Dear Kenneth and Andy, Thanks so much.
This works fine. It is truly the simplest way for me to post-processing the data. In this way, almost all the serial algorithm can be applied to multi-files. Thanks again for your kind help. Best regards. Rilin Shen Division of Solid Mechanics, School of Astronautics *Harbin Institute of Technology*, Harbin 150001, China Civil Engineering & Engineering Mechanics *Columbia University*, New York 10027, U.S. Tel: (+1) 646-200-2122 Email: [email protected] / [email protected] <[email protected]> 2017-09-07 16:18 GMT-04:00 Moreland, Kenneth <[email protected]>: > Rilin, > > > > I think I found a solution for you that will work at least most of the > time. The solution is to simply write out .vtm files instead of .pvtu > files. vtm, which is the multiblock file format, is similar to the pvt* > format. The main difference is that when VTK reads in vtm files it keeps > the data from different files in different blocks, and that will prevent > ParaView from removing what it thinks are internal faces. I’ve attached an > example vtkm file to this email. > > > > A bit more explanation and a description of where this will fail. As Andy > said the problem is that the files in your dataset have overlapping cells. > When ParaView reads in a pvtu file, it combines all the cells from all > files into a single mesh, and this mesh will have duplicates of the > overlapping cells. By definition, these overlapping cells will share all of > their faces. ParaView’s external faces algorithm assumes that if two cells > have the same face, that face must be internal and can be removed (which is > true in conforming meshes but not when there are duplicate cells). When you > first load your mesh into ParaView, everything seems to be working fine > because the reader is also creating duplicate points so index-wise the > duplicate cells register as different. But many operations (like merge > cells, clip, and D3) will find coincident points and merge them together. > That’s when ParaView removes all the faces of all duplicate cells. > > > > When ParaView reads the vtm file, it keeps the data from each file in a > separate mesh. When ParaView runs algorithms like external faces, it does > so independently from each other. So even if the cells are sharing faces, > they will be across blocks and will still be considered external. The > multiblock structure should remain intact as long as you don’t run a filter > that merges them together like D3 or Merge Blocks. > > > > Hope that helps. > > > > -Ken > > > > *From:* ParaView [mailto:[email protected]] *On Behalf Of *Rilin > Shen > *Sent:* Thursday, September 7, 2017 1:38 PM > *To:* Bauer, Andy (External Contacts) <[email protected]> > *Cc:* [email protected] > *Subject:* [EXTERNAL] Re: [Paraview] paraview display issue on parallel > files > > > > Dear Andy, > > > > Thanks very much. > > > > You can remap the point variables back onto the points using the Resample > with Dataset filter but that won't work for cell data. > > I tried the method you advised. Assuming that the original file name is A > and the file after Clean to Grid and Clean Cells to Grid is B, I tried two > different options for the source for Resample with DataSets and both A and > B are not working. Do I misunderstand something? > > > > I believe that the D3 filter is only available if you have ParaView > built/installed with MPI. Even then it will only work if you're running > with more than a single MPI process. > > I only use serial paraview to process multi-results generated by other > programs. I don't use the parallel paraview to deal with large datasets so > I think D3 filter is not suitable for me. > > > > > > I still suggest writing out the data with either marking the repeated > cells as ghost cells or not including them in the file as any other thing > you do to get around that can become fairly expensive and manually > intensive as you go to bigger datasets. > > I would try to not include repeated cells in the original output file. But > how to mark the repeated cells as ghost cells? I think there should a > vtu/pvtu file format to describe it but I didn't find it on the internet. > Could you please share it to me? > > > > BTW, when I clip a small model with 6700 elements generated by 40 > processors, it looks fine. So my question: is there a limit to deal with > the large dataset for paraview? > > > > Best regards, > > > Rilin Shen > > Division of Solid Mechanics, School of Astronautics > > *Harbin Institute of Technology*, Harbin 150001, China > > Civil Engineering & Engineering Mechanics > > *Columbia University*, New York 10027, U.S. > > Tel: (+1) 646-200-2122 <+1%20646-200-2122> > > Email: [email protected] / [email protected] <[email protected]> > > > > 2017-09-07 15:00 GMT-04:00 Andy Bauer <[email protected]>: > > Hi, > > > > You can remap the point variables back onto the points using the Resample > with Dataset filter but that won't work for cell data. > > > > I believe that the D3 filter is only available if you have ParaView > built/installed with MPI. Even then it will only work if you're running > with more than a single MPI process. > > > > I still suggest writing out the data with either marking the repeated > cells as ghost cells or not including them in the file as any other thing > you do to get around that can become fairly expensive and manually > intensive as you go to bigger datasets. > > > > Andy > > > > On Wed, Sep 6, 2017 at 3:28 PM, Rilin Shen <[email protected]> wrote: > > Dear all, > > > > Thanks for your suggestions. It is exactly what you said. > > > > Marking ghost cell would be non-trival work and I tried the second idea. > But only cell and points information is left, other field information > associated with points seem to be lost. Is that the case? If that is the > case, is there an easy way to attach point data to points again? > > > > BTW, I searched the internet and found that the D3 filter could be a good > option for my unstructured grid information. But I cannot find the D3 > filter as Filters>Alphabetical>D3. So my second question is how to add D3 > filter to my paraview? > > > > Best regards, > > > > > Rilin Shen > > Division of Solid Mechanics, School of Astronautics > > *Harbin Institute of Technology*, Harbin 150001, China > > Civil Engineering & Engineering Mechanics > > *Columbia University*, New York 10027, U.S. > > Tel: (+1) 646-200-2122 <(646)%20200-2122> > > Email: [email protected] / [email protected] <[email protected]> > > > > 2017-09-06 14:50 GMT-04:00 Andy Bauer <[email protected]>: > > Hi, > > Please respond to the entire mailing list so that anyone that wants to > participate or follow along can. > > I think the issue here is that you have the same cell specified in > multiple vtu files and ParaView is getting confused when trying to render > them. These are the overlapping cells at the subdomain boundary. My > recommendation would be to either mark these repeated cells as ghost cells > (see https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for > information on that). Other than that, you could use the Clean to Grid > filter to get rid of coincident points and then use the Clean Cells to Grid > filter to get rid of extra copies of the cell. > > Cheers, > > Andy > > > > > > On Tue, Sep 5, 2017 at 6:24 PM, Rilin Shen <[email protected]> wrote: > > > > * Bone.7z > <https://drive.google.com/file/d/0B1JLvkeOK5PQVXR3cTBHa2lfQjQ/view?usp=drive_web>* > > Dear Andy, > > > > Thanks a lot for your help. > > > > As you said, It looks like a ghost cell issue. I attached my dataset. > Please check it. > > > > If you need any additional information, please let me know. > > > > Best regards, > > > Rilin Shen > > Division of Solid Mechanics, School of Astronautics > > *Harbin Institute of Technology*, Harbin 150001, China > > Civil Engineering & Engineering Mechanics > > *Columbia University*, New York 10027, U.S. > > Tel: (+1) 646-200-2122 <(646)%20200-2122> > > Email: [email protected] / [email protected] <[email protected]> > > > > 2017-09-05 16:54 GMT-04:00 Andy Bauer <[email protected]>: > > Hi, > > This typically happens when ghost cells are marked improperly or the data > set has a node/point partitioning and no cells to bridge between the > subdomains (though the point partitioning issue usually happens with finite > difference simulations instead of FEM simulations). If you could share your > dataset it would be easier to diagnose. > > Best, > > Andy > > > > On Tue, Sep 5, 2017 at 4:23 PM, Rilin Shen <[email protected]> wrote: > > Dear all, > > > > I'm very happy to meet all of you in this society. > > > > I use a finite element software with multiprocessors(40) to solve > problems. > > > > All the .vtu files. associated with each processor are output and then a > file .pvtu is generated. > > > > The original file is displayed perfectly as shown in bone.png. However, > when I try to cut it with a plane, it occurs the following issue as > clip.png, It seems not be displayed correctly. > > > > Would you please tell me what happened to my data? > > > > Best regards, > > > > Rilin Shen > > Division of Solid Mechanics, School of Astronautics > > *Harbin Institute of Technology*, Harbin 150001, China > > Civil Engineering & Engineering Mechanics > > *Columbia University*, New York 10027, U.S. > > Tel: (+1) 646-200-2122 <(646)%20200-2122> > > Email: [email protected] / [email protected] <[email protected]> > > > > _______________________________________________ > 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 > > Search the list archives at: http://markmail.org/search/?q=ParaView > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/paraview > > > > > > > > > > > > >
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