<div dir="ltr">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 <a href="http://nbviewer.ipython.org/url/hub.yt-project.org/notebooks/e209c55b6aaa4a9ab12c55422bb3afdc.ipynb">http://nbviewer.ipython.org/url/hub.yt-project.org/notebooks/e209c55b6aaa4a9ab12c55422bb3afdc.ipynb</a> <div>
<br></div><div>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: </div>
<div><br></div><div><span class="Apple-style-span" style="font-size:14px;line-height:20px"><pre style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;font-family:Monaco,Menlo,Consolas,'Courier New',monospace;font-size:13px;color:rgb(51,51,51);border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;display:block;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;line-height:20px;word-break:break-all;word-wrap:break-word;white-space:pre-wrap;background-color:transparent;border-top-style:none;border-right-style:none;border-bottom-style:none;border-left-style:none;border-width:initial;border-color:initial">
<span class="c" style="color:rgb(64,128,128);font-style:italic"># This is where the halo appears to be centered, although the halo center on the Agora website is somewhat different</span></pre><pre style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;font-size:13px;border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;display:block;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;line-height:20px;word-break:break-all;word-wrap:break-word;white-space:pre-wrap;background-color:transparent;border-top-style:none;border-right-style:none;border-bottom-style:none;border-left-style:none;border-width:initial;border-color:initial">
<span class="c"><font class="Apple-style-span" face="arial, helvetica, sans-serif" color="#000000"><br></font></span></pre><pre style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;font-size:13px;border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;display:block;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;line-height:20px;word-break:break-all;word-wrap:break-word;white-space:pre-wrap;background-color:transparent;border-top-style:none;border-right-style:none;border-bottom-style:none;border-left-style:none;border-width:initial;border-color:initial">
<font class="Apple-style-span" face="arial, helvetica, sans-serif" color="#000000">center=np.array([29.754, 32.1, 28.29])</font></pre><pre style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;font-size:13px;border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;display:block;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;line-height:20px;word-break:break-all;word-wrap:break-word;white-space:pre-wrap;background-color:transparent;border-top-style:none;border-right-style:none;border-bottom-style:none;border-left-style:none;border-width:initial;border-color:initial">
<font class="Apple-style-span" color="#000000" face="arial, helvetica, sans-serif"><br></font></pre><pre style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;font-size:13px;border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;display:block;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;line-height:20px;word-break:break-all;word-wrap:break-word;white-space:pre-wrap;background-color:transparent;border-top-style:none;border-right-style:none;border-bottom-style:none;border-left-style:none;border-width:initial;border-color:initial">
<font class="Apple-style-span" color="#000000" face="arial, helvetica, sans-serif">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,</font></pre>
<pre style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;font-size:13px;border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;display:block;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;line-height:20px;word-break:break-all;word-wrap:break-word;white-space:pre-wrap;background-color:transparent;border-top-style:none;border-right-style:none;border-bottom-style:none;border-left-style:none;border-width:initial;border-color:initial">
<font class="Apple-style-span" color="#000000" face="arial, helvetica, sans-serif"><br></font></pre><pre style="padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;font-size:13px;border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;display:block;margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;line-height:20px;word-break:break-all;word-wrap:break-word;white-space:pre-wrap;background-color:transparent;border-top-style:none;border-right-style:none;border-bottom-style:none;border-left-style:none;border-width:initial;border-color:initial">
<font class="Apple-style-span" color="#000000" face="arial, helvetica, sans-serif">Andrew Weis</font></pre></span></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Feb 25, 2014 at 3:16 PM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Did you 'activate' the yt installation? The install script builds an<br>
isolated environment using its own python interpreter.<br>
<br>
More detail here:<br>
<a href="http://yt-project.org/docs/dev/installing.html#activating-your-installation" target="_blank">http://yt-project.org/docs/dev/installing.html#activating-your-installation</a><br>
<br>
The load function is in convenience.py:<br>
<a href="https://bitbucket.org/yt_analysis/yt/src/61e6b84f875cc8fcf25b5b1e67ddd501a19daf68/yt/convenience.py?at=yt#cl-29" target="_blank">https://bitbucket.org/yt_analysis/yt/src/61e6b84f875cc8fcf25b5b1e67ddd501a19daf68/yt/convenience.py?at=yt#cl-29</a><br>
<br>
Cheers,<br>
<br>
Nathan<br>
<div class="HOEnZb"><div class="h5"><br>
On Tue, Feb 25, 2014 at 12:03 PM, Andrew Philip Weis<br>
<<a href="mailto:apw2133@columbia.edu">apw2133@columbia.edu</a>> wrote:<br>
> Thank you for the detailed response, Nathan. To clarify, this is the YT<br>
> method paper?<br>
> <a href="http://iopscience.iop.org/0067-0049/192/1/9/pdf/0067-0049_192_1_9.pdf" target="_blank">http://iopscience.iop.org/0067-0049/192/1/9/pdf/0067-0049_192_1_9.pdf</a><br>
><br>
> Does the fact that these simulations only contain dark matter affect what<br>
> you say at all?<br>
><br>
> I will probably have more questions in the near future; at the moment,<br>
> though, I am confused about where in the source code to find certain<br>
> functions. For instance, the load function appears to be called after we<br>
> do:<br>
><br>
> from yt.mods import *<br>
><br>
> but when I try this line in the terminal, I get an error that says there is<br>
> "no module named yt.mods." Why might this be? I downloaded and installed<br>
> the source code from:<br>
> <a href="http://hg.yt-project.org/yt/raw/yt-3.0/doc/install_script.sh" target="_blank">http://hg.yt-project.org/yt/raw/yt-3.0/doc/install_script.sh</a> but I cannot<br>
> find yt.mods or yt/frontends. Where would those be? Is there further<br>
> software I may need to install? Thanks again,<br>
><br>
> Andrew Weis<br>
><br>
><br>
> On Mon, Feb 24, 2014 at 4:58 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>><br>
> wrote:<br>
>><br>
>> Hi Andrew,<br>
>><br>
>> Thanks for writing. I'm responding since I've had some experience<br>
>> working with yt's SPH frontends. Matt and others might have more<br>
>> information as well.<br>
>><br>
>> Support for Gadget data is still not finished. In the yt-3.0 branch<br>
>> of the development repository, you'll should be able to load the data<br>
>> and do some basic visualization and analysis tasks. The data is<br>
>> available both in its raw form as particles and also by depositing the<br>
>> particle data onto an octree and then visualization and analyzing the<br>
>> octree. The first notebook you linked to describes the basic of<br>
>> loading, visualizating, and analyzing SPH data.<br>
>><br>
>> If you want to work with a more stable codebase (although one that is<br>
>> not being actively developed) you should be able to do many analysis<br>
>> and viz tasks using the yt-3.0 branch of the main development<br>
>> repository: <a href="https://bitbucket.org/yt_analysis/yt" target="_blank">https://bitbucket.org/yt_analysis/yt</a><br>
>><br>
>> The 3.0 branch was a big refactoring of the underlying data selection<br>
>> algorithms yt uses to load data off disk. This made it possible to<br>
>> present the same user interface for visualizing datasets from particle<br>
>> codes like Gadget, octree AMR codes like Ramses, and patch-based AMR<br>
>> codes like Enzo.<br>
>><br>
>> Support for SPH smoothing is available in a separate repository. In<br>
>> this experimental development repository we've refactored the code to<br>
>> use a symbolic units library to handle unit conversions and detect<br>
>> code bugs using dimensional analysis. We've also completely<br>
>> refactored the way frontends are written and fields are set up and<br>
>> detected.<br>
>><br>
>> If you want to dive in to the code, I'd suggest starting with the<br>
>> experimental version of yt. This may be a bit more rocky at first -<br>
>> there might be bugs - but will be more rewarding in the end as this is<br>
>> the direction the codebase is going. The work is ongoing in the<br>
>> yt-3.0 branch on Matt Turk's fork of yt:<br>
>> <a href="https://bitbucket.org/MatthewTurk/yt" target="_blank">https://bitbucket.org/MatthewTurk/yt</a><br>
>><br>
>> In both cases there is unfortunately not a lot of documentation at the<br>
>> moment. This is something that we're working on right now. Mailing<br>
>> list archives as well as the YTEP listing<br>
>> (<a href="http://ytep.readthedocs.org/" target="_blank">http://ytep.readthedocs.org/</a>) might prove to be useful.<br>
>><br>
>> As for your questions about yt internals, I've written some basic<br>
>> description below. I would also encourage you to read the yt method<br>
>> paper and to take a look YTEP-0001 and YTEP-0005, which describe the<br>
>> new geometry system.<br>
>><br>
>> The basic data structure yt uses to represent an on-disk dataset is<br>
>> the StaticOutput class. The SPH frontend defines a GadgetStaticOutput<br>
>> class as well as a GadgetHDF5StaticOutput subclass to represent HDF5<br>
>> Gadget datasets. You can create a new StaticOutput instance using the<br>
>> 'load' function or by directly instantiating an instance of a<br>
>> StaticOutput subclass defined in one of the frontends. You'll need to<br>
>> look at the parameters of the __init__ method to figure out exactly<br>
>> how to load the data. For Gadget, the 'load' convenience function only<br>
>> works with HDF5 datasets, so if you are have data written in Gadget's<br>
>> binary format, you'll need to load your data by calling<br>
>> GadgetStaticOutput directly.<br>
>><br>
>> StaticOutput instances have as an attribute an instance of<br>
>> GeometryHandler. This class handles the indexing and selection of<br>
>> data. This is really the heart of yt's hard-core numerics, and is<br>
>> written in a way that is very accessible at a high level. If you want<br>
>> to dive into the algorithms, I think it would help to look over the<br>
>> GeometryHandler class as well as its subclass the<br>
>> ParticleGeometryHandler. That said, yt's interface is more or less<br>
>> agnostic to the underlying algorithm used to index the data.<br>
>><br>
>> Do you have specific questions about how to load and visualize your<br>
>> datasets?<br>
>><br>
>> Hope that's helpful and not too much of a manifesto :)<br>
>><br>
>> -Nathan<br>
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</div></div></blockquote></div><br></div>