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refactor(io): remove bundled Gmsh reader and document I/O policy
The core package keeps the mesh and assembly stack type-stable without shipping a Gmsh dependency or an always-loaded ASCII parser, and the IO README now states where format readers should live going forward. - Delete `src/io/gmsh_reader.jl` (`GmshReader`, `read_gmsh_mesh`, `GmshMesh`) including its Dict-heavy parsing path - Rewrite `src/io/README.md` to describe policy-only `src/io/` (weakdeps/extensions or separate packages), point legacy `.inp`/`.med` readers at `src/legacy/io/` behind `JULIAFEM_ENABLE_LEGACY=1`, and warn against unconditional `include` growth for heavy I/O
This commit is contained in:
Jukka Aho
+13
-18
@@ -1,24 +1,19 @@
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# src/io/
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Mesh readers that ship with the current 0.x package surface.
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Policy for **external mesh formats** (Gmsh, Netgen, Abaqus, Code Aster, …).
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The Abaqus `.inp` and Code Aster `.med` readers were built around the
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older `Element(Poi1, ...)` constructors and the Dict-based field
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system; they have been moved into the optional `JuliaFEM.Legacy`
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submodule (see `src/legacy/io/`). Set the environment variable
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`JULIAFEM_ENABLE_LEGACY=1` before `using JuliaFEM` to load them.
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The core package owns the type-stable mesh model (`Mesh{N, T}` under
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`src/mesh/`) and assembly; it does **not** ship format-specific parsers in
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`src/io/`. Converters that read third-party files and build `Mesh{…}`,
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`element_sets`, and `node_sets` should live in **separate packages** or in
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**JuliaFEM package extensions** wired through `[weakdeps]` / `[extensions]` in
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`Project.toml`, mirroring the MPI extension pattern (`JuliaFEMMPIExt`).
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## Files
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Legacy `.inp` / `.med` readers tied to the pre-reset API remain under
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`src/legacy/io/` and load only with `JULIAFEM_ENABLE_LEGACY=1`.
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- `gmsh_reader.jl`
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Self-contained Gmsh `.msh` (ASCII format 4.1) reader.
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Defines its own `JuliaFEM.GmshReader` submodule with `GmshMesh`,
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`read_gmsh_mesh`. Has no dependency on legacy types and is loaded
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unconditionally.
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## This directory
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## Future work
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A current-API replacement for the Abaqus reader (returning
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`Mesh{T<:AbstractTopology, N}` and elements built via `create_elements!`)
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is on the roadmap. When it lands it will live here next to
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`gmsh_reader.jl`.
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This folder holds **documentation only** until a new extension or companion
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package is added. Do not grow unconditional `include("io/*.jl")` paths in
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`JuliaFEM.jl` for heavy or format-specific I/O.
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@@ -1,173 +0,0 @@
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"""
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Simple Gmsh mesh reader for tetrahedral meshes
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Reads .msh format (ASCII version 4.1) and extracts:
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- Nodes (coordinates)
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- Elements (Tet4 connectivity)
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- Physical groups (for boundary conditions)
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"""
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module GmshReader
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export read_gmsh_mesh, GmshMesh
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using LinearAlgebra
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"""
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Mesh data structure
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"""
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struct GmshMesh
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nodes::Matrix{Float64} # 3 × n_nodes
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elements::Matrix{Int} # 4 × n_elems (Tet4)
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physical_groups::Dict{String,Vector{Int}} # Name → element/node indices
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end
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"""
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Read Gmsh mesh file (ASCII format 4.1)
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"""
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function read_gmsh_mesh(filename::String)
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@info "Reading Gmsh mesh" filename
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# Storage
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nodes = Dict{Int,Vector{Float64}}()
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elements = Vector{Tuple{Int,Int,Int,Int}}()
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physical_names = Dict{Int,String}()
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element_groups = Dict{Int,Vector{Int}}()
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open(filename, "r") do io
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while !eof(io)
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line = strip(readline(io))
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# Parse physical names
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if line == "\$PhysicalNames"
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n_names = parse(Int, readline(io))
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for _ in 1:n_names
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parts = split(readline(io))
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dim = parse(Int, parts[1])
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tag = parse(Int, parts[2])
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name = strip(parts[3], '"')
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physical_names[tag] = name
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end
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readline(io) # \$EndPhysicalNames
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end
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# Parse nodes (format 4.1)
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if line == "\$Nodes"
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header = split(readline(io))
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numEntityBlocks = parse(Int, header[1])
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numNodes = parse(Int, header[2])
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for _ in 1:numEntityBlocks
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# Entity block header: entityDim entityTag parametric numNodesInBlock
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block_header = split(readline(io))
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numNodesInBlock = parse(Int, block_header[4])
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# Read node IDs
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node_ids = Int[]
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for _ in 1:numNodesInBlock
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push!(node_ids, parse(Int, readline(io)))
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end
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# Read coordinates
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for node_id in node_ids
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coords = split(readline(io))
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x = parse(Float64, coords[1])
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y = parse(Float64, coords[2])
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z = parse(Float64, coords[3])
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nodes[node_id] = [x, y, z]
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end
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end
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readline(io) # \$EndNodes
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end
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# Parse elements (format 4.1)
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if line == "\$Elements"
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header = split(readline(io))
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numEntityBlocks = parse(Int, header[1])
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numElements = parse(Int, header[2])
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for _ in 1:numEntityBlocks
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# Entity block header: entityDim entityTag elementType numElementsInBlock
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block_header = split(readline(io))
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entityTag = parse(Int, block_header[2])
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elementType = parse(Int, block_header[3])
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numElementsInBlock = parse(Int, block_header[4])
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for _ in 1:numElementsInBlock
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parts = split(readline(io))
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elem_id = parse(Int, parts[1])
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# Tet4 element (type 4)
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if elementType == 4
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n1 = parse(Int, parts[2])
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n2 = parse(Int, parts[3])
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n3 = parse(Int, parts[4])
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n4 = parse(Int, parts[5])
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push!(elements, (n1, n2, n3, n4))
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# Track physical group (entity tag is the physical group)
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if entityTag > 0
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if !haskey(element_groups, entityTag)
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element_groups[entityTag] = Int[]
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end
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push!(element_groups[entityTag], length(elements))
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end
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end
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end
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end
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readline(io) # \$EndElements
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end
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end
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end
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# Convert nodes to matrix (3 × n_nodes)
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n_nodes = length(nodes)
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node_matrix = zeros(3, n_nodes)
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for (node_id, coords) in nodes
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node_matrix[:, node_id] = coords
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end
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# Convert elements to matrix (4 × n_elems)
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n_elems = length(elements)
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elem_matrix = zeros(Int, 4, n_elems)
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for (i, elem) in enumerate(elements)
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elem_matrix[:, i] = [elem[1], elem[2], elem[3], elem[4]]
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end
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# Build physical groups with names
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groups = Dict{String,Vector{Int}}()
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for (tag, elem_ids) in element_groups
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name = get(physical_names, tag, "Group_$tag")
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groups[name] = elem_ids
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end
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mesh = GmshMesh(node_matrix, elem_matrix, groups)
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@info "Gmsh mesh loaded" nodes = size(node_matrix, 2) elements = size(elem_matrix, 2) physical_groups = collect(keys(groups))
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return mesh
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end
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"""
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Extract nodes on a boundary surface
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"""
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function get_surface_nodes(mesh::GmshMesh, surface_name::String)
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# For now, return nodes where X ≈ 0 (fixed end) or Z ≈ max (top)
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# This is a placeholder - proper implementation would track surface elements
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if surface_name == "FixedEnd"
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# Find nodes with X ≈ 0
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x_min = minimum(mesh.nodes[1, :])
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tol = 1e-6
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return findall(abs.(mesh.nodes[1, :] .- x_min) .< tol)
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elseif surface_name == "PressureSurface"
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# Find nodes with Z ≈ max
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z_max = maximum(mesh.nodes[3, :])
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tol = 1e-6
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return findall(abs.(mesh.nodes[3, :] .- z_max) .< tol)
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else
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return Int[]
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end
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end
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end # module
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