Rosenbrock DAE Constraint Count

.claude/commands/debug-test.md

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+# Debug Test
+
+Debug a failing MICM test with tracing support.
+
+## Usage
+
+- `/debug-test <test_name>` - Debug a specific test
+
+## Instructions
+
+When the user invokes this skill with a test name:
+
+1. **Run the test first** to confirm failure:
+   ```bash
+   ctest --test-dir /Users/fillmore/EarthSystem/MICM/build --output-on-failure -R "<test_name>" -V
+   ```
+
+2. **If the test passes**, report success and exit.
+
+3. **If the test fails**, analyze the output:
+   - Look for NaN, Inf, or exploding values
+   - Check for assertion failures
+   - Identify which solver component failed
+
+4. **For numerical failures** (NaN/Inf/explosion):
+   - Offer to add debug tracing to `rosenbrock.inl`
+   - Key trace points:
+     - After `AlphaMinusJacobian`: print diagonal values
+     - After linear solve: print K values
+     - In forcing: print residual values
+
+5. **Add tracing code** (with user confirmation):
+   ```cpp
+   // In rosenbrock.inl Solve() loop, after LinearFactor call:
+   std::cerr << "=== Step " << result.stats_.number_of_steps_ << " ===" << std::endl;
+   std::cerr << "H = " << H << ", alpha = " << (1.0 / (H * parameters.gamma_[0])) << std::endl;
+   for (std::size_t i = 0; i < state.jacobian_.NumColumns(); ++i)
+     std::cerr << "Diag[" << i << "] = " << state.jacobian_.DiagonalElement(0, i) << std::endl;
+   ```
+
+6. **Rebuild and rerun** with tracing enabled.
+
+7. **Analyze trace output**:
+   - Compare diagonal magnitudes (should be similar)
+   - Check K value scaling (should scale with H)
+   - Look for sign errors
+
+8. **Clean up** tracing code when done.
+
+## Common Issues
+
+| Symptom | Likely Cause | Check |
+|---------|--------------|-------|
+| Values explode to 10^16+ | Ill-conditioned matrix | Diagonal magnitudes |
+| NaN after linear solve | Singular matrix | Zero diagonals |
+| Wrong steady state | Sign error in Jacobian | SubtractJacobianTerms signs |
+| Constraint not satisfied | Missing projection step | Post-solve enforcement |

.claude/commands/micm-test.md

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+# MICM Test Runner
+
+Build and run MICM tests efficiently.
+
+## Usage
+
+- `/micm-test` - Build and run all tests
+- `/micm-test build` - Build only (no tests)
+- `/micm-test <pattern>` - Run tests matching pattern (e.g., `constraint`, `rosenbrock`)
+
+## Instructions
+
+When the user invokes this skill:
+
+1. **Parse the argument** (if any):
+   - No argument or empty: run all tests
+   - `build`: build only
+   - Any other string: use as test filter pattern
+
+2. **Build the project**:
+   ```bash
+   cmake --build /Users/fillmore/EarthSystem/MICM/build -j$(sysctl -n hw.ncpu)
+   ```
+
+3. **Run tests** (unless build-only):
+   - All tests: `ctest --test-dir /Users/fillmore/EarthSystem/MICM/build --output-on-failure`
+   - Filtered: `ctest --test-dir /Users/fillmore/EarthSystem/MICM/build --output-on-failure -R "<pattern>"`
+
+4. **Report results**:
+   - Show pass/fail count
+   - If failures, show which tests failed
+   - Suggest `/debug-test <name>` for failed tests
+
+## Example Output
+
+```
+Building MICM...
+Build successful.
+
+Running tests matching "constraint"...
+3/3 tests passed:
+  - constraint
+  - constraint_set
+  - equilibrium (contains constraint tests)
+```

.claude/commands/solver-debug.md

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+# Solver Debug Agent
+
+Investigate numerical issues in MICM solvers.
+
+## Usage
+
+- `/solver-debug` - Start numerical debugging investigation
+
+## Instructions
+
+When the user invokes this skill, launch an investigation of solver numerical issues.
+
+### Phase 1: Gather Context
+
+1. **Ask the user** what symptom they're seeing:
+   - Values exploding (which variable?)
+   - NaN or Inf appearing
+   - Wrong steady state
+   - Solver not converging
+   - Step size going to minimum
+
+2. **Read the relevant solver file**:
+   - For Rosenbrock: `include/micm/solver/rosenbrock.inl`
+   - For Backward Euler: `include/micm/solver/backward_euler.inl`
+
+### Phase 2: Trace Data Flow
+
+For Rosenbrock solver issues, trace through:
+
+1. **Forcing calculation** (`AddForcingTerms`):
+   - ODE forcing: `rates_.AddForcingTerms()`
+   - Constraint forcing: `constraints_.AddForcingTerms()`
+   - Expected magnitude: O(rate × concentration)
+
+2. **Jacobian calculation** (`SubtractJacobianTerms`):
+   - Stores `-J_true` (negative of true Jacobian)
+   - ODE Jacobian: `rates_.SubtractJacobianTerms()`
+   - Constraint Jacobian: `constraints_.SubtractJacobianTerms()`
+
+3. **Matrix formation** (`AlphaMinusJacobian`):
+   - Adds `alpha = 1/(H * gamma)` to ALL diagonals
+   - Result should have all diagonals of similar magnitude
+   - If constraint diagonals are much smaller → ill-conditioning
+
+4. **Linear solve**:
+   - Solves `(αI - J) * K = forcing`
+   - K values should scale with H
+
+5. **Stage computation**:
+   - Uses `c/H * K` terms
+   - If K doesn't scale with H → c/H amplifies errors
+
+### Phase 3: Identify Root Cause
+
+Common patterns:
+
+| Symptom | Root Cause | Solution |
+|---------|------------|----------|
+| Constraint var explodes | Missing alpha on constraint diagonal | Check AlphaMinusJacobian |
+| All vars explode | Singular Jacobian | Check for zero rate constants |
+| Wrong equilibrium | Sign error | Check SubtractJacobianTerms |
+| Slow convergence | Step too large | Reduce h_max |
+
+### Phase 4: Recommend Fix
+
+Based on the root cause:
+
+1. **Code fix**: If a bug is found, show the fix
+2. **Parameter tuning**: Suggest solver parameter changes
+3. **Usage fix**: Suggest projection steps or smaller time steps
+4. **Test addition**: Suggest a test case to prevent regression
+
+## Key Files Reference
+
+- `rosenbrock.inl:52-60` - Forcing calculation
+- `rosenbrock.inl:62-71` - Jacobian calculation
+- `rosenbrock.inl:224-261` - AlphaMinusJacobian (both versions)
+- `constraint_set.hpp` - Constraint forcing/Jacobian methods