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Introduces the constraint class hierarchy for algebraic constraints in DAE (Differential-Algebraic Equation) systems: - Constraint: Abstract base class defining the interface - EquilibriumConstraint: Implements equilibrium relationships (K_eq = products/reactants) - ConstraintSet: Manager for collections of constraints with Jacobian support Includes comprehensive unit tests for all constraint functionality. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Prepares the solver infrastructure to support algebraic constraints: State changes: - Add number_of_constraints_ to StateParameters - Add constraint_size_ and upper_left_identity_diagonal_ to State - Size jacobian for species + constraints SolverBuilder changes: - Add SetConstraintCount() and SetConstraintNames() methods - Update Build() to include constraint variables in state This is backward compatible - when constraint_count_=0 (default), behavior is unchanged from before. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Completes the DAE constraint system by wiring constraints into the Rosenbrock solver loop: Solver changes: - Add ConstraintSet member to RosenbrockSolver - Call AddForcingTerms() and SubtractJacobianTerms() in solve loop - Add SetConstraints() to SolverBuilder with full Build() integration Key implementation details: - AlphaMinusJacobian adds alpha to ALL diagonals (ODE and algebraic) - This treats algebraic constraints as stiff ODEs (ε*z' = g with ε=hγ) - Constraint Jacobian elements merged with ODE elements at build time Integration tests: - test_equilibrium.cpp demonstrates working DAE equilibrium solving Documentation: - ARCHITECTURE.md: Implementation details and sign conventions - TESTS.md: Test case specifications - CLAUDE.md: Project context and build instructions - Custom Claude Code skills for testing and debugging Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add educational walkthrough of Constraint, EquilibriumConstraint, and ConstraintSet classes (constraint_classes_walkthrough.md) - Add line-by-line explanation of reactant loop indexing logic (reactant_loop_explanation.md) - Add comparison of ProcessSet vs ConstraintSet Jacobian computation (forcing_jacobian_parallel.md) - Fix incorrect @param comments in Constraint base class - Remove unused <map> include from constraint.hpp Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Use consistent notation across documentation and code: - y for state variables - F(y) for forcing (uppercase) - G(y) for constraints (uppercase) Add note on DAE notation conventions explaining the y/z distinction from DAE literature and why MICM uses a unified state vector. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Rename reactant_loop_explanation.md to indexing_patterns.md to better reflect its broader scope. Add detailed comparison of 2-level indirection (ProcessSet) vs 3-level indirection (Constraint classes), explaining: - How ProcessSet pre-computes global indices at construction - How Constraint receives indices as a parameter for decoupling - The ConstraintSet bridge that connects them - Performance implications and potential optimization paths - Design philosophy trade-offs (OO vs data-oriented) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Architecture Overview section: - Data flow diagram showing how constraints integrate with solver - Component responsibilities for Constraint, EquilibriumConstraint, ConstraintSet, and Rosenbrock Solver - Parallel structure comparison of ProcessSet and ConstraintSet Test Coverage section: - Summary table of EquilibriumConstraint tests - Summary table of ConstraintSet tests - Key scenarios covered by each test suite - Notes on what's not yet tested (future work) - Instructions for running constraint tests Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
New section "Flat Array Memory Layout and Strides" explains: - How MICM uses flat arrays with stride-based access - Dense matrix access pattern (rows=cells, cols=species) - Sparse Jacobian access via AsVector() and FlatBlockSize() - Pre-computed jacobian_flat_ids_ for efficient sparse access - Note that vectorized variants exist in ProcessSet but not yet in ConstraintSet (planned for future optimization) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Rename to constraintset_mirrors_processset.md to better describe the document's purpose: showing how ConstraintSet mirrors ProcessSet's design for Jacobian computation. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Move documentation files from root to docs/design/ - Remove branch name reference from walkthrough intro - Replace std::pair<std::string, double> with Yield type for reactants_ and products_ in EquilibriumConstraint - Fix dead code in Jacobian calculation (removed unused assignment) - Update test files to use Yield(Species(...), coeff) syntax Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add MICM_ERROR_CATEGORY_CONSTRAINT and error codes to error.hpp - Create constraint_error.hpp with MicmConstraintErrc enum and error category - Replace std::invalid_argument with std::system_error in EquilibriumConstraint - Replace std::runtime_error with std::system_error in ConstraintSet - Update tests to expect std::system_error Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Address PR feedback from K20shores and Copilot regarding performance: - K20shores (line 199): "make Residual operate on the dense matrix directly" - K20shores (line 247): "agreed" with Copilot on SubtractJacobianTerms Refactor Residual() and Jacobian() to use pointers instead of vectors, eliminating temporary allocations in the inner grid cell loop: - Change Constraint interface from vector-based to pointer-based - Add dependency_offset_ and jacobian_flat_offset_ to ConstraintInfo for O(1) access to pre-computed index arrays - Add max_dependencies_ for reusable Jacobian buffer allocation - AddForcingTerms: access row data directly via &cell_state[0] - SubtractJacobianTerms: use single reusable jac_buffer across all constraints and grid cells Performance impact: - Eliminates per-cell vector copy of concentrations (was N species) - Eliminates per-constraint vector copy of indices - Eliminates per-constraint Jacobian vector allocation Update documentation to reflect the new interface. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Address Copilot review suggestions: - Validate reactants is not empty (EmptyReactants error) - Validate products is not empty (EmptyProducts error) - Validate all stoichiometric coefficients are positive (InvalidStoichiometry error) Adds corresponding error codes and test cases. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dae-2-state-infrastructure #909 +/- ##
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+ Coverage 94.20% 94.79% +0.59%
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Files 70 69 -1
Lines 3432 3440 +8
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+ Hits 3233 3261 +28
+ Misses 199 179 -20 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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remove md files, and update the test names
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Closing, this PR is superceded by #931 |
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Closing, this PR is superceded by #931 |
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