[yt-dev] Docs and 2.4 roundup (help!)

Matthew Turk matthewturk at gmail.com
Mon Jul 30 13:29:53 PDT 2012 

Hi all,

John has issued a Pull Request on this topic:

https://bitbucket.org/yt_analysis/yt/pull-request/228/redefining-the-entropy-field-so-it-is

Does this seem to address the use cases for Entropy?

-Matt

On Sun, Jul 29, 2012 at 12:06 AM, Greg Bryan <gbryan at astro.columbia.edu> wrote:
> John -- Sorry, I'm not sure.  I would guess "game" since it seems more
> fundamental.
>
> Greg
>
> On Jul 27, 2012, at 1:26 PM, John ZuHone <jzuhone at gmail.com> wrote:
>
> I'm +1 on Greg's suggestion of replacing the number density with just the
> density, but that still leaves us with the problem of gamma. If gamma is a
> field (as it sometimes is in FLASH, don't know about any other codes) then
> it should be incorporated somehow.
>
> Does anybody know which gamma would be part of the entropy definition?
> "gamc" (as defined from the sound speed) or "game" (as defined from the
> energy-pressure relation), which can be different?
>
> On Jul 25, 2012, at 6:40 PM, Greg Bryan wrote:
>
> John has an excellent point.  However, I think having a built in Entropy
> definition is so useful, that I have a different conclusion -- instead I
> would be +1 on using the physical density instead of the number density
> (T/rho^(gamma-1)), since this is the standard thermodynamic definition for
> an ideal gas.  Of course: (i) this is not the real entropy, (the real
> entropy is Nk times the log of our definition, plus a constant) , and (ii)
> individual research areas have their own estimate of this quantity, as John
> points out, but that can be added on a per-user basis.  As always, feel free
> to ignore...
>
> Cheers,
> Greg
>
> On Jul 25, 2012, at 5:22 PM, John Zuhone wrote:
>
> In what context is the Entropy field supposed to apply? If you're talking
> galaxy clusters, then it's typically the number density of electrons that is
> in the definition, not the number density of _everything_.
>
> In multispecies runs you should be able to define it using Abar and Zbar
> fields, but keep in mind that typically in these cases we also have a
> possibly spatially varying gamma.
>
> I'd actually be -1 in retaining the field, since it seems that its
> definition could be very context-dependent.
>
> John
>
> On Wed, Jul 25, 2012 at 4:53 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>>
>> FLASH has eos_singleSpeciesA, which is equivalent to Mu in enzo.  I'm not
>> sure if there is an equivalent parameter in FLASH 2 and 3.
>>
>> Of course in multispecies runs eos_singleSpeciesA is not defined so you
>> would need to build the number density field as in the enzo frontend.  FLASH
>> allows for an arbitrary species specification - I'm not sure how that is
>> represented in the data dumps since I've never run a true multispecies
>> simulation.
>>
>> I can't speak to the other codes.
>>
>> Cheers,
>>
>> Nathan
>>
>> On Jul 25, 2012, at 1:47 PM, Matthew Turk wrote:
>>
>> > New build: http://yt-project.org/docs/2.4/
>> > The cookbook in particular is coming along:
>> > http://yt-project.org/docs/2.4/cookbook/index.html
>> >
>> > Thanks for taking on the making_plots.rst, Nathan.  Britton, don't
>> > worry about the testing stuff, we can push it off for now.  As for
>> > NumberDensity, is there a mu value we could use?  Otherwise, we can
>> > build it from the species fields as we do for Enzo.  I'm also in
>> > support of searching out problematic fields; I think the particle
>> > fields in particular may have a handful of issues.
>> >
>> > On Wed, Jul 25, 2012 at 2:28 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> > wrote:
>> >>> * Rewrite the remaining docs that use PlotCollection.  Specifically,
>> >>> orientation/making_plots.rst needs to be completely redone.  Can
>> >>> someone volunteer to rewrite this document?
>> >>
>> >> I can take care of that one.
>> >>
>> >>>
>> >>> https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-for-non-enzo
>> >>
>> >> This will require defining a NumberSpecies field, currently only
>> >> defined in the enzo frontend.  Really, NumberDensity should be a univseral
>> >> field but I guess its definition will be highly code-dependent with respect
>> >> to how different codes handle multispecies simulations.  Each of the
>> >> maintainers for the different codes will have to update their frontend to
>> >> include the NumberDensity field.
>> >>
>> >> While we're thinking about this, are there any other universal fields
>> >> that depend on enzo-only fields?
>> >>
>> >> Cheers,
>> >>
>> >> Nathan
>> >>
>> >> On Jul 25, 2012, at 11:19 AM, Matthew Turk wrote:
>> >>
>> >>> Hi all,
>> >>>
>> >>> There's been a flurry of activity on the docs this week.
>> >>>
>> >>> * All the cookbook recipes have been moved into the docs and the
>> >>> cookbook shut down.  We now have 45 cookbook recipes, and they're
>> >>> integrated much better into the docs.
>> >>> * Most of the docs have been rewritten to remove PlotCollection
>> >>> * The data index is now part of the website repo.  It's up, but the
>> >>> files are still copying.
>> >>>
>> >>> Here's my current draft of the changelog for 2.4.  Did I forget
>> >>> anything?
>> >>>
>> >>>
>> >>> https://bitbucket.org/MatthewTurk/yt-doc/src/b57d3621ff70/source/changelog.rst
>> >>>
>> >>> We're just about good to go.  These things still need to be done:
>> >>>
>> >>> * Rewrite the remaining docs that use PlotCollection.  Specifically,
>> >>> orientation/making_plots.rst needs to be completely redone.  Can
>> >>> someone volunteer to rewrite this document?
>> >>> * Volume rendering docs need to be rewritten en masse, as they are
>> >>> quite out of date and don't reflect best practices or new
>> >>> functionality (ticket #382).
>> >>> * Do we want to put answer testing docs in for this release, or
>> >>> should we push that off to a point release at a slightly later date?
>> >>> * Write docs about the Hub, which I will do.
>> >>> * Check to make sure that everything that SHOULD be documented in the
>> >>> API docs IS documented.
>> >>>
>> >>> In the past we've also talked about slides demonstrating new
>> >>> functionality, as well as the possibility of doing screencasts.  I'm
>> >>> going to throw together some HTML slides, but if anybody wants to do a
>> >>> screencast that would be outstanding.  We actually have gotten *many*
>> >>> views in the past of screencasts.
>> >>>
>> >>> I think that's about it.  There are two additional technical tickets
>> >>> that should be addressed:
>> >>>
>> >>>
>> >>> https://bitbucket.org/yt_analysis/yt/issue/401/entropy-field-does-not-work-for-non-enzo
>> >>>
>> >>> https://bitbucket.org/yt_analysis/yt/issue/390/transfer-function-bounds
>> >>>
>> >>> I can do the second, but I don't know what to do about the first.
>> >>>
>> >>> Thanks all,
>> >>>
>> >>> -Matt
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>
>
>
> --
> John ZuHone
>
> Postdoctoral Researcher
> NASA/Goddard Space Flight Center
>
> jzuhone at gmail.com
> john.zuhone at nasa.gov
>
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>
> ----------------------------------
> Greg Bryan
> Associate Professor of Astronomy
> Department of Astronomy, Columbia University
> 1325 Pupin Physics Laboratories, Mail Code 5246
> 550 West 120th Street
> New York, New York 10027 (USA)
>
> email: gbryan at astro.columbia.edu
> phone: +1(212)854-6837
> fax  : +1(212)854-8121
>
>
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