[yt-users] Trouble projecting a derived field

[Matthew Turk]

Hi Nathan,

On Wed, Sep 7, 2011 at 3:30 AM, Nathan Goldbaum <goldbaum at ucolick.org> wrote:
> Hi Andrew,
> Thanks for the idea.  Unfortunately, that doesn't seem to be the problem.  I
> just tried taking the absolute value of R cross V before taking the square
> root and got the exact same results.

Your script actually did not work for me on a standard AMR dataset.
The axes of the result of the cross product were transposed from what
they should be; my script died on a grid of size (18, 16, 16) because
the result of the cross product was (16, 16, 18) and the
CylinderRadius variable was (18, 16, 16).  Naively applying a
transpose (although I am not sure why I had to do this) and Andrew's
suggestion of na.abs produced plots that looked vaguely correct.  I
recognize this is perhaps not a satisfying answer, but I would
encourage you to investigate how the axes in the na.cross function are
modified and returned; I also noted that only specifying "axis=0"
instead of "axisa=0" and "axisb=0" got me the same result.  I suspect
that not specifying "axisc=0" is the cause of the problem.  Another
note is that I end up with a singularity at the y=z line.

If you end up wanting to do this *not* aligned with the axes, the
off-axis projection method will probably be of some help.  It would be
very nice if we had some kind of recipe or script for calculating
Toomre Q; I have done it myself, but unfortunately the script I used
to calculate it was not backed up and was wiped out in a colossal and
deep-cutting hard drive failure at SDSC, and so I am unable to share
it.

Best,

Matt

> -Nathan
> On Sep 6, 2011, at 11:43 PM, Andrew Myers wrote:
>
> Hi Nathan,
>
> This is just a guess, but do you really mean to be taking the square root of
> R cross V, at line 30? That quantity could potentially be negative,
> depending on the sense in which the fluid is spinning.
>
> -Andrew Myers
>
>
> On Tue, Sep 6, 2011 at 5:54 PM, Nathan Goldbaum <goldbaum at ucolick.org>
> wrote:
>>
>> Hello all,
>> Right now I'm trying to generate maps of the Toomre Q in an isolated
>> galaxy simulation.  To do so, I'm using yt to generate maps of the gas
>> column density as well as density-weighted projections of the sound speed
>> and orbital frequency, which I'm using as a proxy for the epicyclic
>> frequency.
>> Unfortunately, I'm having some trouble making projected maps of the
>> orbital frequency.  I've defined two new derived fields, CylinderRadius and
>> AngularVelocity (http://paste.yt-project.org/show/1784/).
>> When I try to project the AngularVelocity field, I get what looks like
>> garbage: http://i.imgur.com/PkYhe.png
>> However, slices work just fine: http://i.imgur.com/NnEbq.png
>> I've written the derived fields in a coordinate-dependent way, since I'll
>> always be doing projections down a fixed axis.  Is that where my problem
>> lies?  My understanding of how yt does projections is too shallow to figure
>> out exactly what's going wrong here, so I'm hoping the collective wisdom of
>> the yt developers and user base can come to the rescue.
>> Best regards,
>> Nathan Goldbaum
>> Graduate Student
>> Astronomy & Astrophysics, UCSC
>> goldbaum at ucolick.org
>> http://www.ucolick.org/~goldbaum
>>
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