src: add periodicorbit/Collocation.jl to test new BVP interface in PO…#329
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rveltz wants to merge 14 commits into
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src: add periodicorbit/Collocation.jl to test new BVP interface in PO…#329rveltz wants to merge 14 commits into
rveltz wants to merge 14 commits into
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… context - add abstract types to BVP
12 tasks
…hase conditions
- Extract phase condition structures into `src/bvp/Sections.jl` with `AbstractSection`.
- Implement `SectionSS`, `SectionTrapeze`, and `SectionCollocation` to encapsulate phase condition data (normals, centers, ϕ, xπ, ∂ϕ) and their respective `update!` methods.
- Refactor `Shooting`, `Trapeze`, and `Collocation` structs in `periodicorbit` to use the new section fields rather than raw vectors.
- Move generic vector `_duplicate` utility to `src/periodicorbit/Sections.jl` specifically for `SectionPS` and `NormalForms` usage, removing the mathematically incorrect duplication for Standard Shooting.
- Fix `LA.dot` scope issue in `PeriodicOrbitTrapeze.jl` for GPU compatibility.
- Ensure type stability in `DiscretizedPO` type aliases with explicit `where {Tf, 𝒯}` bounds in `Collocation.jl`.
- Add default values to `Shooting` discretizer fields (`M=1`, `alg=nothing`, `parallel=false`).
- Update all associated periodic orbit tests to reflect the new BVP interfaces.
…d accessors - Add `(sect::SectionTrapeze)(u)` and `(sect::SectionTrapeze)(u, T)` functors to match the `SectionSS` design and respect the generic `AbstractSection` interface. - Implement explicit getter functions across all section types: - `SectionSS` (`get_normal`, `get_center`) - `SectionTrapeze` (`get_ϕ`, `get_xπ`) - `SectionCollocation` (`get_ϕ`, `get_∂ϕ`) - `SectionPS` (`get_normals`, `get_centers`, `get_normals_bar`, `get_centers_bar`) - Update `PeriodicOrbitTrapeze.jl` to evaluate phase conditions and its Jacobian using the new `SectionTrapeze` functor rather than explicit dot products. - Refactor `PeriodicOrbitTrapeze.jl` to use `get_ϕ` accessors, storing them in local variables for improved code readability and robustness.
…tructure** This commit transitions the `Collocation` methods for periodic orbits away from the monolithic legacy implementation towards the new, modular `DiscretizedBVP` and `DiscretizedPO` infrastructure. It establishes a solid and highly optimized foundation for the BVP solver before implementing analytical Jacobians. **Key Changes:** * **Optimized BVP Residual:** Implemented `__bvp_residual_collocation` in `src/bvp/collocation/residual.jl`. The new inner loop avoids memory allocations when evaluating the vector field `model.F(u, p)` by using pre-allocated buffers from `cache.coll_cache.tmp`. * **Removed `po_coll` Dependencies:** Fully decoupled the mesh adaptation and continuation logic in `src/bvp/BVPBifProblem.jl` from the legacy `po_coll` object. All operations (including `_compute_error!` and `__interpolate_posolution`) now rely strictly on the new `mesh_cache`. * **Phase Condition Updates:** Wired the phase condition updates (`updatesection!`) into the new architecture. The underlying math (`ϕ`, `∂ϕ`, and `∇phase` updates) is cleanly isolated in `src/bvp/collocation/section.jl` and properly called during the continuation loop in `__update_bvp_coll!`. * **Legacy Code Preservation:** Restored the legacy `CollocationDisc` methods (`po_residual`, `po_jacobian`, and utility getters) as commented-out reference code in `src/periodicorbit/Collocation.jl` to document the transition and preserve the old mathematical logic. * **Testing:** Validated the new architecture against `stuartLandauCollocationDisc.jl` using `AutoDiffDense`. **Next Steps:** - Re-implement exact dense and sparse analytical Jacobians for `Collocation`. - Port the numerical integration function (`∫`) to use `mesh_cache`.
… Orbits
This commit fixes critical bugs in the continuation loop and mesh adaptation for DiscretizedPO that were introduced during the transition to the new BVP infrastructure.
Key Changes:
Fixed Phase Condition Updates: The updatesection! function was failing to trigger during continuation because __update_bvp_coll! only accepted a DiscretizedBVP. We extended its signature to Union{DiscretizedBVP, DiscretizedPO} and added specific BK.update! overloads for BVPBifProblem{<:DiscretizedPO}. This ensures the DiscretizedPO wrapper is passed down, allowing updatesection!(::DiscretizedPO) to properly dispatch and update ϕ and ∂ϕ.
Fixed Cache Access Errors: Replaced direct field accesses like d_bvp.cache.mesh_cache (which caused a FieldError for DiscretizedPO) with the generic getter get_cache(d_bvp).mesh_cache in __update_bvp_coll!. This guarantees compatibility regardless of whether the underlying object is a pure BVP or a Periodic Orbit.
Cleaned up save_solution: Fixed save_solution for pure DiscretizedBVPs which erroneously still referenced the legacy po_coll object. It now correctly relies on get_cache(bvp).mesh_cache and correctly returns nothing for the phase condition, as expected for pure BVPs.
…legacy issues - Fix state extraction in `bvp_jacobian_dense!`: replace hardcoded `u[1:end-1]` (period stripping) with generic `_bvp_coll_get_Xm` and `_bvp_coll_get_T` accessors to support both `DiscretizedBVP` and `DiscretizedPO` seamlessly. - Refactor internal jacobian API: `bvp_jacobian_dense!` and `bvp_jacobian_sparse_blocks!` now accept a pure `BifFunction` instead of the whole `BifurcationProblem` wrapper, making the codebase cleaner and preventing side-effect programming. - Fix `BifurcationProblem` construction in `jacobian.jl` to use `lens=1` instead of `nothing`, preventing `AssertionError` crashes during problem instantiation. - Fix spurious `BK.` module prefixes for `meshadapt` and `get_times` inside `BVPBifProblem.jl` and `DiscretizedBVP.jl` which broke BVP saving. This successfully restores full BVP collocation continuation tests (`test/bvp/bratu_collocation.jl`).
…ation and address review feedback This commit introduces the full suite of analytical Jacobians (dense, sparse blocks, and sparse in-place) for the generic `DiscretizedBVP` and `DiscretizedPO` collocation API, while also incorporating recent code review feedback. Key changes: - **Jacobian Implementations**: - Added `bvp_jacobian_dense!` for analytical dense Jacobian evaluation. - Added `bvp_jacobian_sparse_blocks!` for out-of-place sparse block generation. - Added `bvp_jacobian_sparse_inplace!` for highly optimized, zero-allocation updates directly modifying the underlying `nzval` of `SparseMatrixCSC`. - **Sparse Indexing Fix**: Fixed `get_blocks` in `Collocation.jl` to correctly map block indices to `nzval` memory offsets using `findnz`, resolving `MethodError` and `Float64` invalid index crashes during in-place updates. - **API Cleanups**: - Removed `Reexport.@reexport using .BVP` in `BifurcationKit.jl` in favor of explicit `export` declarations for better namespace control. - Introduced the `get_mesh_cache` accessor in `DiscretizedBVP.jl` and replaced direct `.mesh_cache` property accesses across `BVPBifProblem.jl`. - **Type Stability for AD**: Removed hardcoded `Float64` allocations (`zeros(0)` and `[1.0]`) when instantiating local `BifurcationProblem`s inside `jacobian.jl`. Replaced with generic `T = eltype(u)` to ensure type-stability and proper support for ForwardDiff Dual numbers. Tests (including `stuartLandauCollocationDisc.jl`) run successfully with the new generic API.
…dPO interface This commit introduces a parallel implementation of the Condensation of Parameters (COP) linear solver that operates entirely on the new BVP architecture (DiscretizedPO). Changes included: - Renamed `src/periodicorbit/cop.jl` to `cop_legacy.jl` to preserve the legacy functionality untouched. - Implemented a new `src/periodicorbit/cop.jl` leveraging the standardized BVP getters (`BVP.get_coll_cache`, `BVP.state_dimension`, etc.) instead of directly accessing fields from the legacy `Collocation` struct. - Refactored `COPCACHE` and `COPBLS` structs to use outer constructors instead of inner constructors, adhering to standard Julia practices and allowing easier generic instantiation. - Added a comparative test suite (`cop_new_vs_legacy.jl`) confirming that the new implementation provides exact numerical matches for dim=0, 1, 2 and performs similarly or slightly faster (less GC overhead). WARNING: The new COP solver is currently restricted to `DiscretizedPO` (Periodic Orbits) rather than any generic `DiscretizedBVP`. This is because the underlying COP algorithm currently hardcodes Periodic Boundary Conditions (injecting `In` and `-In` identity blocks) and explicitly assumes the period `T` is part of the external unknowns. Further refactoring is required to generalize this solver to arbitrary Boundary Value Problems.
…izers This commit cleans up the internal BVP mechanics by strictly enforcing the use of getters, removing direct field accesses and hardcoded shape assumptions across all discretization schemes. Changes included: - Replaced all hardcoded `reshape(@view(X[...]), n, M)` calls in `Shooting`, `Trapeze`, and `Collocation` residuals/jacobians with a unified `get_time_slices(d_bvp, X)` interface. - Updated `get_time_slices` to safely extract only the time-domain state variables, automatically ignoring trailing parameters (such as the period `T`). - Forwarded `get_time_interval` correctly from `DiscretizedPO` and `DiscretizedBVP` down to the `BVPModel`. - Replaced direct struct field accesses (like `bvp.discretizer.M` or `disc.Ntst`) in BVP integration and residual routines with the standard getters (`mesh_size`, `get_ntst`, `get_m`). - Added `get_ntst` and `get_m` accessors for the `Collocation` discretizer in `Discretizers.jl`.
Replace hardcoded BK.update! specializations on BVPBifProblem{<:DiscretizedPO}
with a clean singleton-based dispatch mechanism.
- Add `struct UpdateFunctionForPOFunctional end` as a callable singleton
with methods for standard and codim-2 continuation
- Fix `BK.update!` delegation to forward `prob` as first argument to the
stored callable (was missing, making the singleton pattern impossible)
- Add `POBifProblem` convenience constructor that wraps `BVPBifProblem`
with `update! = UpdateFunctionForPOFunctional()`
- Remove 4 hardcoded `BK.update!` methods on `DiscretizedPO` collocation
- Clean up: remove dead code, unused `oldmesh` variable, redundant alias
- Export `POBifProblem` and `UpdateFunctionForPOFunctional` from `BVP` module
and top-level `BifurcationKit`; fix double export of `BVPBifProblem`
- Add end-to-end tests for `POBifProblem` (residual + PALC continuation)
- Fix missing `_test_sorted` helper in `stuartLandauTrap.jl` test file
All 4341 tests pass.
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close #328