[yt-users] 2D FLASH data again

Nathan Goldbaum nathan12343 at gmail.com
Tue Sep 18 15:57:01 PDT 2012


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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