0002_H_AO_SVD: volume mesh nodes and face nodes don't match

[ktbolt]

Description

Running an svMultiPhysics simulation for the 0002_H_AO_SVD VMR entry fails with

[svMultiPhysics::gnnb] ERROR: The 'aorta2_inlet' face node 0 could not be matched to a node in the 'fluid_mesh' volume mesh.

Reproduction

Download 0002_H_AO_SVD and create a simulation using the CFD Simulation Tool.

Expected behavior

I would expect the simulation to not fail.

Additional context

No response

Code of Conduct

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[ktbolt]

svMultiPhysics generates node IDs for face coordinates using a hash table created from the volume mesh nodal coordinates. When performing this operation no face coordinates are found in the hash table and the solver fails.

Searching for a face nodal coordinate by computing the minimum distance to all mesh nodal coordinates produces a minimum distance of around 1e-6, not 0.0 as you would expect. For example, I see

Volume coordinate: -5.96297979354858398437500000000000e-01  -3.77122998237609863281250000000000e-01 9.61583042144775390625000000000000e+00
       
Closest face coordinate: -5.96297621726989746093750000000000e-01, -3.77122700214385986328125000000000e-01,9.61583518981933593750000000000000e+00

which differ in the sixth decimal place. It is not clear why the face and volume mesh would be different since the face nodal coordinates are taken from the volume mesh.

[ktbolt]

The nodal coordinates in the 0002_H_AO_SVD/Meshes/0064_1001.vtp mesh exterior surface file don't match exactly those in the 0002_H_AO_SVD/Meshes/0064_1001.vtu volume mesh file; only match within around 1e-6.

A SimVascular mesh exterior surface file in SV_PROJECT/Meshes should have only three VTK data arrays

However, the 0002_H_AO_SVD/Meshes/0064_1001.vtp mesh exterior surface file has a bunch of additional VTK arrays

so this does not look like a standard mesh surface file; not clear how it was generated.

[ktbolt]

Generating a new mesh using the SimVascular SV Meshing Tool creates a new mesh with matching surface and volume mesh nodal coordinates.

[ktbolt]

The original mesh has refined meshing at vessel junctions

Generating a new mesh using the SimVascular SV Meshing Tool will not reproduced this local mesh refinement.

The surface mesh coordinates will thus need to be reset using the volume mesh coordinates; I wrote a script to do this.