[yt-users] cylindrical coordinates in Athena

Sam Skillman samskillman at gmail.com
Fri Nov 16 10:31:44 PST 2012


I think that sounds fine.  I think Kaitlin was working off my fork to begin
with, so it's probably good to go.  I think there are probably things I
could clean up when I get the time, but I unfortunately don't have much of
that right now.


On Fri, Nov 16, 2012 at 11:29 AM, John ZuHone <jzuhone at gmail.com> wrote:

> 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 at 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 at 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 at 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 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
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> yt-users mailing list
> >>>>> yt-users at lists.spacepope.org
> >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users at lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users at lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users at lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20121116/8b4ffe63/attachment.htm>


More information about the yt-users mailing list