[yt-users] GADGET visualization

Sun Mar 2 16:32:48 PST 2014

Sorry for the delayed reply.  I had forgotten that step, as it turns out.
 Thank you for those links.  I activated the installation, and endeavored
to follow the steps at
http://nbviewer.ipython.org/url/hub.yt-project.org/notebooks/e209c55b6aaa4a9ab12c55422bb3afdc.ipynb

Most of the steps appeared to work, but when I tried to display the
projection plot with pw.show(), nothing appeared.  I think the issue may
lie with the definition of center; is the definition on the website a
general definition, or specific to one simulation?  I am referring to the
lines:

# This is where the halo appears to be centered, although the halo
center on the Agora website is somewhat different

center=np.array([29.754, 32.1, 28.29])

What do these numbers mean?  It is possible they may be different for
my simulations, I would think, but how do we know that a particular
halo is centered there?  Thanks again,

Andrew Weis

On Tue, Feb 25, 2014 at 3:16 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> Did you 'activate' the yt installation?  The install script builds an
> isolated environment using its own python interpreter.
>
> More detail here:
> http://yt-project.org/docs/dev/installing.html#activating-your-installation
>
> The load function is in convenience.py:
>
> https://bitbucket.org/yt_analysis/yt/src/61e6b84f875cc8fcf25b5b1e67ddd501a19daf68/yt/convenience.py?at=yt#cl-29
>
> Cheers,
>
> Nathan
>
> On Tue, Feb 25, 2014 at 12:03 PM, Andrew Philip Weis
> <apw2133 at columbia.edu> wrote:
> > 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
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> >
> >
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