[yt-users] GDF format issue

[Nathan Goldbaum]

Hi Andrea,

In your script, you have that the dimensions of the root grid are 2x2x2,
but you have a grid on AMR level 1 that goes from 0.25 to 0.75 along z.
This means that the grid on AMR level 1 partially overlaps with some of the
root grid zones. This means that there are zones in your root grid that are
"half" refined. In yt's AMR implementation this is not allowed, grids must
be strictly nested (i.e. the boundary of a child grid *must* fall on a zone
boundary of the enclosing parent grid).

I think that's causing your issue.

In principle load_amr_grids should be able to detect this case and raise an
error message that the AMR grid structure is not well-formed.

Was that a formatting error in your test script, or is this what your
"real" data look like?

-Nathan

On Fri, Nov 4, 2016 at 12:58 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> We've opened an issue to track this:
>
> https://bitbucket.org/yt_analysis/yt/issues/1295/gdf-
> writing-and-loading-dataset-yields
>
> -Nathan
>
> On Fri, Nov 4, 2016 at 12:39 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Fri, Nov 4, 2016 at 12:36 PM, Andrea Negri <negri.andre at gmail.com>
>> wrote:
>>
>>> Hi Nathan,
>>>
>>> yt version returns
>>>
>>> ---
>>> Version = 3.4-dev
>>> Changeset = 334cceb2c6e1 (yt) tip
>>> ---
>>>
>>>
>>> Now I'll try to switch to the stable version.
>>>
>>
>> If it's broken there it's broken on stable too.
>>
>> Kacper is taking a look at this right now.
>>
>>
>>>
>>> On 4 November 2016 at 18:32, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>> >
>>> > On Fri, Nov 4, 2016 at 12:28 PM, Nathan Goldbaum <
>>> nathan12343 at gmail.com>
>>> > wrote:
>>> >>
>>> >> Hi Andrea
>>> >>
>>> >> Different how?
>>> >
>>> >
>>> > Ah I see it's in the script you attached, sorry for the confusion.
>>> >
>>> >>
>>> >> I recently fixed a bug in the GDF writer that would cause the field
>>> data
>>> >> for some grids not to get written out properly That fix should be in
>>> yt
>>> >> 3.3.2 so if you're using an older version you might want to update.
>>> Here's
>>> >> the PR with the fix:
>>> >>
>>> >>
>>> >> https://bitbucket.org/yt_analysis/yt/pull-requests/2296/iter
>>> ate-over-all-grids-in-the-gdf-writer/diff
>>> >>
>>> >> Nathan
>>> >>
>>> >> On Friday, November 4, 2016, Andrea Negri <negri.andre at gmail.com>
>>> wrote:
>>> >>>
>>> >>> Hi all,
>>> >>>
>>> >>> As you have already noted, I'm trying to use the GDF format. Just as
>>> >>> an example I created a simple AMR grid, loaded into yt with load_amr
>>> >>> and plotted a slice. I then write down the dataset to a gdf file
>>> using
>>> >>> yt.utilities.grid_data_format.writer.write_to_gdf,  and after
>>> loading
>>> >>> the very same dataset and doint the slice again, the result is
>>> >>> different (verything is in the attached script).
>>> >>>
>>> >>> Curiously, if I load the sedov dataset downloaded from
>>> >>> http://yt-project.org/data/, the slice seems to be OK, I think (but
>>> I
>>> >>> could be wrong) that there is a problem in the gdf writer.
>>> >>>
>>> >>>
>>> >>> Cheers,
>>> >>> Andrea
>>> >
>>> >
>>> >
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>>
>
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