Remove the standalone CSC utilities file now superseded by
`src/legacy/sparse_helpers.jl` and dropped from `sparse.jl`.
- Drop `src/sparse/sparsematrixcsc.jl`.
Stop pulling deleted CSC helper includes into `sparse.jl`, adopt SPDX lines,
and drop unused dense helpers that duplicated `Legacy` utilities.
- Document that `SparseMatrixCOO` is legacy-oriented vs raw assembler triplets.
- Use `resize!(..., 0)` for `empty!` and qualify `Base.append!`.
- Remove `get_nonzero_rows`/`get_nonzero_columns` and `resize_sparse` helpers from
this file (see `src/legacy/sparse_helpers.jl`).
Clarify why `integration_points` converts the quadrature `SVector` to a `Tuple`
for downstream destructuring while noting compile-time stack usage.
- Refresh comments around `default_quadrature` / `_quadrature_topology_type`.
Drop the unused topology×basis doc signature and align comments with the
actually implemented order/topology paths plus `_infer_basis_order`.
- Remove stale `AbstractBasis` overload documentation.
- Renumber the topology-only path as the third dispatch tier.
Drop a duplicated example line and remove the commented-out Fluid placeholder
that suggested unfinished velocity dispatch.
- Clarify `Thermal{Dim}` wording; delete stale `Fluid{Dim}` sketch.
Replace the long `Physics{...}` narrative with short placeholders that explain
how `assemble!`/`solve!`/BC hooks are extended by assemblers or Legacy only.
- Document the kernel + assembler workflow as the active surface.
- Point Dirichlet/Neumann reservations at matrix-free BC and load value types.
- Keep generic function declarations for Legacy method attachment.
Replace stale `Physics{...}` API docs with the actual 0.x role: a lightweight
trait root for `Elasticity`/`Thermal` tags and material dispatch, with legacy
`Physics` confined to `JuliaFEM.Legacy`.
- Shorten `AbstractPhysics` docstring and drop obsolete interface/examples.
Delete the Dict-era `Physics` implementation file that duplicated boundary
condition plumbing removed from the modern kernel-centric surface.
- Drop `src/physics.jl` (unused relative to `JuliaFEM.jl` includes).
Document that only structured bricks are supported here and route box mesh
construction through the keyword outer constructor.
- Clarify the `Hex8`-only structured entry point in the docstring.
- Replace positional `Mesh{Hex8}(..., sets...)` with keyword `element_sets` /
`node_sets` arguments.
Use explicit `Mesh{8, Hex8}` signatures, SPDX banner lines, and the keyword
`Mesh{T}(nodes, conn; ...)` outer constructor after the mesh core refactor.
- Update docstrings and method signatures from `Mesh{Hex8}` to `Mesh{8, Hex8}`.
- Build refined meshes via `element_sets`/`node_sets` keywords.
Strip experimental permutation/coloring/ghost/named-ID baggage from the
concrete mesh type, adopt SPDX headers, and route boundary extraction through
an explicit `surface_topology` trait with clearer limitations.
- Replace the legacy banner with SPDX lines and tighten the struct/docstring to
the fields that actually ship today.
- Drop bandwidth/permutation maps, industrial ID dictionaries, and parallel
coloring/ghost sets from `Mesh` plus their helpers.
- Introduce `surface_topology(::Type{<:AbstractTopology})` for Tet/Hex volumes
and guard `extract_surface` with `hasmethod` errors for unsupported solids.
- Remove `create_node_set_from_element_set!` (surface workflows should build sets
explicitly or use topology-aware helpers later).
- Document that `extract_surface` still assumes the first `nnodes(FaceT)` nodes
per volume element describe the boundary patch.
Document that multi-topology meshes are still unsupported and replace the old
`Physics` wording with kernel-centric language about shared meshes.
- Swap the future `MixedMesh` bullet for an explicit limitation note.
- Describe mesh ownership vs kernel references for multiphysics reuse.
Replace marketing-heavy prose with a short map of the active files, the
parametric `Mesh{N,T}` role, refinement usage, and where import/tests live now.
- Drop duplicated API inventories and speculative future-work bullets.
- Point readers at `src/io/` for ingest and `llm/design/legacy-tests/mesh/` for
retired parallel/coloring coverage.
Remove the `required_state_variables(::Type{<:AbstractMaterial})` shim that
instantiated materials just to query traits; callers should pass instances or
specialize on concrete types directly.
- Delete the default `required_state_variables(::Type{T}) = …` definition from
`traits.jl`.
Add typed slots for damage equivalent strain, eigenstrain, creep strain, and
indexed Chaboche backstress components so advanced models can declare IP state
without ad hoc symbols.
- Define `DamageEquivalentStrain`, `Eigenstrain`, `CreepStrain`, and
`ChabocheAlpha{N}` with `state_variable_type` / `default_symbol` hooks.
Stop defining `symmetric_identity_tensor` inside `perfect_plasticity.jl` now
that `materials/symmetric_fourth_identity.jl` provides the shared definition.
- Remove `include(\"abstract_material.jl\")`.
- Delete the local `symmetric_identity_tensor` implementation (call sites keep
resolving against the earlier include in `JuliaFEM.jl`).
Expose physics/state-variable traits for hyperelastic assembly and accept
`NamedTuple` IP states alongside `nothing` while sharing one implementation.
- Drop the stale `abstract_material.jl` include.
- Declare `supported_physics` / `required_state_variables` for 3D elasticity.
- Factor `_compute_stress_neo_hookean` and add a `compute_stress` path for
`state_old::NamedTuple`.
- Normalize `where {T}` clauses on public stress APIs.
`AbstractElasticMaterial` already comes from `materials/api.jl`, and IP state
is inferred via `required_state_variables`, so drop the stale include and
`state_type` hook.
- Remove `include(\"abstract_material.jl\")` and redundant trait comments.
- Delete `state_type(::Type{LinearElastic}) = EmptyState`.
Replace the legacy banner with SPDX lines and document how each
`MaterialBehavior` maps to assembly and `GlobalMaterialCache`, dropping the
unused `AbstractMaterialState` / `state_type` surface in favor of
`material_state_type` NamedTuples.
- Switch the file banner to `SPDX-FileCopyrightText` /
`SPDX-License-Identifier: MIT`.
- Remove `AbstractMaterialState`, `EmptyState`, and `state_type`; point readers
at `material_state_type` / `required_state_variables`.
- Enlarge `StatelessConstantTangent`, `StatelessStrainDependent`, and
`StatefulStrainDependent` docstrings with representative models, tangent
caveats, and explicit coverage gaps.
Spell out that SPDX tags must use native comments (`#` in code and TOML,
HTML comments in Markdown/Quarto) and call out formats like JSON that cannot
carry in-file blocks.
- Add an SPDX section with concrete examples and the strict-JSON caveat.
Delete the older compositional cache draft now replaced by
`global_material_cache.jl` + assembler-local workspaces.
- Drop `src/materials/material_cache.jl`.
Remove the unused multiplicative-decomposition J2 sketch that was never wired
into `JuliaFEM.jl` includes.
- Drop `src/materials/finite_strain_plasticity.jl`.
Delete the stale `AbstractMaterial` hierarchy file that duplicated the trait
surface now defined alongside concrete models.
- Drop `src/materials/abstract_material.jl` (unused include target).
Remove the standalone eigen/modal pipeline that was never reached from
`Legacy.jl`.
- Drop `src/legacy/solvers_modal.jl` (problem orchestration + Lanczos hooks).
Remove the plane-stress/strain specialization layer that duplicated the 3D
path but stayed disconnected from `Legacy` includes.
- Drop `src/legacy/problems_elasticity_2d.jl`.
Delete the Dict-based continuum elasticity `Problem` implementation that was
never wired into `Legacy.jl`.
- Drop `src/legacy/problems_elasticity.jl` (assembly over legacy elements).
Remove the mortar-style 3D contact assembly path that lived outside the active
`Legacy` include list.
- Drop `src/legacy/problems_contact_3d.jl` (projection helpers + assembler glue).
Remove the standalone abstract elasticity layer that duplicated concepts now
owned by `src/physics/` and was never included from `Legacy.jl`.
- Delete `src/legacy/physics_api.jl` (`AbstractMesh`, `AbstractMaterial`,
formulation stubs, and helper hooks).
Stop re-exporting `create_surface_elements` from top-level `JuliaFEM`
(which no longer defines it) and bind the compatibility submodule against the
Legacy implementation instead.
- Replace `using JuliaFEM: create_surface_elements` with `import
..create_surface_elements` inside `Legacy.Abaqus`.
Replace unconditional `println` chatter with structured `@info` events so
library callers can filter noise via the standard logging pipeline.
- Log the filename when ingest starts and emit a single summary record with
node/element counts plus physical group keys.
Rewrite the module README now that Abaqus/Code_Aster stacks live behind the
opt-in Legacy flag and only Gmsh ASCII ingest ships unconditionally.
- Document `JULIAFEM_ENABLE_LEGACY=1` and `src/legacy/io/` for vendor parsers.
- Focus the file list on `gmsh_reader.jl` / `GmshReader` instead of deleted stubs.
- Trim emoji/status tables and stale usage snippets; note roadmap for a native
`.inp` path aligned with `Mesh{T}` / `create_elements!`.
Jukka Aho