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[feature.FEM.EdgeAndCornerConnectivity] New Feature: Edge and Vertex connectivity, needed for a FEM solver #51

Merged
merged 31 commits into from
Feb 13, 2024
Merged

[feature.FEM.EdgeAndCornerConnectivity] New Feature: Edge and Vertex connectivity, needed for a FEM solver #51

merged 31 commits into from
Feb 13, 2024

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fhindenlang
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@fhindenlang fhindenlang commented Nov 24, 2023 •
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We introduce a new version 1.3.0 of HOPR, where the mesh file is extended to provide element edge connectivity and element corner or "Vertex" connectivity, which is needed for (high order) Finite Element solvers.

Version 1.3.0

  • fixed 2d GMSH testcase, was failing now because all stop calls have been replaced by abort
  • read-in flag to activate FEM output via GenerateFEMConnectivity=T/F (default is F)
  • HDF5 meshfile variable names of lower versions are kept, and new ones are added for GenerateFEMConnectivity=T
    see documentation for the updated mesh format. The following changes to the meshfile are important:
    • additional information on the element level is stored in FEMElemInfo
    • edge connectivity information ( arrays EdgeInfo and EdgeConnectInfo )
    • vertex connectivity information ( arrays VertexInfo and VertexConnectInfo)
  • Visualization of FEM connectivity of the mesh in paraview:
    - DebugMesh_Faces.vtu visualizes all element faces with their element ID and uniqueFaceID.
    - DebugMesh_Edges.vtu visualizes all element edges (1D lines) with their element ID and uniqueEdgeID, and VertexIDs and their master/slave status
  • Note that the edge and vertex connectivity has been implemented only for conforming meshes. If a non-conforming mesh is found, the default GenerateFEMConnectivity=F will be used.

TODOs before merge:

  • Add read-in flag GenerateFEMConnectivity=T/Fto activate FEM output with new container FEMElemInfo in order to not change the original container ElemInfo
  • implement vertex connectivity
  • check edge+vertex connectivity implementation in simulations @OttTs
    • non-periodic
    • periodic
    • unstructured
  • Descriptions for new/changed routines
    • Short header description (do not just spell out the name of the subroutine, units for important variables if applicable)
    • Workflow
      • Short summary in the header
      • Inside the routine at the appropriate positions
  • Regression tests
    • GenerateFEMConnectivity=T/F (default is F) @fhindenlang
      • non-periodic
      • periodic
      • unstructured
      • curved $N=2,3$: Case(4) used
  • Check if all STOP additionally return != 0, replace with abort() @scopplestone
  • Remove line breaks from all abort() calls @scopplestone
  • Check correct deallocation of new pointer structures by running memory checker for leaks @kopperp
  • Remove leading white spaces from all old and new .ini files @scopplestone
  • Visualize FEM connectivity of the mesh in paraview:
    - DebugMesh_Faces.vtu visualizes all element faces with their element ID and uniqueFaceID.
    - DebugMesh_Edges.vtu visualizes all element edges (1D lines) with their element ID and uniqueEdgeID, and VertexIDs and their master/slave status

Florian Hindenlang and others added 8 commits November 22, 2023 12:02
First commit for new feature:
c851085 
  - build and write edge and corner connectivity for FEM solvers
  - removed unused supernode
  - added local edge pointer
@project-fluxo-old
extend docu of meshformat, for describing edge and vertex connectivit…
56adc78 
…y, needed for FEM solver
@project-fluxo-old
started building the edge connectivity, not yet clear if it really wo…
721cd0c 
…rks, but compiles and runs.
@project-fluxo-old
building element to local edge and the connectivity for each edge (an…
88ab9da 
…d periodic edge...)
@project-fluxo-old
WRITE DATA TO HDF5 FILE.
0378f54
@project-fluxo-old
WRITE DATA TO HDF5 FILE...
0023b64
@OttTs
Update building of Edge and LocalEdge, added counters for geometric a…
963284b 
…nd FEM edges, write EdgeInfo and EdgeConnectInfo to HDF5 file (to be filled)
@project-fluxo-old
update documentation with size of connections for edge and vertex. fi…
82ffe5d 
…lled edgeInfo and edgeConnectionInfo. compiles and runs, but result not yet checked.
@fhindenlang
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Hi everbody, lets dicuss here the further developments.

project-fluxo-old and others added 6 commits November 24, 2023 16:48
@project-fluxo-old
prepare the vertex connection lists in the build Edges. counting and …
8de8f10 
…output to hdf5 still missing.
@scopplestone
Added python script for creating a hopr .h5 mesh file with 2 elements…
02e23a1 
… and fully periodic boundaries. This also includes edge and vertex information.
@project-fluxo-old
replaced stops by aborts, such that tests are marked as failed. debug…
0bc245e 
…ged a little, but still there are bugs with periodic edges and vertices...
@project-fluxo-old
introduced a parameterfile flag called generateFEMconnectivity, defa…
472bb90 
…ult is false, such that previously running tests work. added a new tutorials folder with cases that test that new feature explicitly, and the periodic ones still fail...
@project-fluxo-old
more fixes to build and wirte edge connectivity. now compiles and run…
7161bb4 
…s all examples, for all kinds of periodic meshes (all internal checks go through). Output file data still need to be checked if they are correct.
@project-fluxo-old
mesh_basis:
9023a2d 
- its important to check for the periodic edges, when both firstlocaledges  already exist, if they point onto the same, and if not re-pointer.
  this then makes all common periodic edges pointing to the same firstlocalEdge. all other edges are already unique, and thus always point to one firstlocaledge.
- Analogously done for the periodic vertices.
output to hdf5:
- add a FEMconnect="OFF"/"ON" variable, to be able to know if the edge and vertex connectivity has been generated and written to file (paramterflag `generateFEMconnectivity=T`)
- changed from modified ElemInfo back to original ElemInfo, moved edge and vertex offsets into a new FEMElemInfo.
- added vertex connectivity information to hdf5.
- updated the documentation of the meshformat.
@fhindenlang
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ok, so I think we have now a running version with edge and vertex connectivity.

I changed the elemInfo back to its original, and added the Flag FEMconnect="ON"/"OFF" to the hdf5 file. (Mortar meshes will still have that flag being "OFF", since mortar edges are not yet implemented!)

  • We wanted current hdf5 readers to have no problem with the eleminfo being larger.
  • DG code users can decide if they even need the FEM edge and vertex connectivity information.
  • only if FEMconnect="ON", we write the FEMElemInfo;EdgeInfo;EdgeConnectInfo;VertexInfo;VertexConnectInfo arrays to the meshfile!
    TODOS:
  • We still need (with a FEM code) if the information now given in the HDF5 file is meaningful!!

@fhindenlang
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So I added some cases for the "sphere in cube" in tutorials/4-02, which are conforming curved meshes of a box in [-1,1], and there are mulitple
cases for full/2D/1D/no periodicity.
@OttTs These meshes can be used for testing against an exact solution with dirichlet BCs.

@fhindenlang
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I also added a visualization of the FEM connectivity in vtu files:

  • DebugMesh_Faces visualizes all element faces with their element ID and uniqueFaceID.
  • DebugMesh_Edges visualizes all element edges (1D lines) with their element ID and uniqueEdgeID, and VertexIDs and their master/slave status

@fhindenlang fhindenlang mentioned this pull request Feb 1, 2024
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@fhindenlang
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opened an issue #56, since checks are failing, but not only because of the new feature. Actually, the meshdim=2d does not work in the gmsh test.

@project-fluxo-old
fix deallocate issue in readintools. fix gmsh readin for meshdim=2, w…
d9a93d8 
…hich fixes case tutorials/4-05. the problem was that the triangles were not created, and the fill2.5mesh did not see this. Added abort in Fill2.5 mesh, if anything else than prism or hexa are in the mesh. In the screen output for the element types, the names prism and pyramids had to be interchanged.
@project-fluxo-old
added aborts in readin_CGNS. added more periodic tests, which have th…
285c776 
…e same problem.
@fhindenlang
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I did not yet fix the FEMconnectivity cases, they seem to have a problem with periodicity...

@project-fluxo-old
fix FEM edge connect for unstructured periodic testcases, as fas as h…
5e1c928 
…opr can check it. A FEM solver should run on these meshes, to be sure.
@fhindenlang
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@OttTs Now that the unstructured meshes in tutorials/4-02-unstruct_curved_FEMconnect are working, could you try to run them with your FEM solver?

@OttTs
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OttTs commented Feb 5, 2024

@OttTs Now that the unstructured meshes in tutorials/4-02-unstruct_curved_FEMconnect are working, could you try to run them with your FEM solver?

The meshes all seem to work. For the fully periodic case, I'm having some trouble getting the convergence test to work due to the constant offset.

@fhindenlang
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fhindenlang commented Feb 5, 2024 via email •
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@fhindenlang
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TITEL OF RELEASE:
Build and write FEM "Edge" and "Vertex" connectivity information (flag: GenerateFEMConnectivity=T/F, default is F). Adds new variables to existing hdf5 meshfile.

@scopplestone scopplestone changed the title New Feature: Edge and Vertex connectivity, needed for a FEM solver [feature.FEM.EdgeAndCornerConnectivity] New Feature: Edge and Vertex connectivity, needed for a FEM solver Feb 13, 2024
@scopplestone scopplestone merged commit 0a27c88 into master Feb 13, 2024
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@scopplestone scopplestone deleted the feature.FEM.EdgeAndCornerConnectivity branch February 13, 2024 13:55
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@kopperp kopperp kopperp approved these changes

@scopplestone scopplestone Awaiting requested review from scopplestone

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