Thanks for the suggestions. I did try to stitch the meshes together using
misc example 10, but it failed to find any boundary nodes. For the 2D mesh
I used boundary_id_type 0, 1, 2, 3 for bottom, right, top and left,
respectively. I note when loading the mesh it says "Mesh Dimension: 3"
though, which is odd. Using:
SerialMesh mesh(init.comm());
SerialMesh mesh2(init.comm());
ExodusII_IO(mesh).read("bfstep1.e");
mesh.prepare_for_use();
ExodusII_IO(mesh2).read("bfstep2.e");
mesh2.prepare_for_use();
mesh.stitch_meshes(mesh2, 1, 3, TOLERANCE, true, true, false, false);
I obtain for retrieving the mesh and the stitching:
Mesh Dimension: 3
Number of Nodes: 1089
Number of elements: 1024
Number of elt blocks: 1
Number of node sets: 0
Number of side sets: 0
Nodal data retrieved successfully.
Nodal numbering map retrieved successfully.
[0] node_num_map[i] = 1, 2, 35, 34, 3, 36, 4, 37, 5, 38, ... 1089
All block IDs retrieved successfully.
All block names retrieved successfully.
Element numbering map retrieved successfully.
[0] elem_num_map[i] = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... 1024
Reading a block of 1024 quad(s) having 4 nodes per element.
Info retrieved successfully for block: 0.
Connectivity retrieved successfully for block: 0.
All side set names retrieved successfully.
All node set names retrieved successfully.
Mesh Dimension: 3
Number of Nodes: 429
Number of elements: 384
Number of elt blocks: 1
Number of node sets: 0
Number of side sets: 0
Nodal data retrieved successfully.
Nodal numbering map retrieved successfully.
[0] node_num_map[i] = 1090, 1091, 1104, 1103, 1092, 1105, 1093, 1106,
1094, 1107, ... 1518
All block IDs retrieved successfully.
All block names retrieved successfully.
Element numbering map retrieved successfully.
[0] elem_num_map[i] = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ... 384
Reading a block of 384 quad(s) having 4 nodes per element.
Info retrieved successfully for block: 0.
Connectivity retrieved successfully for block: 0.
All side set names retrieved successfully.
All node set names retrieved successfully.
In SerialMesh::stitch_meshes:
This mesh has 0 nodes on boundary 1.
Other mesh has 0 nodes on boundary 3.
No elements on specified surfaces.
In SerialMesh::stitch_meshes:
Found 0 matching nodes.
If that helps.
There's definitely overlapping nodes on the boundary between two adjacent
subdomains (the mesh is partly visualized on
http://turbmodels.larc.nasa.gov/backstep_grids.html), i.e., zone 1 & 2, 2 &
3, and 3 & 4 have overlapping nodes on their adjacent boundaries. The 2D
plot3d files do not come with so-called neutral map files, containing the
boundary info, so it's basically just a file with node positions.
I'm a first timer on this topic so I'm not very familiar with what info is
needed for the mesh to be stitched together. Is it possible to set these
sidesets in libMesh such that stitching would work? Or would I need a
meshing software? I'd still like to use this test case for my Master's
thesis, but if too difficult I'll have to see if I can generate a simpler
mesh myself.
Pepijn
On Thu, Apr 28, 2016 at 12:07 AM, John Peterson <jwpeter...@gmail.com>
wrote:
>
>
> On Wed, Apr 27, 2016 at 3:46 PM, Pepijn Kessels <pepijnkess...@gmail.com>
> wrote:
>
>> Hi there,
>>
>> I'm trying to import a structured mesh for the 2D backward facing step
>> problem given on the nasa site. I transformed the original plot3d format
>> into exodus format using paraview. I could import the mesh into libMesh
>> without problems, but I ran into some issues when trying to run a
>> simulation.
>>
>> The problem is that the mesh is comprised of 4 subdomains and they are not
>> stitched together, but seen as seperate entities. I read somewhere on the
>> forum that if the nodes on the boundary exactly overlap (which they do)
>> they should automatically be stitched together. I also tried to manually
>> stitch the seperate subdomains together using "stitch_meshes" , but this
>> did not work either as it did not find any nodes on the boundary. I
>> suppose
>> my problem is that boundary information is missing on this mesh. Is there
>> a(n) (easy) way to fix this, such that the 4 subdomains are seen as one
>> domain?
>>
>
> This could be caused if there are duplicate nodes in the Exodus file...
> then find_neighbors() won't detect them as actually being neighbors because
> there will be an infinitely thin "slit" between them.
>
> There's a utility [0] you can use to see if this is the case.
>
> [0]: https://gist.github.com/jwpeterson/7a36f9f794df67d51126
>
> As far as stitching the meshes together goes, I don't think this will work
> if there are no sidesets in the Exodus mesh. It's possible the conversion
> from plot3d -> Exodus dropped these somehow.
>
> --
> John
>
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