[yt-dev] field line tracing problems

[Sam Skillman]

Hi Jeff,

I tried to catch you on IRC but I keep failing. I can't seem to reproduce
this with load_uniform_grid, but haven't yet tried on an AMR simulation.
 Just to be clear, after you integrate the streamlines, you call the
.clean_streamlines() before calling path(stream_number)?

Any chance you could share the data with me to help debug?  Or can we find
a time to hack on this together?

Sorry for all the trouble.

Sam


On Thu, Mar 13, 2014 at 1:08 PM, j s oishi <jsoishi at gmail.com> wrote:

> 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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>>>>>
>>>>>
>>>>
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