[yt-users] cylindrical coordinates in Athena

Kaitlin Kratter kaitlin.kratter at jila.colorado.edu
Fri Nov 16 10:18:22 PST 2012


Ok, great. And yes, I have 3D, too. If there is a specific type of data that would be useful to you, I'm of course happy to produce a file.

Kaitlin


On Nov 16, 2012, at 11:11 AM, John ZuHone <jzuhone at gmail.com> wrote:

> Hi Kaitlin,
> 
> Right now, that is the sequence of events that you should try. Please let us know if you see anything odd. Do you have 3D datasets as well?
> 
> Best,
> 
> John
> 
> On Nov 16, 2012, at 1:07 PM, Kaitlin Kratter <kaitlin.kratter at jila.colorado.edu> wrote:
> 
>> Hi John, Sam,
>> 
>> I was using Sam's athena branch.  Should I switch to the main development branch, get Sam's PR?
>> 
>> Kaitlin
>> 
>> 
>> On Nov 15, 2012, at 7:34 PM, John ZuHone <jzuhone at gmail.com> wrote:
>> 
>>> Hi Kaitlin,
>>> 
>>> Are you using the main development version or Sam's Athena-specific branch? I think we're using different yt code, since we're getting different output. I'm using the main development branch. In that branch, if domain_right_edge doesn't equal -domain_left_edge, you have to set it explicitly. 
>>> 
>>> When I just load the file, I get this:
>>> 
>>> In [4]: pf = load("cyl_disk.0000.vtk")
>>> yt : [INFO     ] 2012-11-15 21:28:49,259 Please set 'domain_right_edge' in parameters dictionary argument if it is not equal to -domain_left_edge.
>>> yt : [INFO     ] 2012-11-15 21:28:49,260 Parameters: current_time              = 0.0
>>> yt : [INFO     ] 2012-11-15 21:28:49,260 Parameters: domain_dimensions         = [ -36.57142857  127.99998696           nan]
>>> yt : [INFO     ] 2012-11-15 21:28:49,261 Parameters: domain_left_edge          = [ 1.       -1.570796  0.      ]
>>> yt : [INFO     ] 2012-11-15 21:28:49,261 Parameters: domain_right_edge         = [-1.        1.570796 -0.      ]
>>> yt : [INFO     ] 2012-11-15 21:28:49,262 Parameters: cosmological_simulation   = 0.0
>>> 
>>> As you can see, the INFO that I get about the domain edges is different from yours. 
>>> 
>>> When I set domain_right_edge explicitly, I get this: 
>>> 
>>> In [5]: pf = load("cyl_disk.0000.vtk", parameters={'domain_right_edge':[15.,np.pi/2.,1.0]})
>>> yt : [INFO     ] 2012-11-15 21:25:27,282 Parameters: current_time              = 0.0
>>> yt : [INFO     ] 2012-11-15 21:25:27,283 Parameters: domain_dimensions         = [ 256.          128.00000028           inf]
>>> yt : [INFO     ] 2012-11-15 21:25:27,283 Parameters: domain_left_edge          = [ 1.       -1.570796  0.      ]
>>> yt : [INFO     ] 2012-11-15 21:25:27,291 Parameters: domain_right_edge         = [ 15.           1.57079633   1.        ]
>>> yt : [INFO     ] 2012-11-15 21:25:27,291 Parameters: cosmological_simulation   = 0.0
>>> 
>>> So the "inf" in the last domain dimension isn't right, but at least it has the r and z dimensions correct. 
>>> 
>>> I suspect that what has happened is that you might be using a revision of Sam's Athena-specific yt branch which probably does not have 2D support built in, since that was put in just a few days ago. If you use the main development branch and update to the latest revision, you should get the same result that I did above.
>>> 
>>> I have a feeling I know how to fix the "inf" in the last dimension, but I should probably try Sam's updates that he mentioned and seeing what happens then. 
>>> 
>>> Best,
>>> 
>>> John
>>> 
>>> 
>>> On Nov 15, 2012, at 5:36 PM, Kaitlin Kratter wrote:
>>> 
>>>> 
>>>> 
>>>> Hi,
>>>> 
>>>> I gather that cylindrical geometries aren't supported. Is it possible to force yt to read in cylindrical coordinates as though they were cartesian?
>>>> 
>>>> 
>>>> When I try to load an athena vtk in cylindrical, I get:
>>>> 
>>>> In [32]: pf = load("cyl_disk.0001.vtk")
>>>> yt : [INFO     ] 2012-11-15 15:31:26,443 Temporarily setting domain_right_edge = -domain_left_edge. This will be corrected automatically if it is not the case.
>>>> yt : [INFO     ] 2012-11-15 15:31:26,445 Parameters: current_time              = 0.001080635
>>>> yt : [INFO     ] 2012-11-15 15:31:26,445 Parameters: domain_dimensions         = [        -37         128 -2147483648]
>>>> yt : [INFO     ] 2012-11-15 15:31:26,445 Parameters: domain_left_edge          = [ 1.       -1.570796  0.      ]
>>>> yt : [INFO     ] 2012-11-15 15:31:26,445 Parameters: domain_right_edge         = [-1.        1.570796 -0.      ]
>>>> yt : [INFO     ] 2012-11-15 15:31:26,445 Parameters: cosmological_simulation   = 0.0
>>>> 
>>>> 
>>>> This is a 256 by 128 grid, and the dimensions should be -pi/2, pi/2 and 1, 15. 
>>>> 
>>>> 
>>>> Thanks,
>>>> Kaitlin
>>>> 
>>>> 
>>>> 
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