<div>I might be able to answer myself.</div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">in the $Nodes section, the mid-face nodes are included with dimension 2 a.k.a faces; e.g. the ninth node</div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><span>2 6 0 1 <-- 2 is the element dimension, 6 is the tag<br></span><div><span>9</span></div><div><span>0.5 0.5 1.0</span></div><span></span></div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">So when creating groups for the surfaces, these nodes are also included into their own physical groups, which PETSc adds into Vertex Sets.<br></div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">I don't quite get why these nodes have dimension 2, but that's probably a gmsh-related question.<br></div><div style="font-family: Arial, sans-serif; font-size: 14px; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><br></div><div class="protonmail_quote">
On Thursday, June 12th, 2025 at 7:08 PM, Noam T. <dontbugthedevs@proton.me> wrote:<br>
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<div style="font-family: Arial, sans-serif; font-size: 14px;">Hello,</div><div style="font-family: Arial, sans-serif; font-size: 14px;"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px;">In the mesh attached, a 1x1x1 cube with 8 nodes, physical groups are defined for the 6 bounding faces only. According to the GUI, and looking at the MSH file in $Entities, there are no physical groups for nodes.</div><div style="font-family: Arial, sans-serif; font-size: 14px;"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px;">Using the following code:</div><div style="font-family: Arial, sans-serif; font-size: 14px;"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px;">---<br></div><div style="font-family: Arial, sans-serif; font-size: 14px;"><span>#include <stdio.h></span><div><span>#include <petscdmplex.h></span></div><div><br></div><div><span>int main(int argc, char *argv[]) {</span></div><div><br></div><div><span> DM dm;</span></div><div><span> PetscInt v;</span></div><div><br></div><div><span> PetscCall(PetscInitialize(&argc, &argv, NULL, NULL));</span></div><div><br></div><div><span> PetscCall(PetscOptionsInsertString(NULL, " -dm_plex_gmsh_mark_vertices "));</span></div><div><span> PetscCall(DMPlexCreateFromFile(PETSC_COMM_WORLD, "mesh.msh", "test", PETSC_TRUE, &dm));</span></div><div><span> PetscCall(DMGetLabelSize(dm, "Vertex Sets", &v));</span></div><div><span> printf("\nVertex set size %d\n", v);</span></div><div><br></div><div><span> PetscCall(PetscFinalize());</span></div><div><span>}</span></div><span></span></div><div style="font-family: Arial, sans-serif; font-size: 14px;">---<br></div><div style="font-family: Arial, sans-serif; font-size: 14px;">it says "Vertex Sets" has size 6, with IS [1, 2, 3, 4, 5, 6]. Is that intended behavior? Up until now I relied on having an empty set whenever physical tags where not explicitly defined, but this one mesh seems to be an exception.</div><div style="font-family: Arial, sans-serif; font-size: 14px;"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px;">Thanks.</div><div style="font-family: Arial, sans-serif; font-size: 14px;"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px;">Noam<br></div><div style="font-family: Arial, sans-serif; font-size: 14px;"><br></div><div style="font-family: Arial, sans-serif; font-size: 14px;">PS: The size is v = 0 when removing the flag "<span>-dm_plex_gmsh_mark_vertices".</span><br></div>
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