[yt-users] Generic UniGrid Data

John ZuHone jzuhone at gmail.com
Fri May 23 14:19:26 PDT 2014 

Hi Junhwan,

I'm having trouble finding anything wrong with your script, actually. 

I would recommend changing this:

ds = load_uniform_grid(data, data['density'][0].shape, 3.086e24, bbox=bbox, nprocs=4)

to this:

ds = load_uniform_grid(data, data['density'][0].shape, length_unit=(1.0,"Mpc"), bbox=bbox, nprocs=4)

but I doubt that would make much of a difference. 

Have you inspected what data["density"][0] is in your script, and what npart is? I set up an example on my own with random particle data, and I set the number_of_particles dictionary key to a variable npart that was set previously, and saw no issues there. 

If it's possible to post the file that this script works with somewhere, that would enable me to reproduce the buggy behavior.

Best,

John Z

On May 22, 2014, at 6:19 PM, John ZuHone <jzuhone at gmail.com> wrote:

> 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,
> 
> 
> 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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