[yt-users] halo finding on a volume subset

[Irina Dvorkin]

Hi Christine,

Here's what I did (probably not the smartest way, but I'm also a  
python beginner). I modified the file HaloFinding.py (in the older yt  
version). There, you have class HOPHaloFinder(GenericHaloFinder,  
HOPHaloList) and its function _init_ . There it reads the data source  
using the function partition_hierarchy_3d. I disabled that (of course  
a more elegant way exists) as following:

# Irina - trying to run HF on a subvolume
	if box is True:
		self.padding=0.0
		LE, RE = self.pf["DomainLeftEdge"].copy(), self.pf["DomainRightEdge"].copy()
		LEbox, REbox = self.pf["RefineRegionLeftEdge"].copy(),  
self.pf["RefineRegionRightEdge"].copy()
		self._data_source = self.hierarchy.region(self.center, LEbox, REbox)
		self.bounds = (LEbox, REbox)
	else:
         	self.padding = padding #* pf["unitary"] # This should be clevererer
         	padded, LE, RE, self._data_source =  
self._partition_hierarchy_3d(padding=self.padding)
         	self.bounds = (LE, RE)

-end-of-code-

box is just a flag I use, when box=True I run HOP on a subvolume, so  
the -else- part is what the code looked like originally. The subvolume  
itself is given by pf["RefineRegionLeftEdge"] and same for RightEdge,  
but that's good just for my application since I have these variables  
anyway, I suppose these can be given as a separate input.

I hope this helps,
Irina

Quoting "Christine Simpson" <csimpson at astro.columbia.edu>:

> Hi all,
>
> This is a follow up on this discussion from a month ago.  I want to do
> the same thing Irina wanted to do--run hop on a smaller region in my
> simulation box.  I read this discussion, but I'm a python neophyte and
> I'm not sure I follow what to do.  Could someone post an example script?
> I'd really appreciate it.
>
> Thanks
> Christine
>
> On Tue, 2010-09-21 at 14:57 +0200, Irina Dvorkin wrote:
>> Matt and Stephen,
>>
>> I followed Matt's idea and it worked great in my simple case.
>> Thanks a lot, it saves quite a lot of time!
>>
>> Irina
>>
>> Quoting "Matthew Turk" <matthewturk at gmail.com>:
>>
>> > Stephen,
>> >
>> > This *was* possible.  Until Irina emailed, I was under the impression
>> > it still was; I don't know why the functionality was removed.
>> >
>> > I believe that changing the data_source check and construction should
>> > make this possible, similarly to how the projection mechanism checks
>> > if a source has been provided.  The only variables that are required
>> > to be initialized in __init__ related to the data_source are padding
>> > and _data_source; if _data_source is supplied (i.e., add on
>> > data_source to the contructor) and "is not None" then it should simply
>> > set padding to 0.0 and set self._data_source equal to the supplied
>> > source.
>> >
>> > -Matt
>> >
>> > On Mon, Sep 20, 2010 at 8:40 AM, Stephen Skory
>> > <stephenskory at yahoo.com> wrote:
>> >> Irina,
>> >>
>> >>
>> >>
>> >>> Is there a way to run the halo finder on part of the  simulation volume?
>> >>> For example, I have a box 256 Mpc on a side but I only  want to  
>> find halos
>> >>> inside a smaller box, say 20 Mpc on a side.
>> >>
>> >>
>> >> Unfortunately, this is not currently possible in yt. However, it  
>> should be
>> >> possible if the right modifications are done. Something along these
>> >> lines is how
>> >> HOP/FOF are parallelized, so it should be translateable to your
>> >> problem. I am
>> >> not making promises that I will do this, but that it is  
>> possible. I'll think
>> >> about it.
>> >>
>> >> However, I wonder why you only want halos in a small region? Do  
>> you have a
>> >> nested simulation? Does it seem like the halo finding is taking too
>> >> long? Are
>> >> you looking for substructure? Depending on the answers to these
>> >> questions, the
>> >> modifications discussed above may not be required.
>> >>
>> >>  _______________________________________________________
>> >> sskory at physics.ucsd.edu o__ Stephen Skory
>> >> http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
>> >> ________________________________(_)_\(_)_______________
>> >>
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