def getFamilyAttributeSum(center2,r,family,attribute):
"""Integrates attributes of a given family over a given sphere."""
charm.createGroupAttributeSphere('group', 'All', 'position', center2[0], center2[1], center2[2], r)
charm.createGroup_Family('group','group',family)
sum = charm.getAttributeSum('group', family, attribute)
charm.deleteGroup('group')
return sum
def getGalDensity(center2, r):
charm.createGroupAttributeSphere(virialGroup, "All", "position", center[0], center[1], center[2], r)
totMass = 0.0
for fam in charm.getFamilies():
totMass += charm.getAttributeSum(virialGroup, fam, "mass")
v = (4 * math.pi / 3.0) * r ** 3
density = totMass / v
return density
def getNormalStarAngMom(center2, radius, comVel=None):
"""Calculates the stellar angular momentum vector given a center and radius. By default the COM velocity is calculated unless it is passed."""
if (comVel==None):vCM=getVelCMStars(center2, radius)
else: vCM = comVel
charm.createGroupAttributeSphere('groupAll', 'All', 'position', center2[0], center2[1], center2[2], radius)
charm.createGroup_Family('groupStar', 'groupAll', 'star')
starAngMom1 = charm.reduceParticle('groupStar', getParticleAngMomentum, sumAngMomentum, [center2,vCM])
starAngMom = (starAngMom1[0][1],starAngMom1[0][2],starAngMom1[0][3])
starAngMomMag = math.sqrt(starAngMom[0]**2+starAngMom[1]**2+starAngMom[2]**2)
starAngMom = (starAngMom[0]/starAngMomMag,starAngMom[1]/starAngMomMag,starAngMom[2]/starAngMomMag)
return starAngMom
def setsphere(group, *args) :
"""Select particles within radius from coordinate."""
import charm
try :
# parse args
if len(args) < 3 : raise TypeError('Too few arguments')
if type(args[0]) == str :
if args[0] == 'pot' or args[0] == 'potential ':
center = charm.findAttributeMin(args[1], 'potential')
radius = args[2]
if(len(args) == 4) : parent = args[3]
else : parent = 'All'
elif args[0] == 'com' :
if type(args[1]) != str : raise StandardError('third argument should be a group')
if args[2] == 'all' or args[2] == 'All' :
center = charm.getCenterOfMass(args[1])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
elif args[2] == 'gas' :
charm.createGroup_Family("__tmpgroup", args[1], 'gas')
center = charm.getCenterOfMass(args[1])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
elif args[2] == 'dark' :
charm.createGroup_Family("__tmpgroup", args[1], 'dark')
center = charm.getCenterOfMass(args[1])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
elif args[2] == 'star' :
charm.createGroup_Family("__tmpgroup", args[1], 'star')
center = charm.getCenterOfMass(args[1])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
else : raise StandardError('unknown particle type: ' + args[2])
else : raise StandardError('unknown center type: ' + args[0])
else :
center = (args[0], args[1], args[2])
radius = args[3]
if(len(args) == 5) : parent = args[4]
else : parent = 'All'
# check if simulation loaded
if charm.getGroups() == None :
raise StandardError('Simulation not loaded')
charm.createGroupAttributeSphere(group, parent, 'position', center[0], center[1],
center[2], radius)
except :
print traceback.format_exc()
def findCenter(group2='All', method = 'pot' ):
"""Finds the center of a given group based on method as 'com' or 'pot'"""
if (method=='pot'):
if (group2=='All'):
charm.createGroup_AttributeRange('highres', 'All', 'mass', -1, 7e-12)
cntHr = charm.getCenterOfMass('highres')
charm.createGroupAttributeSphere('centerhr', 'All', 'position', cntHr[0], cntHr[1], cntHr[2], 1000./136986.30137)
cnt = charm.findAttributeMin('centerhr', 'potential')
else:
cnt = charm.findAttributeMin(group2, 'potential')
elif (method=='com'):
cnt = charm.getCenterOfMass(group2)
return cnt
def getVelCMStars(center2, radius):
"Returns the vector for the center of mass velocity of a group of stars defined by center2 coordinates and a radius."
charm.createGroupAttributeSphere('tmpGal', 'All', 'position', center2[0], center2[1], center2[2], radius) #use cmVelCompare2.py to choose length
charm.createGroup_Family('tmpStarGroup', 'tmpGal', 'star') #select star particles only
massStar = charm.getAttributeSum('tmpGal', 'star', 'mass')
mass = massStar #calculate total mass
vmomentStar = charm.reduceParticle('tmpStarGroup', centMassVelMap, centMassReduce, None)
vmoment = [vmomentStar[0][1],vmomentStar[0][2],vmomentStar[0][3]]
vcm = (vmoment[0]/mass, vmoment[1]/mass, vmoment[2]/mass)
#Clean up
charm.deleteGroup('tmpGal')
charm.deleteGroup('tmpStarGroup')
return vcm #return the COM velocity vector
def calcGalacticCoordinates(angMomGroup=None, center ='pot'):
'''Assigns particles a position in the galactic coordinate system. galVelocity = (v+Hr). angMomGroup'''
#===========================================================================
# --Overview--
# 1.Form transformation matrix
# 2.Translate the coordinates to the center of the galaxy (or COM velocity)
# 3.Rotate the coordinate system to be aligned with the angular momentum vector
# 4.Write information to vector attributes
#===========================================================================
if ((angMomGroup in charm.getGroups())==False) & (angMomGroup!=None):
print "Group does not exist, please try again."
return
##############################
# Actual Routine
##############################
if (angMomGroup==None):
angMomGroup = 'angMomGroup'
cnt = findcenter.findCenter(method=center)
virialRadius = virialgroup.getVirialGroup()
charm.createGroupAttributeSphere('angMomGroup', 'All', 'position', cnt[0], cnt[1], cnt[2], virialRadius*quesoConfig.rgalFraction)
charm.createGroup_Family('angMomGroup', 'angMomGroup', 'gas')
charm.createGroup_AttributeRange('angMomGroup', 'angMomGroup', 'temperature', 0, quesoConfig.coldGasTemp)
else:
cnt = findcenter.findCenter(group2=angMomGroup,method=center)
angmom.getAngMomVector(group=angMomGroup,center=center)
# Transformation Matrix
galZ = vectormath.normalizeVector(angmom.getAngMomVector(group=angMomGroup,center=center))
galX = vectormath.normalizeVector(vectormath.crossVectors((0,1,0),galZ))
galY = vectormath.normalizeVector(vectormath.crossVectors(galZ,galX))
transMatrix = (galX,
galY,
galZ)
fHubble = quesoConfig.fHubble0*math.sqrt(quesoConfig.omega0/charm.getTime()**3+(1-quesoConfig.omega0))
# Galactic Position
charm.createVectorAttribute('star','galPosition')
charm.createVectorAttribute('gas', 'galPosition')
charm.createVectorAttribute('dark','galPosition')
param = (cnt, transMatrix)
charm.runLocalParticleCodeGroup('All', calcGalPosition, param)
# Galactic velocity
vCM=angmom.getVelCM(angMomGroup)
param = (cnt, transMatrix,vCM, fHubble)
charm.createVectorAttribute('star','galVelocity')
charm.createVectorAttribute('gas', 'galVelocity')
charm.createVectorAttribute('dark','galVelocity')
charm.runLocalParticleCodeGroup('All', calcGalVelocity, param)
return
def SFRSurfaceProfile(minRadius=.1, numBins=50,tstep='00512',nbins=500):
"""Returns the list of tuples (radius, SFR, diskSFR, bulgeSFR) in solar masses/year! (for the 0.5Gyr preceding each time)"""
#read in initial masses from file
filename = quesoConfig.dataDir + quesoConfig.preTimestepFilename + tstep + ".massform"
charm.readTipsyArray(filename,'initialMass')
virialRadius = virialgroup.getVirialGroup()
rgal = quesoConfig.rgalFraction*virialRadius
center = findcenter.findCenter()
radialStep = ((math.log10(rgal)-math.log10(minRadius))/(float(numBins)-1))
simTime = getSimTime(timestep=tstep)/quesoConfig.timeunit #time in simulation units
sfr = [[]]*numBins
#initialize relevant attributes
galcoord.calcGalacticCoordinates()
#create sphere of stars
charm.createGroupAttributeSphere('galStar', 'All', 'position', center[0], center[1], center[2], rgal)
charm.createGroup_Family('galStar', 'galStar', 'star')
formHigh = simTime
formLow = formHigh-quesoConfig.sfrLookback/quesoConfig.timeunit
param = (formLow, formHigh, radialStep, quesoConfig.kpcunit*charm.getTime(), minRadius)
reduceResult = charm.reduceParticle('galStar' , mapSFRProfile, reduceSFRProfile, param)
print reduceResult
print (formLow,formHigh)
maxbin=0
for i in range(0,len(reduceResult)):
if (reduceResult[i][0]>maxbin):maxbin=reduceResult[i][0]
for i in range(0,len(reduceResult)):
radiusOut = math.pow(10, radialStep*reduceResult[i][0])
radiusInside = math.pow(10, radialStep*(reduceResult[i][0]-1))
radius = (radiusOut+radiusInside)/2
area = math.pi*(radiusOut**2-radiusInside**2)
formationRate = reduceResult[i][1]*quesoConfig.msolunit/quesoConfig.sfrLookback/area #msolar/yr/kpc^2
bin = reduceResult[i][0]+numBins-maxbin-1
sfr[bin]=(radius, formationRate)
print sfr[bin]
for i in range(0,numBins):
if (sfr[i] == []):
radiusOut = math.pow(10, radialStep*(i+1))
radiusInside = math.pow(10, radialStep*i)
radius = (radiusOut+radiusInside)/2
sfr[i]=(radius,0,0,0)
sfrData = [[],[]]
for i in range(len(sfr)):
sfrData[0].append(sfr[i][0])
sfrData[1].append(sfr[i][1])
return sfrData
def getSFRTimeProfile(nbins=500):
"""Returns the list of tuples (time, SFR) in solar masses/year! (for the 0.5Gyr preceding each time)"""
#read in initial masses from file
filename = quesoConfig.dataDir + quesoConfig.preTimestepFilename + quesoConfig.nTimesteps + ".massform"
charm.readTipsyArray(filename,'initialMass')
simTime = getSimTime()/quesoConfig.timeunit #time in simulation units
profileTStep = simTime/nbins
sfr = [(0,0)]*nbins
center = findcenter.findCenter()
rgal = virialgroup.getVirialGroup()*quesoConfig.rgalFraction
charm.createGroupAttributeSphere('galStar', 'star', 'position', center[0], center[1], center[2], rgal) #Particles within galactic radius
charm.createGroup_Family('galStar', 'galStar', 'star')
param = (profileTStep, nbins)
reduceResult = charm.reduceParticle('galStar' , mapSFR, reduceSFR, param)
#sum = 0.0
for i in range(0,len(reduceResult)):
#try:
formationRate = reduceResult[i][1]*quesoConfig.msolunit/(profileTStep*quesoConfig.timeunit) #msolar/yr
age = (simTime -reduceResult[i][0]*profileTStep)*quesoConfig.timeunit/1e9 #in gyr
sfr[reduceResult[i][0]-1] =(age, formationRate)
return sfr
def getEpsilonDist(group='gal', nBins=50, epsCut=2., center='pot'):
"""Returns a histogram of dimension 2 x nbins of stellar epsilons (jz/jcirc) and mass-fraction. epsCut defines the histogram bound in both directions. Center can be either 'pot' or 'com'"""
numRotBins = 400 #number of points at which we linearly interpolate
radiusVCM = 0.25 #fraction of group radius to use when calculating COM velocity
radiusAngMom = 0.25 #fraction of group radius to use when calculating stellar angular momentum
a = charm.getTime()
if ((group in charm.getGroups()==False)) & (group !='gal'):
print "Group does not exist, please try again."
return
if (group == 'gal'):
rgal = quesoConfig.rgalFraction*virialgroup.getVirialGroup()
center=findcenter.findCenter(group2='virialGroup', method=center)
charm.createGroupAttributeSphere('gal', 'All', 'position', center[0], center[1], center[2], rgal)
else:
center=findcenter.findCenter(group2=group, method=center)
# Find maximum radius
charm.createGroup_Family('tmp',group,'star')
maxRad = getgroupradius.getGroupRadius('tmp', center)
massDist = [0]*(numRotBins+1)
rad = [0]*(numRotBins+1)
radialStep = maxRad/numRotBins
#populate mass bins
for i in range(numRotBins+1):
charm.createGroupAttributeSphere('tmp', 'All', 'position', center[0], center[1], center[2], radialStep*i)
massDist[i] = charm.getAttributeSum('tmp','star','mass')
massDist[i] += charm.getAttributeSum('tmp','dark','mass')
massDist[i] += charm.getAttributeSum('tmp','gas' ,'mass')
#Note: I tried shells instead of spheres and it made no real difference.
rad[i] = radialStep*i
vCM = getVelCMStars(center2=center, radius=radiusVCM*maxRad) #COM velocity
angMomVec = getNormalStarAngMom(center2=center, radius=radiusAngMom*maxRad, comVel=vCM) #Ang Mom Velocity
#vCM = getVelCMStars(center2=center, radius=10/(a*quesoConfig.kpcunit)) #COM velocity
#angMomVec = getNormalStarAngMom(center2=center, radius=6/(a*quesoConfig.kpcunit), comVel=vCM) #Ang Mom Velocity
param = (center, vCM, angMomVec, maxRad, numRotBins,massDist, nBins,epsCut)
charm.createGroupAttributeSphere('tmp', 'All', 'position', center[0], center[1], center[2], maxRad)
charm.createGroup_Family('tmp',group,'star')
#calc total stellar mass for mass weighted average
reduceResult = charm.reduceParticle('tmp', mapEpsilon, reduceEpsilon, param)
sMass = charm.getAttributeSum('tmp','star', 'mass')
epsilonDist = [0]*nBins
eps = [0]*nBins
for i in range(nBins): eps[i] = -epsCut+ 2*epsCut/nBins*(i)
for i in range(len(reduceResult)):
try:
bin = reduceResult[i][0]
epsilonDist[bin] = reduceResult[i][1]/sMass #return the mass fraction
except:{}
return (eps, epsilonDist)
def getVirialGroup(group="All", center2="pot", virialGroup="virialGroup"):
"""This method returns the virial radius of a given group, bases around a center that can be given by one of three options: Default 'pot' finds the potential minimum, 'com' uses the center of mass, or a tuple of length 3 can be given. virialGroup specifies the group name of the resulting """
global center
if center2 == "pot":
cnt = findcenter.findCenter(group2=group, method="pot")
elif center2 == "com":
cnt = findcenter.findCenter(group2=group, method="com")
elif len(center2) == 3:
cnt = center2
center = cnt # use center variable at later times.
# ===========================================================================
# Use center coordinates to find virial radius and return group
# Returns virial radius in sim units via bisection method.
# If this doesn't converge, try larger bounds or adjust the
# other parameters in source.
# ===========================================================================
def getGalDensity(center2, r):
charm.createGroupAttributeSphere(virialGroup, "All", "position", center[0], center[1], center[2], r)
totMass = 0.0
for fam in charm.getFamilies():
totMass += charm.getAttributeSum(virialGroup, fam, "mass")
v = (4 * math.pi / 3.0) * r ** 3
density = totMass / v
return density
# ================================================================
# Specify bounds of bisection. Default is 0.1 to 400kpc (at redshift zero)
epsilon = 0.001 # maximum error in density convergence
count = 0
maxIterations = 200
leftr = 0.1 / quesoConfig.kpcunit
rightr = 4000.0 / quesoConfig.kpcunit
# ================================================================
from queso.quesoConfig import virialRadiusDensity
midpoint = (leftr + rightr) / 2
leftDensity = getGalDensity(center, leftr) - virialRadiusDensity # Initialize values
rightDensity = getGalDensity(center, rightr) - virialRadiusDensity # offset so we can find root
midDensity = getGalDensity(center, midpoint) - virialRadiusDensity # offset so we can find root
# Bisection to find virial radius as defined in quesoConfig
# Run until values converge within epsilon or reach max count
while (count < maxIterations) & (math.fabs(leftDensity - rightDensity) > epsilon):
midpoint = (leftr + rightr) / 2
leftDensity = getGalDensity(center, leftr) - virialRadiusDensity # offset so we can find root
rightDensity = getGalDensity(center, rightr) - virialRadiusDensity # offset so we can find root
midDensity = getGalDensity(center, midpoint) - virialRadiusDensity # offset so we can find root
if leftDensity * midDensity < 0:
rightr = midpoint
elif rightDensity * midDensity < 0:
leftr = midpoint
elif midDensity == 0:
break
elif (leftDensity * midDensity > 0) & (rightDensity * midDensity > 0):
print "\nVirial radius calculation will not converge. Try larger bounds."
return
count += 1
# Don't get stuck in a loop
if count == maxIterations:
print "\nDid not converge in " + str(
maxIterations
) + " iterations. Try smaller bounds or raise epsilon in source."
return
charm.createGroupAttributeSphere(virialGroup, "All", "position", center[0], center[1], center[2], midpoint)
return midpoint # in sim units
def writeBoxAscii(boxRadius, filename, angMomGroup=None, centerMethod ='pot'):
"""Writes out an tipsy-ascii (filename) representation for a box aligned with the galactic coordinate system spanning +-boxRadius (given in kpc) in the galcoord directions. center can be 'pot' or 'com'. Default angMomGroup is cold galactic gas."""
if (angMomGroup==None):
angMomGroup = 'angMomGroup'
center = findcenter.findCenter(method=centerMethod)
virialRadius = virialgroup.getVirialGroup()
charm.createGroupAttributeSphere('angMomGroup', 'All', 'position', center[0], center[1], center[2], virialRadius*quesoConfig.rgalFraction)
charm.createGroup_Family('angMomGroup', 'angMomGroup', 'gas')
charm.createGroup_AttributeRange('angMomGroup', 'angMomGroup', 'temperature', 0, quesoConfig.coldGasTemp)
else:
center = findcenter.findCenter(group2=angMomGroup,method=center)
boxRad1 = boxRadius/(charm.getTime()*quesoConfig.kpcunit)
print 'here'
galcoord.calcGalacticCoordinates(angMomGroup=angMomGroup, center=centerMethod)
galZ = vectormath.normalizeVector(angmom.getAngMomVector(angMomGroup))
galX = vectormath.normalizeVector(vectormath.crossVectors((0,1,0),galZ))
galY = vectormath.normalizeVector(vectormath.crossVectors(galZ,galX))
#===========================================================================
# Create the cube
#===========================================================================
cornerVec = vectormath.addVectors(vectormath.multVectorScalar(boxRad1, galX),vectormath.multVectorScalar(boxRad1, galY))
cornerVec = vectormath.addVectors(cornerVec,vectormath.multVectorScalar(boxRad1, galZ))
cornerVec = vectormath.subVectors(center, cornerVec)
edge1 = vectormath.multVectorScalar(2*boxRad1,galX)
edge2 = vectormath.multVectorScalar(2*boxRad1,galY)
edge3 = vectormath.multVectorScalar(2*boxRad1,galZ)
charm.createGroupAttributeBox('galBox', 'All', 'position',
cornerVec[0],cornerVec[1],cornerVec[2],
edge1[0] ,edge1[1] ,edge1[2],
edge2[0] ,edge2[1] ,edge2[2],
edge3[0] ,edge3[1] ,edge3[2])
numStars = charm.getNumParticles('galBox','star')
numGas = charm.getNumParticles('galBox','gas')
numDark = charm.getNumParticles('galBox','dark')
numTotal = numStars + numGas + numDark
#===========================================================================
# This region outputs the ascii file to be read in by tipsy
#===========================================================================
f = open(filename, 'w') # overwrites pre-existing file
f.write(str(numTotal) + ' ' + str(numGas) + ' ' + str(numStars))
f.write('\n3')
f.write('\n'+ str(charm.getTime())+ '\n')
f.close()
for each in ['star','dark','gas']:charm.createScalarAttribute(each, 'tmpWorking')
def writeAndAppend(attribute):
charm.writeGroupArray('tmpGalBox', attribute, '/tmp/out.tmp')
os.system('tail -n +2 /tmp/out.tmp >> ' + filename)
return
families = ['gas','dark','star']
for each in families:
charm.createGroup_Family('tmpGalBox', 'galBox', each)
writeAndAppend('mass')
# Positions
for i in range(0,3):
for each in families:
charm.createGroup_Family('tmpGalBox', 'galBox', each)
charm.runLocalParticleCodeGroup('tmpGalBox', vectorWriter, ('pos', i))
writeAndAppend('tmpWorking')
# Velocities
for i in range(0,3):
for each in families:
charm.createGroup_Family('tmpGalBox', 'galBox', each)
charm.runLocalParticleCodeGroup('tmpGalBox', vectorWriter, ('vel', i))
writeAndAppend('tmpWorking')
# Star and dark softening
for each in ['dark', 'star']:
charm.createGroup_Family('tmpGalBox', 'galBox', each)
writeAndAppend('softening')
# Gas attributes
charm.createGroup_Family('tmpGalBox', 'galBox', 'gas')
for each in ['density','temperature','softening','metals']:
writeAndAppend(each)
#Star stuff
charm.createGroup_Family('tmpGalBox', 'galBox', 'star')
for each in ['metals','formationtime']:
writeAndAppend(each)
#potential
for each in families:
charm.createGroup_Family('tmpGalBox', 'galBox', each)
writeAndAppend('potential')
charm.deleteGroup('tmpGalBox')
#print 'num lines in ' + filename + ' should be: ' + str(9*numTotal+3*numGas+2*numStars+3)
return
