[yt-users] Generic UniGrid Data

Nathan Goldbaum nathan12343 at gmail.com
Thu May 15 21:29:13 PDT 2014


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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