[yt-users] GADGET visualization

Andrew Weis aweis at astro.columbia.edu
Sat Mar 8 11:48:58 PST 2014 

Realized I hadn't sent this from my astro account, so sending it from that
one, just to be sure it sends.

Andrew Weis


On Sat, Mar 8, 2014 at 2:22 PM, Andrew Philip Weis <apw2133 at columbia.edu>wrote:

> 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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