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@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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