[yt-dev] problem with non-periodic domain and rendering

Nathan Goldbaum nathan12343 at gmail.com
Mon Apr 14 21:48:25 PDT 2014


There is an open YTEP about this issue:
http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-0006.html


On Mon, Apr 14, 2014 at 9:38 PM, Sam Skillman <samskillman at gmail.com> wrote:

> Hi Michael,
>
> Unfortunately the rendering framework currently relies upon being able to
> create a smoothed covering grid to calculate vertex centered data, which
> has not been implemented for non-periodic boundary conditions.  If the
> quality of the rendering using no_ghost=True is not good enough, then
> perhaps try creating a region that is the entire volume except the outer
> cell:
>
> root_dds = pf.domain_width/pf.domain_dimensions
> half_w = pf.domain_width/2. - root_dds
> reg = pf.region(pf.domain_center, pf.domain_center-half_w,
> pf.domain_center+half_w)
>
> then supply that reg to the camera as data_source=reg in the constructor.
>  This requires being on yt-3.0, which I think you are.
>
> I *think* that should allow the no_ghost=False to get the vertex centered
> data using a smoothed covering grid the size of the full domain (but not
> beyond).
>
> The longer term fix is to use meaningful boundary conditions to calculate
> covering grids that extend beyond the domain.  I'm not sure what the
> roadmap for that is...
>
> Best,
> Sam
>
>
> On Mon, Apr 14, 2014 at 7:05 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:
>
>>
>>
>> On Monday, April 14, 2014, Michael Zingale <
>> michael.zingale at stonybrook.edu> wrote:
>>
>>> Recently I made the Maestro BoxLib frontend set the correct boundary
>>> periodicity for a data set, and I can confirm this when I load the data in
>>> yt and look at periodicity.  However, when I try to volume render, with
>>> no_ghost=False, I get an error in the non-periodic direction (we are
>>> periodic in x and y, and non-periodic in z).
>>>
>>> The error is:
>>>
>>> Error: bad Region in non-periodic domain: -24.0 code_length 0.0
>>> code_length 408.0 code_length 4608.0 code_length
>>>
>>> for reference, the domain size is:
>>>
>>> Parameters: domain_left_edge          = [ 0.  0.  0.]
>>> Parameters: domain_right_edge         = [ 1536.  1536.  4608.]
>>>
>>> (aside, these should be cm, but the error reports them as code_length --
>>> should I be setting that somwhere in the frontend?  we are always CGS).
>>>
>>>
>> I can't speak to the volume rendering issue but this is the as-designed
>> behavior.  This has to be code_length because other codes do not have CGS
>> as the internal unit system and this code has to work for all frontends,
>> irrespective of the internal unit system.
>>
>>
>>> Any thoughts on what I may be missed setting up for non-periodic BCs is
>>> appreciated.
>>>
>>> Mike
>>>
>>> --
>>> Michael Zingale
>>> Associate Professor
>>>
>>> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
>>> 11794-3800
>>> *phone*:  631-632-8225
>>> *e-mail*: Michael.Zingale at stonybrook.edu
>>> *web*: http://www.astro.sunysb.edu/mzingale
>>>
>>
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>>
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