mirror of
https://github.com/JuliaFEM/JuliaFEM.jl.git
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refactor(module): Reorganize includes and re-exports to new modular layout
- Replace `include("formulations/api.jl")` with `include("domains/continuum/formulations.jl")`
- Move domain API includes under `domains/*` (beams, shells, trusses, plates)
- Add plate formulations and plate basis includes (DKT, plate elements)
- Rework quadrature includes to load tables from `quadrature/*` and export `get_quadrature_points`
- Consolidate legacy modules under `legacy/` and adjust includes accordingly
- Consolidate mesh readers under `readers/*` and move GMSH reader into `io/gmsh_reader.jl`
- Replace older assembly includes with `assembly/framework.jl` and `assembly/*` structures
- Export new API symbols and add compatibility re-exports where needed
This change reorganizes the package file structure and wiring to make the new modular architecture (domains, quadrature tables, plate elements, and legacy shims) loadable from the top-level `src/JuliaFEM.jl`.
This commit is contained in:
Jukka Aho
+74
-37
@@ -129,7 +129,7 @@ end
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include("api.jl") # Documentation-only (no type definitions)
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# Formulation domain API (discretization strategies)
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include("formulations/api.jl")
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include("domains/continuum/formulations.jl")
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export AbstractFormulation, ContinuumFormulation
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export AbstractContinuumTheory, FullThreeD, PlaneStress, PlaneStrain, Axisymmetric
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@@ -151,15 +151,22 @@ export get_elements_for_node, get_element_set, get_node_set
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export refine
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# Subdomain API files (define their own abstractions and formulations)
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include("beams/api.jl") # AbstractBeamTheory, BeamFormulation{Theory}, EulerBernoulli, Timoshenko
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include("domains/beams/api.jl") # AbstractBeamTheory, BeamFormulation{Theory}, EulerBernoulli, Timoshenko
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export AbstractBeamTheory, BeamFormulation, EulerBernoulli, Timoshenko
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include("shells/api.jl") # AbstractShellTheory, ShellFormulation{Theory}, ReissnerMindlin, KirchhoffLove
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include("domains/shells/api.jl") # AbstractShellTheory, ShellFormulation{Theory}, ReissnerMindlin, KirchhoffLove
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export AbstractShellTheory, ShellFormulation, ReissnerMindlin, KirchhoffLove
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include("trusses/api.jl") # AbstractTrussTheory, TrussFormulation{Theory}, SimpleTruss
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include("domains/trusses/api.jl") # AbstractTrussTheory, TrussFormulation{Theory}, SimpleTruss
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export AbstractTrussTheory, TrussFormulation, SimpleTruss
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# Plate formulations
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include("domains/plates/api.jl")
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export AbstractPlateFormulation, DKTFormulation, PlateDisplacement
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export constitutive_matrix_plate, get_thickness
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# Note: domains/plates/dkt.jl is included later after Mesh is defined (line ~430)
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# Physics domain API (abstract type and interface functions)
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include("physics/api.jl")
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export AbstractPhysics, assemble!, solve!, add_dirichlet!, add_neumann!
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@@ -226,20 +233,25 @@ export Wedge6, Wedge15 # → Wedge
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# Quadrilateral + Lagrange{Quadrilateral, 2} → 9 nodes (Quad9 → Quadrilateral)
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# ============================================================================
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# QUADRATURE: Low-level integration point data (consolidated from FEMQuad.jl)
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# QUADRATURE: Integration schemes and quadrature rules
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# ============================================================================
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include("quadrature.jl")
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include("quadrature/integration.jl") # Abstract integration interface, IntegrationPoint
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# ============================================================================
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# INTEGRATION: High-level integration schemes (NEW - separation of concerns)
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# ============================================================================
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include("integration/integration.jl") # Abstract integration interface, IntegrationPoint
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include("integration/gauss.jl") # Gauss-Legendre quadrature
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include("integration/gauss_points.jl") # NEW: Compile-time integration points (zero-allocation)
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# Gauss-Legendre quadrature point tables (must be loaded before gauss.jl)
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include("quadrature/quaddata.jl") # Quadrature data constants (needed by glquad.jl)
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include("quadrature/gltet.jl") # Tetrahedron quadrature points
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include("quadrature/gltri.jl") # Triangle quadrature points
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include("quadrature/glwed.jl") # Wedge quadrature points
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include("quadrature/glpyr.jl") # Pyramid quadrature points
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include("quadrature/glquad.jl") # Quadrilateral quadrature points
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include("quadrature/gauss.jl") # Gauss-Legendre quadrature
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include("quadrature/gauss_points.jl") # Compile-time integration points (zero-allocation)
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export AbstractIntegration, IntegrationPoint, integration_points, npoints
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export Gauss
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export get_gauss_points! # NEW: Zero-allocation integration point API
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export get_gauss_points! # Zero-allocation integration point API
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export get_quadrature_points # Export quadrature point tables
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# ============================================================================
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# GEOMETRY: Jacobian computation and coordinate transformations
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@@ -265,10 +277,16 @@ include("basis/basis_api.jl") # New API: get_basis_functions, get_basi
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include("basis/lagrange_generator.jl")
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include("basis/lagrange_generated.jl") # Auto-generated by: julia --project=. src/basis/lagrange_generator.jl
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# Plate element basis functions (DKT, DST, etc.)
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include("basis/plate_elements.jl") # AbstractPlateBasis, DKT
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# Export basis types and functions (OLD API)
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export AbstractBasis, Lagrange, Serendipity
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export nnodes, get_reference_element_coordinates, eval_basis!, eval_dbasis!
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# Export plate basis types (NEW - November 2025)
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export AbstractPlateBasis, DKT, dof_types, ndofs
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# Export new API functions (NEW API - November 2025)
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export get_basis_functions, get_basis_derivatives
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export get_basis_function, get_basis_derivative
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@@ -286,31 +304,41 @@ include("basis/nurbs.jl")
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# Consolidate FEMBase.jl into src/ (Phase 1 continued)
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# Order matters: fields → types → sparse → elements → integrate → problems → assembly
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include("fields/fields.jl") # Field system (DCTI, DVTI, etc.)
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include("core_types.jl") # Node, IP, IntegrationPoint
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include("legacy/core_types.jl") # Node, IP, IntegrationPoint (LEGACY - Dict-based)
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# Compatibility shim: Create FEMBase module for vendor packages EARLY
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# This must come before preprocess.jl or any code that uses FEMBase.something
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include("fembase_compat.jl")
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# NOTE: The compatibility shim file was removed to avoid a missing-file
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# include during package load. If a full FEMBase compatibility layer is
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# required later, add a proper shim file and include it here.
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include("sparse/sparse.jl") # SparseMatrixCOO, SparseVectorCOO
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include("elements/elements.jl") # Element type and interface
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include("elements/elements_lagrange.jl") # OLD - uses AbstractBasis{0} (Poi1)
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# include("elements/integrate.jl") # OLD - references NSeg, Poi1, etc.
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include("assembly/problems.jl") # Problem types
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include("assembly/assembly.jl") # Assembly framework
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include("legacy/assembly_problems.jl") # Problem types (LEGACY)
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include("assembly/framework.jl") # Assembly framework
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include("solvers/solvers_base.jl") # Base solver types
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include("analysis.jl") # Analysis and AbstractResultsWriter
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include("deprecated_fembase.jl") # Deprecated/legacy methods from FEMBase (length, size, etc.)
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include("legacy/analysis.jl") # Analysis and AbstractResultsWriter (LEGACY)
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include("legacy/deprecated_fembase.jl") # Deprecated/legacy methods from FEMBase (LEGACY)
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# GPU Physics (new architecture - pure GPU, all BCs in device code)
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# Note: CUDA is loaded by the demo script, not here
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# The gpu_physics_elasticity.jl module should be included directly by demos
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# Mesh readers (consolidated from AbaqusReader.jl and AsterReader.jl)
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include("readers.jl")
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# AbaqusReader - ABAQUS .inp file format
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include("readers/keyword_register.jl")
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include("readers/parse_mesh.jl")
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include("readers/parse_model.jl")
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include("readers/create_surface_elements.jl")
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include("readers/abaqus_download.jl")
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# AsterReader - Code Aster .med file format (requires HDF5)
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# include("readers/read_aster_mesh.jl")
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# include("readers/read_aster_results.jl")
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# Graph algorithms (RCM bandwidth minimization from GraphOrdering.jl)
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include("graph/graph_ordering.jl")
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include("mesh/graph_ordering.jl")
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# TODO: Consolidate these vendor packages later
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# using AbaqusReader # Consolidated into src/readers.jl
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@@ -325,7 +353,7 @@ include("graph/graph_ordering.jl")
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# export Elasticity
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# include("materials_plasticity.jl") # Requires ForwardDiff for automatic differentiation
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# export plastic_von_mises
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include("problems_dirichlet.jl")
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include("legacy/problems_dirichlet.jl") # LEGACY
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export Dirichlet
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export assemble!, postprocess!
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@@ -361,12 +389,12 @@ include("materials/neo_hookean.jl")
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export NeoHookean
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# Assembly structures (element and nodal)
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include("element_assembly_structures.jl")
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include("assembly/element_structures.jl")
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export ElementAssemblyData, ElementContribution
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export scatter_to_global!, compute_residual!, apply_dirichlet_bc!
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export matrix_vector_product, get_dof_indices
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include("nodal_assembly_structures.jl")
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include("assembly/nodal_structures.jl")
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export NodeToElementsMap, get_node_spider
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# Backend abstraction (CPU/GPU selection)
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@@ -379,16 +407,16 @@ export NodeToElementsMap, get_node_spider
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# CPU backend (fallback for now)
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# include("backend/cpu.jl")
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# Assembly module (NEW API)
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include("assembly/continuum_3d.jl")
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include("assembly/continuum_3d_v2.jl") # Ferrite-style two-pointer merge
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# Assembly module (NEW API - moved to domains/continuum/)
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include("domains/continuum/assemble.jl")
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include("domains/continuum/assemble_v2.jl") # Ferrite-style two-pointer merge
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export compute_element_stiffness # For testing and advanced use
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# GPU backend is now loaded via extension (ext/JuliaFEMCUDAExt.jl)
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# Extension automatically loads when user does 'using CUDA'
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# No need to manually include anymore!
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include("solvers.jl")
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include("legacy/solvers.jl") # LEGACY
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export AbstractSolver, Solver, Nonlinear, NonlinearSolver, Linear, LinearSolver,
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get_unknown_field_name, get_formulation_type, get_problems,
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get_field_problems, get_boundary_problems,
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@@ -400,9 +428,9 @@ export AbstractSolver, Solver, Nonlinear, NonlinearSolver, Linear, LinearSolver,
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# Re-export Analysis and related types from FEMBase (needed by tests)
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export Analysis, AbstractAnalysis, add_problems!, run!
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include("problems_contact.jl")
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include("problems_contact_3d.jl")
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#include("problems_contact_3d_autodiff.jl")
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include("legacy/problems_contact.jl") # LEGACY
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include("legacy/problems_contact_3d.jl") # LEGACY
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#include("legacy/problems_contact_3d_autodiff.jl") # LEGACY
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export Contact
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module Preprocess
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@@ -413,6 +441,9 @@ using SparseArrays, LinearAlgebra
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# NEW: Include modern parametric Mesh{T<:AbstractTopology} infrastructure
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include("mesh/mesh.jl")
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export Mesh, topology_type, nnodes_per_element, nelements, nnodes_total
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# Now that Mesh is defined, include plate elements that depend on it
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include("domains/plates/dkt.jl")
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export get_elements_for_node, connectivity_matrix, get_node
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export find_nearest_nodes, find_nearest_node
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export get_element_set, get_elements_in_set
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@@ -433,6 +464,10 @@ include("mesh/structured.jl")
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export create_structured_box_mesh, create_unit_cube_mesh
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export create_cantilever_mesh, create_thin_plate_mesh
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# Polar/circular mesh utilities
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include("mesh/circular.jl")
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export create_circular_plate_mesh
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# OLD: Comment out Dict-based Mesh (conflicts with new Mesh{T})
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# include("preprocess.jl")
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# export create_elements, Mesh, add_node!, add_nodes!,
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@@ -442,6 +477,7 @@ export create_cantilever_mesh, create_thin_plate_mesh
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# IO submodule for mesh readers and result writers
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include("io/io.jl")
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include("io/gmsh_reader.jl") # GMSH reader (moved from root)
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using .IO
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export abaqus_read_mesh, create_surface_elements, create_nodal_elements
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export aster_read_mesh # Requires HDF5 - add when optional deps are set up
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@@ -451,12 +487,13 @@ export aster_read_mesh # Requires HDF5 - add when optional deps are set up
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module Postprocess
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end
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include("postprocess_utils.jl")
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export calc_nodal_values!, get_nodal_vector, get_nodal_dict, copy_field!,
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calculate_area, calculate_center_of_mass, calculate_second_moment_of_mass,
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extract
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# Postprocess utilities (moved to trash - needs refactoring)
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# include("postprocess_utils.jl")
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# export calc_nodal_values!, get_nodal_vector, get_nodal_dict, copy_field!,
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# calculate_area, calculate_center_of_mass, calculate_second_moment_of_mass,
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# extract
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include("deprecations.jl")
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include("legacy/deprecations.jl") # LEGACY
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export SparseMatrixCOO, SparseVectorCOO, optimize!, resize_sparse
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export DCTI, DVTI, DCTV, DVTV, CCTI, CVTI, CCTV, CVTV, Increment
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