inputfile = './galacticus_stages_19.hdf5'
h5file = tables.openFile(inputfile, "r")
timeTable = getData.getTimestepTable(h5file)
print timeTable
# In order to plot the physical values we need h
h = 0.72
# Boxsize in Mpc, for easy centering
boxSize = 32000 / 1000
# Calculate the center of mass coordinates
# Get dataset at z=0
nodeData = getData.getOutput(h5file, timeTable[len(timeTable) - 1, 0])
#print 'Check time at center of mass calculation: ', timeTable[len(timeTable)-1,1]
nHalos = len(nodeData.positionX)
comCoord = np.zeros(3)
for i in range(nHalos):
comCoord[0] += nodeData.positionX[i]
comCoord[1] += nodeData.positionY[i]
comCoord[2] += nodeData.positionZ[i]
comCoord = comCoord / nHalos / timeTable[len(timeTable) - 1, 2] * h
print 'Coordinates of the center of mass: ', comCoord[0], comCoord[
1], comCoord[2]
tStart = 0
tEnd = len(timeTable)
for i in range(tStart, tEnd):
#for i in range(tstep,tstep+1):
inputfile = 'inputtemp' h5file = tables.openFile(inputfile,"r") timeTable = getData.getTimestepTable(h5file) print timeTable # In order to plot the physical values we need h h = 0.73 # Boxsize in Mpc, for easy centering #boxSize = 32000/1000 # Calculate the center of mass coordinates # Get dataset at z=0 nodeData = getData.getOutput(h5file,timeTable[len(timeTable)-1,0]) #print 'Check time at center of mass calculation: ', timeTable[len(timeTable)-1,1] nHalos = len(nodeData.positionX) comCoord = np.zeros(3) for i in range(nHalos): comCoord[0] += nodeData.positionX[i] comCoord[1] += nodeData.positionY[i] comCoord[2] += nodeData.positionZ[i] comCoord = comCoord/nHalos/timeTable[len(timeTable)-1,2]*h maxCoord = np.zeros(3) print 'Coordinates of the center of mass: ', comCoord[0], comCoord[1], comCoord[2] maxCoord[0] = nodeData.positionX[0] maxCoord[1] = nodeData.positionY[0] maxCoord[2] = nodeData.positionZ[0]
if xlog == 'log':
ax.set_xscale('log')
ax.set_xlabel(xlabel)
ax.set_ylabel('#')
ax.set_title(title)
fig.text(0.82, 0.95, r'z = %.2f' % timeTable[tstep, 3])
title = (savepath + title + 'inputtemp' + ' ' + str(tstep).zfill(4) + '.' +
fileformat).replace(" ", "_")
plt.savefig(title, dpi=savedpi, format=fileformat)
# loop over timesteps
for i in range(tStart, tEnd):
tstep = i
nodeData = getData.getOutput(h5file, timeTable[tstep, 0])
makeHistogram('Histogram of Disk Gas Masses', nodeData.diskGasMass[:],
10**np.linspace(6, 15,
25), (0.8, 4000), 'log', 'log', r'M$_\odot$')
makeHistogram('Histogram of Disk Gas Metallicity',
nodeData.diskGasMetals[:] / nodeData.diskGasMass[:] / 0.02,
np.linspace(0, 20, 40), (0.8, 4000), 'nonlog', 'log',
r'solar abundances')
makeHistogram('Histogram of Outflowed Metals', nodeData.outflowedMetals[:],
10**np.linspace(0, 11,
40), (0.8, 4000), 'log', 'log', r'M$_\odot$')
makeHistogram('Histogram of Disk Stellar Mass',
nodeData.diskStellarMass[:], 10**np.linspace(6, 15, 20),
(0.8, 4000), 'log', 'log', r'M$_\odot$')
makeHistogram('Histogram of Disk Gas Fraction',
nodeData.diskGasMass[:] / nodeData.nodeMass[:],
ax.set_ylim(ylimits)
if xlog == 'log':
ax.set_xscale('log')
ax.set_xlabel(xlabel)
ax.set_ylabel('#')
ax.set_title(title)
fig.text(0.82,0.95,r'z = %.2f'%timeTable[tstep,3])
title = (savepath+title+'inputtemp'+' '+str(tstep).zfill(4)+'.'+fileformat).replace(" ","_")
plt.savefig(title,dpi=savedpi,format=fileformat)
# loop over timesteps
for i in range(tStart,tEnd):
tstep=i
nodeData = getData.getOutput(h5file,timeTable[tstep,0])
makeHistogram('Histogram of Disk Gas Masses',nodeData.diskGasMass[:],
10**np.linspace(6,15,25),(0.8,4000),'log','log',r'M$_\odot$')
makeHistogram('Histogram of Disk Gas Metallicity',nodeData.diskGasMetals[:]
/nodeData.diskGasMass[:]/0.02,np.linspace(0,20,40),(0.8,4000)
,'nonlog','log',r'solar abundances')
makeHistogram('Histogram of Outflowed Metals',nodeData.outflowedMetals[:],
10**np.linspace(0,11,40),(0.8,4000),'log','log',r'M$_\odot$')
makeHistogram('Histogram of Disk Stellar Mass' ,nodeData.diskStellarMass[:],
10**np.linspace(6,15,20),(0.8,4000),'log','log',r'M$_\odot$')
makeHistogram('Histogram of Disk Gas Fraction' ,nodeData.diskGasMass[:]/nodeData.nodeMass[:],
10**np.linspace(-8,1,20),(0.8,4000),'log','log',r'M$_\odot$')
makeHistogram('Histogram of SFR (combined)' ,nodeData.spheroidStarFormationRate[:]+nodeData.diskStarFormationRate[:],
10**np.linspace(-5,12,20),(0.8,4000),'log','log',r'M$_\odot$')
makeHistogram('Histogram of Virial Radii',nodeData.nodeVirialRadius[:],
np.linspace(0,2,40),(0.8,4000),'nonlog','log',r'Mpc')
if(timeTable[i,1] == nodeHistory[0].time): tIndexNodeDataStart = i #print 'First halo data at tIndex ', i break if tIndexNodeDataStart == len(timeTable)-1: print 'Attention, halo is only present at z=0?' sys.exit(1) if tIndexNodeDataStart > tIndexEnd: print 'Attention, no halo data in selected time range' # loop over the timesteps from tIndexStart to tIndexEnd for tIndex in range(tIndexStart,tIndexEnd+1): print 'tstep ', tIndex, 'time: ', timeTable[tIndex,1] # get the nodeData for tIndex nodeData = getData.getOutput(h5file,timeTable[tIndex,0]) nHalos = len(nodeData.positionX) # number of halos in that timestep # ATTENTION: Positions seem to be in Mpc/h # ATTENTION: Also check for the masses positionX = nodeData.positionX[0:nHalos]/timeTable[tIndex,2]*h positionY = nodeData.positionY[0:nHalos]/timeTable[tIndex,2]*h positionZ = nodeData.positionZ[0:nHalos]/timeTable[tIndex,2]*h # Put nodeHistory[tIndex] into plotData values for easier plotting if tIndex>=tIndexNodeDataStart: # put the data to be plotted into the plotData array # the data vector should have length of tIndex-tIndexStart+1 plotData1 = np.zeros(tIndex-tIndexNodeDataStart+1) plotData2 = np.zeros(tIndex-tIndexNodeDataStart+1) plotData3 = np.zeros(tIndex-tIndexNodeDataStart+1) plotData4 = np.zeros(tIndex-tIndexNodeDataStart+1)
# The time table starts at highest redshift # and goes to redshift = 0. Its length corresponds # to the number of timesteps in our galacticus file # Format: nodeDataIndex, time since big bang, scale factor, z # output the timeTable for debugging purposes print timeTable galacticusTimesteps = h5file.root.Outputs._v_nchildren # Make a list of nodes nodeHistory = [ NodeClass() ] # Index of z=0 in our timeTable (end of our simulation) tIndexEnd = len(timeTable)-1 # Get z=0 Output nodeData = getData.getOutput(h5file,timeTable[tIndexEnd,0]) # Select the node to trace (at z=0) # by giving the table index in the nodeData field (starting with 0) #aIndex = 150 nodeHistory[0].arrayIndex = aIndex # Get the properties for the selected node at z=0 nodeHistory[0].time = timeTable[tIndexEnd,1] # time in Gyr nodeHistory[0].nodeIndex = nodeData.nodeIndex[aIndex] # nodeIndex nodeHistory[0].diskStarFormationRate = nodeData.diskStarFormationRate[aIndex] nodeHistory[0].diskGasMass = nodeData.diskGasMass[aIndex] nodeHistory[0].positionX = nodeData.positionX[aIndex] nodeHistory[0].positionY = nodeData.positionY[aIndex] nodeHistory[0].positionZ = nodeData.positionZ[aIndex] nodeHistory[0].virialRadius = nodeData.nodeVirialRadius[aIndex] nodeHistory[0].diskScaleLength = nodeData.diskScaleLength[aIndex] nodeHistory[0].outflowedMass = nodeData.outflowedMass[aIndex]
tIndexNodeDataStart = i #print 'First halo data at tIndex ', i break #if tIndexNodeDataStart == len(timeTable)-1: #print 'Attention, halo is only present at z=0?' #sys.exit(1) #if tIndexNodeDataStart > tIndexEnd: #print 'Attention, no halo data in selected time range' # loop over the timesteps from tIndexStart to tIndexEnd for tIndex in range(tIndexStart,tIndexEnd+1): print 'indstart:', tIndexStart, 'tindexend:', tIndexEnd print 'tstep ', tIndex, 'time: ', timeTable[tIndex,1] # get the nodeData for tIndex nodeData = getData.getOutput(h5file,timeTable[tIndex,0]) nHalos = len(nodeData.positionX) # number of halos in that timestep # ATTENTION: Positions seem to be in Mpc/h # ATTENTION: Also check for the masses positionX = nodeData.positionX[0:nHalos]/timeTable[tIndex,2]*h positionY = nodeData.positionY[0:nHalos]/timeTable[tIndex,2]*h positionZ = nodeData.positionZ[0:nHalos]/timeTable[tIndex,2]*h # Put nodeHistory[tIndex] into plotData values for easier plotting if tIndex>=tIndexNodeDataStart: # put the data to be plotted into the plotData array # the data vector should have length of tIndex-tIndexStart+1 plotData1 = np.zeros(tIndex-tIndexNodeDataStart+1) plotData2 = np.zeros(tIndex-tIndexNodeDataStart+1) plotData3 = np.zeros(tIndex-tIndexNodeDataStart+1) plotData4 = np.zeros(tIndex-tIndexNodeDataStart+1)