[yt-users] 2D Axisymmetric BoxLib Dataset Issue

Max Katz maxpkatz at gmail.com
Mon Jan 18 14:37:53 PST 2016


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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>>>>>>
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