[yt-users] cylindrical coordinates in Athena

[Kaitlin Kratter]

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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