[yt-users] RadMC3DWriter and Ramses data
Nathan Goldbaum
nathan12343 at gmail.com
Mon Oct 5 17:31:38 PDT 2015
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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