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 catbox(group1, group2, group3) :
"""Concatenate two groups to make a third group. Side effect:
creates a new attribute to define the third group."""
import charm
tmpAttr = 'cat_'+group1+group2;
for fam in ['gas', 'dark', 'star'] :
charm.createScalarAttribute(fam, tmpAttr)
charm.runLocalParticleCodeGroup('All', zeroTmp, tmpAttr)
charm.runLocalParticleCodeGroup(group1, assignTmp, tmpAttr)
charm.runLocalParticleCodeGroup(group2, assignTmp, tmpAttr)
charm.createGroup_AttributeRange(group3, 'All', tmpAttr, 0.5, 2.0)
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 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 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 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
