[yt-users] Generic UniGrid Data

John ZuHone jzuhone at gmail.com
Thu May 15 21:56:04 PDT 2014


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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