[yt-users] Gadget blocks' configuration

Mon Sep 26 11:36:02 PDT 2016

Hi Bernhard,

The "gas" alias points to a version of the fields that has been deposited
on the octtree.  For the ion-specific fields, Trident will take care of
adding this for you as long as the element fields are added correctly.  I
am at the end of my day here, but I can take a look at the dataset you've
uploaded tomorrow.

On Mon, Sep 26, 2016 at 6:51 PM, Bernhard Röttgers <
broett at mpa-garching.mpg.de> wrote:

> Got the new fields. I had a little typo in the names.
> Couldn’t  solve the problems with the unit system though.
> And I have the additional problem, that I need to define a particle group
> “gas” for trident. How do I do this?
>
> Cheers,
> Bernhard
>
> On 26 Sep 2016, at 18:55, Bernhard Röttgers <broett at MPA-Garching.MPG.DE
> <broett at mpa-garching.mpg.de>> wrote:
>
> Okay, so the (HDF5) snapshot is now available at:
> http://use.yt/upload/09111d2e
>
> I used the FIRE frontend by Britton (https://bitbucket.org/
> brittonsmith/yt_fire) as a basis to create my own:
> https://bitbucket.org/broett/my_yt/overview (it’s git, not hg!)
>
> I can load a snapshot with the front-end, but I still don’t have the
> self-defined fields. Meaning that after
>
> ds = my_yt.MyGadgetDataset(‘path/to/snapshot/snap_M0664_4x_940.hdf5',
> unit_base=…, bounding_box=…)
> ds.index
> ad = ds.all_data()
>
> the following fails:
> ad[('PartType0','metallicity’)]
>
> I also cannot use self.ds.unit_system["code_metallicity”] in class
> MyGadgetFieldInfo(GadgetFieldInfo) as Britton did.
>
>
> Cheers,
> Bernhard
>
>
>
> On 26 Sep 2016, at 18:10, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>
>
> 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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