[yt-dev] proper handling species fields

[Chris Malone]

For the calculations we do, which mainly use nuclear reactions - our nuclei
are completely ionized.  So we know the charge just based on the element or
Z (# of protons).  The p/m designator, as Mike said, is irrelevant.  What
we have been doing is something like ('gas', 'Ne20_density') or ('gas',
'Ne22_density'), etc.  For us, this works and doesn't clash with the
"chemistry" side of things.

I'm not sure how the PyNE folks do things, so I'd be curious to hear their
input.

I agree, we should update YTEP-003.  Mike and I agreed to at least add a
section on treating nuclear species, but I'd like some more feedback before
we proceed.

Chris

On Tue, Oct 7, 2014 at 8:52 AM, Britton Smith <brittonsmith at gmail.com>
wrote:

> I would rather not change the field names to denote the domain, but
> instead only optionally make fields available with varying naming
> convention based on loaded field plugins.  For example, you might have in
> astrophysical_species:
> ("gas", "H_number_density")
> ("gas", "H_p1_number_density")
>
> but in nuclear_physics_species:
> ("gas", "H1_number_density")
> ("gas", "H1_p1_number_density")
> ("gas", "H2_number_density")
> ("gas", "H2_p1_number_density")
> to denote different isotopes.
>
> On Tue, Oct 7, 2014 at 10:46 AM, Cameron Hummels <chummels at gmail.com>
> wrote:
>
>> I like the idea of having context-specific field domains.  It seems to me
>> that is why the field system was generalized to have two parts in the first
>> place.  Perhaps we could move the nuclear fields to ('nuclear',
>> 'Ytterbium_V') or something like that?  Either way, I'm in favor of
>> expanding YTEP-0003.  Good suggestions everyone.
>>
>> Cameron
>>
>> On Tue, Oct 7, 2014 at 7:37 AM, Britton Smith <brittonsmith at gmail.com>
>> wrote:
>>
>>> Hi Chris,
>>>
>>> Thanks for starting this discussion.  As you have stated, trying to
>>> encompass all domains with a single nomenclature probably won't work.
>>> Currently, the field system is set up to load all field plugins for every
>>> dataset, but I think we should be able to move to having different
>>> frontends declare which plugins they want and only load those.  With that
>>> in place, for example, the current species field plugin can be renamed to
>>> be astrophysics-specific and another one can be created that is nuclear
>>> physics-specific.  If people are in favor of something like this, then I
>>> would suggest that we try to expand YTEP-0003 to different domains and
>>> establish the naming conventions there.
>>>
>>> Britton
>>>
>>> On Mon, Oct 6, 2014 at 7:29 PM, Chris Malone <chris.m.malone at gmail.com>
>>> wrote:
>>>
>>>> At Britton's great suggestion, let's move the discussion of what to do
>>>> with species fields from BitBucket comments to here.  For reference, see
>>>> the discussion in the comments here [1].  Note that the current situation
>>>> is outlined in YTEP-003, specifically the section on species names [2].
>>>>
>>>> The main issue is that yt supports a wide range of codes, which are
>>>> applicable in various domains of science and sometimes the nomenclature
>>>> clashes.  What is meant by 'species' is a prime example.  'Species' can
>>>> mean atomic elements, ions, or nuclei (perhaps others?), and the definition
>>>> of each of these should - if it is possible - be made explicit.
>>>>
>>>> Agreeing on the yt-internal nomenclature for this explicitness requires
>>>> some discussion.
>>>>
>>>> [1]
>>>> https://bitbucket.org/yt_analysis/yt/pull-request/1240/bugfix-fixing-nuclei-density-fields/diff
>>>> [2]
>>>> http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0003.html#molecular-and-atomic-species-names
>>>>
>>>> Chris
>>>>
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>>>>
>>>>
>>>
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>>>
>>
>>
>> --
>> Cameron Hummels
>> Postdoctoral Researcher
>> Steward Observatory
>> University of Arizona
>> http://chummels.org
>>
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>>
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