[yt-users] GADGET visualization

Andrew Philip Weis apw2133 at columbia.edu
Sat Mar 8 11:22:32 PST 2014


Ok thanks.  I am indeed looking at a cosmology simulation; I am trying to
locate the dark matter filaments in the simulation, using the ORIGAMI code,
and am essentially trying to use YT to confirm that the filament particles
are appropriately identified.  I hope that makes things clearer?

Andrew Weis


On Sun, Mar 2, 2014 at 8:07 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> On Sun, Mar 2, 2014 at 4:32 PM, Andrew Weis <aweis at astro.columbia.edu>
> wrote:
> > 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.
>
> Were you running those steps inside of an IPython notebook?  If so,
> what happens when you add '%matplotlib inline' to the top of the
> notebook?
>
> If you weren't running of a notebook, that is the expected behavior.
> You can save the plot to disk using pw.save() instead.
>
> > 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,
> >
>
> My guess is that Matt chose those as the location of an interesting
> halo in the dataset he was looking at.  You will need to supply a
> different center if you are looking at a different dataset.
>
> If you're looking at a cosmology simulation, you will need to run a
> halo finder to get the positions of the halos you want to look at.
>
> >
> > 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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