[yt-users] Halo finder changes

Matthew Turk matthewturk at gmail.com
Thu Apr 23 10:21:00 PDT 2009


Hi everyone,

Stephen Skory has added the Friends-of-friends halo finder to the yt
trunk (not yt-1.0) and we've now enabled it as a possibility for
finding halos in a simulation.  Because there are now two mechanisms
for finding halos, we've also changed the API a little bit and made
the halo finders available through yt.mods.  So to run the HOP halo
finder you would do the following:

from yt.mods import *
pf = load("data0001")
halo_list = HaloFinder(pf)

and to run FOF you have to call it slightly differently:

from yt.mods import *
pf = load("data0001")
halo_list = FOFHaloFinder(pf)

To get FOF to compile, you'll have to rerun "python setup.py develop"
or "python setup.py install" depending on how yt was installed
initially.  (The install_script does the former, but most
hand-installs do the latter.)  With this new API, both halo finders
run in parallel.  I'll save any discussion of that for Stephen,
however, as there are some caveats to running HOP in parallel.
Additionally, as of right now they dont scale as well as we'd like --
but we're working on it.

Additionally, as a result of this change we have intentionally broken
compatibility by removing the import of the 'hop' module in
yt/mods.py.  Hopefully this has not caused too many problems; all of
the old, largely duplicated-in-multiple-places classes and interfaces
have now been consolidated and placed in yt/lagos/HaloFinding.py.

Thanks to Stephen for his hard work adding in FOF and working with the
parallel interface!

Best wishes, and let us know if there are any problems,

Matt



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