[yt-users] Gadget blocks' configuration

Desika Narayanan desika.narayanan at gmail.com
Wed Sep 28 08:35:34 PDT 2016 

Hi Bernhard,

Is there any chance you're using the Scannapieco/Naab et al. version of
Gadget (with their metallicity blocks)?

-d

On Wed, Sep 28, 2016 at 11:28 AM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> On Wed, Sep 28, 2016 at 10:22 AM, Britton Smith <brittonsmith at gmail.com>
> wrote:
>
>> Hi Bernhard,
>>
>> Yes, I think I agree with you, but I'm not 100% sure.  If someone knows
>> of an instance where that might happen, please speak up.  You should be
>> able to pass units of "" (i.e., no units).  It looks like you're using
>> "code_metallicity", which looks to be the same thing.  "Zsun" should be
>> defined, so you can do:
>> ds.r["gas", "metallicity"].to("Zsun")
>> to see things in solar.  The metallicities will be in linear units.
>>
>> Does anyone else have any ideas?
>>
>> Britton
>>
>> On Wed, Sep 28, 2016 at 3:56 PM, Bernhard Röttgers <
>> broett at mpa-garching.mpg.de> wrote:
>>
>>> Hi Britton,
>>>
>>> thanks a lot! I finally can access the metallicity block :)
>>> However, I am stilled puzzled by the result: The maximum value I have
>>> for the particles is ~0.08, but the maximum value I see in yt is ~0.10.
>>> That seems be to wrong. Regardless of the details of the mapping onto a
>>> grid, I should never get larger metallicities than for the individual
>>> particles, right?
>>>
>>
> Hi Bernhard,
>
> Can you share the code snippet that generates that result?
>
> -Nathan
>
>
>>
>>> And what units do I have to pass? Did I correctly understand that yt
>>> always assumes the metallicities to be in solar metallicities? And is it in
>>> linear units or logarithmic units?
>>>
>>> Cheers,
>>> Bernhard
>>>
>>> On 28 Sep 2016, at 16:03, Britton Smith <brittonsmith at gmail.com> wrote:
>>>
>>> Hi Bernhard,
>>>
>>> Sorry, the previous suggestion I gave you was completely wrong.
>>>
>>> The issue is that the step where the ("gas", "metallicity") field is
>>> being created is happening before your setup_gas_particle_fields function
>>> is getting called.  The field never gets created because the ("PartType0",
>>> "metallicity") field does not yet exist.  I think yt is expecting it to be
>>> there because "metallicity" is typically aliased to a specific field on
>>> disk and that step happens earlier on.  Some rearranging of the order or
>>> operations might make this possible, but this simplest solution is to
>>> directly add the ("gas", "metallicity") field in your
>>> setup_gas_particle_fields.  If did it in the following way and it worked
>>> for me:
>>>
>>> from yt.fields.particle_fields import \
>>>     add_volume_weighted_smoothed_field
>>>
>>> # end of setup_gas_particle_fields
>>>         num_neighbors = 64
>>>         fn = add_volume_weighted_smoothed_field(
>>>             ptype, "particle_position", "particle_mass",
>>>             "smoothing_length", "density", "metallicity",
>>>             self, num_neighbors)
>>>         self.alias(("gas", "metallicity"), fn[0])
>>>
>>> Britton
>>>
>>> On Wed, Sep 28, 2016 at 2:44 PM, Bernhard Röttgers <
>>> broett at mpa-garching.mpg.de> wrote:
>>>
>>>> Never mind! `sum` also accepts generator expressions
>>>> <https://www.python.org/dev/peps/pep-0289/>. So in my little example
>>>> the last statement is equivalent with a+b+c. Since the addition of
>>>> numpy arrays
>>>> <http://docs.scipy.org/doc/numpy/reference/generated/numpy.add.html> of
>>>> the same shape is defined as an element-wise operation, we end up with the
>>>> intended result.
>>>>
>>>> The thing that does not work is the for loop with the if-statement.
>>>> This combination is only allowed in list comprehension and generator
>>>> expressions.
>>>>
>>>> Cheers,
>>>> Bernhard
>>>>
>>>>
>>>> On 28 Sep 2016, at 15:34, Britton Smith <brittonsmith at gmail.com> wrote:
>>>>
>>>> Hi Bernhard,
>>>>
>>>> My apologies, I was not familiar with that syntax.  yt arrays will
>>>> behave like NumPy arrays, so if that works as in your example, it should
>>>> work in that function.  Can you elaborate at why my suggestion doesn't work
>>>> in Python 2.7?  I will try to debug this here.
>>>>
>>>> Britton
>>>>
>>>> On Wed, Sep 28, 2016 at 2:29 PM, Bernhard Röttgers <
>>>> broett at mpa-garching.mpg.de> wrote:
>>>>
>>>>> PS:
>>>>> I also cannot access (‘PartType0’,’metallicity’) including you
>>>>> attempt to fix.
>>>>>
>>>>> On 28 Sep 2016, at 15:27, Bernhard Röttgers <
>>>>> broett at MPA-Garching.MPG.DE <broett at mpa-garching.mpg.de>> wrote:
>>>>>
>>>>> Hi Britton,
>>>>>
>>>>> thanks for spotting this error! So that means yt arrays do not behave
>>>>> like numpy arrays, since:
>>>>> In [2]: a = np.arange(10)
>>>>>
>>>>> In [3]: b = np.arange(10)
>>>>>
>>>>> In [4]: c = np.arange(10)
>>>>>
>>>>> In [5]: sum( x for x in [a,b,c] )
>>>>> Out[5]: array([ 0,  3,  6,  9, 12, 15, 18, 21, 24, 27])
>>>>> Which is what I had in mind, but apparently does not happen with yt
>>>>> arrays.
>>>>>
>>>>> However, you proposed code seem to have problems, too. First of all
>>>>> the loop you propose is not Python 2.7, which I use. And second, even after
>>>>> fixing that, the problem is not solved. Actually even the particle_mass
>>>>> block seems to be broken somehow. I cannot access it by (“gas”,
>>>>> “particle_mass”) but only via (“partType0”, “particle_mass”).
>>>>>
>>>>> Cheers,
>>>>> Bernhard
>>>>>
>>>>>
>>>>> On 28 Sep 2016, at 15:08, Britton Smith <brittonsmith at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hi Bernhard,
>>>>>
>>>>> I'm just starting to look at this now.  I haven't looked to closely
>>>>> yet, but I noticed an issue with your _metal_mass field function.  Right
>>>>> now, you've got:
>>>>>
>>>>>         def _metal_mass(field, data):
>>>>>             return sum( data[(ptype, "%s_mass"%el)]
>>>>>                     for el in self.nuclei_names if el not in
>>>>> ["H","He"] )
>>>>>
>>>>> The sum function is going to reduce the entire field array to a single
>>>>> number.  I think you need something like this:
>>>>>
>>>>> field_data = np.zeros_like(data[ptype, "particle_mass"])
>>>>> for el in self.nuclei_names if el not in ["H","He"]:
>>>>>     field_data += data[ptype, "%s_mass"% el]
>>>>>
>>>>> The metallicity field is likely not showing up because it is quietly
>>>>> erroring.  This may fix that.  Let us know how it goes.
>>>>>
>>>>> Britton
>>>>>
>>>>> On Wed, Sep 28, 2016 at 1:44 PM, Bernhard Röttgers <
>>>>> broett at mpa-garching.mpg.de> wrote:
>>>>>
>>>>>> Hi there,
>>>>>>
>>>>>> I still have problems with the “gas”. I can access (“PartType0”,
>>>>>> “metallicity”) but not (“gas”, “metallicity”). Why is the alias not being
>>>>>> created automatically as I understood it should?
>>>>>>
>>>>>> Cheers,
>>>>>> Bernhard
>>>>>>
>>>>>> On 26 Sep 2016, at 20:36, Britton Smith <brittonsmith at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> 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/britton
>>>>>>> smith/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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