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 <[email protected]> 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 <[email protected]>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, [email protected] wrote: >> >> Message: 2 >> Date: Sat, 31 Aug 2013 11:19:17 -0400 >> From: George Zagaris <[email protected]> >> <[email protected]> >> Subject: Re: [Paraview] viewing Gadget2 simulations >> To: Tim Haines <[email protected]> <[email protected]> >> Cc: ParaView <[email protected]> <[email protected]> >> Message-ID: >> <CAP6Wa3gkiTtmJHnOKALccaM7vk46us5q=8a6evz+kwdtoxa...@mail.gmail.com> >> <CAP6Wa3gkiTtmJHnOKALccaM7vk46us5q=8a6evz+kwdtoxa...@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 <[email protected]> <[email protected]> >> Subject: Re: [Paraview] viewing Gadget2 simulations >> To: Tim Haines <[email protected]> <[email protected]> >> Cc: "[email protected]" <[email protected]> <[email protected]> >> <[email protected]> >> Message-ID: >> <CANjZAi9cQtyYszXBa1z8xgr+HKAzGOd5g-Z6nG85vMyHR_4o=g...@mail.gmail.com> >> <CANjZAi9cQtyYszXBa1z8xgr+HKAzGOd5g-Z6nG85vMyHR_4o=g...@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 >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Please keep messages on-topic and check the ParaView Wiki at: >> http://paraview.org/Wiki/ParaView >> >> Follow this link to subscribe/unsubscribe: >> http://www.paraview.org/mailman/listinfo/paraview >> >> > >
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