[Yt-dev] more non-unique particles in enzo and how to deal with them

[Eric Hallman]

Stephen,
   so is this fix (to enzo) only in WOC and not in the dev trunk?


On Dec 4, 2009, at 4:37 PM, Stephen Skory wrote:

> Britton,
>
>> Stephen's latest update of his new parallel hop to check for unique- 
>> ness of particle indices has shed light on another problem.  In a  
>> recent simulation run with the devel/trunk version of enzo, I have  
>> found the particle numbers are no longer unique when star particles  
>> are generated.  Originally, the star particle indices by adding to  
>> the number of dark matter particles, such that if you had N dm  
>> particles and M star particles, the dm particle indices when from 0  
>> to N-1 and the star particle indices went from N to N+M-1.
>
> Unfortunately, Ji-hoon Kim addressed this issue last month <http://hg.spacepope.org/week-of-code/rev/bc61ccd0f247 
> >, which you may not be aware of. Obviously it's too late for this  
> dataset!
>
>> However, now it seems that the star particles simply go from 0 to  
>> M.  Before I go any further, I will mention that the star particles  
>> can be differentiated from the dark matter particles by the  
>> particle_type data, so we're not totally screwed.  The point is  
>> that for the time being, hop no longer works.  The question is  
>> this: what is the best solution for dealing with this?  I am more  
>> than willing to write something to remap the particle indices, but  
>> that doesn't fix the underlying problem.  I have already done  
>> something similar to this for a different application, so I can do  
>> it quickly.  OR, something can be done to hop to read in particle  
>> type.  Clearly, this question is mainly for Stephen, but anyone  
>> should feel free to weigh in.  What is the best solution?
>
> I see several options. You could filter out all the stars like this:
>
> notstars = (self._data_source["particle_type"] != star)
>
> and then in HaloFinding.py add a '[notstars]' to all the arrays  
> where the particle data is handled and handed off to Parallel HOP.  
> If you have 'creation_time' you could just try setting  
> 'dm_only=True' in the HaloFinder call.
>
> I think you could easily write a script to fix the dataset itself  
> (on a copy, not the original, of course). Use h5py to open the  
> files, and read in the particle_index and particle_type fields. SO  
> something like this:
>
> pi = file["Grid00000234"]["particle_index"]
> ct = file["Grid00000234"]["particle_type"]
> tochange = (ct == star)
> tochange *= (number of dark matter particles)
> pi += tochange
>
> and then delete the old particle_index field from the file, and  
> replace it with this new pi array.
>
> I'll let you know what else I come up with.
>
> Good luck!
>
> _______________________________________________________
> sskory at physics.ucsd.edu           o__  Stephen Skory
> http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
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Eric Hallman
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