[yt-users] Fwd: cylindrical coordinates in Athena

[John ZuHone]

Hi Sam,

I'll definitely be up for testing this. 

Kaitlin,

I agree that we should support binary files as well. I'd be happy to work on that (Sam, I'm not sure if you've done any legwork on this already).

Best,

John

On Nov 15, 2012, at 6:14 PM, Sam Skillman <samskillman at gmail.com> wrote:

> Hi all,
> 
> I just posted a PR: https://bitbucket.org/yt_analysis/yt/pull-request/343/athena-upgrades that combines some work that Stephanie Tonnesen and I did a while back to fix some various ways of reading in Athena data.  It doesn't address the cylindrical data (unless it is somehow does coincidentally!), but I figured there might be a bit of momentum here and I should get this code PR'd before it bitrots away into nothingness.
> 
> Cheers!
> Sam
> 
> 
> On Thu, Nov 15, 2012 at 6:05 PM, Kaitlin Kratter <kaitlin.kratter at jila.colorado.edu> wrote:
> Hi John,
> 
> I've put the inputs file and the first output file in vtk and binary format at:
> 
> http://jila.colorado.edu/~kakr3691/Athena/
> 
> I'm using the development branch (though not necessarily up to date). One thing Matt and I discussed was that using the athena binary data might ultimately be better than the vtk files. My uneducated guess is that the binary data would read in like the 2D cartesian, much like Flash.
> 
> -Kaitlin
> 
> 
> 
> On Nov 15, 2012, at 3:49 PM, John ZuHone <jzuhone at gmail.com> wrote:
> 
>> Hi Kaitlin,
>> 
>> At the moment yt supports 2D and 3D cartesian data for Athena (the former only very recently in the yt development tree). 
>> 
>> True cylindrical coordinate support (for all codes) is planned for yt 3.0. FLASH 2D cylindrical reads in fine, but this is mostly by accident since the data format in the file is the same as 2D cartesian. I'm guessing this means that the Athena vtk files for cylindrical coordinates are set up slightly differently from the cartesian coordinates.
>> 
>> Are you using the stable or development version of yt? We might be able to get something working along the same lines as FLASH if you have a file you wouldn't mind providing, as a stepping-stone to true support for cylindrical coordinates. 
>> 
>> 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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