME")+"/workspace/Voids/multidark/"
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figDir = os.getenv("PWD")+"/../figs/multidark/"
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logDir = os.getenv("PWD")+"/../logs/multidark/"
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# where to place the pipeline scripts
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scriptDir = os.getenv("PWD")+"/multidark/"
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# simulation or observation?
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dataType = "simulation"
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# available formats for simulation: gadget, multidark
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dataFormat = "multidark"
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dataUnit = 1 # as multiple of Mpc/h
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# place particles on the lightcone?
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useLightCone = True
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# common filename of particle files
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particleFileBase = "mdr1_particles_z"
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# list of file numbers for the particle files
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# to get particle file name, we take particleFileBase+fileNum
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fileNums = (("0.0", "0.53", "1.0"))
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# redshift of each file in the above list
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redshifts = (("0.0", "0.53", "1.0"))
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# how many independent slices along the z-axis?
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numSlices = 4
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# how many subdivisions along the x- and y- axis?
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# ( = 2 will make 4 subvolumes for each slice, = 3 will make 9, etc.)
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numSubvolumes = 1
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# prefix to give all outputs
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prefix = "md_"
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# list of desired subsamples
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subSamples = ((0.1, 0.05, 0.01, 0.002, 0.001, 0.0004, 0.0002))
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# simulation information
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numPart = 1024*1024*1024
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lbox = 1000 # Mpc/h
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omegaM = 0.27
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hubble = 0.70
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# END CONFIGURATION
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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LIGHT_SPEED = 299792.458
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@ -85,12 +36,25 @@ parser.add_argument('--halos', dest='halos', action='store_const',
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help='write halos')
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parser.add_argument('--hod', dest='hod', action='store_const',
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const=True, default=False,
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help='write hos')
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help='write hod')
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parser.add_argument('--all', dest='all', action='store_const',
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const=True, default=False,
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help='write everything')
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parser.add_argument('--parmFile', dest='parmFile',
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default="",
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help='path to parameter file')
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args = parser.parse_args()
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filename = args.parmFile
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print " Loading parameters from", filename
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if not os.access(filename, os.F_OK):
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print " Cannot find parameter file %s!" % filename
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exit(-1)
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parms = imp.load_source("name", filename)
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globals().update(vars(parms))
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#------------------------------------------------------------------------------
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def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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@ -253,6 +217,7 @@ newSample.addStack({zMin}, {zMax}, {minRadius}+18, {minRadius}+24, True, False)
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#------------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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if not os.access(scriptDir, os.F_OK): os.mkdir(scriptDir)
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if not os.access(catalogDir, os.F_OK): os.mkdir(catalogDir)
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#------------------------------------------------------------------------------
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# first the directly downsampled runs
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@ -288,45 +253,73 @@ for thisSubSample in subSamples:
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redshifts,
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numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
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subsample=thisSubSample, suffix="")
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elif dataFormat == "random":
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writeScript(setName, "ran.ss"+str(thisSubSample)+"_z",
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scriptDir, catalogDir, fileNums,
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redshifts,
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numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
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subsample=1.0)
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if args.subsample or args.all:
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print " Doing subsample", thisSubSample
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for (iRedshift, redshift) in enumerate(redshifts):
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print " redshift", redshift
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dataFile = catalogDir+"/"+particleFileBase+fileNums[iRedshift]
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inFile = open(dataFile, 'r')
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sampleName = "md.ss"+str(thisSubSample)+"_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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if dataFormat == "multidark":
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dataFile = catalogDir+"/"+particleFileBase+fileNums[iRedshift]
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inFile = open(dataFile, 'r')
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outFile.write("%f\n" %(lbox))
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outFile.write("%s" %(omegaM))
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outFile.write("%s" %(hubble))
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outFile.write("%s\n" %(redshift))
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outFile.write("%d\n" %(maxKeep))
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sampleName = "md.ss"+str(thisSubSample)+"_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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numKept = 0
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for line in inFile:
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if np.random.uniform() > keepFraction: continue
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numKept += 1
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if numKept > maxKeep: break
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line = line.split(',')
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x = float(line[0])
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y = float(line[1])
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z = float(line[2])
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vz = float(line[3])
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outFile.write("%f\n" %(lbox))
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outFile.write("%s\n" %(omegaM))
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outFile.write("%s\n" %(hubble))
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outFile.write("%s\n" %(redshift))
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outFile.write("%d\n" %(maxKeep))
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outFile.write("%e %e %e %e\n" %(x,y,z,vz))
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numKept = 0
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for line in inFile:
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if np.random.uniform() > keepFraction: continue
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numKept += 1
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if numKept > maxKeep: break
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line = line.split(',')
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x = float(line[0])
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y = float(line[1])
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z = float(line[2])
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vz = float(line[3])
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outFile.write("%e %e %e %e\n" %(x,y,z,vz))
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outFile.write("-99 -99 -99 -99\n")
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inFile.close()
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outFile.close()
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elif dataFormat == "random":
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sampleName = "ran.ss"+str(thisSubSample)+"_z"+redshift
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("%f\n" %(lbox))
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outFile.write("%s\n" %(omegaM))
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outFile.write("%s\n" %(hubble))
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outFile.write("%s\n" %(redshift))
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outFile.write("%d\n" %(maxKeep))
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for i in xrange(int(maxKeep)):
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x = np.random.uniform()*lbox
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y = np.random.uniform()*lbox
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z = np.random.uniform()*lbox
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outFile.write("%e %e %e %e\n" %(x,y,z, 0.))
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outFile.write("-99 -99 -99 -99\n")
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outFile.close()
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outFile.write("-99 -99 -99 -99\n")
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print "KEEPING:", numKept, "...predicted:", maxKeep
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inFile.close()
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outFile.close()
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# -----------------------------------------------------------------------------
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# now halos
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if args.script or args.all:
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if (args.script or args.all) and dataFormat == "multidark":
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print " Doing halo scripts"
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dataFile = catalogDir+"/mdr1_halos_z"+fileNums[0]
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@ -362,8 +355,8 @@ if args.halos or args.all:
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outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
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outFile.write("%f\n" %(lbox))
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outFile.write("%s" %(omegaM))
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outFile.write("%s" %(hubble))
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outFile.write("%s\n" %(omegaM))
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outFile.write("%s\n" %(hubble))
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outFile.write("%s\n" %(redshift))
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outFile.write("%d\n" %(numPart))
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@ -425,7 +418,7 @@ BOX_SIZE {boxSize}
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root_filename hod
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"""
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if args.script or args.all:
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if (args.script or args.all) and dataFormat == "multidark":
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print " Doing DR7 HOD scripts"
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if dataFormat == "multidark":
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setName = prefix+"hod_dr72dim2"
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@ -467,16 +460,16 @@ if args.hod or args.all:
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# -----------------------------------------------------------------------------
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# now the BOSS HOD
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if args.script or args.all:
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if (args.script or args.all) and dataFormat == "multidark":
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print " Doing DR9 HOD scripts"
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if dataFormat == "multidark":
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setName = prefix+"hod_dr9mid"
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writeScript(setName, "md.hod_dr9mid_z",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, False, lbox, 5, omegaM)
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writeScript(prefix, "md.hod_dr9mid_z",
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numSubvolumes, numSlices, False, lbox, 15, omegaM)
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writeScript(setName, "md.hod_dr9mid_z",
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scriptDir, catalogDir, fileNums, redshifts,
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numSubvolumes, numSlices, True, lbox, 5, omegaM)
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numSubvolumes, numSlices, True, lbox, 15, omegaM)
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if args.hod or args.all:
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print " Doing DR9 HOD"
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@ -1,246 +0,0 @@
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#!/usr/bin/env python
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# script which prepares inputs for gadget-based void run
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import numpy as np
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import os
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import sys
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import void_python_tools as vp
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import argparse
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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# CONFIGURATION
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# directory for the input simulation/observational particle files
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catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/gadget/"
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# where to put the final void catalog, figures, and output logs
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voidOutputDir = os.getenv("HOME")+"/workspace/Voids/gadget/"
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figDir = os.getenv("PWD")+"/../figs/gadget/"
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logDir = os.getenv("PWD")+"/../logs/gadget/"
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# where to place the pipeline scripts
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scriptDir = os.getenv("PWD")+"/gadget/"
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# simulation or observation?
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dataType = "simulation"
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# available formats for simulation: gadget, multidark
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dataFormat = "gadget"
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dataUnit = 1 # as multiple of Mpc/h
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# place particles on the lightcone?
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useLightCone = False
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# common filename of particle files
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particleFileBase = "mdr1_particles_z"
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# list of file numbers for the particle files
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# to get particle file name, we take particleFileBase+fileNum
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fileNums = (("0.0", "0.53", "1.0"))
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# redshift of each file in the above list
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redshifts = (("0.0", "0.53", "1.0"))
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# how many independent slices along the z-axis?
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numSlices = 4
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# how many subdivisions along the x- and y- axis?
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# ( = 2 will make 4 subvolumes for each slice, = 3 will make 9, etc.)
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numSubvolumes = 1
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# prefix to give all outputs
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prefix = "gadget_"
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# list of desired subsamples
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subSamples = [ 1.0, 0.1 ]
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# simulation information
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numPart = 1024*1024*1024
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lbox = 1000 # Mpc/h
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omegaM = 0.27
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hubble = 0.70
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# END CONFIGURATION
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# -----------------------------------------------------------------------------
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# -----------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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LIGHT_SPEED = 299792.458
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def getSampleName(setName, redshift, useVel, iSlice=-1, iVol=-1):
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sampleName = setName
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if useVel: setName += "_pv"
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if iSlice != -1: sampleName += "_s" + str(iSlice)
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if iVol != -1: sampleName += "_d" + iVol
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return sampleName
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#------------------------------------------------------------------------------
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# for given dataset parameters, outputs a script for use with analyzeVoids
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def writeScript(setName, dataFileNameBase,
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scriptDir, catalogDir, fileNums, redshifts, numSubvolumes,
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numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0,
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suffix=".dat"):
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if useVel: setName += "_pv"
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scriptFileName = scriptDir + "/" + setName + ".py"
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scriptFile = open(scriptFileName, 'w')
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scriptFile.write("""#!/usr/bin/env/python
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import os
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from void_python_tools.backend.classes import *
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continueRun = False
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startCatalogStage = 1
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endCatalogStage = 4
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startAPStage = 1
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endAPStage = 7
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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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freshStack = True
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errorBars = "CALCULATED"
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numIncoherentRuns = 100
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ranSeed = 101010
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useLCDM = False
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bias = 1.16
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dataPortions = ["central"]
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dataSampleList = []
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""")
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dataInfo = """
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setName = "{setName}"
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workDir = "{voidOutputDir}/{setName}/"
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inputDataDir = "{inputDataDir}"
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figDir = "{figDir}/{setName}/"
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logDir = "{logDir}/{setName}/"
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"""
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scriptFile.write(dataInfo.format(setName=setName, figDir=figDir,
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logDir=logDir, voidOutputDir=voidOutputDir,
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inputDataDir=catalogDir))
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sampleInfo = """
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newSample = Sample(dataFile = "{dataFile}",
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dataFormat = "{dataFormat}",
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dataUnit = {dataUnit},
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fullName = "{sampleName}",
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nickName = "{sampleName}",
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dataType = "simulation",
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zBoundary = ({zMin}, {zMax}),
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zRange = ({zMin}, {zMax}),
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zBoundaryMpc = ({zMinMpc}, {zMaxMpc}),
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omegaM = {omegaM},
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minVoidRadius = {minRadius},
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includeInHubble = True,
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partOfCombo = False,
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isCombo = False,
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boxLen = {boxLen},
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usePecVel = {usePecVel},
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numSubvolumes = {numSubvolumes},
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mySubvolume = "{mySubvolume}",
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numSubDivisions = 4,
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useLightCone = {useLightCone},
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subsample = {subsample})
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dataSampleList.append(newSample)
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"""
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for (iFile, redshift) in enumerate(redshifts):
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fileNum = fileNums[iFile]
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zBox = float(redshift)
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Om = float(omegaM)
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zBoxMpc = LIGHT_SPEED/100.*vp.angularDiameter(zBox, Om=Om)
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boxMaxMpc = zBoxMpc + lbox
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# converter from redshift to comoving distance
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zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
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zVsDX = np.zeros(len(zVsDY))
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for i in xrange(len(zVsDY)):
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zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
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if useLightCone:
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boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
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LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
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dzSafe = 0.03
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else:
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boxWidthZ = lbox*100./LIGHT_SPEED
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dzSafe = 0.0
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for iSlice in xrange(numSlices):
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sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-dzSafe)/numSlices
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sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-dzSafe)/numSlices
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sliceMinMpc = sliceMin*LIGHT_SPEED/100.
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sliceMaxMpc = sliceMax*LIGHT_SPEED/100.
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sliceMin = "%0.2f" % sliceMin
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sliceMax = "%0.2f" % sliceMax
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sliceMinMpc = "%0.1f" % sliceMinMpc
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sliceMaxMpc = "%0.1f" % sliceMaxMpc
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dataFileName = dataFileNameBase + fileNum + suffix
|
||||
|
||||
for iX in xrange(numSubvolumes):
|
||||
for iY in xrange(numSubvolumes):
|
||||
|
||||
mySubvolume = "%d%d" % (iX, iY)
|
||||
|
||||
sampleName = getSampleName(setName, redshift, useVel,
|
||||
iSlice=iSlice, iVol=mySubvolume)
|
||||
|
||||
scriptFile.write(sampleInfo.format(dataFile=dataFileName,
|
||||
dataFormat=dataFormat,
|
||||
dataUnit=dataUnit,
|
||||
sampleName=sampleName,
|
||||
zMin=sliceMin,
|
||||
zMax=sliceMax,
|
||||
zMinMpc=sliceMinMpc,
|
||||
zMaxMpc=sliceMaxMpc,
|
||||
omegaM=Om,
|
||||
boxLen=lbox,
|
||||
usePecVel=useVel,
|
||||
minRadius=minRadius,
|
||||
numSubvolumes=numSubvolumes,
|
||||
mySubvolume=mySubvolume,
|
||||
useLightCone=useLightCone,
|
||||
subsample=subsample))
|
||||
|
||||
scriptFile.close()
|
||||
return
|
||||
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
#------------------------------------------------------------------------------
|
||||
if not os.access(scriptDir, os.F_OK): os.mkdir(scriptDir)
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
# first the directly downsampled runs
|
||||
# Note: ss0.002 ~ SDSS DR7 dim2
|
||||
# ss0.0004 ~ SDSS DR9 mid
|
||||
baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
|
||||
for thisSubSample in subSamples:
|
||||
|
||||
keepFraction = float(thisSubSample) / baseResolution
|
||||
maxKeep = keepFraction * numPart
|
||||
minRadius = int(np.ceil(lbox/maxKeep**(1./3)))
|
||||
|
||||
print " Doing subsample", thisSubSample, " scripts"
|
||||
setName = prefix+"ss"+str(thisSubSample)
|
||||
writeScript(setName, particleFileBase, scriptDir, catalogDir, fileNums,
|
||||
redshifts,
|
||||
numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
|
||||
subsample=thisSubSample, suffix="")
|
||||
writeScript(setName, particleFileBase, scriptDir, catalogDir, fileNums,
|
||||
redshifts,
|
||||
numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
|
||||
subsample=thisSubSample, suffix="")
|
||||
|
||||
|
|
@ -106,7 +106,7 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
|
|||
else:
|
||||
useLightConeString = ""
|
||||
|
||||
if sample.dataFormat == "multidark":
|
||||
if sample.dataFormat == "multidark" or sample.dataFormat == "random":
|
||||
dataFileLine = "multidark " + datafile
|
||||
elif sample.dataFormat == "gadget":
|
||||
dataFileLine = "gadget " + datafile
|
||||
|
|
@ -197,8 +197,10 @@ def launchZobov(sample, binPath, zobovDir=None, logDir=None, continueRun=None):
|
|||
if os.access(zobovDir+"/voidDesc_"+sampleName+".out", os.F_OK):
|
||||
os.unlink(zobovDir+"/voidDesc_"+sampleName+".out")
|
||||
|
||||
cmd = "%s/vozinit %s 0.1 1.0 2 %s %g %s %s %s >& %s" % \
|
||||
(binPath, datafile, \
|
||||
numThreads = 2
|
||||
|
||||
cmd = "%s/vozinit %s 0.1 1.0 %g %s %g %s %s %s >& %s" % \
|
||||
(binPath, datafile, numThreads, \
|
||||
"_"+sampleName, sample.numSubDivisions, \
|
||||
binPath, zobovDir, maskIndex, logFile)
|
||||
os.system(cmd)
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue