[yt-users] xstick label in yt slice plot

[Jiang, Yanfei]

Hi John,

   I just paste the script. You can replay the filename with the data  you
have (I forget which file I sent to you before).

   I should say that at minimum, I should do region selection so that the
progress bar for mesh construction shows up. Then the memory leaking issue
also shows up.

On Fri, May 20, 2016 at 3:25 PM, John Zuhone <jzuhone at gmail.com> wrote:

> Yan-Fei,
>
> Can you send a script that shows this?
>
> Try pasting the script with paste.yt-project.org
>
> Best,
>
> John
>
> On May 20, 2016, at 3:24 PM, Jiang, Yanfei <yanfei.jiang at cfa.harvard.edu>
> wrote:
>
> OK.
>
> By the way, the memory leaking issue with the new function for Athena++
> seems to come from mesh construction. I tried a case with yt just reading
> the data without any plot, the memory usage still goes up with time.
>
> On Fri, May 20, 2016 at 3:13 PM, John Zuhone <jzuhone at gmail.com> wrote:
>
>> Hi Yan-Fei,
>>
>> And in the athena_pp bookmark I will set this to the default for
>> cylindrical and spherical coordinates instead of “domain” which is what I
>> had it set to.
>>
>> John
>>
>> On May 20, 2016, at 3:12 PM, Jiang, Yanfei <yanfei.jiang at cfa.harvard.edu>
>> wrote:
>>
>> Thank you, Nathan. This indeed is what I need.
>>
>> On Fri, May 20, 2016 at 3:09 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> Hi Yanfei,
>>>
>>> So I looked a little closer at the code. It looks like the 'domain'
>>> origin sets the origin of the plot at the lower-left-hand corner of the
>>> *domain*, which for your dataset is *not* the same thing as setting the
>>> origin of the plot at the origin of the simulation's coordinate system.
>>>
>>> What you want is to set the origin to 'native', which sets the origin to
>>> be the same as the origin of the simulation coordinate system. Here is an
>>> example with that choice:
>>>
>>> https://gist.github.com/e61ac07b44e5083ea88fcf1bf24a3459
>>>
>>> Hope that's helpful,
>>>
>>> Nathan
>>>
>>> On Thu, May 19, 2016 at 3:29 PM, Jiang, Yanfei <
>>> yanfei.jiang at cfa.harvard.edu> wrote:
>>>
>>>> Hi Nathan,
>>>>
>>>>    Here is a much smaller data file that you can try:
>>>>
>>>>
>>>> https://drive.google.com/file/d/0ByTG4wYr-7aOdUxUR0dMWGZVQmM/view?usp=sharing
>>>>
>>>> Now the inner boundary is 28 and it is labeled as 0.
>>>>
>>>>
>>>> On Thu, May 19, 2016 at 3:07 PM, Nathan Goldbaum <nathan12343 at gmail.com
>>>> > wrote:
>>>>
>>>>> Hi Yanfei,
>>>>>
>>>>> John ZuHone gave me access to your dataset - I think the issue is that
>>>>> ds.domain_left_edge is [2, 0, 0], and that is confusing the code that
>>>>> generates the plot coordinates for spherical geometries.
>>>>>
>>>>> I don't think this is an issue with the frontend, but a general issue
>>>>> with plotting data in spherical coordinates with an inner radial boundary.
>>>>>
>>>>> I don't have any test datasets besides yours that look like this, and
>>>>> yours is pretty large, so it would be nice to have a smaller dataset to
>>>>> play with.
>>>>>
>>>>> -Nathan
>>>>>
>>>>> On Thu, May 19, 2016 at 10:59 AM, Jiang, Yanfei <
>>>>> yanfei.jiang at cfa.harvard.edu> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>>    I am trying to make a slice plot with the new capability for
>>>>>> spherical polar grid in Athena++ data John developed. The attached
>>>>>> notebook.png shows what I am doing. I take a slice and the origin is set to
>>>>>> "domain". The image.png is the image from the notebook. In the slice image,
>>>>>> the empty space near the center corresponds to the inner radial boundary of
>>>>>> the original spherical coordinate, which is 2 in this case. Therefore, I
>>>>>> think the x stick where is 0 in the plot should be 2. Do you know any way
>>>>>> to fix this?
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> --
>>>>>> Yan-Fei Jiang
>>>>>>
>>>>>> Einstein Fellow
>>>>>> Harvard-Smithsonian Center for Astrophysics
>>>>>> 60 Garden Street, Cambridge MA USA 02138
>>>>>>
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>>>>>>
>>>>>>
>>>>>
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>>>>
>>>>
>>>> --
>>>> Yan-Fei Jiang
>>>>
>>>> Einstein Fellow
>>>> Harvard-Smithsonian Center for Astrophysics
>>>> 60 Garden Street, Cambridge MA USA 02138
>>>>
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>>
>> --
>> Yan-Fei Jiang
>>
>> Einstein Fellow
>> Harvard-Smithsonian Center for Astrophysics
>> 60 Garden Street, Cambridge MA USA 02138
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>
>
> --
> Yan-Fei Jiang
>
> Einstein Fellow
> Harvard-Smithsonian Center for Astrophysics
> 60 Garden Street, Cambridge MA USA 02138
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-- 
Yan-Fei Jiang

Einstein Fellow
Harvard-Smithsonian Center for Astrophysics
60 Garden Street, Cambridge MA USA 02138
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