[yt-users] RadMC3DWriter and Ramses data

Andrew Myers atmyers2 at gmail.com
Mon Oct 5 18:11:53 PDT 2015 

I did the merge and updated the pull request so that it has that bugfix.
Now the revision hash is 0b2aab9
<https://bitbucket.org/atmyers/yt/commits/0b2aab975b9e24b723bebc9df4fc9161b4342da9?at=yt>,
but other than that you should be able to update to it using the same
process as before.

Best,
Andrew

On Mon, Oct 5, 2015 at 5:31 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> This is an issue that was fixed a while ago, but after Andrew opened his
> pull request. Since you're updating to the PR head, you're updating to a
> version before the fix was applied.
>
> You should be able to avoid the error by executing the clean.sh script at
> the root of the yt repository:
>
> $ bash clean.sh
>
> And then rebuilding yt:
>
> $ python setup.py develop
>
> You could also temporarily merge Andrew's pull request with the latest
> development version, but you might need to resolve some merge conflicts.
> Andrew could also do the merge and update his PR.
>
> HTH,
>
> Nathan
>
> On Mon, Oct 5, 2015 at 7:26 PM, Marc Schartmann <mschartmann at swin.edu.au>
> wrote:
>
>> Thanks!
>> Unfortunately, it didn’t work out for me.
>> After merging the PR locally into a new installation of yt (with the
>> standard install script), I get the following
>> error already after importing yt.
>>
>>
>>
>> Python 2.7.9 (default, Oct  6 2015, 10:48:03)
>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-16)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> import yt
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File
>> "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/__init__.py",
>> line 132, in <module>
>>     frontends = _frontend_container()
>>   File
>> "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/frontends/api.py",
>> line 48, in __init__
>>     setattr(self, frontend, importlib.import_module(_mod))
>>   File
>> "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/importlib/__init__.py",
>> line 37, in import_module
>>     __import__(name)
>>   File
>> "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/frontends/artio/api.py",
>> line 17, in <module>
>>     from .data_structures import \
>>   File
>> "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/frontends/artio/data_structures.py",
>> line 22, in <module>
>>     from ._artio_caller import \
>>   File "yt/geometry/particle_deposit.pxd", line 98, in init
>> yt.frontends.artio._artio_caller (yt/frontends/artio/_artio_caller.c:27347)
>> ValueError: yt.geometry.particle_deposit.ParticleDepositOperation has the
>> wrong size, try recompiling
>>
>>
>>
>>
>>
>> On 6 Oct 2015, at 5:42 am, Andrew Myers <atmyers2 at gmail.com> wrote:
>>
>> Hi Marc,
>>
>> In that case, you should be able to try out the PR by doing:
>>
>> 1. Make sure yt is activated
>> 2. cd $YT_DEST/src/yt-hg/
>> 3. hg pull -r 7674674 https://bitbucket.org/atmyers/
>> 4. hg update -C 7674674
>> 5. python setup.py develop
>>
>> The "-C" option to hg update will wipe any uncommited changes in your
>> working copy, so be wary.
>>
>> -Andrew
>>
>> On Sun, Oct 4, 2015 at 10:57 PM, Marc Schartmann <mschartmann at swin.edu.au
>> > wrote:
>>
>>> Thanks a lot.
>>> I installed the Dev branch via the install script.
>>>
>>>
>>>
>>>
>>>
>>> On 5 Oct 2015, at 2:41 pm, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>> There's an open pull request that adds support for actree style outputs
>>> to the radmc3d exporter:
>>>
>>>
>>> https://bitbucket.org/yt_analysis/yt/pull-requests/1688/wip-adding-support-for-octree-style-output
>>>
>>> If you merge that pull request in locally you could try it out. If you
>>> share how you've set up your yt installation (install script? pip? from a
>>> mercurial checkout? anaconda?) one of us could give instructions on how to
>>> test out the PR.
>>>
>>> On Sun, Oct 4, 2015 at 10:30 PM, Marc Schartmann <
>>> mschartmann at swin.edu.au> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I am trying to export the density distribution from a RAMSES run to
>>>> RADMC-3D using RadMC3DWriter.
>>>> Whereas the example with the “StarParticle” data set works perfectly,
>>>> it fails for any RAMSES data
>>>> I tried (e.g. the “ramses_mhd_amr” one).
>>>>
>>>> Below is the output, complaining about a missing attribute in the
>>>> RAMSES frontend.
>>>> I am not a yt expert, any help with how to fix this would be
>>>> appreciated.
>>>>
>>>> Thanks a lot.
>>>>
>>>> Best wishes,
>>>>
>>>> Marc
>>>>
>>>>
>>>>
>>>> >>> writer = RadMC3DWriter(ds)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,236 Loading field plugins.
>>>> yt : [INFO     ] 2015-10-05 14:20:04,237 Loaded angular_momentum (8 new
>>>> fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,237 Loaded astro (15 new fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,237 Loaded cosmology (22 new
>>>> fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,238 Loaded fluid (63 new fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,238 Loaded fluid_vector (95 new
>>>> fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded geometric (111 new
>>>> fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded local (111 new fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded magnetic_field (119 new
>>>> fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded my_plugins (119 new
>>>> fields)
>>>> yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded species (121 new fields)
>>>> Traceback (most recent call last):
>>>>   File "<stdin>", line 1, in <module>
>>>>   File
>>>> "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py",
>>>> line 148, in __init__
>>>>     sorted_grids = sorted(ds.index.grids, key=lambda x: x.Level)
>>>> AttributeError: 'RAMSESIndex' object has no attribute 'grids'
>>>>
>>>>
>>>>
>>>>
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>>>>
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