[yt-users] GADGET visualization

Andrew Philip Weis apw2133 at columbia.edu
Tue Feb 25 12:03:41 PST 2014


Thank you for the detailed response, Nathan.  To clarify, this is the YT
method paper?
http://iopscience.iop.org/0067-0049/192/1/9/pdf/0067-0049_192_1_9.pdf

Does the fact that these simulations only contain dark matter affect what
you say at all?

I will probably have more questions in the near future; at the moment,
though, I am confused about where in the source code to find certain
functions.  For instance, the load function appears to be called after we
do:

from yt.mods import *

but when I try this line in the terminal, I get an error that says there is
"no module named yt.mods."  Why might this be?  I downloaded and installed
the source code from:
http://hg.yt-project.org/yt/raw/yt-3.0/doc/install_script.sh   but I cannot
find yt.mods or yt/frontends.  Where would those be?  Is there further
software I may need to install?  Thanks again,

Andrew Weis


On Mon, Feb 24, 2014 at 4:58 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> Hi Andrew,
>
> Thanks for writing.  I'm responding since I've had some experience
> working with yt's SPH frontends.  Matt and others might have more
> information as well.
>
> Support for Gadget data is still not finished.  In the yt-3.0 branch
> of the development repository, you'll should be able to load the data
> and do some basic visualization and analysis tasks.  The data is
> available both in its raw form as particles and also by depositing the
> particle data onto an octree and then visualization and analyzing the
> octree. The first notebook you linked to describes the basic of
> loading, visualizating, and analyzing SPH data.
>
> If you want to work with a more stable codebase (although one that is
> not being actively developed) you should be able to do many analysis
> and viz tasks using the yt-3.0 branch of the main development
> repository: https://bitbucket.org/yt_analysis/yt
>
> The 3.0 branch was a big refactoring of the underlying data selection
> algorithms yt uses to load data off disk.  This made it possible to
> present the same user interface for visualizing datasets from particle
> codes like Gadget, octree AMR codes like Ramses, and patch-based AMR
> codes like Enzo.
>
> Support for SPH smoothing is available in a separate repository.  In
> this experimental development repository we've refactored the code to
> use a symbolic units library to handle unit conversions and detect
> code bugs using dimensional analysis.  We've also completely
> refactored the way frontends are written and fields are set up and
> detected.
>
> If you want to dive in to the code, I'd suggest starting with the
> experimental version of yt.  This may be a bit more rocky at first -
> there might be bugs - but will be more rewarding in the end as this is
> the direction the codebase is going.  The work is ongoing in the
> yt-3.0 branch on Matt Turk's fork of yt:
> https://bitbucket.org/MatthewTurk/yt
>
> In both cases there is unfortunately not a lot of documentation at the
> moment.  This is something that we're working on right now.  Mailing
> list archives as well as the YTEP listing
> (http://ytep.readthedocs.org/) might prove to be useful.
>
> As for your questions about yt internals, I've written some basic
> description below.  I would also encourage you to read the yt method
> paper and to take a look YTEP-0001 and YTEP-0005, which describe the
> new geometry system.
>
> The basic data structure yt uses to represent an on-disk dataset is
> the StaticOutput class.  The SPH frontend defines a GadgetStaticOutput
> class as well as a GadgetHDF5StaticOutput subclass to represent HDF5
> Gadget datasets.  You can create a new StaticOutput instance using the
> 'load' function or by directly instantiating an instance of a
> StaticOutput subclass defined in one of the frontends.  You'll need to
> look at the parameters of the __init__ method to figure out exactly
> how to load the data. For Gadget, the 'load' convenience function only
> works with HDF5 datasets, so if you are have data written in Gadget's
> binary format, you'll need to load your data by calling
> GadgetStaticOutput directly.
>
> StaticOutput instances have as an attribute an instance of
> GeometryHandler.  This class handles the indexing and selection of
> data.  This is really the heart of yt's hard-core numerics, and is
> written in a way that is very accessible at a high level.  If you want
> to dive into the algorithms, I think it would help to look over the
> GeometryHandler class as well as its subclass the
> ParticleGeometryHandler.  That said, yt's interface is more or less
> agnostic to the underlying algorithm used to index the data.
>
> Do you have specific questions about how to load and visualize your
> datasets?
>
> Hope that's helpful and not too much of a manifesto :)
>
> -Nathan
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20140225/ab282bec/attachment.htm>


More information about the yt-users mailing list