[yt-users] 2D Axisymmetric BoxLib Dataset Issue

[Nathan Goldbaum]

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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