[yt-users] Fwd: cylindrical coordinates in Athena

[Sam Skillman]

Hi John,

Nope, I've never done any work with binary Athena files.

Sam


On Thu, Nov 15, 2012 at 7:03 PM, John ZuHone <jzuhone at gmail.com> wrote:

> 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-upgradesthat 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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