[yt-users] Gadget blocks' configuration

Mon Sep 26 09:10:57 PDT 2016

On Mon, Sep 26, 2016 at 11:07 AM, Bernhard Röttgers <
broett at mpa-garching.mpg.de> wrote:

> Okay, then I upload HDF5 for now. Called the file “snap_M6782_4x_470.hdf5”.
> So what are we gonna do with it?
>
>
You can upload it using the yt curldrop:

$ curl -T snap_M6782_4x_470.hdf5 http://use.yt/upload/

That will print out a URL once the upload is finished, just share that URL
here.

Alternatively generating a share link via google drive or dropbox will also
work.

> Oops… I mixed up the field info and the data structure classes. My bad!
>
> Cheers,
> Bernhard
>
>
> On 26 Sep 2016, at 17:55, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>
>
> On Mon, Sep 26, 2016 at 10:42 AM, Bernhard Röttgers <broett at mpa-garching.
> mpg.de> wrote:
>
>> Hi Nathan,
>>
>> Yes, I have some smaller (~85MB) sample I could upload. I guess it should
>> ideally be HDF5? (Originally it is format 2, but I can easily convert.)
>> What naming should I use?
>> I would guess, my format is pretty much “the standard” except for the
>> metallicity block (which in fact is element masses for 12 different
>> elements).
>>
>
> The naming and format doesn't matter too much. HDF5 is probably easiest to
> deal with, although yt supports both binary formats as well.
>
>
>>
>> So again, how am I supposed the data set class I derive from
>> GadgetHDF5Dataset? Simply replacing `yt.load` yields an exception
>> complaining that the `bounding_box` keyword argument is unexpected.
>>
>
> I think all you need to do is declare the subclass and then load your
> dataset directly:
>
> my_ds = MyGadgetHDF5DatasetSubclass(unit_base=..., bbox=...)
>
> It should also be possible to make your subclass work with yt.load() (i'm
> not sure how to do that offhand as I've never tried to add a new Dataset
> subclass outside of yt), but instantiating your subclass directly should be
> fine for now.
>
>
>>
>> Cheers,
>> Bernhard
>>
>> On 26 Sep 2016, at 17:24, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>>
>>
>>
>> On Mon, Sep 26, 2016 at 10:15 AM, Bernhard Röttgers <broett at mpa-garching.
>> mpg.de> wrote:
>>
>>> Hi Britton,
>>>
>>> thanks for the answer and sorry for my late answer!
>>>
>>> No, I don’t have OWLS/EAGLE/Gizmo snapshots. I actually just wanted to
>>> compare my results with yt/trident, but your solution does not seem to be
>>> too complicated. How, am I supposed to use it? (Sorry for asking dump
>>> questions. I’m not familiar with yt.) I understood that I can load a Gadget
>>> snapshot with like:
>>>
>>> ds = yt.load(YT_FNAME, unit_base=UNIT_BASE, bounding_box=bbox)
>>> ds.index
>>>
>>> The data structure `ds` then is what is passed to trident. Where does
>>> the new frontend come into play?
>>>
>>
>> Right now yt makes certain assumptions about the structure and meaning of
>> data in Gadget output files. The assumptions currently used in yt are based
>> on the public data the yt developers have access to (e.g. the datasets on
>>  yt-project.org/data) and are only valid in so far as those datasets are
>> representative of Gadget data in general. Due to the history of the
>> Gadget's code, there are in reality many different flavors of Gadget that
>> make different assumptions about what the data they write to disk means,
>> and it seems yt doesn't currently make incorrect assumptions for your
>> flavor of Gadget data.
>>
>> Do you happen to have a test dataset that you can share? In principle the
>> necessary modification should be simple, and having a dataset to test with
>> would be helpful. One way to share files with us is to use the yt curldrop:
>>
>> https://docs.hub.yt/services.html#curldrop
>>
>>
>>>
>>> And some more questions:
>>> What exactly are the code metallicity units? In my case yt says its in
>>> units of 1. Is this interpreted as absolute units or in solar metallicity?
>>>
>>
>> In units of solar metallicity. There is also the metal_density, which
>> should have units of g/cm**3 (by default, if may be different if you
>> specified a value for the `unit_system` keyword when you called the load()
>> function.
>>
>>
>>>
>>> Cheers,
>>> Bernhard
>>>
>>>
>>> On 19 Sep 2016, at 15:04, Britton Smith <brittonsmith at gmail.com> wrote:
>>>
>>> Hi Bernhard,
>>>
>>> Does your data come from a specific flavor of Gadget that is supported
>>> by yt?  For example, we currently support OWLS, EAGLE, and Gizmo data that
>>> have fields for individual elements.  If not, then it is probably best to
>>> try and put together a new frontend for this data.  If the type of data
>>> that you're working with is not public or widely used, the best thing may
>>> be to create a frontend that exists as a yt extension (an external module
>>> not inside the main yt codebase).  Here is an example of one that I created
>>> a while back for the FIRE simulation data:
>>> https://bitbucket.org/brittonsmith/yt_fire
>>>
>>> If the only thing that is different about your data is the way that the
>>> metallicity fields are defined, then it shouldn't be too difficult to
>>> create a subclass of an existing Gadget frontend that overrides the field
>>> definitions.  Please, let us know if you're interested in pursuing this and
>>> we can work with you.
>>>
>>> Britton
>>>
>>> On Sat, Sep 17, 2016 at 11:45 AM, Bernhard Röttgers <
>>> broett at mpa-garching.mpg.de> wrote:
>>>
>>>> Hello!
>>>>
>>>> I am trying to use trident
>>>> <https://bitbucket.org/trident-project/trident> (yt-based code) to
>>>> generate spectra out of my Gadget simulations (stored in HDF5). I could get
>>>> the code running, but the spectra are scaled weirdly. I was able to track
>>>> the problem down to a weirdly scaled metallicity block within yt. I am
>>>> guessing that the issue is related to the fact, that my block “Metallicity”
>>>> is in fact element masses for individual elements, i.e. for each particle I
>>>> have an array of masses for the 12 elements He, C, Mg, O, Fe, Si, H, N, Ne,
>>>> S, Ca, and the rest (I know, a crappy naming for such a block, but that’s
>>>> the way it is).
>>>>
>>>> Is there a way to force yt to create the metallicity block correctly?.
>>>>
>>>> Cheers,
>>>> Bernhard
>>>>
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