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https://github.com/JuliaFEM/JuliaFEM.jl.git
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feat(core): reorder includes and add FEDiscretization plus Gauss tuples
Partition metadata loads before DOF-based caches, new kernels and column helpers wire into the load order, Gmsh leaves the default include graph, and MPI docstrings describe kernel-less overloads plus internal-force hook. - Add reference_gauss_tuples.jl and dof_based_pass1; include poroelastic and thermo_poroelastic kernels after thermo_elastic - Hoist partitioning, halo_exchange, packed_layout, redundant_kernel_depwarn, ka_column_homogeneity, kernel_column ahead of dof_based_coo.jl - Add physics/discretization.jl (FEDiscretization); drop gmsh_reader include - Extend MPI matvec docstrings; declare mpi_partitioned_internal_force_owned!
This commit is contained in:
Jukka Aho
+69
-13
@@ -89,6 +89,7 @@ include("quadrature/gl_triangles.jl")
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include("quadrature/gl_wedges.jl")
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include("quadrature/gl_pyramids.jl")
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include("quadrature/gl_tensor_product.jl")
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include("quadrature/reference_gauss_tuples.jl")
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include("quadrature/gauss.jl")
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include("geometry/jacobian.jl")
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@@ -165,6 +166,7 @@ include("domains/continuum/kernel.jl")
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include("domains/continuum/update_geometry_cache.jl")
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include("domains/continuum/update_element_cache.jl")
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include("domains/continuum/update_material_cache.jl")
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include("domains/continuum/dof_based_pass1.jl")
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include("domains/continuum/mixed_up_kernel.jl")
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include("domains/continuum/stokes_mixed_kernel.jl")
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include("domains/continuum/hellinger_reissner_kernel.jl")
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@@ -176,6 +178,8 @@ include("domains/darcy/mixed_rt0.jl")
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include("domains/darcy/mixed_rt0_hex.jl")
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include("domains/thermo_elastic/kernel.jl")
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include("domains/poroelastic/kernel.jl")
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include("domains/thermo_poroelastic/kernel.jl")
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# ============================================================================
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# Level 7 - Concrete mesh + DOFHandler + DOF-based assembler + matrix-free
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@@ -198,17 +202,23 @@ include("dofs/dof_connectivity.jl")
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include("interface/interface_mesh.jl")
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include("interface/interface_dof_handler.jl")
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# DOF-based assembler — CPU plus the backend-agnostic KernelAbstractions
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# port (CPU(), CUDABackend(), MetalBackend(), AMDGPUBackend(), oneAPIBackend();
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# locally validated against CPU()).
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include("assemblers/dof_based/dof_based_coo.jl")
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include("assemblers/dof_based/dof_based_coo_ka.jl")
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# Partition metadata + multiply-buffer layouts (MPI/GPU hooks; default is
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# single-process identity).
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# Partition metadata + packed layouts must load before `dof_based_coo.jl`
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# (method signatures use `PartitionPackedLayout`). `packed_layout.jl` depends on
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# `MeshPartitionLayout` / halo helpers from `partitioning.jl` / `halo_exchange.jl`.
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include("assemblers/partitioning.jl")
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include("assemblers/halo_exchange.jl")
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include("assemblers/packed_layout.jl")
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include("assemblers/redundant_kernel_depwarn.jl")
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# DOF-based assembler — CPU plus the backend-agnostic KernelAbstractions
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# port (CPU(), CUDABackend(), MetalBackend(), AMDGPUBackend(), oneAPIBackend();
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# locally validated against CPU()).
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include("assemblers/dof_based/ka_column_homogeneity.jl")
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include("assemblers/dof_based/kernel_column.jl")
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include("assemblers/dof_based/dof_based_coo.jl")
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include("assemblers/dof_based/dof_based_coo_ka.jl")
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include("assemblers/partitioned_matvec.jl")
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# Matrix-free path: declarative Dirichlet / MPC constraints, declarative
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@@ -222,6 +232,8 @@ include("assemblers/matrix_free/preconditioners.jl")
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include("assemblers/matrix_free/eigensolve.jl")
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include("assemblers/matrix_free/loads.jl")
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include("physics/discretization.jl")
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# ============================================================================
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# Level 8 - Mesh utilities and I/O
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# ============================================================================
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@@ -230,9 +242,8 @@ include("mesh/structured.jl")
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include("domains/continuum/material_element_lab.jl")
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# Self-contained Gmsh mesh reader (defines its own `JuliaFEM.GmshReader`
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# submodule with `read_gmsh_mesh` / `GmshMesh`).
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include("io/gmsh_reader.jl")
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# External mesh formats (Gmsh, Abaqus, Netgen, …) → `Mesh{…}` belong in
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# optional package extensions or side packages; see `src/io/README.md`.
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# ============================================================================
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# Optional older API surface (Problem / Assembly / Solver / Analysis,
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@@ -284,16 +295,28 @@ on the local partition, summed with [`MPI.Allreduce`](@ref). Requires `using MPI
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function mpi_owned_dot_global end
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"""
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mpi_partitioned_operator_matvec!(
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Ap, p, packed, work, recv_vals, send_vals,
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layout, exchange, cache, assembler, mesh, comm;
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dirichlet = nothing, mpi_requests = nothing,
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configuration = nothing, global_material_cache = nothing, Δt = 0.0,
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)
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mpi_partitioned_operator_matvec!(
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Ap, p, packed, work, recv_vals, send_vals,
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layout, exchange, cache, assembler, kernel, mesh, comm;
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dirichlet = nothing, mpi_requests = nothing,
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configuration = nothing, global_material_cache = nothing, Δt = 0.0,
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)
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Replicated-global matrix-free product including optional [`PenaltyDirichlet`](@ref) post-hook.
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Loads `JuliaFEMMPIExt` when both `JuliaFEM` and `MPI` are imported.
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Keyword `mpi_requests` is forwarded to [`exchange_matvec_halos_mpi!`](@ref).
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The primary form reads the volume kernel from `cache.kernel_column`. The overload
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with `kernel` ignores it (backward compatibility).
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Keywords `mpi_requests` (to [`exchange_matvec_halos_mpi!`](@ref)) and
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`configuration` / `global_material_cache` / `Δt` (to [`apply_K_owned_rows!`](@ref), nonlinear continuum Pass~1)
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are forwarded when `JuliaFEMMPIExt` is loaded.
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"""
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function mpi_partitioned_operator_matvec! end
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@@ -307,10 +330,17 @@ entries only (aligned with [`copy_owned_subset_to_packed_owned_prefix!`](@ref)).
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function mpi_owned_dot_local end
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"""
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mpi_partitioned_operator_matvec_owned!(
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Ap_owned, p_owned, packed, recv_vals, send_vals,
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layout, exchange, cache, assembler, mesh, comm;
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dirichlet = nothing, mpi_requests = nothing,
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configuration = nothing, global_material_cache = nothing, Δt = 0.0,
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)
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mpi_partitioned_operator_matvec_owned!(
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Ap_owned, p_owned, packed, recv_vals, send_vals,
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layout, exchange, cache, assembler, kernel, mesh, comm;
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dirichlet = nothing, mpi_requests = nothing,
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configuration = nothing, global_material_cache = nothing, Δt = 0.0,
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)
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Lean MPI matvec: [`copy_owned_subset_to_packed_owned_prefix!`](@ref), halo exchange,
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@@ -318,10 +348,36 @@ Lean MPI matvec: [`copy_owned_subset_to_packed_owned_prefix!`](@ref), halo excha
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No `ndofs_global`-length trial workspace — trial DOFs stay in `packed`. **No** full-vector
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[`MPI.Allreduce!`](@ref) on `Ap`.
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Keyword `mpi_requests` is forwarded to [`exchange_matvec_halos_mpi!`](@ref).
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The primary form uses `cache.kernel_column`; the overload with `kernel` ignores it.
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Keywords `mpi_requests` and `configuration` / `global_material_cache` / `Δt` are forwarded when
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`JuliaFEMMPIExt` is loaded.
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Supports [`PenaltyDirichlet`](@ref) only on this path.
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"""
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function mpi_partitioned_operator_matvec_owned! end
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"""
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mpi_partitioned_internal_force_owned!(
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f_int_owned, u_owned, packed, work, recv_vals, send_vals,
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layout, exchange, cache, assembler, mesh, comm;
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mpi_requests = nothing,
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configuration = nothing, global_material_cache = nothing, Δt = 0.0,
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)
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mpi_partitioned_internal_force_owned!(
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f_int_owned, u_owned, packed, work, recv_vals, send_vals,
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layout, exchange, cache, assembler, kernel, mesh, comm;
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mpi_requests = nothing,
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configuration = nothing, global_material_cache = nothing, Δt = 0.0,
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)
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Lean MPI path for [`assemble_internal_force!`](@ref) on owned rows: pack owned
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`u`, halo exchange, then [`apply_f_int_owned_rows_from_packed!`](@ref). The
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`work` buffer must have length `cache.ndofs` (expand + Pass~1 scratch).
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The overload with `kernel` ignores it (backward compatibility). Requires
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`using MPI` after `JuliaFEM` so `JuliaFEMMPIExt` is loaded.
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"""
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function mpi_partitioned_internal_force_owned! end
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end # module JuliaFEM
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@@ -0,0 +1,53 @@
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# SPDX-FileCopyrightText: 2015-2026 Jukka Aho
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# SPDX-License-Identifier: MIT
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"""
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FEDiscretization(elements, handler, mesh, cache, assembler)
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Lightweight bundle of the usual DOF-based finite-element assembly inputs:
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`elements` from [`create_elements!`](@ref), the [`DOFHandler`](@ref), the
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[`AbstractMesh`](@ref), a pre-built [`DOFBasedCOOCache`](@ref) (whose
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[`kernel_column`](@ref) holds the volume kernel), and a
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[`DOFBasedCOOAssembler`](@ref) tag.
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Use [`assemble!`](@ref)`(fe)` then [`linear_system`](@ref)`(fe)` to obtain
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`(K, f)` without threading several separate variables through driver code.
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This is intentionally minimal: it does not own the mesh or elements, impose
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boundary conditions, or choose a solver. The kernel is read from
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`fe.cache.kernel_column` only; there is no separate redundant kernel field.
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"""
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struct FEDiscretization{E,H,M,C,A}
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elements::Vector{E}
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handler::H
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mesh::M
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cache::C
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assembler::A
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end
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@inline function assemble!(fe::FEDiscretization; kwargs...)
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return assemble!(fe.cache, fe.assembler, fe.mesh; kwargs...)
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end
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@inline function assemble_internal_force!(f::AbstractVector{Float64}, fe::FEDiscretization; kwargs...)
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return assemble_internal_force!(f, fe.cache, fe.assembler, fe.mesh; kwargs...)
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end
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@inline function nonlinear_equilibrium_residual!(
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r::AbstractVector{Float64},
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f_ext::AbstractVector{Float64},
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f_work::AbstractVector{Float64},
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fe::FEDiscretization,
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u::AbstractVector{Float64};
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kwargs...,
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)
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return nonlinear_equilibrium_residual!(
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r, f_ext, f_work, fe.cache, fe.assembler, fe.mesh, u; kwargs...,
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)
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end
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@inline function linear_system(fe::FEDiscretization)
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return extract_system(fe.cache)
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end
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@inline total_dofs(fe::FEDiscretization) = fe.handler.total_dofs
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@@ -0,0 +1,34 @@
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# SPDX-FileCopyrightText: 2015-2026 Jukka Aho
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# SPDX-License-Identifier: MIT
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# Reference-domain Gauss-Legendre tuples for hand-coded integrals. Values match
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# `get_quadrature_points` for the same rule (see `gl_tensor_product.jl`, `gl_triangles.jl`),
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# including the 3-point triangle rule (`REF_GAUSS_TRIANGLE_ORDER2`).
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"Two-point Gauss-Legendre on reference segment `[-1, 1]`; each tuple is `(ξ, w)`; weights sum to `2`."
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const REF_GAUSS_SEGMENT_ORDER2 = ((-1.0 / √3, 1.0), (1.0 / √3, 1.0))
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"Tensor-product 2×2 Gauss-Legendre on reference square `[-1, 1]²`; each tuple is `(ξ, η, w)`."
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const REF_GAUSS_QUAD_2X2 = (
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(-1.0 / √3, -1.0 / √3, 1.0),
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(1.0 / √3, -1.0 / √3, 1.0),
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(1.0 / √3, 1.0 / √3, 1.0),
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(-1.0 / √3, 1.0 / √3, 1.0),
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)
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"One-point centroid rule on the unit-area-right-triangle natural coordinates; tuple `(ξ, η, w)` with `w = 1/2`."
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const REF_GAUSS_TRIANGLE_CENTROID = ((1.0 / 3.0, 1.0 / 3.0, 0.5),)
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"""
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Three-point Gauss-Legendre rule (degree 2) on the reference triangle `ξ, η ≥ 0`,
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`ξ + η ≤ 1` (area `1/2`). Each tuple is `(ξ, η, w)` with `w = 1/6`.
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Same weights as `get_quadrature_points(Triangle{3}, GaussLegendre{2}())` in
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`gl_triangles.jl` (default 3-point rule); point order matches
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`MixedDarcyTet4BoundaryNormalFluxLoad` in `matrix_free/loads.jl`.
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"""
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const REF_GAUSS_TRIANGLE_ORDER2 = (
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(1.0 / 6.0, 1.0 / 6.0, 1.0 / 6.0),
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(2.0 / 3.0, 1.0 / 6.0, 1.0 / 6.0),
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(1.0 / 6.0, 2.0 / 3.0, 1.0 / 6.0),
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)
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