Opening cgns file in visualiser software

[PhDFlo]

Hi everyone,

I have compiled CGNS-4.2.0 (with hdf5-1.12.0 and zlib-1.2.11) with intel 19.0.5 and intel mpi 19.0.5. I'm coding in Fortran, and for now I was able to do what I want on structured meshes in fully parallel and can visualize the data in Paraview 5.9.1.

Now I'm trying to work with unstructured meshes which is a bit more tough... I cannot find any examples on the internet using NGONS but saw that there are some Fortran examples in the source folder. I run all the examples successfully and can watch the CGNS tree with cgnslist or cgnsview. I'm especially interested in the Test_mixed_elements example (cgwrite.F) which is basically what i want to do. However, I struggle to open the result mesh with Paraview. I wonder if someone already had such issue with opening unstructured meshes with Paraview.

I receive the following error: "Mixed definition of unstructured zone by elements and by faces is not valid."

[brtnfld]

You might try Paraview 5.10.0. I think it supports this.

[mennodeij]

I don't think ParaView 5.10.x will do any different.

What I understand from the error message is this: An unstructured zone in CGNS cannot contain MIXED elements that are defined by faces. You should split this into an unstructured zone that contains only NGON_n (and NFACE_n if you're using polyhedra) definitions, and an unstructured zone that contains only MIXED "simple" elements (tri, quad, tetra, hexa, prism, etc.)

See for c++ code an example can be found in https://gitlab.kitware.com/paraview/paraview/-/blob/master/VTKExtensions/IOCGNS/vtkCGNSWriter.cxx

[brtnfld]

You are correct. I did not realize that ParaView moved the CGNS reader out of the source in 5.10, it looks like it is in VTK/IO/CGNS now. So I did not find that error message any longer, it is still there in VTK/IO/CGNS

[PhDFlo]

So, I've tried with Paraview 5.10.1 and as said by @mennodeij it does not change anything.

I'm not totally sure what my CGNS tree should look like. For now my CGNS tree is:

HDF5 MotherNode
+-CGNSLibraryVersion
+-MixedElementBase
+-UnstructuredZone#1
+-ZoneType
+-GridCoordinates
| +-CoordinateX
| +-CoordinateY
| +-CoordinateZ
+-MixedElements
| +-ElementRange
| +-ElementStartOffset
| +-ElementConnectivity
+-NGON_n(3)
+-ElementRange
+-ElementStartOffset
+-ElementConnectivity

To be fully honest i don't really get what the example result should be, I'm beginner in CGNS format. I'm trying to find a Fortran example of creating a simple unstructured mesh with tetras, prisms, ... Maybe this example is too complicated to understand how it works

[mennodeij]

If you are mixing topologically 3D (tetras, prisms) and 2D elements (triangles, quads, polygons), you should use 2 bases and set the cell dimensions correctly. In our case it looks something like this:

HDF5 MotherNode
  +-CGNSLibraryVersion
  +-Base_Volume_elements
  | +-SimulationType
  | +-TimeIterValues
  | | +-TimeValues
  | +-Zone_Interior
  |   +-ZoneType
  |   +-GridCoordinates
  |   | +-DataClass
  |   | +-CoordinateX
  |   | +-CoordinateY
  |   | +-CoordinateZ
  |   +-Elements
  |   | +-ElementRange
  |   | +-ElementConnectivity
  |   +-FlowSolution-00000100
      <cut many fields>
 +-Base_Surface_elements
    +-SimulationType
    +-TimeIterValues
    | +-TimeValues
    +-Zone_BCSymmetryPlane
    | +-ZoneType
    | +-GridCoordinates
    | | +-DataClass
    | | +-CoordinateX
    | | +-CoordinateY
    | | +-CoordinateZ
    | +-Elements
    | | +-ElementRange
    | | +-ElementConnectivity
    | +-BoundSolution-00000100
      <cut many fields>
 +-Zone_BCWall
    | +-ZoneType
    | +-GridCoordinates
    | | +-DataClass
    | | +-CoordinateX
    | | +-CoordinateY
    | | +-CoordinateZ
    | +-Elements
    | | +-ElementRange
    | | +-ElementConnectivity
    | +-BoundSolution-00000100
      <cut many fields>
+-Zone_BCInflow
    | +-ZoneType
    | +-GridCoordinates
    | | +-DataClass
    | | +-CoordinateX
    | | +-CoordinateY
    | | +-CoordinateZ
    | +-Elements
    | | +-ElementRange
    | | +-ElementConnectivity
    | +-BoundSolution-00000100
<and so on, for each family on the boundary>

[PhDFlo]

Ok I got it, I managed to write my first unstructured field with CGNS that opens with Paraview. I saw that there is no cgp_poly_section_write function for Fortran, is there a reason for that ?
Is the solution to create the NGON and NFACE zone by more generic parallel functions ?

[brtnfld]

Just an oversight, we'll add it for Fortran. I've created an issue for tracking, https://cgnsorg.atlassian.net/browse/CGNS-276

[PhDFlo]

I've looked at CGNS documentation this morning and here are the parallel Fortran functions that seem to be missing:

• cgp_coord_general_write_data_f
• cgp_coord_general_read_data_f
• cgp_poly_section_write_f
• cgp_poly_elements_write_data_f
• cgp_field_general_write_data_f
• cgp_field_general_read_data_f
• cgp_array_general_write_data_f
• cgp_array_general_read_data_f
  I'll use only the function cgp_poly_section_write_f for now, so I will test if it works properly or no. Mentioning the others just in case.

[PhDFlo]

Great ! If you want I can provide you my short Fortran scripts that create a small unstructured domain with ngon and nface (that can be opened in Paraview !) for the examples. There are no examples of that on internet, maybe it can help someone ...

[brtnfld]

Yes, that would be great! I will add it to the examples.

[PhDFlo]

Here are the examples I've made, not sure all are necessary. I've also added an image from Paraview of how it looks like.
examples_fortran_unstruct.tar.gz