[yt-users] 2D FLASH data again

John Forbes jforbes at ucolick.org
Tue Sep 18 15:44:24 PDT 2012


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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