[yt-users] yt-3.0 density gradient

[Nathan Goldbaum]

Hi Lile,

This is due to a known issue in yt-3.0.  Right now ghost zone generation
has only been implemented for periodic boundary conditions. In yt-2, all
simulations were assumed to have periodic boundary conditions, so it would
incorrectly assume that for your dataset and generate ghost zones as if it
were periodic.

Instead of silently generating incorrect results, yt-3 now issues the error
you're seeing when trying to select data outside of the simulation domain
for non-periodic datasets.

Improving support for ghost zones at the simulation boundary for
non-periodic datasets is on the roadmap for yt 3.1:
https://trello.com/c/lLlqF0zp

You should be able to "cheat" and tell yt that your dataset is periodic
when it really isn't by doing the following:

ds = yt.load(filename)
ds.periodicity = (True, True, True)

Hope that's helpful,

Nathan


On Fri, Aug 8, 2014 at 2:58 PM, Lile Wang <wll9004 at gmail.com> wrote:

>  Hi all,
>
> I am just worried about the problem associated to the density gradient
> field in yt-3.0.
>
> When I was trying to get the gradient of density field along z (actually
> any) direction, I got this error message (last few lines) when calling
> data[ 'density_gradient_z' ]:
>
> ~/lilew/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in
> selector(self)
>     529         if sclass is None:
>     530             raise YTDataSelectorNotImplemented(self._type_name)
> --> 531         self._selector = sclass(self)
>     532         return self._selector
>     533
>
> ~/lilew/yt-x86_64/src/yt-hg/yt/geometry/selection_routines.so in
> yt.geometry.selection_routines.RegionSelector.__init__
> (yt/geometry/selection_routines.c:20276)()
>
> RuntimeError: Error: bad Region in non-periodic domain along dimension 0.
> Region left edge = -0.01171875 code_length, Region right edge = 0.13671875
> code_lengthDataset left edge = 0.
> 0 code_length, Dataset right edge = 1.0 code_length
>
> Similar things happen for the pressure gradient.
>
> The data input was generated by Enzo with AMR. In comparison, it works
> well with yt-2.6, where I refer to the gradient by data[ 'gradDensityZ' ].
>
> Any ideas are appreciated. Thanks!
>
> Cheers,
> Lile
>
>
> -----------------------------------------------------------
> Lile 'Patrick' Wang
> Dept. of Astroph. Sci., Princeton University, NJ 08544 USA
> Website     : http://www.astro.princeton.edu/~lilew/
> Tel (Mobile): +1-(734)-834-3936
> Tel (GVoice): +1-(510)-926-6831
> -----------------------------------------------------------
>
>
> _______________________________________________
> 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/20140808/5d242abb/attachment.html>