[yt-users] 2D FLASH data again

[Matthew Turk]

Hi all,

Nathan submitted a fix which looks good to me, but I am holding off on
accepting until after we can get 2D FLASH data into the answer testing
suite.  Because of some inflexibility in the tests, this may take a
short while, but thanks very much to Nathan and John for tracking this
down.

-Matt

On Tue, Sep 18, 2012 at 6:57 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> Hey John,
>
> Thanks for the report.  We've been adjusting the way yt loads 2D FLASH data in response to a report from Ji Suoqing over the weekend.  Clearly things aren't working properly yet.
>
> For now, I would suggest updating to the revision before we made these changes.  To do so, make sure the yt environment is activated and do the following:
>
> $ cd $YT_DEST/src/yt-hg
> $ hg up af06f14fcd9e
> $ python setup.py develop
>
> We'll take a look at this and try to get it fixed soon.
>
> Cheers,
>
> Nathan
>
> On Sep 18, 2012, at 3:44 PM, John Forbes wrote:
>
>> Hi all,
>>
>> I updated yt today, and a problem with my 2D FLASH data has arisen again.
>>
>> As of last week, all of my cells' z values were at
>> pf.domain_left_edge[2], and all the dz values were 1.
>>
>> I think ideally I would want my z-values to be (upper + lower)/2, and
>> my dz-values to be upper-lower, where by upper and lower I mean
>> pf.domain_right_edge[2] and pf.domain_left_edge[2], respectively. So,
>> things were working, just not in precisely the way I would have
>> expected.
>>
>>
>> With the current version of yt ( d77fb0031d39 ) , it appears that I
>> get a range of z-values and dz-values, from 0 to upper/2, with dz = 2
>> z. These appear to be correlated with the refinement level. An example
>> of what happens in this situation when I try to generate a slice plot
>> is shown below. I also attempted to shift the center of the plot
>> collection up by 1.0, but got the same set of errors.  The file which
>> I'm using in the session below is still available here:
>> http://www.ucolick.org/~jforbes/cloud_hdf5_plt_cnt_0000
>>
>> Thank you,
>> John
>>
>>
>>
>>
>>
>>>>> from yt.mods import *
>>>>> pf = load("cloud_hdf5_plt_cnt_0000")
>> yt : [WARNING  ] 2012-09-18 15:18:10,923 integer runtime parameter
>> checkpointfilenumber overwrites a simulation scalar of the same name
>> yt : [INFO     ] 2012-09-18 15:18:10,928 Parameters: current_time
>>        = 0.0
>> yt : [INFO     ] 2012-09-18 15:18:10,928 Parameters: domain_dimensions
>>        = [ 8 32  1]
>> yt : [INFO     ] 2012-09-18 15:18:10,928 Parameters: domain_left_edge
>>        = [ -2.46854420e+22   0.00000000e+00  -2.46854420e+22]
>> yt : [INFO     ] 2012-09-18 15:18:10,928 Parameters: domain_right_edge
>>        = [  2.46854420e+22   1.97483536e+23   2.46854420e+22]
>> yt : [INFO     ] 2012-09-18 15:18:10,929 Parameters:
>> cosmological_simulation   = 0.0
>>>>> pc=PlotCollection(pf)
>> yt : [INFO     ] 2012-09-18 15:18:43,245 Max Value is 1.67330e-26 at
>> -430910425537109360640.0000000000000000
>> 24248504855224609931264.0000000000000000 0.0000000000000000 in grid
>> FLASHGrid_0649 ([8 8 1]) at level 10 (0, 7, 0)
>> yt : [INFO     ] 2012-09-18 15:18:43,245 Created plot collection with
>> default plot-center = [-4.3091042553710936e+20, 2.424850485522461e+22,
>> 0.0]
>>>>> pc.add_slice("Density",2)
>> Traceback (most recent call last):
>>  File "<stdin>", line 1, in <module>
>>  File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py",
>> line 431, in add_slice
>>    center=center, **field_parameters)
>>  File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 1045, in __init__
>>    self._refresh_data()
>>  File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 315, in _refresh_data
>>    self.get_data()
>>  File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 830, in get_data
>>    self._generate_coords()
>>  File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 1079, in _generate_coords
>>    for grid in self._get_grids():
>>  File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
>> line 898, in _get_grids
>>    return ObjectIterator(self, attr='_grids')
>>  File "/Users/jforbes/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
>> line 102, in __init__
>>    raise YTNoDataInObjectError(pobj)
>> yt.utilities.exceptions.YTNoDataInObjectError: The object requested
>> has no data included in it.  It may lie on a grid face.  Try
>> offsetting slightly.
>>>>> dd=pf.h.all_data()
>>>>> print dd['dz'].min(), dd['dz'].max(), dd['z'].min(), dd['z'].max()
>> yt : [INFO     ] 2012-09-18 15:19:27,137 Getting field dz from 3648
>> yt : [INFO     ] 2012-09-18 15:19:28,476 Getting field z from 3648
>> 0.0 2.4685442e+22 0.0 1.2342721e+22
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