[yt-users] Generic UniGrid Data

John ZuHone jzuhone at gmail.com
Thu May 22 15:19:15 PDT 2014 

Hi Junhwan,

Sorry, I kind of got lost in some other things--I'll have a look at your script tonight and get back to you.

Best,

John Z

On May 22, 2014, at 6:17 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.
> 
> 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
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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