[yt-users] 2D Axisymmetric BoxLib Dataset Issue

Max Katz maxpkatz at gmail.com
Tue Jan 19 06:52:43 PST 2016


I also tried removing yt and reinstalling the latest version on the
development branch, but I see the same behavior.

Max Katz
Ph.D. Candidate, Department of Physics and Astronomy
Stony Brook University
http://astro.sunysb.edu/mkatz/

On Mon, Jan 18, 2016 at 5:37 PM, Max Katz <maxpkatz at gmail.com> wrote:

> The current version and changeset for the code is:
>
> ---
> Version = 3.2.2
> Changeset = d7acb82ef450 (stable) @
> ---
>
>
> Max Katz
> Ph.D. Candidate, Department of Physics and Astronomy
> Stony Brook University
> http://astro.sunysb.edu/mkatz/
>
> On Mon, Jan 18, 2016 at 5:26 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> Which yt version are you using? I'm able to create a covering grid of
>> your dataset with the following script using the latest dev version of yt.
>>
>> import yt
>> ds = yt.load('plt00000/')
>> ds.periodicity = (True, True, True)
>>
>> cg = ds.covering_grid(0, [0, 0, 0], ds.domain_dimensions)
>> cg['density']
>>
>>
>> On Mon, Jan 18, 2016 at 4:20 PM, Max Katz <maxpkatz at gmail.com> wrote:
>>
>>> Sure, here's the link to the dataset (10 MB, tgz format):
>>> http://use.yt/upload/7bcd9429
>>>
>>> Max Katz
>>> Ph.D. Candidate, Department of Physics and Astronomy
>>> Stony Brook University
>>> http://astro.sunysb.edu/mkatz/
>>>
>>> On Mon, Jan 18, 2016 at 5:08 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>> I'm not able to reproduce this with any of the 2D datasets I have on
>>>> hand.
>>>>
>>>> Would it be ok to share the dataset you're having trouble with or a
>>>> test dataset that triggers the same error? You can use the curldrop Kacper
>>>> set up to do this, which allows you to upload a file using:
>>>>
>>>> $ curl -T file.name http://use.yt/upload/
>>>>
>>>> You could also use e.g. dropbox or google drive.
>>>>
>>>> -Nathan
>>>>
>>>> On Mon, Jan 18, 2016 at 3:40 PM, Max Katz <maxpkatz at gmail.com> wrote:
>>>>
>>>>> That results in the following:
>>>>>
>>>>> Traceback (most recent call last):
>>>>>   File "analyze.py", line 78, in <module>
>>>>>     wdmerger.rho_T_scatterplot(eps_filename, output_dir + pltfile)
>>>>>   File "/home/mkatz/codes/wdmerger/analysis/wdmerger.py", line 617, in
>>>>> rho_T_scatterplot
>>>>>     grid = ds.covering_grid(level=0, left_edge = problo, dims = [1024,
>>>>> 2048, 1])
>>>>>   File
>>>>> "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
>>>>> line 506, in __init__
>>>>>     rdx[np.where(np.array(dims) - 2 * num_ghost_zones <= 1)] = 1   #
>>>>> issue 602
>>>>> IndexError: index 2 is out of bounds for axis 1 with size 2
>>>>>
>>>>>
>>>>> Max Katz
>>>>> Ph.D. Candidate, Department of Physics and Astronomy
>>>>> Stony Brook University
>>>>> http://astro.sunysb.edu/mkatz/
>>>>>
>>>>> On Mon, Jan 18, 2016 at 3:32 PM, Kacper Kowalik <
>>>>> xarthisius.kk at gmail.com> wrote:
>>>>>
>>>>>> On 01/18/2016 11:59 AM, Max Katz wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I'm trying to use yt for analysis of a 2D axisymmetric (R-z) dataset
>>>>>>> using
>>>>>>> the BoxLib frontend. After I load the dataset I am trying to make a
>>>>>>> covering grid with the following commands:
>>>>>>>
>>>>>>>      ds = yt.load(pltfile)
>>>>>>>
>>>>>>>      problo = ds.domain_left_edge.v
>>>>>>>      probhi = ds.domain_right_edge.v
>>>>>>>      dim    = ds.domain_dimensions
>>>>>>>
>>>>>>>      grid = ds.covering_grid(level=0, left_edge = problo, dims = dim)
>>>>>>>
>>>>>>> That leads to the following output at the terminal:
>>>>>>>
>>>>>>> yt : [INFO     ] 2016-01-18 01:35:47,516 Parameters:
>>>>>>> current_time              = 0.0
>>>>>>> yt : [INFO     ] 2016-01-18 01:35:47,516 Parameters:
>>>>>>> domain_dimensions         = [1024 2048]
>>>>>>> yt : [INFO     ] 2016-01-18 01:35:47,517 Parameters:
>>>>>>> domain_left_edge          = [  0.00000000e+00  -5.12000000e+09
>>>>>>> 0.00000000e+00]
>>>>>>> yt : [INFO     ] 2016-01-18 01:35:47,517 Parameters:
>>>>>>> domain_right_edge         = [  5.12000000e+09   5.12000000e+09
>>>>>>> 6.28318531e+00]
>>>>>>> Traceback (most recent call last):
>>>>>>>    File "analyze.py", line 78, in <module>
>>>>>>>      wdmerger.rho_T_scatterplot(eps_filename, output_dir + pltfile)
>>>>>>>    File "/home/mkatz/codes/wdmerger/analysis/wdmerger.py", line 615,
>>>>>>> in
>>>>>>> rho_T_scatterplot
>>>>>>>      grid = ds.covering_grid(level=0, left_edge = problo, dims = dim)
>>>>>>>    File
>>>>>>>
>>>>>>> "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
>>>>>>> line 503, in __init__
>>>>>>>      self.ActiveDimensions = self._sanitize_dims(dims)
>>>>>>>    File
>>>>>>>
>>>>>>> "/gpfs/home/mkatz/codes/yt-x86_64/src/yt-hg/yt/data_objects/construction_data_containers.py",
>>>>>>> line 552, in _sanitize_dims
>>>>>>>      "Length of dims must match the dimensionality of the dataset")
>>>>>>> RuntimeError: Length of dims must match the dimensionality of the
>>>>>>> dataset
>>>>>>>
>>>>>>> Thoughts? It seems like the code has some inconsistency in what the
>>>>>>> dimensionality of the dataset is. The Castro plot file in question
>>>>>>> doesn't
>>>>>>> provide that third angular dimension of size 2*pi.
>>>>>>>
>>>>>>
>>>>>> Could you try dims=[1024, 2048, 1] ?
>>>>>>
>>>>>> Cheers,
>>>>>> Kacper
>>>>>>
>>>>>> Max Katz
>>>>>>> Ph.D. Candidate, Department of Physics and Astronomy
>>>>>>> Stony Brook University
>>>>>>> http://astro.sunysb.edu/mkatz/
>>>>>>>
>>>>>>>
>>>>>>>
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