Re: [yt-users] yt and PLUTO
Hi Marc (cc: yt-users),
Thanks for your interest in yt! I have not used yt and pluto, but I have used yt with some other Chombo data in the past. I would strongly suggest you join the yt-users mailing list, which you can do here:
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
or dropping by our IRC chat room,
http://yt-project.org/irc.html
I believe Andrew Myers, who is active on yt-users, has the most experience using Chombo data in yt. However, the mailing list is the best way to get help. If you do post to yt-users, please include some details about exactly what is going wrong when you try to load your Pluto data. This will help get you going faster.
take care, and welcome to yt!
yours,
Jeff
On Wed, Mar 6, 2013 at 8:43 AM, Marc Schartmann schartmann@mpe.mpg.de wrote:
Dear Jeff Oishi,
I would very much like to use yt for analyzing my PLUTO simulations. I saw that there is supposed to be support for the Chombo hdf5 files, but it does not seem to work for me (maybe not for PLUTO 4.0?). Do you know of anybody who is working with PLUTO + yt, I might contact?
Thanks a lot.
Best regards from Munich,
Marc
--
Marc Schartmann | Tel. 089-30000-3712 Max-Planck-Institut für | (Tuesday-Thursday) extraterrestrische Physik | Giessenbachstrasse | Fax: 089-30000-3569 85748 Garching | schartmann@mpe.mpg.de
and
Universitätssternwarte | Tel. 089-2180-6028 Scheinerstrasse 1 | (Monday & Friday) 81679 München |
Hi Marc,
I'm not surprised that yt doesn't work quite out-of-the box with Pluto data, but the Chombo HDF5 frontend definitely works, and could probably be made to handle Pluto data with minimal hassle. Probably you just need to do things like specifying the field names, where to find stuff like 'gamma', etc. If you want help with that, I'd be happy to point you to the right places in the code. It would also help if you could provide the traceback for the error you are seeing when you try to load the dataset.
Best, Andrew
On Wed, Mar 6, 2013 at 8:54 AM, j s oishi jsoishi@gmail.com wrote:
Hi Marc (cc: yt-users),
Thanks for your interest in yt! I have not used yt and pluto, but I have used yt with some other Chombo data in the past. I would strongly suggest you join the yt-users mailing list, which you can do here:
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
or dropping by our IRC chat room,
http://yt-project.org/irc.html
I believe Andrew Myers, who is active on yt-users, has the most experience using Chombo data in yt. However, the mailing list is the best way to get help. If you do post to yt-users, please include some details about exactly what is going wrong when you try to load your Pluto data. This will help get you going faster.
take care, and welcome to yt!
yours,
Jeff
On Wed, Mar 6, 2013 at 8:43 AM, Marc Schartmann schartmann@mpe.mpg.de wrote:
Dear Jeff Oishi,
I would very much like to use yt for analyzing my PLUTO simulations. I
saw
that there is supposed to be support for the Chombo hdf5 files, but it
does
not seem to work for me (maybe not for PLUTO 4.0?). Do you know of anybody who is working with PLUTO + yt, I might contact?
Thanks a lot.
Best regards from Munich,
Marc
--
Marc Schartmann | Tel. 089-30000-3712 Max-Planck-Institut für | (Tuesday-Thursday) extraterrestrische Physik | Giessenbachstrasse | Fax: 089-30000-3569 85748 Garching | schartmann@mpe.mpg.de
and
Universitätssternwarte | Tel. 089-2180-6028 Scheinerstrasse 1 | (Monday & Friday) 81679 München |
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Or, if possible, a sample dataset.
On Mar 6, 2013, at 6:41 PM, Andrew Myers atmyers@berkeley.edu wrote:
Hi Marc,
I'm not surprised that yt doesn't work quite out-of-the box with Pluto data, but the Chombo HDF5 frontend definitely works, and could probably be made to handle Pluto data with minimal hassle. Probably you just need to do things like specifying the field names, where to find stuff like 'gamma', etc. If you want help with that, I'd be happy to point you to the right places in the code. It would also help if you could provide the traceback for the error you are seeing when you try to load the dataset.
Best, Andrew
On Wed, Mar 6, 2013 at 8:54 AM, j s oishi jsoishi@gmail.com wrote: Hi Marc (cc: yt-users),
Thanks for your interest in yt! I have not used yt and pluto, but I have used yt with some other Chombo data in the past. I would strongly suggest you join the yt-users mailing list, which you can do here:
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
or dropping by our IRC chat room,
http://yt-project.org/irc.html
I believe Andrew Myers, who is active on yt-users, has the most experience using Chombo data in yt. However, the mailing list is the best way to get help. If you do post to yt-users, please include some details about exactly what is going wrong when you try to load your Pluto data. This will help get you going faster.
take care, and welcome to yt!
yours,
Jeff
On Wed, Mar 6, 2013 at 8:43 AM, Marc Schartmann schartmann@mpe.mpg.de wrote:
Dear Jeff Oishi,
I would very much like to use yt for analyzing my PLUTO simulations. I saw that there is supposed to be support for the Chombo hdf5 files, but it does not seem to work for me (maybe not for PLUTO 4.0?). Do you know of anybody who is working with PLUTO + yt, I might contact?
Thanks a lot.
Best regards from Munich,
Marc
--
Marc Schartmann | Tel. 089-30000-3712 Max-Planck-Institut für | (Tuesday-Thursday) extraterrestrische Physik | Giessenbachstrasse | Fax: 089-30000-3569 85748 Garching | schartmann@mpe.mpg.de
and
Universitätssternwarte | Tel. 089-2180-6028 Scheinerstrasse 1 | (Monday & Friday) 81679 München |
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Dear Jeff, Andrew, Nathan and all,
thanks a lot.
I have put a sample data file here (including parameter files, at least the pluto.ini seems to be read):
http://www.mpe.mpg.de/~mschartm/download/
data.0000.hdf5 pluto.ini definitions.h
And the error message I receive:
pf = load("data.0000.hdf5")
yt : [WARNING ] 2013-03-07 09:16:19,293 Setting 1.0 in code units to be 1.0 cm yt : [WARNING ] 2013-03-07 09:16:19,293 No time units. Setting 1.0 = 1 second. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/data01/mschartm/software/yt/yt-x86_64/src/yt-hg/yt/ convenience.py", line 77, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/data01/mschartm/software/yt/yt-x86_64/src/yt-hg/yt/frontends/ chombo/data_structures.py", line 225, in __init__ StaticOutput.__init__(self,filename,data_style) File "/data01/mschartm/software/yt/yt-x86_64/src/yt-hg/yt/ data_objects/static_output.py", line 97, in __init__ self._set_units() File "/data01/mschartm/software/yt/yt-x86_64/src/yt-hg/yt/frontends/ chombo/data_structures.py", line 249, in _set_units self.units['unitary'] = 1.0 / (self.domain_right_edge - self.domain_left_edge).max() AttributeError: 'ChomboStaticOutput' object has no attribute 'domain_right_edge'
It would be great if you could point me to the locations where I need to adapt the code. This would save me a lot of time.
Thanks a lot and best wishes,
Marc
On Mar 7, 2013, at 3:45 AM, Nathan Goldbaum wrote:
Or, if possible, a sample dataset.
On Mar 6, 2013, at 6:41 PM, Andrew Myers atmyers@berkeley.edu wrote:
Hi Marc,
I'm not surprised that yt doesn't work quite out-of-the box with Pluto data, but the Chombo HDF5 frontend definitely works, and could probably be made to handle Pluto data with minimal hassle. Probably you just need to do things like specifying the field names, where to find stuff like 'gamma', etc. If you want help with that, I'd be happy to point you to the right places in the code. It would also help if you could provide the traceback for the error you are seeing when you try to load the dataset.
Best, Andrew
On Wed, Mar 6, 2013 at 8:54 AM, j s oishi jsoishi@gmail.com wrote: Hi Marc (cc: yt-users),
Thanks for your interest in yt! I have not used yt and pluto, but I have used yt with some other Chombo data in the past. I would strongly suggest you join the yt-users mailing list, which you can do here:
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
or dropping by our IRC chat room,
http://yt-project.org/irc.html
I believe Andrew Myers, who is active on yt-users, has the most experience using Chombo data in yt. However, the mailing list is the best way to get help. If you do post to yt-users, please include some details about exactly what is going wrong when you try to load your Pluto data. This will help get you going faster.
take care, and welcome to yt!
yours,
Jeff
On Wed, Mar 6, 2013 at 8:43 AM, Marc Schartmann <schartmann@mpe.mpg.de
wrote: Dear Jeff Oishi,
I would very much like to use yt for analyzing my PLUTO
simulations. I saw
that there is supposed to be support for the Chombo hdf5 files,
but it does
not seem to work for me (maybe not for PLUTO 4.0?). Do you know of anybody who is working with PLUTO + yt, I might
contact?
Thanks a lot.
Best regards from Munich,
Marc
--
Marc Schartmann | Tel. 089-30000-3712 Max-Planck-Institut für | (Tuesday-Thursday) extraterrestrische Physik | Giessenbachstrasse | Fax: 089-30000-3569 85748 Garching | schartmann@mpe.mpg.de
and
Universitätssternwarte | Tel. 089-2180-6028 Scheinerstrasse 1 | (Monday & Friday) 81679 München |
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Marc,
Thanks for providing that sample dataset. I just submitted a pull request that should add basic support for reading in Pluto datasets, provided they are in the Chombo HDF5 output format. You should be able to get it once it's accepted. This isn't super well-tested yet, but at least I can make slices and projections from the dataset you sent in:
from yt.mods import *
pf = load('data.0000.hdf5') sl = SlicePlot(pf, 0, 'Density') sl.annotate_grids() sl.save()
and
from yt.mods import *
pf = load('data.0000.hdf5') proj = ProjectionPlot(pf, 0, 'Density') proj.save()
You'll probably want to modify things a bit, but that should at least get you started. The files you'll most likely need to change are these three:
yt/frontends/pluto/data_structures.py yt/frontends/pluto/fields.py yt/frontends/pluto/io.py
"data_structures.py" is where the grid levels and locations are read in from the hdf5 file, and also where the pluto.ini file is parsed for the domain dimensions. "fields.py" is where the basic fields are set up. Right now it mostly just includes the ones in the hdf5 file, but you'll probably want to modify this to define some derived fields and also if you have a data dump with another set of physics options. Finally, "io.py" contains the methods that actually read the data from the hdf5 file.
You can look at the other frontends to see how all this stuff works. You might also find these pieces of documentation helpful:
http://yt-project.org/doc/analyzing/creating_derived_fields.html http://yt-project.org/doc/advanced/creating_frontend.html
Good luck, and please feel free to email the list if you need any help.
Andrew
On Thu, Mar 7, 2013 at 12:38 AM, Marc Schartmann schartmann@mpe.mpg.dewrote:
Dear Jeff, Andrew, Nathan and all,
thanks a lot.
I have put a sample data file here (including parameter files, at least the pluto.ini seems to be read):
http://www.mpe.mpg.de/~mschartm/download/
data.0000.hdf5 pluto.ini definitions.h
And the error message I receive:
pf = load("data.0000.hdf5")
yt : [WARNING ] 2013-03-07 09:16:19,293 Setting 1.0 in code units to be 1.0 cm yt : [WARNING ] 2013-03-07 09:16:19,293 No time units. Setting 1.0 = 1 second. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/data01/mschartm/software/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 77, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/data01/mschartm/software/yt/yt-x86_64/src/yt-hg/yt/frontends/chombo/data_structures.py", line 225, in __init__ StaticOutput.__init__(self,filename,data_style) File "/data01/mschartm/software/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 97, in __init__ self._set_units() File "/data01/mschartm/software/yt/yt-x86_64/src/yt-hg/yt/frontends/chombo/data_structures.py", line 249, in _set_units self.units['unitary'] = 1.0 / (self.domain_right_edge - self.domain_left_edge).max() AttributeError: 'ChomboStaticOutput' object has no attribute 'domain_right_edge'
It would be great if you could point me to the locations where I need to adapt the code. This would save me a lot of time.
Thanks a lot and best wishes,
Marc
On Mar 7, 2013, at 3:45 AM, Nathan Goldbaum wrote:
Or, if possible, a sample dataset.
On Mar 6, 2013, at 6:41 PM, Andrew Myers atmyers@berkeley.edu wrote:
Hi Marc,
I'm not surprised that yt doesn't work quite out-of-the box with Pluto data, but the Chombo HDF5 frontend definitely works, and could probably be made to handle Pluto data with minimal hassle. Probably you just need to do things like specifying the field names, where to find stuff like 'gamma', etc. If you want help with that, I'd be happy to point you to the right places in the code. It would also help if you could provide the traceback for the error you are seeing when you try to load the dataset.
Best, Andrew
On Wed, Mar 6, 2013 at 8:54 AM, j s oishi jsoishi@gmail.com wrote:
Hi Marc (cc: yt-users),
Thanks for your interest in yt! I have not used yt and pluto, but I have used yt with some other Chombo data in the past. I would strongly suggest you join the yt-users mailing list, which you can do here:
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
or dropping by our IRC chat room,
http://yt-project.org/irc.html
I believe Andrew Myers, who is active on yt-users, has the most experience using Chombo data in yt. However, the mailing list is the best way to get help. If you do post to yt-users, please include some details about exactly what is going wrong when you try to load your Pluto data. This will help get you going faster.
take care, and welcome to yt!
yours,
Jeff
On Wed, Mar 6, 2013 at 8:43 AM, Marc Schartmann schartmann@mpe.mpg.de wrote:
Dear Jeff Oishi,
I would very much like to use yt for analyzing my PLUTO simulations. I
saw
that there is supposed to be support for the Chombo hdf5 files, but it
does
not seem to work for me (maybe not for PLUTO 4.0?). Do you know of anybody who is working with PLUTO + yt, I might contact?
Thanks a lot.
Best regards from Munich,
Marc
--
Marc Schartmann | Tel. 089-30000-3712 Max-Planck-Institut für | (Tuesday-Thursday) extraterrestrische Physik | Giessenbachstrasse | Fax: 089-30000-3569 85748 Garching | schartmann@mpe.mpg.de
and
Universitätssternwarte | Tel. 089-2180-6028 Scheinerstrasse 1 | (Monday & Friday) 81679 München |
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (4)
-
Andrew Myers -
j s oishi -
Marc Schartmann -
Nathan Goldbaum