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

[John Forbes]

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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