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 markgal(group, max_temp, min_rho) :
"""Mark all the gas particles in group that have temperatures less
than or equal to max_temp and densities greater than or equal to
min_rho. This command can be used to mark those gas particles that
are likely to be in galaxies."""
# check if simulation loaded
if charm.getGroups() == None :
raise StandardError('Simulation not loaded')
# get opposing boundaries from simulation values
max_rho = charm.getAttributeRange('gas', 'density')[1]
min_temp = charm.getAttributeRange('gas', 'temperature')[0]
# play the createGroup shuffle
charm.createGroup_Family('tmp_group_fam', group, 'gas')
charm.createGroup_AttributeRange('tmp_group1', 'tmp_group_fam', 'density',
min_rho, max_rho)
charm.createGroup_AttributeRange('tmp_group2', 'tmp_group1',
'temperature', min_temp, max_temp)
charm.markParticlesGroup('tmp_group2')
# remove the temporary groups to avoid clutter
charm.deleteGroup('tmp_group_fam')
charm.deleteGroup('tmp_group1')
charm.deleteGroup('tmp_group2')
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 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 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 markgal(group, maxTemp, minRho) :
"""Mark gas particles that are likely to be in galaxies based on selected
temperature and density thresholds. Marked particles are stored in a group
called "mark" which will be replaced every time a marking command is run."""
# check if simulation loaded
if charm.getGroups() == None :
raise StandardError('Simulation not loaded')
# take only gas particles
charm.createGroup_Family('mark', group, 'gas')
# get min temp, get max density
minTemp = charm.getAttributeRangeGroup('mark', 'gas', 'temperature')[0]
maxRho = charm.getAttributeRangeGroup('mark', 'gas', 'density')[1]
# reduce members according to criteria
charm.createGroup_AttributeRange('mark', 'mark', 'temperature', minTemp, maxTemp)
charm.createGroup_AttributeRange('mark', 'mark', 'density', minRho, maxRho)
def getMeanMetals(group , family='bar'):
if ((group in charm.getGroups())==False):
print "Group does not exist, please try again."
return
metalStar = [(0,0,0)]
metalGas = [(0,0,0)]
numStar = charm.getNumParticles(group, 'star')
numGas = charm.getNumParticles(group, 'gas')
if (numStar !=0) & (family=='bar' or family=='star'):
charm.createGroup_Family('groupMetStar',group, 'star')
metalStar = charm.reduceParticle('groupMetStar',massMetal,reduceMassMetal,None)
if (numGas !=0) & (family=='bar' or family=='gas'):
charm.createGroup_Family('groupMetGas',group , 'gas')
metalGas = charm.reduceParticle('groupMetGas' ,massMetal,reduceMassMetal,None)
if (numGas==0) & (numStar==0):
return 0
metals = (metalStar[0][1] + metalGas[0][1])/(metalStar[0][2]+metalGas[0][2])
return metals
def metalProfile(group, nbins=20, center="pot", family="bar"):
if (group in charm.getGroups()) == False:
print "Group does not exist, please try again."
return
if (family in ["star", "bar", "gas"]) == False:
print 'Invalid family. Need "bar","gas", or "star"'
return
center = findcenter.findCenter(group2=group, method=center)
radialStep = getgroupradius.getGroupRadius(group, center) / nbins
metalRad = [0] * (nbins)
metalProf = [0] * (nbins)
numStar = charm.getNumParticles(group, "star")
numGas = charm.getNumParticles(group, "gas")
if (numGas == 0) & (numStar == 0):
return metalProf
if (numStar != 0) & (family == "star"):
charm.createGroup_Family("groupMetStar", group, "star")
metalStar = charm.reduceParticle("groupMetStar", massMetal, reduceMassMetal, (radialStep, center))
for i in range(len(metalStar)):
metalProf[metalStar[i][0]] = metalStar[i][1] / metalStar[i][2]
if (numGas != 0) & (family == "gas"):
charm.createGroup_Family("groupMetGas", group, "gas")
metalGas = charm.reduceParticle("groupMetGas", massMetal, reduceMassMetal, (radialStep, center))
for i in range(len(metalGas)):
metalProf[metalGas[i][0]] = metalGas[i][1] / metalGas[i][2]
if family == "bar":
charm.createGroup_Family("groupMetGas", group, "gas")
charm.createGroup_Family("groupMetStar", group, "star")
metalProfGas = [[0, 0]] * nbins
metalProfStar = [[0, 0]] * nbins
metalGas = charm.reduceParticle("groupMetGas", massMetal, reduceMassMetal, (radialStep, center))
for i in range(len(metalGas)):
metalProfGas[metalGas[i][0]][0] = metalGas[i][1]
metalProfGas[metalGas[i][0]][1] = metalGas[i][2]
metalStar = charm.reduceParticle("groupMetStar", massMetal, reduceMassMetal, (radialStep, center))
for i in range(len(metalStar)):
metalProfStar[metalStar[i][0]][0] = metalStar[i][1]
metalProfStar[metalStar[i][0]][1] = metalStar[i][2]
for i in range(len(metalProf)):
metalTot = metalProfStar[i][0] + metalProfGas[i][0]
massTot = metalProfStar[i][1] + metalProfGas[i][1]
if massTot != 0:
metalProf[i] = metalTot / massTot
for i in range(nbins):
metalRad[i] = (i + 0.5) * radialStep
return (metalRad, metalProf)
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 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 boxstat(group, family='all') :
"""Print statistics for a group as in the tipsy boxstat command
Arguments are group and family
Return physical parameters of particles:
number, mass, center of box, size of box, center of mass,
center of mass's velocity, angular momentum vector.
Format output to say if gas, dark, star, baryon, or all.
Check error cases: Bad input, Not a proper data type, Box not loaded."""
import charm
# check if simulation loaded
if charm.getGroups() == None :
raise StandardError('Simulation not loaded')
# There is a potential issue with the capitalization of "all" being mixed
# in different implementations. Take either.
if family == 'All':
family = 'all'
if group == 'all':
group = 'All'
# Prepare values based on selected family
if family == 'all':
nPartGas = charm.getNumParticles(group, 'gas')
nPartDark = charm.getNumParticles(group, 'dark')
nPartStar = charm.getNumParticles(group, 'star')
mass = charm.getAttributeSum(group, 'gas', 'mass')
mass += charm.getAttributeSum(group, 'dark', 'mass')
mass += charm.getAttributeSum(group, 'star', 'mass')
bBox = list(charm.getAttributeRangeGroup(group, 'gas', 'position'))
bBoxTmp = charm.getAttributeRangeGroup(group, 'dark', 'position')
bBox[0] = map(lambda x, y : min(x,y), bBox[0], bBoxTmp[0])
bBox[1] = map(lambda x, y : max(x,y), bBox[1], bBoxTmp[1])
bBoxTmp = charm.getAttributeRangeGroup(group, 'star', 'position')
bBox[0] = map(lambda x, y : min(x,y), bBox[0], bBoxTmp[0])
bBox[1] = map(lambda x, y : max(x,y), bBox[1], bBoxTmp[1])
groupfamname = group
elif family == 'baryon':
nPartGas = charm.getNumParticles(group, 'gas')
nPartStar = charm.getNumParticles(group, 'star')
mass = charm.getAttributeSum(group, 'gas', 'mass')
mass += charm.getAttributeSum(group, 'star', 'mass')
bBox = list(charm.getAttributeRangeGroup(group, 'gas', 'position'))
bBoxTmp = charm.getAttributeRangeGroup(group, 'star', 'position')
bBox[0] = map(lambda x, y : min(x,y), bBox[0], bBoxTmp[0])
bBox[1] = map(lambda x, y : max(x,y), bBox[1], bBoxTmp[1])
groupfamname = group
else :
nPart = charm.getNumParticles(group, family)
mass = charm.getAttributeSum(group, family, 'mass')
bBox = charm.getAttributeRangeGroup(group, family, 'position')
groupfamname = group + 'FAM' + family
charm.createGroup_Family(groupfamname, group, family)
# Derive box properties
size = map(lambda min, max : max - min, bBox[0], bBox[1])
center = map(lambda min, max : 0.5*(max + min), bBox[1], bBox[0])
mmoment = charm.reduceParticle(groupfamname, centmassmap, centmassreduce, None)
cm = [mmoment[0][1]/mass, mmoment[0][2]/mass, mmoment[0][3]/mass]
vmoment = charm.reduceParticle(groupfamname, centmassVelmap, centmassreduce, None)
vcm = [vmoment[0][1]/mass, vmoment[0][2]/mass, vmoment[0][3]/mass]
angmom1 = charm.reduceParticle(groupfamname, angmomMap, centmassreduce, None)
# Apply parallel axis theorem and make specific
angmom = [0,0,0]
angmom[0] = (angmom1[0][1] - mass*(cm[1]*vcm[2] - cm[2]*vcm[1]))/mass
angmom[1] = (angmom1[0][2] - mass*(cm[2]*vcm[0] - cm[0]*vcm[2]))/mass
angmom[2] = (angmom1[0][3] - mass*(cm[0]*vcm[1] - cm[1]*vcm[0]))/mass
# Write output header according to type of particles
if family == 'all' :
print 'number of dark, gas and star particles =', nPartDark, nPartGas, nPartStar
elif family == 'baryon' :
print 'number of baryon particles =', (nPartGas + nPartStar)
else:
print 'number of', family, 'particles =', nPart
# Write physical parameters
print 'mass =', mass
print 'center coordinates =', center
print 'size =', size
print 'center of mass coordinates =', cm
print 'center of mass velocity =', vcm
print 'angular momentum vector =', angmom
def writeGroupAscii(group='All', filename='groupAscii.dat'):
"""Writes out a tipsy-ascii file for the group (filename='groupAscii.dat')."""
numStars = charm.getNumParticles(group,'star')
numGas = charm.getNumParticles(group,'gas')
numDark = charm.getNumParticles(group,'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
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
def profile(group='All', center='pot', family='all', projection='sph', bin_type='log', nbins=30, filename='profile.DAT', min_radius=0., fit_radius=0.) :
"""Perform the Tipsy profile() function.
profile is a command that produces a file of name, file-
name, that contains various physical profiles as a func-
tion of radius for particles of type particle in group.
The center of the radial distribution is taken to be the
center of mass of the particles of the type particle in
group center. If the string "pot" is given instead of
a group name for the argument center, the particle in
group with the lowest potential energy is used as the
center of the radial bins.
The projection argument refers to the shape of the bins
and the bin_type argument refers to how the particles are
binned, either linearly or log in radius. There are nbins
bins distributed equally in either radius or log radius
between min_radius and the size of group.
The output file has the following columns: radius, number
in bin, density, cumulative mass (M(<r)), circular veloc-
ity (sqrt(M(<r)/r)), radial velocity, radial velocity dis-
persion, tangential velocity, tangential velocity disper-
sion, specific angular momentum (j),j_theta, j_phi. The
j_theta and j_phi angles specify the direction of the spe-
cific angular momentum vector (in degrees). If family is
is either gas, baryon, or all, four additional columns
containing the mean mass weighted gas density, mass weigh-
ted gas temperature, mass weighted gas pressure, and mass
weighted gas entropy are added. If particle is either
star, baryon, or all an additional column containing the
stellar luminosity in the Johnson V band is added. This
is calculated using the ages of the star particles
as in Katz (Ap.J. 391: 502, 1992).
Note: some rarer configuration options are not implemented
e.g. non-uniform UV for star luminosity calculation."""
try:
import charm
# check initialization state of meanmwt attribute
if family in ['all', 'gas', 'baryon'] and not 'meanmwt' in charm.getAttributes('gas') :
print 'Attribute meanmwt not initialized. Initializing...'
import load_meanmwt
load_meanmwt.do_meanmwt()
print '\n'
# these should be moved to tipsyf
# fn to take the dot product of two vectors in R3
def dotprod(a, b) :
return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]
# fn to take the cross product of two vectors in R3
def crossprod(a, b) :
return [a[1]*b[2] - a[2]*b[1], a[2]*b[0] - a[0]*b[2], a[0]*b[1] - a[1]*b[0]]
# fn to multiply a vector v by a scalar c
def scalevec(c, v) :
return [c * v[0], c * v[1], c * v[2]]
# fn to add two vectors
def addvec(a, b) :
return [a[0] + b[0], a[1] + b[1], a[2] + b[2]]
# fn to subtract vector b from vector a
def subvec(a, b) :
return [a[0] - b[0], a[1] - b[1], a[2] - b[2]]
# fn to find the length of a vector
def vlength(a) :
import math
return math.sqrt(pow(a[0], 2) + pow(a[1], 2) + pow(a[2], 2))
# fn to combine two vectors, weighting by their corresponding mass scalars
def weightvecs(m1, x1, m2, x2) :
return [(x1[0]*m1 + x2[0]*m2)/(m1+m2), (x1[1]*m1 + x2[1]*m2)/(m1+m2), (x1[2]*m1 + x2[2]*m2)/(m1+m2)]
# scrub input
# check if simulation loaded, store group list
groups = charm.getGroups()
if groups == None :
raise StandardError('Simulation not loaded')
# case is inconsistent between groups and families, work for either
if group == 'all' :
group = 'All'
if family == 'All' :
family = 'all'
# deal with group or center group does not exist
if group not in groups :
raise StandardError('Group does not exist!')
if (center not in groups) and (center != 'pot') :
raise StandardError('Center group does not exist!')
# set up families iterator and throw family related exceptions
families = charm.getFamilies()
if families == None :
raise StandardError('Simulation loaded but no families present.')
isbaryon = 0
if family == 'baryon' :
isbaryon = 1
if 'dark' in families:
families.remove('dark')
if len(families) == 0 :
raise StandardError('No baryon particles present in simulation.')
if (family != 'all') and (family != 'baryon') :
if family not in families :
raise StandardError('Family not present in simulation.')
else :
families = [family]
if len(families) == 0 :
raise StandardError('List of families to process has zero length.')
# create groups containing one family each, store names in famgroups list
famgroups = []
for each in families :
famgroup = group + 'FAM' + each
charm.createGroup_Family(famgroup, group, each)
if charm.getNumParticles(famgroup, each) != 0 :
famgroups += [famgroup]
if len(famgroups) == 0 :
raise StandardError('No particles in group of selected type.')
# validate other inputs
if bin_type == 'linear' :
bin_type = 'lin'
elif bin_type == 'logarithmic' :
bin_type = 'log'
elif bin_type not in ['lin', 'log'] :
raise StandardError('Value of bin_type must be lin or log.')
if (int(nbins) != nbins) or (nbins < 1) :
raise StandardError('Value of nbins must be a positive integer.')
if not min_radius >= 0 :
raise StandardError('Value of min_radius cannot be negative.')
if min_radius == 0 and bin_type == 'log' :
min_radius = config.LOG_MIN
print 'Parameter min_radius set to ' + str(min_radius) + ' to accomodate logarithmic binning.'
if not fit_radius >= 0 :
raise StandardError('Value of fit_radius cannot be negative.')
# begin calculating parameters
# find center point
if center == 'pot' :
center = charm.findAttributeMin(group, 'potential')
else:
center = charm.getCenterOfMass(center)
# get center_vel and center_angular_mom
# families must be parsed individually then combined
vmdata = charm.reduceParticle(famgroups[0], vmmap, vmreduce, None)
if vmdata == None :
raise StandardError('MapReduce returned NoneType object.')
center_vel = vmdata[0][2]
center_angular_mom = vmdata[0][3]
# if there are additional families, parse each then combine results weighting by mass
if len(famgroups) > 1 :
old_mass = vmdata[0][1]
for i in range(len(famgroups)-1) :
vmdata = charm.reduceParticle(famgroups[i+1], vmmap, vmreduce, None)
new_mass = vmdata[0][1]
center_vel = weightvecs(old_mass, center_vel, new_mass, vmdata[0][2])
center_angular_mom = weightvecs(old_mass, center_angular_mom, new_mass, vmdata[0][3])
old_mass += new_mass
# for an elliptical projection, use Katz to get shape & then find vel, mom
# when restoring this, find out what happened to center_ell?
if projection == 'ell' :
if fit_radius == 0. :
print 'fit_radius = 0 in an elliptical projection.\nusing all particles in batch to find shape of ellipses.'
ell_matrix = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]]
center_ell = [0., 0., 0.]
ba = ca = phi = theta = psi = 0.
center = list(center)
shape_data = elliptical.find_shape(famgroups, center, fit_radius, ell_matrix, center_ell)
center = tuple(center)
if type(shape_data) == type(None) :
print 'find_shape() did not succeed'
return
# raise StandardError('Problem in elliptical.find_shape(): no fit found.')
else :
ba, ca, phi, theta, psi = shape_data
print 'b/a = %g, c/a = %g' % (ba, ca)
center = [0.]*config.MAXDIM
center_vel = [0.]*config.MAXDIM
center_angular_mom = [0.]*config.MAXDIM
vel_data = elliptical.find_vel(famgroups,center,center_vel,center_angular_mom, ell_matrix, center_ell, ba, ca, fit_radius)
else :
ba, ca, phi, theta, psi, center_ell, ell_matrix = (0., 0., 0., 0., 0., [0.]*config.MAXDIM, [[0.]*config.MAXDIM]*config.MAXDIM)
# find max_radius
# maxradmap iterates over all particles and compares each radius to the previous max found
p_param = (center)
max_radius = 0.
if family == 'all' :
max_radius = charm.reduceParticle(group, maxradmap, maxradreduce, p_param)[0][1]
else :
for i in range(len(famgroups)) :
fam_radius = charm.reduceParticle(famgroups[i], maxradmap, maxradreduce, p_param)[0][1]
max_radius = max(max_radius, fam_radius)
# TIPSY uses an approximation for max_radius which can't be adequately emulated here.
# for the run99 data file, the value of max_radius is 8.18829; set it manually.
# max_radius = 8.18829
# determine bin_size
# if min_radius > 0, then bin 0 should have the specified radius.
# other than this exception, all bins have constant size in either lin or log space as specified
if min_radius > max_radius and nbins > 1 :
raise StandardException('Value for min_radius encompasses all particles; cannot bin data.')
# min_radius > 0 case creates a scenario where nbins = 1 would create a /0 error, must handle here.
if nbins == 1 :
bin_size = max_radius
# bin_type and min_radius are superfluous to nbins = 1 case
bin_type = 'lin'
min_radius = 0.
# find size in lin space
elif bin_type == 'lin' :
if min_radius > 0. :
bin_size = (max_radius - min_radius) / float(nbins - 1)
else :
bin_size = (max_radius - min_radius) / float(nbins)
# find size in log space
else :
min_radius = math.log10(min_radius)
bin_size = (math.log10(max_radius) - min_radius) / float(nbins - 1)
# calculate bin boundary radii
bounds = [0.] * (nbins + 1)
# the first boundary radius is affected by min_radius, handle
if bin_type == 'lin' and min_radius == 0.:
bounds[1] = bin_size
else :
bounds[1] = min_radius
# each following bound should be bound[previous] + bin_size
for i in range(2, nbins + 1) :
bounds[i] = bounds[i - 1] + bin_size
# if logarithmic binning, convert values into linear space
if bin_type == 'log' :
for i in range(1, nbins + 1) :
bounds[i] = pow(10., bounds[i])
starlf = star_lum.star_lum()
sim_time = charm.getTime()
# do calculations which must see individual particles.
# the set of attributes on a particle varies by family, so each family must be processed seperately
params = [None, isbaryon, bounds, projection, nbins, bin_type, bin_size, min_radius, max_radius, center, center_vel, ell_matrix, center_ell, ba, ca, config.msolunit, config.gasconst, sim_time, config.time_unit, starlf.age, starlf.lum, starlf.lumv_fit, starlf.vv_dat, starlf.vv_fit, starlf.bv_dat, starlf.bv_fit, center_angular_mom]
fam_data = [None] * len(famgroups)
for i in range(len(famgroups)) :
params[0] = families[i]
fam_data[i] = charm.reduceParticle(famgroups[i], basemap, basereduce, tuple(params))
# shows per-family result of MapReduce, sometimes useful for debugging
# if debug_flag == 1 :
# print '\nThe current family is: ' + families[i]
# for line in fam_data[i] :
# print line
if len(fam_data) < 1 or fam_data == None :
raise StandardException('MapReduce for fam_data has length zero or is NoneType.')
# sum results into one list.
# Note that if a bin has no particles, it will be missing from the reduce result. data[] should have no missing rows.
# values are: bin, number, mass, vel_radial, vel_radial_sigma, vel_tang_sigma, angular_mom[x,y,z], lum, density, temp, pressure, entropy, gas_mass
data = [None] * nbins
for i in range(nbins) :
data[i] = [i, 0, 0., 0., 0., 0., [0., 0., 0.], 0., 0., 0., 0., 0., 0.]
for fam in fam_data :
for row in fam :
bin = row[0]
# merge fields 0 thru 5
for i in range(1, 6) :
data[bin][i] += row[i]
# merge field 6 (angular momentum vector)
for i in range(3) :
data[bin][6][i] += row[6][i]
# merge fields 7 thru 12
for i in range(7, 13) :
data[bin][i] += row[i]
if not len(data) == nbins :
raise StandardError('nbins != length of result after basemap')
# calculate remaining "base" values that did not need to be handled in the map
mass_r = 0.
for i in range(nbins) :
# get max radius, min radius, and mean radius
r_max = bounds[i + 1]
r_min = bounds[i]
r_mean = (r_max + r_min) / 2.
# number of particles in bin
number = data[i][1]
# if the bin is empty then some calculations e.g. 1/mass will explode; catch these.
if number != 0 :
# find volume by projection
pi = 3.141592653589793
if projection == 'ell' :
volume = 4. * ba * ca / 3. * pi * (pow((r_max),3) - pow((r_min),3))
elif projection == 'cyl' :
volume = pi * (pow((r_max),2) - pow((r_min),2))
else :
volume = (4. / 3.) * pi * (pow(r_max,3) - pow(r_min,3))
# unpack values. deal with non-sum calculations, largely n / mass
mass = data[i][2]
mass_r += mass
vel_radial = data[i][3] / mass
vel_radial_sigma = data[i][4] / mass
if vel_radial_sigma > vel_radial**2 :
vel_radial_sigma = math.sqrt(vel_radial_sigma - vel_radial**2)
else :
vel_radial_sigma = 0.
vel_tang_sigma = data[i][5] / mass
ang_mom = scalevec(1./mass, data[i][6])
ang = vlength(ang_mom)
if ang > 0.0 :
ang_theta = 180.0 * math.acos(ang_mom[2] / ang) / pi
else :
ang_theta = 0.0
ang_phi = 180.0 * math.atan2(ang_mom[1], ang_mom[0]) / pi
rho = mass / volume
vel_circ = ang / r_mean
c_vel = math.sqrt(mass_r / r_max)
if vel_tang_sigma > vel_circ**2 :
vel_tang_sigma = math.sqrt(vel_tang_sigma - vel_circ**2)
else :
vel_tang_sigma = 0.
# star stuff
lum_den = data[i][7] / volume
# gas stuff
if 'gas' in families and data[i][12] > 0 :
density = data[i][8] / data[i][12]
temp = data[i][9] / data[i][12]
pressure = data[i][10] / data[i][12]
entropy = data[i][11] / data[i][12]
else :
density = 0.
temp = 0.
pressure = 0.
entropy = -config.HUGE
data[i] = [r_max, number, rho, mass_r, c_vel, vel_radial, vel_radial_sigma, vel_circ, vel_tang_sigma, ang, ang_theta, ang_phi, density, temp, pressure, entropy, lum_den]
else :
c_vel = math.sqrt(mass_r / r_max)
data[i] = [r_max, 0, 0., mass_r, c_vel, 0., 0., 0., 0., 0., 0.,
0., 0., 0., 0., 0., 0.]
# build header row
# may need to update the exact text used for clarity or for consistency with TIPSY
headers = ('radius', 'number', 'rho', 'mass_r', 'c_vel', 'vel_radial', 'vel_radial_sigma', 'vel_circ', 'vel_tang_sigma', 'ang', 'ang_theta', 'ang_phi')
if family in ['gas', 'baryon', 'all'] :
headers += ('mmwg_density', 'mwg_temp', 'mwg_pres', 'mwg_entr')
if family in ['star', 'baryon', 'all'] :
headers += ('lum_V',)
# write output to file
f = open(filename, 'w')
# write headers according to families present
f.write('#')
for i in range(len(headers)) :
f.write(' ' + headers[i])
f.write('\n')
# write data according to families present
for i in range(nbins) :
f.write('%g %d %g %g %g %g %g %g %g %g %g %g' % tuple(data[i][0:12]))
if 'gas' in families :
f.write(' %g %g %g %g' % tuple(data[i][12:16]))
if 'star' in families :
f.write(' %g' % tuple(data[i][16:17]))
f.write('\n')
f.close()
# there is no current mechanism to delete groups.
# if one is added, delete temporary working groups here.
except :
print traceback.format_exc()
def do_meanmwt() :
if 'AllFAMgas' not in charm.getGroups() :
charm.createGroup_Family('AllFAMgas', 'All', 'gas')
if 'meanmwt' not in charm.getAttributes('gas') :
charm.createScalarAttribute('gas', 'meanmwt')
charm.runLocalParticleCodeGroup('AllFAMgas', setvals, None)
