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chore(test): delete fundamentals Gmsh reading tutorial script
Remove stale tutorial harness superseded by `test/io/test_gmsh_reader.jl`. - Drop `reading_gmsh_meshes.jl`.
This commit is contained in:
Jukka Aho
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# # Tutorial 2: Reading Meshes with Gmsh
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#
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# Real FEM problems need meshes with many elements. Creating them manually
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# would be tedious! This tutorial shows how to:
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# - Read mesh files generated by Gmsh
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# - Extract nodes and elements
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# - Organize elements by physical groups (for boundary conditions)
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#
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# ## Prerequisites
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#
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# - Tutorial 1 (Creating Elements and Fields)
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# - Basic understanding of mesh concepts (nodes, elements, connectivity)
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using JuliaFEM
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using Gmsh # Mesh generation and reading
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using Test
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# ## The Mesh File
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#
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# We're reading a pre-generated mesh file: `reading_gmsh_meshes.msh`
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#
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# This mesh was created using the Gmsh.jl recipe in `reading_gmsh_meshes_recipe.jl`.
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# The recipe shows how to programmatically generate meshes - very useful for
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# parametric studies!
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#
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# **Mesh specifications:**
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# - Domain: Unit square [0,1] × [0,1]
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# - Elements: 10 Quad4 elements (2×5 structured mesh)
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# - Nodes: 18 nodes
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# - Physical groups: DOMAIN (volume), BOTTOM/RIGHT/TOP/LEFT (boundaries)
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mesh_file = joinpath(@__DIR__, "reading_gmsh_meshes.msh")
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# ## Reading the Mesh with Gmsh.jl
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#
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# Gmsh.jl provides a Julia interface to the Gmsh API. We can read mesh files
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# and extract all the data we need.
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# Initialize Gmsh
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gmsh.initialize()
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# Open and read the mesh file
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gmsh.open(mesh_file)
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# ## Extracting Nodes
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#
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# Nodes are the points in space where we'll compute field values.
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# In Gmsh, nodes are returned as:
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# - `nodeTags`: Node IDs (integers)
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# - `coord`: Coordinates (x, y, z) as a flat vector
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nodeTags, coord, parametricCoord = gmsh.model.mesh.getNodes()
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# The `coord` vector is flat: [x1, y1, z1, x2, y2, z2, ...]
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# Let's reshape it into a more convenient format:
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num_nodes = length(nodeTags)
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nodes = Dict{Int,Vector{Float64}}()
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for i in 1:num_nodes
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node_id = nodeTags[i]
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x = coord[3*(i-1)+1]
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y = coord[3*(i-1)+2]
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z = coord[3*(i-1)+3]
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nodes[node_id] = [x, y, z]
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end
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# Now we have a dictionary mapping node IDs to coordinates!
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# ## Extracting Elements
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#
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# Elements connect nodes and define the interpolation within each region.
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# In Gmsh, we need to query elements by entity (surfaces, volumes, etc.).
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# Get all 2D entities (surfaces in our case)
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entities = gmsh.model.getEntities(2) # 2 = dimension for surfaces
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# For each entity, get the elements
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all_elements = Element[]
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for entity in entities
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dim, tag = entity
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# Get element data for this entity
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elemTypes, elemTags, nodeTags_elem = gmsh.model.mesh.getElements(dim, tag)
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# Loop over element types (we have Quad4 = type 3)
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for (elemType, elemTag, elemNodeTags) in zip(elemTypes, elemTags, nodeTags_elem)
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# Get element properties
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elemName, elemDim, order, numNodes, localNodeCoord, numPrimaryNodes =
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gmsh.model.mesh.getElementProperties(elemType)
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# Create JuliaFEM elements
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for i in 1:length(elemTag)
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# Extract connectivity for this element
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start_idx = (i - 1) * numNodes + 1
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end_idx = i * numNodes
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# Convert UInt64 to Int for JuliaFEM compatibility
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connectivity = Tuple(Int(tag) for tag in elemNodeTags[start_idx:end_idx])
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# Map Gmsh element type to JuliaFEM element type
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if elemType == 3 # Gmsh Quad4
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local elem = Element(Quad4, connectivity)
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else
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@warn "Unknown element type: $elemType ($elemName)"
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continue
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end
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# Add geometry field
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update!(elem, "geometry", nodes)
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push!(all_elements, elem)
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end
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end
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end
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# ## Physical Groups
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#
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# Physical groups let us organize elements by region (for materials)
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# and boundaries (for boundary conditions).
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# Get all physical groups
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physicalGroups = gmsh.model.getPhysicalGroups()
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# We can query which elements belong to each physical group
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# (This would be used to create separate Problems for different regions)
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# ## Cleanup
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gmsh.finalize()
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# ## Validation Tests
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#
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# Let's verify the mesh was read correctly:
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@testset "Gmsh Mesh Reading" begin
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# Correct number of nodes (2×5 structured quad mesh has 3×6 nodes)
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@test length(nodes) == 18
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# Correct number of elements (2 × 5 = 10 quads)
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@test length(all_elements) == 10
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# All elements should be Quad4
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@test all(e -> typeof(e.properties) == Quad4, all_elements)
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# Node coordinates should be in [0,1] × [0,1]
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for (node_id, coord) in nodes
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@test 0.0 <= coord[1] <= 1.0 # x ∈ [0,1]
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@test 0.0 <= coord[2] <= 1.0 # y ∈ [0,1]
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@test coord[3] == 0.0 # z = 0 (2D mesh)
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end
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# Each element should have 4 nodes
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for element in all_elements
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@test length(element.connectivity) == 4
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end
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end
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# ## What We Learned
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#
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# ✅ How to read Gmsh .msh files using Gmsh.jl
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# ✅ Extract nodes (IDs and coordinates)
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# ✅ Extract elements (type, connectivity)
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# ✅ Map Gmsh element types to JuliaFEM types
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# ✅ Physical groups organize elements for BCs and materials
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# ✅ Mesh generation recipes document mesh creation
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#
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# ## Why This Approach?
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#
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# **Pre-generated mesh files** (not generating in tests):
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# - Tests are reliable (don't fail due to mesh generation)
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# - Tests run faster (no mesh generation overhead)
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# - Mesh is version-controlled (reproducible)
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#
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# **Recipe files** (showing how mesh was made):
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# - Educational (teach Gmsh.jl)
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# - Documented (can regenerate if needed)
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# - Transparent (know exactly what the mesh is)
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#
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# ## Next Steps
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#
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# - **Tutorial 3:** Basis functions and shape function evaluation
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# - **Tutorial 4:** Solving 1D elasticity (1-element validation)
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# - **Tutorial 5:** Solving 2D elasticity (realistic 10-element problem)
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#
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# ## Real-World Impact
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#
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# JuliaFEM is being used to **validate other FEM software**!
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# See [Issue #265](https://github.com/JuliaFEM/JuliaFEM.jl/issues/265) where
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# a user validated their FEM code against JuliaFEM results. This is beautiful -
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# we're useful as a reference implementation even after years!
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#
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# That's why we include **1-element validation tests** with analytical solutions
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# and **nice round numbers** (parameters chosen so results are integers). Makes
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# it easy to verify by hand calculation or compare with other codes.
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