Add algebraic constraint support to CUDA ProcessSet kernels

[boulderdaze]

This PR

• Adds algebraic constraint support to CUDA ProcessSet kernels
• Separates the logic inside the process set loop where the current version iterates over process_info.number_of_dependent_reactants_ + 1, combining both dependent reactants and the independent variable in one pass. This change helps improve clarity and readibility.
• Closes CUDA ProcessSet kernels ignore algebraic masks #938
• Closes Create GPU constrained rosenbrock #854

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.61%. Comparing base (257400f) to head (38f83fd).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #944   +/-   ##
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  Coverage   94.61%   94.61%           
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  Files          69       69           
  Lines        3973     3973           
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  Hits         3759     3759           
  Misses        214      214           

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[Copilot]

Pull request overview

Adds end-to-end algebraic constraint (DAE) support with a “replace-species-row” mass-matrix formulation, including honoring algebraic row masks in CUDA ProcessSet kernels (closing the gap described in #938) and expanding test coverage for constraints.

Changes:

• Add constraint plumbing through SolverBuilder → State (mass-matrix diagonal / algebraic IDs) → solvers (Rosenbrock forcing/Jacobian + normalization + clamping).
• Update CPU/CUDA ProcessSet to skip kinetic forcing/Jacobian writes for algebraic rows (including CUDA device-side mask propagation).
• Add/extend unit, integration, and regression tests for equilibrium + linear constraints, and for DAE-specific behaviors (normalization, clamping, state copy).

Reviewed changes

Copilot reviewed 36 out of 36 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/process/process_set.cu	CUDA kernels now honor algebraic-row masks for forcing/Jacobian updates; device memory now carries is_algebraic_variable_.
include/micm/process/process_set.hpp	CPU ProcessSet gains SetAlgebraicVariableIds and skips algebraic rows; Jacobian flat-id generation supports skipped rows.
include/micm/cuda/util/cuda_param.hpp	Adds uint8_t* is_algebraic_variable_ to CUDA params for device-side masking.
include/micm/cuda/process/cuda_process_set.hpp	Propagates algebraic-row mask to device and overrides SetAlgebraicVariableIds.
include/micm/cuda/solver/cuda_rosenbrock.hpp	Updates constructor signature to accept ConstraintSet.
include/micm/constraint/constraint.hpp	Reworks constraints into a std::variant wrapper supporting equilibrium + linear constraints.
include/micm/constraint/equilibrium_constraint.hpp	Refactors equilibrium constraint to concrete type with dependency bookkeeping + algebraic target selection.
include/micm/constraint/linear_constraint.hpp	Introduces LinearConstraint for conservation/linear relations.
include/micm/constraint/constraint_set.hpp	Implements “replace species rows” constraint set (residuals + Jacobian contributions) + algebraic variable ID tracking.
include/micm/solver/solver_builder.hpp	Adds SetConstraints API and stores constraints on the builder.
include/micm/solver/solver_builder.inl	Builds ConstraintSet, marks algebraic rows, prunes kinetic sparsity for those rows, and merges constraint Jacobian sparsity.
include/micm/solver/state.hpp	Adds constraint_size_ and upper_left_identity_diagonal_ (mass-matrix diagonal) to state.
include/micm/solver/state.inl	Initializes mass-matrix diagonal from parameters (or defaults to ODE-only).
include/micm/solver/temporary_variables.hpp	Makes TemporaryVariables polymorphically clonable via pure-virtual Clone().
include/micm/solver/rosenbrock_temporary_variables.hpp	Implements Clone() for Rosenbrock temp vars.
include/micm/solver/backward_euler_temporary_variables.hpp	Implements Clone() for Backward Euler temp vars.
include/micm/solver/rosenbrock.hpp	Rosenbrock solver now stores a ConstraintSet and accepts it via constructor.
include/micm/solver/backward_euler.hpp	Backward Euler solver stores ConstraintSet for API compatibility (not used in algorithm).
include/micm/solver/rosenbrock.inl	Integrates constraints into forcing/Jacobian, mass-matrix scaling in linear stage combinations, and error normalization ignoring algebraic vars.
include/micm/solver/solver.hpp	Post-solve clamping now avoids clamping algebraic variables; supports constraint-aware state handling.
test/unit/solver/test_rosenbrock.cpp	Adds unit tests ensuring NormalizedError ignores algebraic variables.
test/unit/constraint/test_linear.cpp	New unit tests for LinearConstraint residual/Jacobian/algebraic target behavior.
test/unit/constraint/test_constraint_set.cpp	Updates tests for “replace-row” constraint formulation; adds vectorized sparse ordering coverage.
test/unit/constraint/CMakeLists.txt	Adds linear unit test target.
test/integration/test_equilibrium.cpp	Adds broad integration coverage for equilibrium constraints across solver configs (DAE solving, reorder state, stiff coupling, etc.).
test/integration/test_linear_constraint.cpp	Adds integration test for a linear conservation constraint in a DAE solve.
test/integration/CMakeLists.txt	Adds new integration test targets for equilibrium + linear constraints.
test/regression/RosenbrockChapman/regression_test_solve.cpp	Adjusts Chapman regression to use six-stage DAE Rosenbrock parameters.
test/unit/process/test_process_configuration.cpp	Fixes comment spelling (“stoichiometric coefficients”).
test/unit/solver/test_lu_decomposition_policy.hpp	Adds <iomanip> include / minor formatting fix.
test/unit/solver/test_lu_decomposition_in_place_policy.hpp	Adds <iomanip> include / minor formatting fix.
test/unit/solver/test_linear_solver_policy.hpp	Adds <iomanip> include.
test/unit/solver/test_linear_solver_in_place_policy.hpp	Adds <iomanip> include.
test/integration/analytical_policy.hpp	Removes a stray standalone ;.
docs/design/FULL_REVIEW.md	Deleted design review artifact.
docs/design/CODEX_TODO.md	Deleted design TODO artifact.

Comments suppressed due to low confidence (1)

include/micm/constraint/equilibrium_constraint.hpp:12

• EquilibriumConstraint uses std::max but this header doesn’t include <algorithm>. This will fail to compile in translation units that don’t already include <algorithm> before this header. Add #include <algorithm> here (preferred) or avoid std::max in the header.

#include <micm/constraint/constraint_error.hpp>
#include <micm/system/stoich_species.hpp>

#include <cmath>
#include <cstddef>
#include <string>
#include <system_error>
#include <vector>

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Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.

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