mesh_from_gmsh fails when .msh has quadrilateral reference elements

[jfdev001]

In prepping for the periodic boundary condition handling algorithm that is necessary to ensure consistent global ids, I wanted to generate some coarser meshes for ease of visualization with paraview. Commit 2b32a73 contains the quad.msh, which was generated by opening quad.geo in gmsh, then all mesh options > Set 2D Algorithm to "Frontal Delauny for Quads (Experimental)" > Checking "Recombine all triangular meshes" > Set "Element size factor" to 2. Attempting to load this mesh fails, the cause of which is the assertion at src/geometry.jl:1970. This is low priority right now, but thought I'd submit anyways and I or you could come back to it later. An image of the mesh that throws the assertion error is attached along with the error producing code.

import GalerkinToolkit as gk
mesh = gk.mesh_from_gmsh("assets/quad.msh")

ERROR: AssertionError: ldface2 != INVALID_ID
Stacktrace:
[1] generate_face_boundary(Dface_to_vertices::PartitionedArrays.JaggedArray{…}, vertex_to_D
faces::PartitionedArrays.JaggedArray{…}, dface_to_vertices::PartitionedArrays.JaggedArray{…},
vertex_to_dfaces::PartitionedArrays.JaggedArray{…}, Dface_to_refid::Vector{…}, Drefid_to_ldf
ace_to_lvertices::Tuple{…})
@ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:1970
[2] complexify_mesh(mesh::GalerkinToolkit.GenericFEMesh{…})
@ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:1676
[3] complexify(mesh::GalerkinToolkit.GenericFEMesh{Vector{…}, Vector{…}, Vector{…}, Tuple{…
}, Pair{…}, Vector{…}, Nothing})
@ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:1633
[4] mesh_from_gmsh_module(; complexify::Bool)
@ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:707
[5] mesh_from_gmsh_module
@ ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:525 [inlined]
[6] (::GalerkinToolkit.var"#63#64"{Bool, Bool, String})()
@ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:521
[7] with_gmsh(f::GalerkinToolkit.var"#63#64"{Bool, Bool, String}; options::Vector{Pair{Stri
ng, Int64}})
@ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:507
[8] with_gmsh
@ ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:501 [inlined]
[9] mesh_from_gmsh(file::String; complexify::Bool, renumber::Bool, kwargs::@kwargs{})
@ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:517
[10] mesh_from_gmsh(file::String)
@ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:515
[11] top-level scope
@ REPL[24]:1
Some type information was truncated. Use show(err) to see complete types.

[jfdev001]

The gk.cartesian_mesh function doesn't appear to support imposing periodic boundary conditions. So for developing the periodic bc handling algorithm in the context of a two level mesh, would the coarse mesh be a Cartesian mesh and the fine mesh a periodic mesh created from gmsh? See e.g., below for visualization. If this is the case, then either (a) a fix for mesh to gmsh quad reference elements is necessary or (b) the cartesian mesh needs to support periodic bcs on arbitrary sides. I will look into (a) unless otherwise notified.

[fverdugo]

Regarding the first error:

have you added a physical group that covers all cells in the mesh? If not, gmsh does not store connectivity information in the .msh file for the cells. (gmsh only stores connectivity for objects appearing in physical groups)

[fverdugo]

Regarding the periodic BCs:

• Note that you also need periodic BCs in the vertical direction, in addition to the horizontal one.
• gk.cartesian_mesh needs to be extended to support periodic bcs. This is important in many scenarios. For the moment, use a unit cell mesh generated with gmsh.

[jfdev001]

Regarding the first error:

have you added a physical group that covers all cells in the mesh? If not, gmsh does not store connectivity information in the .msh file for the cells. (gmsh only stores connectivity for objects appearing in physical groups)

Commit 8021398 adds physical groups to the simple quad geometry and then meshes using two strategies: (1) recombining triangles to give quadrilateral reference elements, and (2) just using triangular reference elements. Recombining triangles still throws the assertion error despite physical groups now being named.

julia> import GalerkinToolkit as gk
julia> gk.mesh_from_gmsh("assets/quad_recombine_triangles.msh")
Info    : Reading 'assets/quad_recombine_triangles.msh'...
Info    : 9 entities
Info    : 25 nodes
Info    : 36 elements
Info    : Done reading 'assets/quad_recombine_triangles.msh'
ERROR: AssertionError: ldface2 != INVALID_ID
Stacktrace:
  [1] generate_face_boundary(Dface_to_vertices::PartitionedArrays.JaggedArray{…}, vertex_to_Dfaces::PartitionedArrays.JaggedArray{…}, dface_to_vertices::PartitionedArrays.JaggedArray{…}, vertex_to_dfaces::PartitionedArrays.JaggedArray{…}, Dface_to_refid::Vector{…}, Drefid_to_ldface_to_lvertices::Tuple{…})
    @ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:1970
  [2] complexify_mesh(mesh::GalerkinToolkit.GenericFEMesh{…})
    @ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:1676
  [3] complexify(mesh::GalerkinToolkit.GenericFEMesh{Vector{…}, Vector{…}, Vector{…}, Tuple{…}, Pair{…}, Vector{…}, Nothing})
    @ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:1633
  [4] mesh_from_gmsh_module(; complexify::Bool)
    @ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:707
  [5] mesh_from_gmsh_module
    @ ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:525 [inlined]
  [6] (::GalerkinToolkit.var"#63#64"{Bool, Bool, String})()
    @ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:521
  [7] with_gmsh(f::GalerkinToolkit.var"#63#64"{Bool, Bool, String}; options::Vector{Pair{String, Int64}})
    @ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:507
  [8] with_gmsh
    @ ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:501 [inlined]
  [9] mesh_from_gmsh(file::String; complexify::Bool, renumber::Bool, kwargs::@Kwargs{})
    @ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:517
 [10] mesh_from_gmsh(file::String)
    @ GalerkinToolkit ~/.julia/dev/GalerkinToolkit.jl/src/geometry.jl:515
 [11] top-level scope
    @ REPL[48]:1
Some type information was truncated. Use `show(err)` to see complete types.

and

julia> gk.mesh_from_gmsh("assets/quad_triangles.msh")
Info    : Reading 'assets/quad_triangles.msh'...
Info    : 9 entities
Info    : 25 nodes
Info    : 52 elements
Info    : Done reading 'assets/quad_triangles.msh'
GalerkinToolkit.GenericFEMesh(…)