[Paraview] viewing Gadget2 simulations

Sat Sep 7 19:21:43 EDT 2013

Hi Tim,

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.

I'll take a look at that.

Cheers,
George

On Sat, Sep 7, 2013 at 2:08 AM, Tim Haines <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>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 wrote:
>>
>> Message: 2
>> Date: Sat, 31 Aug 2013 11:19:17 -0400
>> From: George Zagaris <george.zagaris at kitware.com> <george.zagaris at kitware.com>
>> Subject: Re: [Paraview] viewing Gadget2 simulations
>> To: Tim Haines <thaines at astro.wisc.edu> <thaines at astro.wisc.edu>
>> Cc: ParaView <paraview at paraview.org> <paraview at paraview.org>
>> Message-ID:
>> 	<CAP6Wa3gkiTtmJHnOKALccaM7vk46us5q=8A6evz+KWdTOXaSgg at mail.gmail.com> <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> <dave.demarle at kitware.com>
>> Subject: Re: [Paraview] viewing Gadget2 simulations
>> To: Tim Haines <thaines at astro.wisc.edu> <thaines at astro.wisc.edu>
>> Cc: "paraview at paraview.org" <paraview at paraview.org> <paraview at paraview.org> <paraview at paraview.org>
>> Message-ID:
>> 	<CANjZAi9cQtyYszXBa1z8xgr+HKAzGOd5g-Z6nG85vMyHR_4o=g at mail.gmail.com> <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
>>
>>
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