mirror of
https://bitbucket.org/cosmicvoids/vide_public.git
synced 2025-07-04 15:21:11 +00:00
466 lines
15 KiB
Python
Executable file
466 lines
15 KiB
Python
Executable file
#!/usr/bin/env python
|
|
|
|
# prepares input catalogs based on multidark simulations
|
|
# (borrows heavily from generateMock, but doesn't hold much in memory)
|
|
# also creates necessary analyzeVoids input files
|
|
|
|
import numpy as np
|
|
import os
|
|
import sys
|
|
from Scientific.IO.NetCDF import NetCDFFile
|
|
import void_python_tools as vp
|
|
import argparse
|
|
|
|
catalogDir = os.getenv("HOME")+"/workspace/Voids/catalogs/multidark/"
|
|
scriptDir = os.getenv("PWD")+"/multidark/"
|
|
hodPath = os.getenv("HOME")+"/projects/Voids/hod/HOD.x"
|
|
|
|
outputDir = os.getenv("HOME")+"/workspace/Voids/multidark/"
|
|
figDir = os.getenv("PWD")+"/../figs/multidark/"
|
|
logDir = os.getenv("PWD")+"/../logs/multidark/"
|
|
|
|
dataFormat = "multidark"
|
|
dataType = "simulation"
|
|
useLightCone = True
|
|
|
|
redshifts = (("0.0", "0.53", "1.0"))
|
|
redshiftFileBase = "mdr1_particles_z"
|
|
numSlices = 4
|
|
numSubvolumes = 1
|
|
|
|
prefix = "md_"
|
|
subSamples = ((0.1, 0.05, 0.01, 0.002, 0.001, 0.0004, 0.0002))
|
|
|
|
numPart = 1024*1024*1024 # number of particles in base catalog
|
|
lbox = 1000
|
|
omegaM = 0.27
|
|
hubble = 0.70
|
|
|
|
# -----------------------------------------------------------------------------
|
|
LIGHT_SPEED = 299792.458
|
|
|
|
parser = argparse.ArgumentParser(description='options')
|
|
parser.add_argument('--scripts', dest='script', action='store_const',
|
|
const=True, default=False,
|
|
help='write scripts')
|
|
parser.add_argument('--subsamples', dest='subsample', action='store_const',
|
|
const=True, default=False,
|
|
help='write subsamples')
|
|
parser.add_argument('--halos', dest='halos', action='store_const',
|
|
const=True, default=False,
|
|
help='write halos')
|
|
parser.add_argument('--hod', dest='hod', action='store_const',
|
|
const=True, default=False,
|
|
help='write hos')
|
|
parser.add_argument('--all', dest='all', action='store_const',
|
|
const=True, default=False,
|
|
help='write everything')
|
|
args = parser.parse_args()
|
|
|
|
#------------------------------------------------------------------------------
|
|
def getSampleName(prefix, base, redshift, useVel, iSlice=-1, iVol=-1):
|
|
useVelString = ""
|
|
if useVel: useVelString = "_pv"
|
|
|
|
sampleName = prefix + base + useVelString + "_z" + redshift
|
|
|
|
if iSlice != -1:
|
|
sampleName += "_s" + str(iSlice)
|
|
|
|
if iVol != -1:
|
|
sampleName += "_d" + iVol
|
|
|
|
return sampleName
|
|
|
|
#------------------------------------------------------------------------------
|
|
# for given dataset parameters, outputs a script for use with analyzeVoids
|
|
def writeScript(prefix, base, scriptDir, catalogDir, redshifts, numSubvolumes,
|
|
numSlices, useVel, lbox, minRadius, omegaM, subsample=1.0,
|
|
suffix=".dat"):
|
|
|
|
setName = prefix + base
|
|
|
|
dataFileNameBase = setName #+ ".dat"
|
|
|
|
if useVel: setName += "_pv"
|
|
|
|
scriptFileName = scriptDir + "/" + "md_" + base
|
|
if useVel: scriptFileName += "_pv"
|
|
scriptFileName += ".py"
|
|
scriptFile = open(scriptFileName, 'w')
|
|
|
|
scriptFile.write("""#!/usr/bin/env/python
|
|
import os
|
|
from void_python_tools.backend.classes import *
|
|
|
|
continueRun = False
|
|
startCatalogStage = 1
|
|
endCatalogStage = 3
|
|
|
|
startAPStage = 1
|
|
endAPStage = 6
|
|
|
|
ZOBOV_PATH = os.getenv("PWD")+"/../zobov/"
|
|
CTOOLS_PATH = os.getenv("PWD")+"/../c_tools/"
|
|
freshStack = True
|
|
errorBars = "CALCULATED"
|
|
numIncoherentRuns = 100
|
|
ranSeed = 101010
|
|
useLCDM = False
|
|
bias = 1.16
|
|
|
|
dataPortions = ["central"]
|
|
dataSampleList = []
|
|
""")
|
|
|
|
dataInfo = """
|
|
catalogName = "{sampleName}"
|
|
|
|
workDir = "{outputDir}/{sampleName}/"
|
|
inputDataDir = "{catalogDir}"
|
|
figDir = "{figDir}/{sampleName}/"
|
|
logDir = "{logDir}/{sampleName}/"
|
|
"""
|
|
scriptFile.write(dataInfo.format(sampleName=setName, figDir=figDir,
|
|
logDir=logDir, outputDir=outputDir,
|
|
catalogDir=catalogDir,
|
|
inputDataDir=catalogDir))
|
|
|
|
sampleInfo = """
|
|
newSample = Sample(dataFile = "{dataFile}",
|
|
dataFormat = "{dataFormat}",
|
|
fullName = "{sampleName}",
|
|
nickName = "{sampleName}",
|
|
dataType = "simulation",
|
|
zBoundary = ({zMin}, {zMax}),
|
|
zRange = ({zMin}, {zMax}),
|
|
zBoundaryMpc = ({zMinMpc}, {zMaxMpc}),
|
|
omegaM = {omegaM},
|
|
minVoidRadius = {minRadius},
|
|
includeInHubble = True,
|
|
partOfCombo = False,
|
|
isCombo = False,
|
|
boxLen = {boxLen},
|
|
usePecVel = {usePecVel},
|
|
numSubvolumes = {numSubvolumes},
|
|
mySubvolume = "{mySubvolume}",
|
|
numSubDivisions = 4,
|
|
useLightCone = {useLightCone},
|
|
subsample = {subsample})
|
|
dataSampleList.append(newSample)
|
|
newSample.addStack({zMin}, {zMax}, {minRadius} , {minRadius}+2, True, False)
|
|
newSample.addStack({zMin}, {zMax}, {minRadius} , {minRadius}+4, True, False)
|
|
newSample.addStack({zMin}, {zMax}, {minRadius}+2, {minRadius}+6, True, False)
|
|
newSample.addStack({zMin}, {zMax}, {minRadius}+6, {minRadius}+10, True, False)
|
|
newSample.addStack({zMin}, {zMax}, {minRadius}+10, {minRadius}+18, True, False)
|
|
newSample.addStack({zMin}, {zMax}, {minRadius}+18, {minRadius}+24, True, False)
|
|
"""
|
|
|
|
for redshift in redshifts:
|
|
zBox = float(redshift)
|
|
Om = float(omegaM)
|
|
zBoxMpc = LIGHT_SPEED/100.*vp.angularDiameter(zBox, Om=Om)
|
|
boxMaxMpc = zBoxMpc + lbox
|
|
|
|
# converter from redshift to comoving distance
|
|
zVsDY = np.linspace(0., zBox+8*lbox*100./LIGHT_SPEED, 10000)
|
|
zVsDX = np.zeros(len(zVsDY))
|
|
for i in xrange(len(zVsDY)):
|
|
zVsDX[i] = vp.angularDiameter(zVsDY[i], Om=Om)
|
|
|
|
if useLightCone:
|
|
boxWidthZ = np.interp(vp.angularDiameter(zBox,Om=Om)+100. / \
|
|
LIGHT_SPEED*lbox, zVsDX, zVsDY)-zBox
|
|
dzSafe = 0.03
|
|
else:
|
|
boxWidthZ = lbox*100./LIGHT_SPEED
|
|
dzSafe = 0.0
|
|
|
|
for iSlice in xrange(numSlices):
|
|
# trim off the first and last 10,000 km/s
|
|
sliceMin = zBox + dzSafe + iSlice*(boxWidthZ-dzSafe)/numSlices
|
|
sliceMax = zBox + dzSafe + (iSlice+1)*(boxWidthZ-dzSafe)/numSlices
|
|
|
|
sliceMinMpc = sliceMin*LIGHT_SPEED/100.
|
|
sliceMaxMpc = sliceMax*LIGHT_SPEED/100.
|
|
|
|
sliceMin = "%0.2f" % sliceMin
|
|
sliceMax = "%0.2f" % sliceMax
|
|
sliceMinMpc = "%0.1f" % sliceMinMpc
|
|
sliceMaxMpc = "%0.1f" % sliceMaxMpc
|
|
|
|
dataFileName = dataFileNameBase + "_z" + redshift + suffix
|
|
|
|
for iX in xrange(numSubvolumes):
|
|
for iY in xrange(numSubvolumes):
|
|
|
|
mySubvolume = "%d%d" % (iX, iY)
|
|
|
|
sampleName = getSampleName(prefix, base, redshift, useVel,
|
|
iSlice=iSlice, iVol=mySubvolume)
|
|
|
|
scriptFile.write(sampleInfo.format(dataFile=dataFileName,
|
|
dataFormat=dataFormat,
|
|
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 = 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)))
|
|
|
|
if args.script or args.all:
|
|
print " Doing subsample", thisSubSample, " scripts"
|
|
if dataFormat == "multidark":
|
|
writeScript(prefix,
|
|
"ss"+str(thisSubSample), scriptDir, catalogDir, redshifts,
|
|
numSubvolumes, numSlices, False, lbox, minRadius, omegaM,
|
|
subsample=1.0)
|
|
writeScript(prefix, "ss"+str(thisSubSample), scriptDir, catalogDir,
|
|
redshifts, numSubvolumes, numSlices, True, lbox, minRadius,
|
|
omegaM, subsample=1.0)
|
|
elif dataFormat == "gadget":
|
|
writeScript("", redshiftFileBase, scriptDir, catalogDir, redshifts,
|
|
numSubvolumes, numSlices, True, lbox, minRadius, omegaM,
|
|
subsample=thisSubSample, suffix="")
|
|
|
|
if args.subsample or args.all:
|
|
print " Doing subsample", thisSubSample
|
|
|
|
for redshift in redshifts:
|
|
print " redshift", redshift
|
|
dataFile = catalogDir+"/"+redshiftFileBase+redshift
|
|
inFile = open(dataFile, 'r')
|
|
|
|
sampleName = getSampleName("ss"+str(thisSubSample), redshift, False)
|
|
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
|
|
|
|
outFile.write("%f\n" %(lbox))
|
|
outFile.write("%s" %(omegaM))
|
|
outFile.write("%s" %(hubble))
|
|
outFile.write("%s\n" %(redshift))
|
|
outFile.write("%d\n" %(maxKeep))
|
|
|
|
numKept = 0
|
|
for line in inFile:
|
|
if np.random.uniform() > keepFraction: continue
|
|
numKept += 1
|
|
if numKept > maxKeep: break
|
|
line = line.split(',')
|
|
x = float(line[0])
|
|
y = float(line[1])
|
|
z = float(line[2])
|
|
vz = float(line[3])
|
|
|
|
outFile.write("%e %e %e %e\n" %(x,y,z,vz))
|
|
|
|
outFile.write("-99 -99 -99 -99\n")
|
|
print "KEEPING:", numKept, "...predicted:", maxKeep
|
|
inFile.close()
|
|
outFile.close()
|
|
|
|
# -----------------------------------------------------------------------------
|
|
# now halos
|
|
if args.script or args.all:
|
|
print " Doing halo scripts"
|
|
|
|
dataFile = catalogDir+"/mdr1_halos_z"+redshifts[0]
|
|
inFile = open(dataFile, 'r')
|
|
numPart = 0
|
|
for line in inFile: numPart += 1
|
|
inFile.close()
|
|
|
|
minRadius = int(np.ceil(lbox/numPart**(1./3.)))
|
|
|
|
if dataFormat == "multidark":
|
|
writeScript(prefix, "halos", scriptDir, catalogDir, redshifts,
|
|
numSubvolumes, numSlices, False, lbox, minRadius, omegaM)
|
|
writeScript(prefix, "halos", scriptDir, catalogDir, redshifts, numSubvolumes,
|
|
numSlices, True, lbox, minRadius, omegaM)
|
|
|
|
if args.halos or args.all:
|
|
print " Doing halos"
|
|
|
|
for redshift in redshifts:
|
|
print " z = ", redshift
|
|
|
|
dataFile = catalogDir+"/mdr1_halos_z"+redshift
|
|
inFile = open(dataFile, 'r')
|
|
numPart = 0
|
|
for line in inFile: numPart += 1
|
|
inFile.close()
|
|
|
|
sampleName = getSampleName("halos", redshift, False)
|
|
|
|
outFile = open(catalogDir+"/"+sampleName+".dat", 'w')
|
|
|
|
outFile.write("%f\n" %(lbox))
|
|
outFile.write("%s" %(omegaM))
|
|
outFile.write("%s" %(hubble))
|
|
outFile.write("%s\n" %(redshift))
|
|
outFile.write("%d\n" %(numPart))
|
|
|
|
inFile = open(dataFile, 'r')
|
|
numKept = 0
|
|
for line in inFile:
|
|
numKept += 1
|
|
line = line.split(',')
|
|
x = float(line[0])
|
|
y = float(line[1])
|
|
z = float(line[2])
|
|
vz = float(line[5])
|
|
|
|
# write to output file
|
|
outFile.write("%e %e %e %e\n" %(x,y,z,vz))
|
|
|
|
inFile.close()
|
|
outFile.close()
|
|
|
|
# -----------------------------------------------------------------------------
|
|
# now the SDSS HOD
|
|
parFileText = """
|
|
% cosmology
|
|
OMEGA_M {omegaM}
|
|
HUBBLE {hubble}
|
|
OMEGA_B 0.0469
|
|
SIGMA_8 0.82
|
|
SPECTRAL_INDX 0.95
|
|
ITRANS 5
|
|
REDSHIFT {redshift}
|
|
|
|
% halo definition
|
|
%DELTA_HALO 200
|
|
DELTA_HALO 740.74 % 200/Om_m
|
|
M_max 1.00E+16
|
|
|
|
% fit function types
|
|
pdfs 11
|
|
pdfc 2
|
|
EXCLUSION 4
|
|
|
|
% hod parameters
|
|
M_min {Mmin}
|
|
GALAXY_DENSITY 0.0111134 % computed automatically if M_min set, use for sanity
|
|
M1 {M1}
|
|
sigma_logM {sigma_logM}
|
|
alpha {alpha}
|
|
M_cut {Mcut}
|
|
|
|
% simulation info
|
|
real_space_xi 1
|
|
HOD 1
|
|
populate_sim 1
|
|
HaloFile {haloFile}
|
|
RESOLUTION {numPartPerSide}
|
|
BOX_SIZE {boxSize}
|
|
|
|
% output
|
|
root_filename hod
|
|
"""
|
|
|
|
if args.script or args.all:
|
|
print " Doing DR7 HOD scripts"
|
|
if dataFormat == "multidark":
|
|
writeScript(prefix,
|
|
"hod_dr72dim2", scriptDir, catalogDir, redshifts,
|
|
numSubvolumes, numSlices, False, lbox, 5, omegaM)
|
|
writeScript(prefix,
|
|
"hod_dr72dim2", scriptDir, catalogDir, redshifts,
|
|
numSubvolumes, numSlices, True, lbox, 5, omegaM)
|
|
|
|
if args.hod or args.all:
|
|
print " Doing DR7 HOD"
|
|
for redshift in redshifts:
|
|
print " z = ", redshift
|
|
|
|
parFileName = "./hod.par"
|
|
parFile = open(parFileName, 'w')
|
|
haloFile = catalogDir+"/mdr1_halos_z"+redshift
|
|
parFile.write(parFileText.format(omegaM=omegaM,
|
|
hubble=hubble,
|
|
redshift=redshift,
|
|
Mmin=1.99526e12,
|
|
M1=3.80189e13,
|
|
sigma_logM=0.21,
|
|
alpha=1.12,
|
|
Mcut=6.91831e11,
|
|
haloFile=haloFile,
|
|
numPartPerSide=numPart**(1/3.),
|
|
boxSize=lbox))
|
|
parFile.close()
|
|
|
|
os.system(hodPath+" "+parFileName+">& /dev/null")
|
|
|
|
sampleName = getSampleName("hod_dr72dim2", redshift, False)
|
|
outFileName = catalogDir+"/"+sampleName+".dat"
|
|
os.system("mv hod.mock" + " " + outFileName)
|
|
|
|
os.system("rm ./hod.*")
|
|
|
|
# -----------------------------------------------------------------------------
|
|
# now the BOSS HOD
|
|
if args.script or args.all:
|
|
print " Doing DR9 HOD scripts"
|
|
if dataFormat == "multidark":
|
|
writeScript(prefix,
|
|
"hod_dr9mid", scriptDir, catalogDir, redshifts,
|
|
numSubvolumes, numSlices, False, lbox, 5, omegaM)
|
|
writeScript(prefix,
|
|
"hod_dr9mid", scriptDir, catalogDir, redshifts,
|
|
numSubvolumes, numSlices, True, lbox, 5, omegaM)
|
|
|
|
if args.hod or args.all:
|
|
print " Doing DR9 HOD"
|
|
for redshift in redshifts:
|
|
print " z = ", redshift
|
|
|
|
parFileName = "./hod.par"
|
|
parFile = open(parFileName, 'w')
|
|
haloFile = catalogDir+"/mdr1_halos_z"+redshift
|
|
parFile.write(parFileText.format(omegaM=omegaM,
|
|
hubble=hubble,
|
|
redshift=redshift,
|
|
Mmin=1.23e13,
|
|
M1=1.e14,
|
|
sigma_logM=0.596,
|
|
alpha=1.0127,
|
|
Mcut=1.19399e13,
|
|
haloFile=haloFile,
|
|
numPartPerSide=numPart**(1/3.),
|
|
boxSize=lbox))
|
|
parFile.close()
|
|
|
|
os.system(hodPath+" "+parFileName+">& /dev/null")
|
|
|
|
sampleName = getSampleName("hod_dr9mid", redshift, False)
|
|
outFileName = catalogDir+"/"+sampleName+".dat"
|
|
os.system("mv hod.mock" + " " + outFileName)
|
|
|
|
os.system("rm ./hod.*")
|
|
|
|
|