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

[Michael Zingale]

Thanks Nathan, I'll look at that YTEP.  Unfortunately the region fix you
suggested did not work -- the error was the same regardless of the region
(even clipping off more than one zone didn't work).  I'll take a deeper
look at this after I teach this morning.  As a stopgap I may decide to go
back to assuming we are triply periodic, even though that is rarely the
case in our simulations.


On Tue, Apr 15, 2014 at 12:48 AM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> 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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-- 
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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