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Hi, George.<br>
<br>
I had noticed the visit bridge subsystem while perusing the
codebase, but I wasn't sure if it was used or not. I have it working
now, but I made a small modification to the Cosmo Gadget reader that
really makes things very nice. By changing the tag attribute from
the particle ID to the particle type (i.e., dark matter, gas, stars,
etc.) I am able to use the threshold mechanism to show only the
particle types I want. I have attached an example image showing only
the disk stars from the simulation output I provided previously.
Once I add gas to my simulations, I can then use the tag to colorize
the particles to further distinguish gas and stars. This isn't
possible to do with the visit bridge as it does not store the mass
(or if it does, it does not show it as a colorization value).<br>
<br>
This change really only works because I can ignore the particle IDs
as my particles are not split across multiple input files, so it's
not really a production-ready solution to getting Gadget
visualizations into ParaView.<br>
<br>
Let me know if I can be of any help with testing ParaView changes
with Gadget data.<br>
<br>
Many thanks for all of your help.<br>
<br>
- Tim<br>
<br>
P.S. An oddity I noticed between the Cosmo Gadget reader and the
Visit Bridge one is that the Visit Bridge reader expects the Gadget2
"enhanced" snapshot format (i.e., SnapFormat=2), but expects the
file extension '.gadget'. While the Cosmo Reader uses the old Gadget
format (i.e., SnapFormat=1), but expects the file extension
'.gadget2'. It's only a small wart, though!<br>
<br>
<br>
<div class="moz-cite-prefix">On 09/12/2013 01:53 PM, George Zagaris
wrote:<br>
</div>
<blockquote
cite="mid:CAP6Wa3iR5VS0ogM49BirvPw2VK9cK29jgudQoL4Hzgc-9BPxxg@mail.gmail.com"
type="cite">
<div dir="ltr">By the way, another alternative is to enable
VisItBridge -- turn PARAVIEW_USE_VISITBRIDGE to ON when you
build ParaView -- and use the Gadget reader that is available
through visit bridge. Currently, it expects a "*.gadget"
extension. Attached is a figure of the dataset you shared with
us, opened with that reader. This might be a better alternative
in the short term.
<div>
<br>
</div>
<div>Best,</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 moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true" href="mailto:george.zagaris@kitware.com" target="_blank"><george.zagaris@kitware.com></a>
Subject: Re: [Paraview] viewing Gadget2 simulations
To: Tim Haines <a moz-do-not-send="true" href="mailto:thaines@astro.wisc.edu" target="_blank"><thaines@astro.wisc.edu></a>
Cc: ParaView <a moz-do-not-send="true" href="mailto:paraview@paraview.org" target="_blank"><paraview@paraview.org></a>
Message-ID:
<a moz-do-not-send="true" 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 moz-do-not-send="true" href="mailto:dave.demarle@kitware.com" target="_blank"><dave.demarle@kitware.com></a>
Subject: Re: [Paraview] viewing Gadget2 simulations
To: Tim Haines <a moz-do-not-send="true" href="mailto:thaines@astro.wisc.edu" target="_blank"><thaines@astro.wisc.edu></a>
Cc: <a moz-do-not-send="true" href="mailto:paraview@paraview.org" target="_blank">"paraview@paraview.org"</a> <a moz-do-not-send="true" href="mailto:paraview@paraview.org" target="_blank"><paraview@paraview.org></a>
Message-ID:
<a moz-do-not-send="true" 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 moz-do-not-send="true" href="tel:518-881-4909" value="+15188814909" target="_blank">518-881-4909</a>
</pre>
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