[yt-users] Generic UniGrid Data

Nathan Goldbaum nathan12343 at gmail.com
Thu May 22 15:45:21 PDT 2014 

On Thu, May 22, 2014 at 3:17 PM, Junhwan Choi (최준환)
<choi.junhwan at gmail.com>wrote:

> Hi,
>
> I have read more about the "generic array data" from the document in yt
> webpage.
> I found that the the how to set data dict and call "load_uniform_grid"
> by yt-2.6 and yt-3.0 are quite different, and it looks that yt-3.0
> supports better unit treatment.
>
> However, my yt-3.0 looks use old formate for load_uniform_grid as follow:
> .....
> def load_uniform_grid(data, domain_dimensions, sim_unit_to_cm, bbox=None,
>                       nprocs=1, sim_time=0.0, periodicity=(True, True,
> True)):
> ....
>
> This load_uniform_grid arguments are different with those presented in
> yt-3.0 document.
> I think this is part of the reason that I have a difficulty.
>
>
Sorry for the difficulty - we're in the middle of updating the docs so
there is still come confusing incorrect information in the 3.0-dev
documentation.


> How can I use that load_uniform_grid for the version shown in yt-3.0
> document?
>
> Thank you,
> Junhwan
>
> On Fri, May 16, 2014 at 11:28 AM, Junhwan Choi (최준환)
> <choi.junhwan at gmail.com> wrote:
> > Here, I post my script in http://paste.yt-project.org/show/4641
> >
> > Thank you,
> > Junhwan
> >
> > On Thu, May 15, 2014 at 11:56 PM, John ZuHone <jzuhone at gmail.com> wrote:
> >> Junhwan,
> >>
> >> Can you post your script somewhere? It might be easier to debug it that
> way.
> >>
> >> Best,
> >>
> >> John Z
> >>
> >> On May 16, 2014, at 12:46 AM, Junhwan Choi <choi.junhwan at gmail.com>
> wrote:
> >>
> >> Hi Nathan,
> >>
> >> I think that I am using the yt 3.0 unless there is stabke yt 3.0
> version.
> >>
> >> Junhwan
> >>
> >>
> >>
> >> On May 15, 2014, at 11:29 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
> >>
> >> Hi Junhwan,
> >>
> >> Just to clarify (since the answers you receive will be different
> depending
> >> on your response) is this for the in-development yt 3.0 release or the
> >> current stable release?
> >>
> >> Nathan
> >>
> >> On Friday, May 16, 2014, Junhwan Choi (최준환) <choi.junhwan at gmail.com>
> wrote:
> >>>
> >>> Dear yt user,
> >>>
> >>> I try to use Generic UnicGrid Data (256^3 gas density cube + position
> >>> of particle that is subset of a huge simulation).
> >>> It is preliminary work, but I still have some questions.
> >>>
> >>> 1. In order to set density unit as cgs, I made following script:
> >>> ......
> >>> data = dict(density = (map, "g/cm**3"))  #map is 256^3 density data
> array
> >>> bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]])
> >>> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24,
> >>> bbox=bbox, nprocs=4)
> >>> .....
> >>>
> >>> Then, I got the following error message:
> >>> Traceback (most recent call last):
> >>>   File "cutout2.py", line 62, in <module>
> >>>     ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24,
> >>> bbox=bbox, nprocs=4)
> >>>   File
> >>>
> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
> >>> line 461, in load_uniform_grid
> >>>     psize = get_psize(np.array(data[key].shape), nprocs)
> >>> AttributeError: 'tuple' object has no attribute 'shape'
> >>>
> >>> Hence, I modify "data = dict(density = (map, "g/cm**3"))" --> "data =
> >>> dict(density = map)" and it work.
> >>> If this is the case, how can I define the density unit and show it
> >>> when I make Slice/Projection?
> >>> In addition, I would like to know how I can set the unit in Generic
> >>> UnicGrid Data in general?
> >>> The length unit can be provide to script in load_uniform_grid(...
> >>> 3.086e24 ....) but I do not know how to set other units.
> >>>
> >>> 2. When I add particle information as follow:
> >>> .....
> >>> npart = 100000  # number of particles
> >>> data = dict(density = map,
> >>>             number_of_particles = npart,
> >>>             particle_position_x = posx,
> >>>             particle_position_y = posy,
> >>>             particle_position_z = posz)
> >>> bbox = np.array([[0., boxsize], [0., boxsize], [0.,boxsize]])
> >>> ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24,
> >>> bbox=bbox, nprocs=4)
> >>> ...
> >>>
> >>> I got the following error message:
> >>> Traceback (most recent call last):
> >>>   File "cutout.py", line 107, in <module>
> >>>     ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24,
> >>> bbox=bbox, nprocs=4)
> >>>   File
> >>>
> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
> >>> line 519, in load_uniform_grid
> >>>     assign_particle_data(spf, pdata)
> >>>   File
> >>>
> "/Users/jhchoi/common/lib/python2.7/site-packages/yt-3.0dev-py2.7-macosx-10.4-x86_64.egg/yt/frontends/stream/data_structures.py",
> >>> line 371, in assign_particle_data
> >>>     pdata.pop("number_of_particles")
> >>> KeyError: 'number_of_particles'
> >>>
> >>> So, I change "number_of_particles = npart," --> "number_of_particles =
> >>> 100000," and it works.
> >>> How could it happen?
> >>>
> >>> 3. Can I do halo finder (hop/fof) using the above particle data?
> >>> Or, what information do I need to provide to do grouping?
> >>> In this case, how can I set the units and linking length?
> >>>
> >>> 4. Can I make particle distribution to particle data like
> >>> data['Dark_Matter_position_x']?
> >>> This process will allow me additional analysis such as profile and
> >>> obtaining total value.
> >>>
> >>> I may ask too many for new tool, but it will help a lot to use yt for
> >>> general data set.
> >>>
> >>> Thank you,
> >>> Junhwan
> >>> _______________________________________________
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