[yt-users] analyze flash data with uniform grid

[Ji Suoqing]

Hi Matt,

Thanks for your prompt response!

I'm not quite sure whether my update is successful or not, but it shows:

----------------------------------------------------------------------------
yt module located at:
    /aphelion/jisuoqing/yt-x86_64/src/yt-hg
The supplemental repositories are located at:
    /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental

The current version of the code is:

---
2ace6373d8a3+ (yt) tip
---

This installation CAN be automatically updated.
Reading configuration from  /aphelion/jisuoqing/yt-x86_64/src/yt-hg/.hg/hgrc
searching for changes
no changes found
Can't rebuild modules by myself.
You will have to do this yourself.  Here's a sample commands:

    $ cd /aphelion/jisuoqing/yt-x86_64/src/yt-hg
    $ hg up
    $ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop
Updated successfully.
----------------------------------------------------------------------------

And I've also rebuilt the modules as what the sample tells. 


----------------------------------------------------------------------------
(yt-x86_64)[jisuoqing at hpcmanage yt-hg]$ hg up
0 files updated, 0 files merged, 0 files removed, 0 files unresolved
(yt-x86_64)[jisuoqing at hpcmanage yt-hg]$ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop
PNG_LOCATION: png.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib
FTYPE_LOCATION: freetype.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib
HDF5_LOCATION: hdf5.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib
running develop
running build_scripts
running egg_info
running build_src
build_src
building py_modules sources
building extension "yt.analysis_modules.halo_finding.fof.EnzoFOF" sources
building extension "yt.analysis_modules.halo_finding.hop.EnzoHop" sources
building extension "yt.frontends.ramses._ramses_reader" sources
building extension "yt.utilities.delaunay._delaunay" sources
building extension "yt.utilities.spatial.ckdtree" sources
building extension "yt.utilities.spatial._distance_wrap" sources
building extension "yt.utilities.lib.CICDeposit" sources
building extension "yt.utilities.lib.ContourFinding" sources
building extension "yt.utilities.lib.DepthFirstOctree" sources
building extension "yt.utilities.lib.fortran_reader" sources
building extension "yt.utilities.lib.freetype_writer" sources
building extension "yt.utilities.lib.geometry_utils" sources
building extension "yt.utilities.lib.Interpolators" sources
building extension "yt.utilities.lib.marching_cubes" sources
building extension "yt.utilities.lib.misc_utilities" sources
building extension "yt.utilities.lib.Octree" sources
building extension "yt.utilities.lib.png_writer" sources
building extension "yt.utilities.lib.PointsInVolume" sources
building extension "yt.utilities.lib.QuadTree" sources
building extension "yt.utilities.lib.RayIntegrators" sources
building extension "yt.utilities.lib.VolumeIntegrator" sources
building extension "yt.utilities.lib.grid_traversal" sources
building extension "yt.utilities.data_point_utilities" sources
building extension "yt.utilities.hdf5_light_reader" sources
building extension "yt.utilities.libconfig_wrapper" sources
building extension "yt.visualization._MPL" sources
building data_files sources
build_src: building npy-pkg config files
writing yt.egg-info/PKG-INFO
writing top-level names to yt.egg-info/top_level.txt
writing dependency_links to yt.egg-info/dependency_links.txt
writing entry points to yt.egg-info/entry_points.txt
reading manifest file 'yt.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'yt.egg-info/SOURCES.txt'
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
running scons
Creating /aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/yt.egg-link (link to .)
yt 2.4dev is already the active version in easy-install.pth
Installing yt script to /aphelion/jisuoqing/yt-x86_64/bin
Installing pyro_queue.py script to /aphelion/jisuoqing/yt-x86_64/bin
Installing iyt script to /aphelion/jisuoqing/yt-x86_64/bin
Installing yt_lodgeit.py script to /aphelion/jisuoqing/yt-x86_64/bin

Installed /aphelion/jisuoqing/yt-x86_64/src/yt-hg
Processing dependencies for yt==2.4dev
Finished processing dependencies for yt==2.4dev
----------------------------------------------------------------------------

But the file-load error still remains.

Best wishes,
Suoqing


在 2012-7-28，下午3:35，Matthew Turk <matthewturk at gmail.com> 写道：

> Hi Suoqing,
> 
> On Sat, Jul 28, 2012 at 3:26 PM, Ji Suoqing <jisuoqing at gmail.com> wrote:
>> Hi all,
>> 
>> Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
>> 
>>>>> pf=load('relax_hdf5_chk_0000')
>> Traceback (most recent call last):
>>  File "<stdin>", line 1, in <module>
>>  File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load
>>    return output_type_registry[candidates[0]](*args, **kwargs)
>>  File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__
>>    StaticOutput.__init__(self, filename, data_style)
>>  File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__
>>    self._parse_parameter_file()
>>  File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file
>>    self.min_level = self.parameters["lrefine_min"] -1
>> KeyError: 'lrefine_min'
>> 
>> So, does YT provides a way to deal with the uniform grid?
> 
> If FLASH4 either doesn't set that parameter anymore or had conditional
> parameter setting, that will need to be taken into account in the
> future.  I've checked and it looks like this parameter is optional (it
> will default to L0) and so I've added a check for it.  If it's not
> present, it sets it to be the most lenient.  This was done in the
> current development branch, in changeset 2ace6373d8a3, so you will
> need to update with "yt update".
> 
> Thanks,
> 
> Matt
> 
>> 
>> Thanks for your care and consideration.
>> 
>> Best wishes,
>> Suoqing
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