[yt-users] Fwd: cylindrical coordinates in Athena
John ZuHone
jzuhone at gmail.com
Thu Nov 15 18:34:03 PST 2012
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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