Two helpful libraries are our modules and analysis tools.
git clone [email protected]:caterpillarproject/modules.git # Python 2.7+git clone [email protected]:caterpillarproject/analysis.git # Python 2.7+
Add these to your
PYTHONPATH environment variable, e.g. for
setenv PYTHONPATH /path/to/modules:$PYTHONPATHsetenv PYTHONPATH /path/to/analysis:$PYTHONPATH
Lastly you will need to install
Once you have the modules ready, uou can load a
ROCKSTAR catalogue for a given snapshot simply as:
rscat = htils.load_rscat(hpath,319,verbose=True) # snapshot = 319 (z = 0)
Once you do this however, you will have access to the following methods:
def __init__(self, dir, snap_num, version=2, sort_by='mvir', base='halos_', digits=2, AllParticles=False):def get_particles_from_halo(self, haloID):# @param haloID: id number of halo. Not its row position in matrix# @return: a list of particle IDs in the Halodef get_subhalos_from_halo(self,haloID):#Retrieve subhalos only one level deep.#Does not get sub-sub halos, etc.def get_subhalos_from_halos(self,haloIDs):#Returns an array of pandas data frames of subhalos. one data frame#for each host halo. returns only first level of subhalos.def get_subhalos_from_halos_flat(self,haloIDs):#Returns a flattened pandas data frame of all subhalos within#the hosts given by haloIDs. Returns only first level of subhalos.def get_hosts(self):# Get host halo frame onlydef get_subs(self):# Get subhalo frame onlydef get_all_subs_recurse(self,haloID):# Retrieve all subhalos: sub and sub-sub, etc.# just need mask of all subhalos, then return data frame subsetdef get_all_subhalos_from_halo(self,haloID):# Retrieve all subhalos: sub and sub-sub, etc.# return pandas data frame of subhalosdef get_all_sub_particles_from_halo(self,haloID):#returns int array of particle IDs belonging to all substructure#within host of haloIDdef get_all_particles_from_halo(self,haloID):#returns int array of all particles belonging to haloIDdef get_all_num_particles_from_halo(self,haloID):# Get the actual number of particles 'total_npart' from halo as opposed to 'npart'.# mainly for versions less than 7def get_block_from_halo(self, snapshot_dir, haloID, blockname, allparticles=True):# quick load a block (hdf5 block) of particles belong to halo.# e.g. you want particle positions for haloid = 10 (use blockname="pos")# this works fastest on snapshots ordered by id and requires import readsnapHDF5_gregdef H(self):#returns hubble parameter for rockstar rundef get_most_gravbound_particles_from_halo(self,snapshot_dir, haloID):# Gets most bound particles just based on potential energy for specific halo IDdef get_most_bound_particles_from_halo(self, snapshot_dir, haloID):# Gets most bound particles for halo based on pot. energy and kin. energy# if potential block does not exist, it is calculate assuming a spherical halodef getversion(self):# returns the version of rockstar the run was done within# this will include versions made by Alex Ji, Greg Dooley & Brendan Griffen
One workflow might look as follows:
import haloutils as htils# load the first 24 halos# (just change 14 to 11 for the lower resolution halos)hpaths = htils.get_paper_paths_lx(14)hpath = hpaths # select first Caterpillar halo# strip down the path to just the halo idparentid = htils.get_parent_hid(hpath)# get the central host id of the zoom-in halo# parentid is named from the parent simulation# the zooms have different idszoomid = htils.load_zoomid(hpath)# Return the pandas data frame with all the halos,# return mvir for examplelastsnap = htils.get_lastsnap(hpath)halos = htils.load_rscat(hpath,lastsnap,verbose=True)mvir_host = halos.ix[zoomid]['mvir'] # units of Msol/h# get one specific parameter of the host at# z = 0 (quick version of above)mvir_host = htils.get_quant_zoom(hpath,'mvir') # units of Msol/h# return all halo virial massesall_mvir = halos['mvir'] # units of Msol/h# get the merger tree of the host and all its subscat = htils.load_mtc(hpath,haloids=[zoomid])# read in every halo's merger treeall_trees = htils.load_mtc(hpath,indexbyrsid=True)tree = all_trees[zoomid]# if you feed more than one id to the above# it would be cat,cat etc.# you can now access the main branch > try tree. then tab complete to see other functionsmainbranch = tree.getMainBranch()# we also have a short hand version:# mainbranch = htils.get_mainbranch(hpath)# which is very fast and skips the reading of the entire progenitor tree if you don't need dit# see further down this page for more options# output the main branch virial massprint mainbranch['mvir']
Here is an example of some of these in action:
# load required modulesimport haloutils as htilsimport numpy as np# select Cat-1 halohpaths = htils.get_paper_paths_lx(14)# select the last snapshot (z = 0)snapshot = htils.get_lastsnap(hpath)# load rockstar id of the host halozoomid = htils.load_zoomid(hpath)#Load Halo Cataloguehalos = htils.load_rscat(hpath,snapshot)#Select host haloshosts = halos.get_hosts()#Select subhalossubs = halos.get_subs()# Get positions of subs and hostsprint hosts[['posX','posY','posZ']]print subs[['posX','posY','posZ']]#Get particle ids from halo of interest (here it is the host)print halos.get_particles_from_halo(zoomid)#Get virial radius of a specific halo id (in this case the host)print halos.ix[zoomid]['rvir'] # units of kpc/h
Similarly the merger tree catalogues (once loaded) have a number of its own functions.
def getMainBranch(self, row=0):"""@param row: row of the halo you want the main branch for. Defaults to row 0Uses getSubTree, then finds the smallest dfid that has no progenitors@return: all halos that are in the main branch of the halo specified by row (in a np structured array)"""def getMMP(self, row):"""@param row: row number (int) of halo considered@return: row number of the most massive parent, or None if no parent"""def getNonMMPprogenitors(self,row):"""return row index of all progenitors that are not the most massiveThese are all the subhalos that were destroyed in the interval"""
These can be used in the following example:
# load required modulesimport haloutils as htilsimport numpy as np# select the caterpillar halo of interest# based on halo id and resolution levelhid = 1387186lx = 14hpath = htils.hid_hpath_lx(hid,lx)# select the last snapshot (z = 0)snapshot = htils.get_lastsnap(hpath)# load rockstar id of the host halozoomid = htils.load_zoomid(hpath)# Load every tree (VERY slow)trees = htils.load_mtc(hpath)# Just look at the first tree# tree = cat# You can access all trees via: cat, cat etc.# If you want to load the tree for a particular ID from the rockstar cataloguetrees = htils.load_mtc(haloids=[zoomid]) # in this case the host (quite slow)tree = cat # tree will contain all progenitors, including subhalos# Just say you want to index the merger tree by the z = 0 root rockstar id# (i.e. the base of the tree). This is quite powerful because you might select# halos of interest in the rockstar catalogue then want to know, just for those# what their merger tree is (e.g. say you just want dwarf systems of a particular size)trees = htils.load_mtc(haloids=[zoomid],indexbyrsid=True)tree = trees[zoomid]# You can just loop through rockstar ids (if you gave it more than one id above)# and get out the accretion histories for a small sample of trees quite quickly# to get the main branchmain_branch = tree.getMainBranch()# print mass evolutionfor mass,scale in zip(main_branch['mvir'],main_branch['scale']):print "%3.2f: %3.2e" % (scale,mass)# output1.00: 2.86e+140.99: 2.89e+140.98: 2.90e+140.97: 2.90e+140.95: 2.88e+140.94: 2.86e+140.93: 2.83e+140.92: 2.80e+140.91: 2.76e+140.90: 2.73e+140.89: 2.64e+140.88: 2.47e+14 ...
A function to find the descendant branch of any halo in merger tree catalogue. You should use it as follows:
# get a tree of interestmtc = haloutils.load_zoom_mtc(hpath)host = mtc.Trees# make a dictionary that maps ids to rowsdesc_map = host.get_desc_map()# get the descendent branch.desc_branch = host.getDescBranch(row, desc_map)# similarly for main branches, you can use a dictionary that speeds up the# getMainBranch call substantially.mmp_map = host.get_mmp_map()main_branch = host.getMainBranch(row, mmp_map)# you can get the branches without making the map as below, but they will be much slower.# only faster if you use ~ < 10 calls to the function.desc_branch = host.getDescBranch(row)main_branch = host.getMainBranch(row)
If you want the Gadget header:
# get the first halo in the cataloguehpaths = htils.get_paper_paths_lx(14)# read its Gadget headerheader = htils.get_halo_header(hpath)# header contains the typical Gadget infoheader.boxsize header.massarr header.omegaLheader.cooling header.metals header.redshiftheader.double header.nall header.sfrheader.feedback header.nall_highword header.stellar_ageheader.filenum header.npart header.timeheader.hubble header.omega0
Be sure to divide the relevant quantities (pos, rvir etc.) by
header.hubble. See the Gadget section in the sidebar for more information on the header and block types available.
If you wanted to get the postions of all the particles for a specific halo (or any block).
pos = htils.load_partblock(hpath,zoomid,"POS ") # units Mpc/h# "VEL ", "ID ", "MASS" etc. also work (notice the space)# check readsnapshots/readsnapHDF5.py for the other block names# you can call in the caterpillar modulesprint pos*1000. # kpc/h# output[ 32085.45117188 57312.79296875 44314.35546875][ 27002.18554688 10062.73242188 9899.70019531][ 26711.08789062 9560.22460938 10165.18847656][ 49757.3515625 21470.00195312 6461.90917969]...
If you want to read in the entire block, use the following:
import haloutils as htilshid = 1387186lx = 14hpath = htils.hid_hpath_lx(hid,lx)pos = htils.load_partblock(hpath,319,"POS ")mass = htils.load_partblock(hpath,319,"MASS")
If you wanted just the ids for a selection of particle ids:
pos = htils.load_partblock(hpath,zoomid,"POS ",partids=[listofids]) # units Mpc/h