[yt-dev] field line tracing problems

j s oishi jsoishi at gmail.com
Thu Mar 13 13:08:57 PDT 2014


Hi Sam,

Thanks for the tips. Unfortunately, I sat down this afternoon to implement
this fix, but it doesn't seem to help at all. Here's what I tried, in diff
format:

http://paste.yt-project.org/show/4377/

I also moved the launching plane 2 root grid cells away from the left edge
of the grid. I get exactly the same results. I wasn't quite sure from
reading the code how many ghost cells the code uses to construct the vertex
data; I assumed it only uses one. Thus, I would think moving the launch
point 2 cells away from the edge would alleviate the problem if it were a
vertex centering issue.

Do you have any further suggestions?

thanks,

Jeff


On Tue, Mar 11, 2014 at 1:14 AM, Sam Skillman <samskillman at gmail.com> wrote:

> Hi Jeff,
>
> (Offline we went back and forth a bit, I think what we came to was
> probably right. I just want to follow up here.)
>
> The issue seems to be that during the construction of vertex-centered
> data, the periodicity of the fields are assumed, and the streamlines go
> nuts.  The ideal fix is to get non-periodic vertex-centered data working,
> but that might take a bit. The quick fix/hack is to modify either the
> get_vertex_centered_data function in yt/data_objects/grid_patch.py or the
> logic in _integrate_through_brick in yt/visualization/streamlines.py.  You
> could cut off the integration when it gets close to dx away from the
> left/right domain edges.
>
> Sorry this was buried, we should probably raise some sort of warning if
> the simulation data is not periodic.
>
> Sam
>
>
> On Fri, Mar 7, 2014 at 3:19 PM, j s oishi <jsoishi at gmail.com> wrote:
>
>> HI Sam,
>>
>> Nope, that gives identical results. Any other thoughts?
>>
>> j
>>
>>
>> On Fri, Mar 7, 2014 at 5:15 PM, Sam Skillman <samskillman at gmail.com>wrote:
>>
>>> Hi Jeff,
>>>
>>> After integrate_trhough_volume, can you call:
>>> streamlines.clean_streamlines()
>>>
>>> In reading this function, I think it will fail since with it complaining
>>> about not having a .magnitudes, so perhaps first edit that function to take
>>> out the references to self.magnitudes?
>>>
>>> The reason I suggest this is that I don't see where in your script it
>>> goes through and cleans up the ones that left the domain.
>>>
>>> If that doesn't help, let me know and I'll dive further in to this.
>>>
>>> Sorry for the hassle,
>>> Sam
>>>
>>>
>>>
>>> On Fri, Mar 7, 2014 at 1:34 PM, j s oishi <jsoishi at gmail.com> wrote:
>>>
>>>> Hi All (especially Sam),
>>>>
>>>> I'm trying to understand some behavior in the streamlines that I don't
>>>> completely understand. I've documented the problem in a notebook here:
>>>>
>>>> https://hub.yt-project.org/nb/2tmwor
>>>>
>>>> The notebook has a full statement of the problem. In essense, I'm not
>>>> sure I understand why streams that I believe should terminate instantly
>>>> upon launch (because they should walk directly out of the box) have
>>>> thousands of elements in them (instead of one). I assume there are one or
>>>> more misconceptions in my understanding, and I'd really welcome any
>>>> suggestions.
>>>>
>>>> thanks,
>>>>
>>>> Jeff
>>>>
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