[Paraview] viewing Gadget2 simulations

Sat Sep 7 02:08:21 EDT 2013

Hi, George.

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).

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.

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].

Thoughts?

Many thanks.

- Tim

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.

On 09/03/2013 10:25 AM, George Zagaris wrote:
> Hi Tim,
>
> I was able to open the dataset you provided. Here are a couple of 
> suggestions:
>
> (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.
>
> (2) Set "rL", i.e., the box-size of the simulation data accordingly
>
> (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.
>
> Attached is an image of what the output looks like when I do the above 
> with rL=100.
>
> Best,
> George
>
>
> On Sat, Aug 31, 2013 at 11:04 PM, Tim Haines <thaines at astro.wisc.edu 
> <mailto:thaines at astro.wisc.edu>> wrote:
>
>     @David,
>
>     I put a snapshot file on github (
>     https://github.com/hainest/Gadget2_test). Let me know if you need
>     more of them.
>
>     @George,
>
>     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.
>
>     Many thanks for all of your help!
>
>     - Tim
>
>
>     On 08/31/2013 11:00 AM, paraview-request at paraview.org
>     <mailto:paraview-request at paraview.org> wrote:
>>     Message: 2
>>     Date: Sat, 31 Aug 2013 11:19:17 -0400
>>     From: George Zagaris<george.zagaris at kitware.com>  <mailto:george.zagaris at kitware.com>
>>     Subject: Re: [Paraview] viewing Gadget2 simulations
>>     To: Tim Haines<thaines at astro.wisc.edu>  <mailto:thaines at astro.wisc.edu>
>>     Cc: ParaView<paraview at paraview.org>  <mailto:paraview at paraview.org>
>>     Message-ID:
>>     	<CAP6Wa3gkiTtmJHnOKALccaM7vk46us5q=8A6evz+KWdTOXaSgg at mail.gmail.com>  <mailto:CAP6Wa3gkiTtmJHnOKALccaM7vk46us5q=8A6evz+KWdTOXaSgg at mail.gmail.com>
>>     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<dave.demarle at kitware.com>  <mailto:dave.demarle at kitware.com>
>>     Subject: Re: [Paraview] viewing Gadget2 simulations
>>     To: Tim Haines<thaines at astro.wisc.edu>  <mailto:thaines at astro.wisc.edu>
>>     Cc:"paraview at paraview.org"  <mailto:paraview at paraview.org>  <paraview at paraview.org>  <mailto:paraview at paraview.org>
>>     Message-ID:
>>     	<CANjZAi9cQtyYszXBa1z8xgr+HKAzGOd5g-Z6nG85vMyHR_4o=g at mail.gmail.com>  <mailto:CANjZAi9cQtyYszXBa1z8xgr+HKAzGOd5g-Z6nG85vMyHR_4o=g at mail.gmail.com>
>>     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:518-881-4909  <tel:518-881-4909>
>
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