[Paraview] viewing Gadget2 simulations
Tim Haines
thaines at astro.wisc.edu
Fri Sep 13 23:00:52 EDT 2013
Hi, George.
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).
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.
Let me know if I can be of any help with testing ParaView changes with
Gadget data.
Many thanks for all of your help.
- Tim
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!
On 09/12/2013 01:53 PM, George Zagaris wrote:
> 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.
>
> Best,
> George
>
>
> On Sat, Sep 7, 2013 at 2:08 AM, Tim Haines <thaines at astro.wisc.edu
> <mailto:thaines at astro.wisc.edu>> wrote:
>
> 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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