[yt-users] RadMC3DWriter and Ramses data

Mon Oct 5 17:26:56 PDT 2015

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<mailto: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<mailto: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<mailto: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<mailto: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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