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

[Nathan Goldbaum]

Oops, didn't see that you were replying to the old thread I linked to.


On Tue, Jul 9, 2013 at 7:43 PM, Nathan Goldbaum <goldbaum at ucolick.org>wrote:

> 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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>>>
>>>
>>>
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>>
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