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Repair holes in surface (from haning nodes)

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Old   February 21, 2014, 13:00
Default Repair holes in surface (from haning nodes)
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Adam Læssøe
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I have hexa-mesh produced with ICEM. The mesh is block-refined in ICEM, so there are hanging nodes in places. It seems Paraview cannot handle hanging nodes, but is there some filter that will either

a) do as the answer in the link suggests - break hanging nodes into tetras, and interpolate values or

b) simply fill the holes? The data there isn't important, but it doesn't look very nice.
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Old   February 21, 2014, 17:50
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Greetings Adam,

Can you provide a simple example file? It would make it easier to diagnose and test how this can be achieved.

Best regards,
Bruno
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Old   February 21, 2014, 18:38
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Sure - this is the smallest working example(18MB) I could get from my data.

To reproduce:
Import with EnSight
CellDataToPointData
Contour[phase_2_vof,0.5]
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Old   February 22, 2014, 15:13
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Hi Adam,

I noticed that you've also asked about this at the mailing list: http://www.paraview.org/pipermail/pa...ry/030632.html

I believe the trick is to use the filter "Tetrahedralize" Keep in mind that this will substantially increase the computational requirements of the resulting mesh (680 kcell went up to 3.9 Mcell).

Attached is shown the results of my investigation into this:
  • The first image shows the pipeline I used to get a proper isosurface, or at least without the unwanted holes in the mesh.
  • The second image shows a similar pipeline, where the only change was regarding the input for the "Tetrahedralize" filter. The missing pipeline is identical to the previous one, with the exception that the "Merge Blocks" filter isn't used.
-------------
edit: Sorry, I didn't properly read your question today You had already tried this and it was too heavy, as you indicated.
OK, try using the filter "Extract cells by region", which can allow you to get only a certain section of the mesh. Then apply the "Tetrahedralize" filter to it.
You can use multiple "Extract cells by region" filters with the "box" sub-filter (instead of "plane") and then use the "Group Datasets" filter or one of the "Append" filters to group all extractions together.

Best regards,
Bruno
Attached Images
File Type: jpg Screenshot from 2014-02-22 19:01:41.jpg (46.8 KB, 17 views)
File Type: jpg Screenshot from 2014-02-22 19:02:11.jpg (48.2 KB, 14 views)

Last edited by wyldckat; February 22, 2014 at 15:19. Reason: see "edit:"
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Old   February 22, 2014, 15:35
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Hi Bruno

Thanks a lot for looking into it!

Yeah, I wasn't sure how much attention was given here so after a day of waiting, I figured I'd try the mailing list

As you say, the Tetrahedralize increases computation a lot. For animating transient data, that might well be a deal breaker. On top of that, the output seems more faceted. Could there be a way to only tetrahedralize the cells with hanging nodes?

For that to work I suppose something like the following would be necessary (with [ ] meaning taken input) :

Full data set (1);
|-Extract cells w/ hanging nodes (2);
| |-Tetrahedralize (3);
|
|-'Mask' using data set [(2)] (4);
|-Merge with dataset [(3)] (5);

But I have no idea how to accomplish (2) - let alone (4) and (5).

/adam
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Old   February 22, 2014, 15:46
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Oh, and I tried VeronoiMergeConnected, thinking it sounded maybe applicable - but ParaView crashes when I apply it.
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Old   February 22, 2014, 16:23
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The steps list you wrote gave me an idea and attached is the resulting pipeline. I'm not sure how much lighter it truly is and the results seem a bit... strange.

The pipeline is essentially:
  1. The case file.
    1. "Mesh quality" filter, using the defaults.
      1. "Threshold" filter with 0 to 1, in regards to the "Quality" field.
        1. Applied the "Tetrahedralize" filter.
      2. "Threshold" filter with 1 to maximum value, in regards to the "Quality" field.
    2. Applied the "Group Dataset" filter, to group the "Tetrahedralize" result and the second "Threshold" filter.
      1. "Merge Blocks" filter. This can be considerably heavy, since it can duplicate the amount of data loaded onto RAM.
        1. "Cell Data to Point Data" filter, without passing the cell data (save a bit of RAM).
          1. "Contour Filter".
Note: after 1.2 and before 1.2.1, you can apply the "Pass Arrays" filter to filter out only the field data you truly need.

edit: never mind, the "Pass Arrays" filter seems to be broken... at least in another test I did.

edit 2: The third image shows another possible pipeline, which may or may not be a little bit lighter.
Attached Images
File Type: jpg Screenshot from 2014-02-22 20:12:22.jpg (52.2 KB, 11 views)
File Type: jpg Screenshot from 2014-02-22 20:12:24.jpg (52.5 KB, 11 views)
File Type: jpg Screenshot from 2014-02-22 20:28:38.jpg (49.0 KB, 15 views)

Last edited by wyldckat; February 22, 2014 at 16:29. Reason: see "edit:" and "edit 2"
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Old   February 22, 2014, 17:47
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That's _exactly_ what I had in mind.

It does look a little weird still, but I suspect no more so than what all the data would have looked like if tetrahedralizing everything.

As for memory, the Information tab reports the full Tetrahedralize as 290MB, while the MergeBlocks is reported as 140 - but then the mesh quality reported 120MB - which sounds weird, so I'm wondering how accurate that panel really is. For some reason, I couldn't select AppendDatasets - 'twas grayed out.
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Old   March 1, 2014, 06:03
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Hi Adam,

Quote:
Originally Posted by AdamAL View Post
For some reason, I couldn't select AppendDatasets - 'twas grayed out.
Usually that happens when the selected items are not of the same type. It's possible that you had one in multi-block mode and another already merged into a single block.

Best regards,
Bruno
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