[yt-users] 2D Axisymmetric BoxLib Dataset Issue

[Nathan Goldbaum]

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/
>>>
>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160118/91b4c7e2/attachment.htm>
-------------- next part --------------
_______________________________________________
yt-users mailing list
yt-users at lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org