<div dir="ltr">Hi Tim,<div><br></div><div>I think you're correct. Indeed, there is such a filter in the code. In the context that this code is being used, the domain is indeed defined in [0, rL]. Your suggestion seems reasonable, but it may be a little more involved, because, that's how the code knows to produce ghost regions across periodic boundaries and we will need to make sure that [0,rL] is not being assumed anywhere else in the code.</div>
<div><br></div><div>I'll take a look at that.</div><div><br></div><div>Cheers,</div><div>George</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Sep 7, 2013 at 2:08 AM, Tim Haines <span dir="ltr"><<a href="mailto:thaines@astro.wisc.edu" target="_blank">thaines@astro.wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi, George.<br>
<br>
I was able to track down the issue. In
ParticleDistribute::readFromBlockFile, there is a filter to
determine the 'active' particles (near line 1300). It requires that
the components of the positions of each particle lie within the
components of the minAlive/maxAlive values (currently set to 0 and
rL, respectively). However, the Gadget2 coordinate system uses an
origin that lies between the two galaxies I was simulating. Hence,
many of the coordinates lied well outside of the [0,rL] boundary
(almost all were negative). Removing the bounding box filter, I get
the expected (and correct!) results (attached; colored by particle
type (tag) - pink is disk, white/blue are dark matter halo).<br>
<br>
My interpretation of this behaviour is that, in general, the
bounding box filter is necessary to ensure only those particles
which the user cares about are rendered. Is this true? If so, the
enforcement of a physical box with **only** positive coordinate
values seems unnecessarily constrained. For tree codes such as
Gadget2, this is especially true since there is no box at all.<br>
<br>
I think the easiest fix is to tweak the interface to allow the user
to specify the bounds of the simulation box rather than relying on
the implicit use of [0,rL].<br>
<br>
Thoughts?<br>
<br>
Many thanks.<span class="HOEnZb"><font color="#888888"><br>
<br>
- Tim<br>
</font></span><br>
P.S. The resulting movie looks great! I really want to use ParaView
for all my simulation visualizations because of the ease and quality
of the movies it makes. I am hopeful we can get Gadget2 to work with
the current importer without too much trouble.<div><div class="h5"><br>
<br>
<br>
<br>
<div>On 09/03/2013 10:25 AM, George Zagaris
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Tim,
<div><br>
</div>
<div>I was able to open the dataset you provided. Here are a
couple of suggestions:</div>
<div><br>
</div>
<div>(1) Make sure to uncheck the "Cosmo Format" checkbox --
this will ensure that the underlying reader will read in the
data as a Gadget file.</div>
<div><br>
</div>
<div>(2) Set "rL", i.e., the box-size of the simulation data
accordingly</div>
<div><br>
</div>
<div>(3) Set overlap to 0 -- This parameter creates ghost zones
between inter-processor and periodic boundaries which you may
need if you are running this in parallel, depending on what
you want to do after you read in the data.</div>
<div><br>
</div>
<div>Attached is an image of what the output looks like when I
do the above with rL=100.</div>
<div><br>
</div>
<div>Best,</div>
<div>George</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
On Sat, Aug 31, 2013 at 11:04 PM, Tim Haines <span dir="ltr"><<a href="mailto:thaines@astro.wisc.edu" target="_blank">thaines@astro.wisc.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> @David,<br>
<br>
I put a snapshot file on github ( <a href="https://github.com/hainest/Gadget2_test" target="_blank">https://github.com/hainest/Gadget2_test</a>).
Let me know if you need more of them.<br>
<br>
@George,<br>
<br>
My apologies, I realize now that my description wasn't
specific enough. I put a screenshot of the snapshot in the
github repo I linked above. When I color the particles by
mass, it appears that they are being rendered using the
velocity values rather than the position values to
determine their coordinate in the volume. I hope that
clarifies things a bit more.<br>
<br>
Many thanks for all of your help!<br>
<br>
- Tim<br>
<br>
<br>
<div>On 08/31/2013 11:00 AM, <a href="mailto:paraview-request@paraview.org" target="_blank">paraview-request@paraview.org</a>
wrote:<br>
</div>
<blockquote type="cite">
<pre>Message: 2
Date: Sat, 31 Aug 2013 11:19:17 -0400
From: George Zagaris <a href="mailto:george.zagaris@kitware.com" target="_blank"><george.zagaris@kitware.com></a>
Subject: Re: [Paraview] viewing Gadget2 simulations
To: Tim Haines <a href="mailto:thaines@astro.wisc.edu" target="_blank"><thaines@astro.wisc.edu></a>
Cc: ParaView <a href="mailto:paraview@paraview.org" target="_blank"><paraview@paraview.org></a>
Message-ID:
<a href="mailto:CAP6Wa3gkiTtmJHnOKALccaM7vk46us5q=8A6evz+KWdTOXaSgg@mail.gmail.com" target="_blank"><CAP6Wa3gkiTtmJHnOKALccaM7vk46us5q=8A6evz+KWdTOXaSgg@mail.gmail.com></a>
Content-Type: text/plain; charset="iso-8859-1"
Hi Tim,
I believe the position vector is used as the xyz position of the particles
that are being rendered, so, you cannot color by the position. Do you see
any particles when you open the file?
Best,
George
------------------------------
Message: 3
Date: Sat, 31 Aug 2013 11:19:35 -0400
From: David E DeMarle <a href="mailto:dave.demarle@kitware.com" target="_blank"><dave.demarle@kitware.com></a>
Subject: Re: [Paraview] viewing Gadget2 simulations
To: Tim Haines <a href="mailto:thaines@astro.wisc.edu" target="_blank"><thaines@astro.wisc.edu></a>
Cc: <a href="mailto:paraview@paraview.org" target="_blank">"paraview@paraview.org"</a> <a href="mailto:paraview@paraview.org" target="_blank"><paraview@paraview.org></a>
Message-ID:
<a href="mailto:CANjZAi9cQtyYszXBa1z8xgr+HKAzGOd5g-Z6nG85vMyHR_4o=g@mail.gmail.com" target="_blank"><CANjZAi9cQtyYszXBa1z8xgr+HKAzGOd5g-Z6nG85vMyHR_4o=g@mail.gmail.com></a>
Content-Type: text/plain; charset="iso-8859-1"
Can you share or point us to a url for a small Gadget2 data set that we can
try with?
David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: <a href="tel:518-881-4909" value="+15188814909" target="_blank">518-881-4909</a>
</pre>
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