[yt-dev] NumberDensity in clumps and on FLASH data

[Nathan Goldbaum]

Hey John,

This is a longstanding issue with the FLASH frontend, see e.g. this e-mail
from last year:
http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2012-October/002579.html

I think your patch is a good starting point and it's probably worth issuing
a pull request about this to at least start a discussion.

-Nathan


On Tue, Jul 9, 2013 at 6:48 PM, John Forbes <jforbes at ucolick.org> wrote:

> Hi everyone,
>
> It looks to me like this issue was never resolved - for instance when I
> attempt to save the clump hierarchy (which I can now find thanks to
> Kacper!), it complains about not finding NumberDensity (traceback here:
> http://pastebin.com/NSuaj8XH ). I got it to work using a potentially
> non-optimal solution, namely adding the following lines to the end of
> yt/frontends/flash/fields.py -- http://pastebin.com/jYWcZCDj
>
> I can imagine this failing if the dataset uses the Helmholtz EoS or maybe
> with multispecies, but maybe it would work (I don't have any datasets handy
> which use these).
>
> Thank you,
> John
>
>
>
> On Thu, Oct 25, 2012 at 4:18 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:
>
>> Hi Matt,
>>
>> There's actually an issue related to this that we closed before the 2.4
>> release:
>> https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-for-non-enzo
>>
>> Basically, we would need to pare the FLASH data dumps, search for the
>> appropriate runtime parameters that control the EOS settings (as described
>> in section 15 of the FLASH docs:
>> http://flash.uchicago.edu/site/flashcode/user_support/flash4_ug/node22.html),
>> and from that back out what mean molecular weight is.
>>
>> I think it would be possible for Mark to define his own NumberDensity
>> field in his .yt/my_plugins file as a stopgap solution.
>>
>> -Nathan
>>
>> On Oct 25, 2012, at 4:09 PM, Matthew Turk wrote:
>>
>> Hi all,
>>
>> Mark Richardson wrote to the yt_analysis project with a problem with
>> clumps on FLASH datasets.  Here's his email:
>>
>> "Below includes my script and the output (it wouldn't let me attach
>> two files). I get some output in the clump file up until I'd expect to
>> see the Jeans Mass dumped. The output makes me think that it can't
>> calculate this point because Gamma is unknown, or some other essential
>> variable needed to get the number density. I've attempted to change
>> the data_structure.py frontend for Flash to alias Gamma to gamc and
>> game but I still get the 'cannot find Gamma' when loading my dataset."
>>
>> The issue from the traceback is that JeansMassMsun requires
>> MeanMolecularWeight which needs NumberDensity.  This can't be
>> generated for his data.
>>
>> I am not an expert on FLASH, but it seems that this should be
>> straightforward to fix, I just don't know how.  Anybody from the FLASH
>> or Clump side have any ideas?
>>
>> -Matt
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