[Yt-dev] Forked depo

Matthew Turk matthewturk at gmail.com
Tue May 10 18:53:45 PDT 2011


Dear Geoffrey,

On Tue, May 10, 2011 at 6:16 PM,  <gso at physics.ucsd.edu> wrote:
> Thanks for the suggestions Stephen and Matt,
>
> Stephen,
> * I fixed up the dim so that it now take into account the possibility of
> different root grid tile dimensions, in cases when it is not a cube.
> * Edited/added more comments.
> * I tried my scatter3D.py and it works on my laptop with python 2.7, has
> anyone else tried?
>
> Matt,
> 1) I just put the calculation in the subsection of AMREllipsoidBase and
> deleted the _InEllipsoid derived field.

Cool!

> 2)
> * I think I would leave it as the e1,2,3 basis vectors for now, because
> the way I am doing the Ellipsoid profiling from the Halo profiles, I don't
> use rotations of any kind, so everything is done vector wise, and the
> results from that will be fed into the ellipsoid object, so at least it
> would be easier for me to use e1,2,3.

Okay.  Let's keep an eye on this and see if we can, in the future,
reduce the over-determination of the object.

> * For an arbitrarily aligned orthogonal basis vector set, I think you'll
> need 3 rotations to align it to another generic orthogonal basis vector
> set, so only Phi and Theta would be insufficient.
> * However, I would only need to record e1, and e2, and just calculate e3
> (e1 cross e2) on the fly at the start of the calculation.  Should I just
> record e1 and e2 or leave it in the file, saves some space...?

Leave it for now, but again, let's revisit this in a little while.  My
feeling is that likely the generation of ellipsoids from halo objects
will be the primary entry point for the foreseeable future.

>
>
> A few questions:
>
> after defining the ellipsoid "ell"
> ell.quantities["TotalQuantity"]("CellMassMsun")
> works fine, but when I change CellMassMsun to ParticleMassMsun, I get the
> following errors, Traceback pasted to
> http://paste.enzotools.org/show/iZ1Ww36ZLFob49xWBfU1
> Is that a bug in my code?  I am not quite sure how to fix it.

I'll fix this after we merge the code.

>
> Ultimately I'd want to analyze the DM and star particles in the ellipsoid
> separately, do I just use the derived field and particle ages to do that
> once the previous problem is solved?

I'll defer to someone else on this.  The way stars are differentiated
in Enzo -- although other codes seem to have gotten this right -- bugs
me in its inconsistencies.  (i.e., ages versus ParticleType.  Not a
fault of enzo, really, just inconsistent conventions for running
simulations.  :)

Nice work, Geoffrey.  Stephen, once you and Geoffrey have adapted the
changes above, I am +1 on merging, so feel free to do so unless
someone else here objects.

-Matt

>
> From
> G.S.
>
>
>
>
>> Hi Geoffrey,
>>
>> Other than Stephen's issue, I have two suggestions then I am +1 for
>> merging.
>>
>> 1) Remove the InEllipsoid field and put that code directly into the
>> masking routine.
>> 2) Minimally define the Ellipse -- right now it's a bit over-defined,
>> in that you have all three unit vectors and all three axis lengths.
>> Maybe A,B,C,theta,phi?
>>
>> This will be a great addition.  And, I don't think I've said this yet,
>> but congrats on your first commit to yt!  Thanks very much.
>>
>> -Matt
>>
>> On Tue, May 10, 2011 at 2:54 PM, Stephen Skory <s at skory.us> wrote:
>>> Geoffrey,
>>>
>>>> To get the ellipsoid changeset you can visit:
>>>> https://bitbucket.org/gsiisg/yt/compare/default..yt_analysis/yt
>>>
>>> I scanned this and I didn't see anything glaringly wrong. You might
>>> want to change the comment block below class
>>> AMREllipsoidBase(AMR3DData) to match an ellipsoid ;). Anyway, very
>>> good work!
>>>
>>> I did run your scripts, and I ran into a couple issues. First, in
>>> _InEllipsoid, I had to make this change to avoid a crash:
>>>
>>> diff -r 676c7f17fb97 yt/data_objects/universal_fields.py
>>> --- a/yt/data_objects/universal_fields.py       Mon May 09 20:46:16 2011
>>> -0700
>>> +++ b/yt/data_objects/universal_fields.py       Tue May 10 15:52:39 2011
>>> -0600
>>> @@ -944,7 +944,7 @@
>>>         # allocate array to be filled with results from eqn of ellipsoid
>>>         Inside = na.zeros(data["x"].shape, dtype='float64')
>>>         # find the dimension length of the grid
>>> -        dim = shape(data["x"])
>>> +        dim = data["x"].shape
>>>         # allocate array for the dot product with the 3 e_vectors
>>>         # need to take into account different grid side sizes
>>>         dot_evec = na.zeros([3,dim[0],dim[1],dim[2]])
>>>
>>> Second, I didn't see anything in the test3D.png image... I haven't
>>> looked into why, but the 2D image looked encouraging!
>>>
>>> Again, good work!
>>>
>>>
>>> --
>>> Stephen Skory
>>> s at skory.us
>>> http://stephenskory.com/
>>> 510.621.3687 (google voice)
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