[yt-users] Clump tracking!

[Eve Lee]

Hi Patrick,

I did something very similar when I tried to track clumps (molecular 
clump in star formation simulation in my case) using the centre of mass 
of the clump (we ended up using the position of the densest pixel 
instead of the centre of mass since CoM tracking gave a huge fluctuation 
in mass) and using the velocity vector of that centre to infer the 
direction of the progenitor of that clump.

What I noticed was that the mass is still quite unstable due to the 
intrinsic definition of the clump. I found that starting lv 3, the mass 
fluctuation is so great I couldn't trust my tracking any more. I'm not 
sure if you'll encounter the same problem.

David Collins has been working on this extensively using tracer 
particles so he should be able to help you more.

Best Regards,

Eve

On 10/5/2012 4:15 PM, Patrick Rieser wrote:
> As I am running a little bit out of time to finish this, I thought 
> about doint this the simple and "brute force" way.
> So this is the current plan: I am going to iterate through all 
> snapshots we have, and write out all clump objects with pickle. 
> Starting at snapshot 0 i am going to estimate the position of the 
> center of mass of the clump in the new snapshot using it's bulk 
> velocity and see if I can find the clump in the surrounding area 
> (looping through all clumps in the following snapshot). If I find one 
> or more, I will compare the mass and identify it as the same or not 
> (if the mass doesn't match maybe i check if a second one vanished). 
> This might not be a very elegant way, but I hope it works for our 
> system (galaxy cluster). I am quite new to this stuff, so if I got any 
> horrible mistakes here, please correct me.
>
>> For instance, we include a Cython
>> kD-tree that we use to provide a nearest-neighbor search when doing
>> merger trees.
>
> Thanks, I will take a look into that!
>
>
>> and you didn't
>> want to go full-on "lagrangian coherent structures"
>
> I took a look at it and it seems really interesting. It's really a 
> pity I don't have enough time at the moment.
>
> best wishes,
> Patrick
>
>
>
> On 2012-10-05 18:07, Matthew Turk wrote:
>> Hi Patrick,
>>
>> Thanks for writing, and welcome to yt-users.  :)
>>
>> On Thu, Oct 4, 2012 at 9:42 AM, Patrick Rieser
>> <patrick.rieser at uibk.ac.at> wrote:
>>> Heya everyone!
>>>
>>> I am trying to track clumps across multiple snapshots (from flash). 
>>> Now my
>>> questions is, has anybody done something like this and would be 
>>> willing to
>>> share his/her code?
>> David Collins wrote some code that did this, a couple years ago.  I
>> don't know the current status.
>>
>> If you wanted to write a new set of code to do this (and you didn't
>> want to go full-on "lagrangian coherent structures") there are some
>> things in yt that could help out.  For instance, we include a Cython
>> kD-tree that we use to provide a nearest-neighbor search when doing
>> merger trees.  This is used in a very simple way in the code in
>> yt/analysis_modules/halo_merger_tree/enzofof_merger_tree.py , where
>> halos are loaded into a variable called halo_kdtree.  This then gets
>> searched with a ball query.  You could in principle load the clumps
>> into the same kdtree structure, perform the search, and then apply
>> selection criteria for clump tracking based on that.  (Of course this
>> is just the first step in identifying clump motion -- but it would be
>> a way to reduce from N^2 searching.)
>>
>> Let us know if you run into any tricks or have any successes -- this
>> is a pretty cool idea, and I'd love to see where it leads you!
>>
>> -Matt
>>
>>> Best Wishes,
>>> Patrick
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