[yt-dev] Issue #619: user-defined outputs with Athena (yt_analysis/yt)

[Anonymous]

New issue 619: user-defined outputs with Athena
https://bitbucket.org/yt_analysis/yt/issue/619/user-defined-outputs-with-athena

Anonymous:

Dear Developers,

I would like to visualize/analyze some streaming-nstability simulation outputs created with Athena with yt. The output is a user-defined variable, such as the particle density enhancement. The (2-d) data is written to a .vtk file which I tried to read with yt using the load command. I Immediately get errors. 

Here is the session information:



pf = load("id0/Streaming2d.0000.difdpar.vtk")


yt : [INFO     ] 2013-08-05 15:30:17,851 Temporarily setting domain_right_edge = -domain_left_edge. This will be corrected automatically if it is not the case.
yt : [INFO     ] 2013-08-05 15:30:17,855 Parameters: current_time              = 0
yt : [INFO     ] 2013-08-05 15:30:17,855 Parameters: domain_dimensions         = [64 64  1]
yt : [INFO     ] 2013-08-05 15:30:17,856 Parameters: domain_left_edge          = [-1. -1.  0.]
yt : [INFO     ] 2013-08-05 15:30:17,857 Parameters: domain_right_edge         = [ 1.  1. -0.]
yt : [INFO     ] 2013-08-05 15:30:17,858 Parameters: cosmological_simulation   = 0.0
yt : [WARNING  ] 2013-08-05 15:30:17,860 Dimensionality less than 3: reverting to overlap_proj
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-3-fa5200178679> in <module>()
----> 1 pf = load("id0/Streaming2d.0000.difdpar.vtk")

/home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/convenience.pyc in load(*args, **kwargs)
     75         if c._is_valid(*args, **kwargs): candidates.append(n)
     76     if len(candidates) == 1:
---> 77         return output_type_registry[candidates[0]](*args, **kwargs)
     78     if len(candidates) == 0:
     79         if ytcfg.get("yt", "enzo_db") != '' \

/home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/frontends/athena/data_structures.pyc in __init__(self, filename, data_style, storage_filename, parameters)
    353         # instantiated so that we can make sure we have the correct left
    354         # and right domain edges.
--> 355         self.h
    356 
    357     def _set_units(self):

/home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/data_objects/static_output.pyc in hierarchy(self)
    201                 raise RuntimeError("You should not instantiate StaticOutput.")
    202             self._instantiated_hierarchy = self._hierarchy_class(
--> 203                 self, data_style=self.data_style)
    204         return self._instantiated_hierarchy
    205     h = hierarchy  # alias

/home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/frontends/athena/data_structures.pyc in __init__(self, pf, data_style)
    129         #self.directory = os.path.dirname(self.hierarchy_filename)
    130         self._fhandle = file(self.hierarchy_filename,'rb')
--> 131         AMRHierarchy.__init__(self, pf, data_style)
    132 
    133         self._fhandle.close()

/home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style)
     70 
     71         mylog.debug("Parsing hierarchy.")
---> 72         self._parse_hierarchy()
     73 
     74         mylog.debug("Constructing grid objects.")

/home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/frontends/athena/data_structures.pyc in _parse_hierarchy(self)
    251                 line = f.readline()
    252             f.close()
--> 253             levels[j] = gridread['level']
    254             glis[j,0] = gridread['left_edge'][0]
    255             glis[j,1] = gridread['left_edge'][1]

KeyError: 'level'