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/ <http://www.astro.princeton.edu/%7Elilew/> Tel (Mobile): +1-(734)-834-3936 Tel (GVoice): +1-(510)-926-6831 -----------------------------------------------------------
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@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 -----------------------------------------------------------
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Hi Nathan, Yep, this really helps. It is relatively easy to guess that the problem is related to the ghost regions, yet I could not find the exact point about it. Thanks a lot! 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 -----------------------------------------------------------
在 Aug 8, 2014，18:04，Nathan Goldbaum <nathan12343@gmail.com> 写道：
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@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 -----------------------------------------------------------
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