I would vote for the ghost points. This is really a cool feature for datasets that doesn't have overlapping cells.
Takuya OSHIMA, Ph.D. Faculty of Engineering, Niigata University 8050 Ikarashi-Ninocho, Nishi-ku, Niigata, 950-2181, JAPAN From: Berk Geveci <[email protected]> Subject: Re: [Paraview] extract surface of multiblock mesh Date: Mon, 6 Apr 2009 19:58:56 -0400 > I did not mean ghost cells. I meant ghost points. If you were to mark > the points at a shared interface as ghost (more appropriately > duplicated), we can easily throw away all polygons that contain all > duplicate points when extracting external surfaces. Even better, if we > had an array that had values like: > > -1 : point not shared > n >= 0 : point shared, owned by process n > > we could make bunch of filters work correctly - mainly statistics ones > and the glyph filter. Is this something that is easy for your > simulation to write? > > -berk > > On Mon, Apr 6, 2009 at 7:41 PM, Renato Elias <[email protected]> wrote: >> Berk, forgive for delaying my response (I was out of my lab...) >> >> Just a silly question: >> >> What do you exactly mean by "Ghost cell"? This silly question is justified >> by the fact that I thought that ghost cells only make sense when we have >> subdomains _overlapped_. In these cases, the number of overlapped cell >> layers should (or could) be considered as "ghost level". >> >> In my case, the subdomains are not overlapped at all. They are just >> partitioned by Metis and the solver can deal with the computations without >> the need to use overlapped elements. Thus, if "ghost cells" can be simply >> defined by "cells somehow touching the parallel interface (even those not >> overlapped)" I think I could try tagging my parallel interface cells as >> "ghost level 0" to see what happens... >> >> Renato. >> >> On Sun, Apr 5, 2009 at 11:53 PM, Chris Kees >> <[email protected]> wrote: >>> >>> Berk, >>> >>> Thanks for correcting me. I'll try adding the vtkGhostLevels to the XDMF >>> and see how that goes. >>> >>> Chris >>> On Apr 4, 2009, at 2:50 PM, Berk Geveci wrote: >>> >>>> The right way to deal with this situation is to mark the ghost cells >>>> as ghost. If you create a cell array called vtkGhostLevels and assign >>>> 0 to inside cells and 1 to ghost cells, you should not need >>>> MergeBlocks or CleanToGrid. Note that this array has to be of type >>>> unsigned char. There are actual benefits to keeping ghost levels since >>>> some algorithms will produce better results. >>>> >>>> -berk >>>> >>>> On Thu, Apr 2, 2009 at 6:37 PM, Chris Kees >>>> <[email protected]> wrote: >>>>> >>>>> I turned off the overlapping domain decomposition (ghost cells) for a >>>>> simple >>>>> problem and the sequence >>>>> >>>>> MergeBlocks->CleantoGrid->ExtractSurface->Clip >>>>> >>>>> shows just the physical boundary of the problem (clipped open so you can >>>>> see >>>>> inside). Also volume visualization and streamline calculation works with >>>>> no >>>>> processor boundary artifacts. >>>>> >>>>> From what I understand, there are no filters in paraview or abstractions >>>>> in >>>>> the XDMF data model at this time that will allow paraview to read in >>>>> overlapping blocks and really make use of the ghost cells correctly. For >>>>> now >>>>> truncating our output to only "owned" elements will solve our problems. >>>>> Thanks again for the help. >>>>> >>>>> Chris >>>>> >>>>> On Mar 30, 2009, at 2:06 PM, Chris Kees wrote: >>>>> >>>>>> Thanks for the help. I also tried suggestions from Paul, Ken, and >>>>>> Berk, >>>>>> but it does seem that I'm stuck right now unless I provide ParaView >>>>>> with >>>>>> more information. Since streamlines are computed correctly on the >>>>>> current >>>>>> multiblock mesh I just generated the mesh on a single processor and >>>>>> used >>>>>> ExtractSurface->Clip on that mesh to visualize the geometry around the >>>>>> streamlines from the multiblock grid. >>>>>> >>>>>> On the first method: Each of my UnstructuredGrids in the Multiblock >>>>>> Grid >>>>>> is a subdomain in an overlapping decomposition of the domain. Each of >>>>>> the >>>>>> subdomains has several elements of overlap (the layer of ghost cells is >>>>>> more >>>>>> than one element thick). Presumably the streamline generation works >>>>>> now on >>>>>> the multiblock grid because the overlap is loaded into ParaView. Is >>>>>> there a >>>>>> way I can just set a cell-centered attributed to identify the ghost >>>>>> cells so >>>>>> that surface extraction and volume visualization will work too? >>>>>> Currently >>>>>> volume visualization of the multiblock grid shows only a single >>>>>> subdomain >>>>>> and volume visualization after MergeBlocks shows the whole domain but >>>>>> with >>>>>> overlap regions being more opaque. >>>>>> >>>>>> On your other method, we have both the external boundary mesh and a >>>>>> pre-mesh polygonal representation of the boundaries available in the >>>>>> simulator. You are suggesting that I just dump one of those to a valid >>>>>> ParaView format as well, is that correct? >>>>>> >>>>>> Chris >>>>>> >>>>>> On Mar 30, 2009, at 9:14 AM, Jean Favre wrote: >>>>>> >>>>>>> Chris Kees wrote: >>>>>>>> >>>>>>>> So far I've tried MergeBlocks->ExtractSurface->FeatureEdges->Clip and >>>>>>>> various permutations that I've seen in previous posts and the wiki, >>>>>>>> but I always end up with the surfaces on the interior of the tank as >>>>>>>> if it still sees each subdomain as a closed surface. >>>>>>> >>>>>>> In fact, it seems to me that ParaView does the best it can. Your >>>>>>> unstructured mesh is partitioned in 512 pieces and [presumably], you >>>>>>> did >>>>>>> not specify ghost-cells at the partition boundaries. Without >>>>>>> ghost-cells, ParaView has no information to help decide whether an >>>>>>> outside face looks towards the outside world, or to another partition. >>>>>>> I >>>>>>> don't think any combination of filters would help you. Removing >>>>>>> duplicate points may only remove duplicate fake boundaries, but these >>>>>>> fake boundaries must be removed all together. >>>>>>> >>>>>>> I use two methods to achieve what you want. Ghost-cells, or another >>>>>>> multi-piece object containing the different boundary types (solid, >>>>>>> symmetries, inflow, outflow, etc) stored as vtkPolyData. These are >>>>>>> read >>>>>>> in from the models on disk. >>>>>>> >>>>>>> Jean -- >>>>>>> Swiss National Supercomputing Center >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>> >>> _______________________________________________ >>> 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 >> >> > _______________________________________________ > 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 _______________________________________________ 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
