Hi Kaitlin, Just go ahead and try the code out on your data to see how it goes, specifically on the 3D data maybe try some projections and whatever other tests you'd like to make sure things look sane. On the basis of that I'll probably accept the PR. Sam, does that sound good to you? Best, John On Nov 16, 2012, at 1:18 PM, Kaitlin Kratter <kaitlin.kratter@jila.colorado.edu> wrote:
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@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@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@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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