Validate Hermite cascade benchmark: Successfully reproduce thesis Figure 3.3 (#48) #114
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…ure 3.3 (#48) **Summary:** Successfully reproduced thesis Figure 3.3 showing m^(-1/2) velocity-space spectrum through systematic parameter investigation. This validates the kinetic physics implementation in the KRMHD solver. **Key Discovery:** Thesis requires much lower forcing amplitude (0.0035) than initially guessed (0.15), combined with νm^6 hypercollision and moderate collision frequency (ν=0.25). **Successful Parameters:** - ν = 0.25 (collision frequency) - hyper_n = 6 (νm^6 hypercollision, explicitly stated in thesis caption) - amplitude = 0.0035 (42× lower than initial guess) - M = 128 (Hermite moments) - resolution = 32³ - Lambda = -1.0 (kinetic parameter α=1.0) **Results:** - Clean m^(-1/2) power law from m=2 to m=20 ✓ - Forward flux dominance: 98.1-98.6% (C^+ >> C^-) ✓ - Sharp collisional cutoff at m~20-30 ✓ - Matches thesis Figure 3.3 qualitatively and quantitatively ✓ **Changes:** 1. **New benchmarks** (examples/benchmarks/): - hermite_forward_backward_flux.py: C+/C- decomposition diagnostic (recommended) - hermite_spectrum_evolution.py: Short diagnostic runs - hermite_cascade_benchmark.py: Long production runs with averaging 2. **Infrastructure improvements:** - Added hyper_n=6 support to config.py validation - Updated forcing.py parameter defaults - Enhanced diagnostics for energy balance monitoring 3. **Documentation:** - docs/HERMITE_CASCADE_INVESTIGATION.md: Comprehensive investigation summary - docs/references/thesis_chapter_3.pdf: Reference material - CLAUDE.md: Updated with validated parameters and usage 4. **Post-processing:** - scripts/plot_hermite_checkpoint_spectrum.py: Checkpoint analysis tool **Quick validation:** ```bash uv run python examples/benchmarks/hermite_forward_backward_flux.py \ --steps 90 --nu 0.25 --hyper-n 6 --amplitude 0.0035 \ --hermite-moments 128 --resolution 32 --thesis-style ``` Runtime: ~2 minutes Output: examples/output/successful_fig_3.3.png Closes #48
Code Review: PR #114 - Hermite Cascade Benchmark ValidationOverall AssessmentStatus: ✅ APPROVE with minor suggestions This PR successfully validates the Hermite moment cascade benchmark (Issue #48) by reproducing thesis Figure 3.3. The work is thorough, well-documented, and represents a significant milestone in validating the kinetic physics implementation. The PR demonstrates excellent scientific rigor with systematic parameter investigation and comprehensive documentation. Strengths1. Excellent Documentation 🌟
2. Scientific Rigor
3. Code Quality
4. Key Physical InsightThe discovery that amplitude = 0.0035 (42× lower than initial guess) is required for energy balance is important physics that should prevent future parameter selection mistakes. Issues & Suggestions1. Config Validation Inconsistency
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Critical fixes before merge: 1. Add scipy import and power law fitting to hermite_forward_backward_flux.py - Import scipy.stats for quantitative spectral slope validation - Add power law fits for C+ and C- spectra (m=3-16 range) - Print slopes with expected values (-0.5 for C+, -1.5 for C-) - Print R² values to assess fit quality - Matches diagnostic rigor in hermite_spectrum_evolution.py 2. Add comprehensive hyper_n=6 validation tests - Update test_hyper_n_valid_values to include all valid values [1,2,3,4,6] - Add test_hyper_n_thesis_value_6 for explicit hyper_n=6 validation - Add test_hyper_n_invalid_value_5 to demonstrate gap is intentional - Update test_hyper_n_invalid_value_8 error message to match config - Fixes test/code mismatch discovered during review All tests pass (4/4 hyper_n tests validated).
Critical Feedback AddressedBoth critical issues have been fixed in commit c74cfc1: 1. ✅ Fixed missing scipy import (hermite_forward_backward_flux.py)Added:
This matches the diagnostic rigor in 2. ✅ Added hyper_n=6 validation tests (test_config.py)Added/Updated:
All tests pass: 4/4 hyper_n tests validated Ready for merge pending optional improvements (config clarity, documentation structure). |
Code Review: Hermite Cascade Validation (Issue #48)SummaryThis PR successfully validates the Hermite moment cascade physics by reproducing thesis Figure 3.3 (m^(-1/2) velocity-space spectrum). The implementation is well-documented, scientifically rigorous, and includes comprehensive diagnostics. This is a major milestone for the kinetic physics validation. ✅ Strengths1. Scientific Rigor
2. Code Quality
3. Documentation Excellence
4. Testing Infrastructure
🔍 Issues FoundCRITICAL: Potential Security/Safety IssueLocation: Issue: The function enforces Hermitian symmetry on both kx=0 and kx=Nyquist planes unconditionally: # Line 204: kx=0 plane
forced_field = forced_field.at[:, :, 0].set(forced_field[:, :, 0].real.astype(forced_field.dtype))
# Line 213-215: kx=Nyquist plane (ALWAYS applied, even when Nx is odd)
nyquist_idx = Nx_rfft - 1
forced_field = forced_field.at[:, :, nyquist_idx].set(
forced_field[:, :, nyquist_idx].real.astype(forced_field.dtype)
)Problem: When Example:
Impact:
Fix Required: # Only enforce reality on Nyquist if Nx is even
if Nx_full % 2 == 0:
nyquist_idx = Nx_rfft - 1
forced_field = forced_field.at[:, :, nyquist_idx].set(
forced_field[:, :, nyquist_idx].real.astype(forced_field.dtype)
)Note: Similar issue in Related: Comment at line 209 acknowledges "For JIT compatibility, we always apply" but this is incorrect—JIT can handle conditional logic on static shapes. MODERATE: Code DuplicationLocations:
Issue: The C+/C- spectrum computation ( Recommendation:
MINOR: Magic NumbersLocation: Issue: E_ref_half = m_ref**(-0.5) * C_plus[3] / (3.0**(-0.5)) # Line 264
E_ref_three_half = m_ref**(-1.5) * C_minus[3] / (3.0**(-1.5)) # Line 273Recommendation: Extract normalization index as named constant: NORMALIZATION_MODE = 3 # Mode number for reference line normalizationMINOR: Parameter ValidationLocation: Issue: Validation accepts Recommendation: Update validator to mention n=6 is validated for thesis reproduction: if v not in {1, 2, 3, 4, 6}:
raise ValueError(
f"hyper_n must be 1, 2, 3, 4, or 6 (got {v}). "
"Use n=1 for standard collisions, n=2 for typical studies, "
"n=3 to match original GANDALF alpha_m=3, n=6 for thesis Figure 3.3 (VALIDATED)."
)📋 Detailed Code Reviewhermite_forward_backward_flux.py (427 lines)✅ Excellent:
hermite_cascade_benchmark.py (738 lines)✅ Excellent:
forcing.py (additions lines 157-356)✅ Otherwise excellent:
🔧 Must fix: Lines 209-215 and 287-295 (conditional Nyquist enforcement) config.py (changes lines 81-102)✅ Good: Added hyper_n=6 validation CLAUDE.md (changes lines 186-728)✅ Excellent documentation:
🧪 TestingWhat's Tested:✅ Existing tests pass (per PR description) What's Missing:
Recommendation: Add tests in follow-up PR: def test_forcing_reality_condition_odd_grid():
"""Test Hermitian symmetry with odd Nx (no Nyquist mode)."""
grid = SpectralGrid3D.create(Nx=33, Ny=32, Nz=32, Lx=1.0, Ly=1.0, Lz=1.0)
# ... test that mode 16 is NOT forced to real🎯 Performance✅ Efficient:
📊 Benchmarked runtimes (from docs):
📚 Documentation✅ Outstanding:
This is exemplary scientific software documentation. 🔒 Security/Safety✅ No malicious code 🏁 RecommendationAPPROVE with required fix: This PR makes a major scientific contribution and is well-implemented. However, the Nyquist enforcement bug must be fixed before merging to avoid silent physics corruption. Action Items:
After Fix:Once the Nyquist bug is corrected, this PR will be ready to merge. The scientific validation is sound, documentation is excellent, and code quality is high. 💡 Positive Highlights
Overall: This is high-quality computational physics research code. Excellent work! 🎉 Reviewer: Claude (AI Code Review) |
**CRITICAL BUG FIX**: Nyquist mode enforcement was being applied unconditionally to highest kx mode, corrupting physics when Nx is odd. Problem: - rfft format: shape [Nz, Ny, Nx//2+1] - Nx even (e.g., 32): Nyquist mode exists at index 16 (must be real) - Nx odd (e.g., 33): NO Nyquist mode at index 16 (regular complex mode) - Code was forcing index Nx_rfft-1 to real regardless of Nx parity - This violated Hermitian symmetry for odd Nx, corrupting high-k physics Fix: - Add Nx_full parameter to three JIT functions to check grid parity - Only enforce reality on Nyquist plane if Nx % 2 == 0 - Use @partial(jax.jit, static_argnums=...) for conditional logic - Update all call sites to pass grid.Nx Affected functions: 1. _gaussian_white_noise_fourier_perp_lowkz_jit (line 71) 2. _gaussian_white_noise_fourier_jit (line 140) 3. _gandalf_forcing_fourier_jit (line 230) Testing: - All 35 forcing tests pass (tests/test_forcing.py) - Reality condition tests specifically validated Impact: - Previous runs with even Nx (32, 64, 128) were NOT affected - Odd Nx grids would have had silent physics corruption at high-k - Hermite cascade validation (PR #114) used Nx=32 (even) - results valid Discovered during PR #114 code review.
Critical Bug Fixed: Nyquist EnforcementFixed the critical Nyquist enforcement bug identified in the latest code review (commit 578e792). ProblemThe forcing functions were unconditionally enforcing reality condition on the highest kx mode ( For rfft format
This bug would silently corrupt physics at high wavenumbers for odd grid sizes. Solution
Affected Functions
Testing
Impact on This PRHermite cascade validation results remain valid because all benchmarks used Nx=32 (even). The m^(-1/2) spectrum and forward flux validation are NOT affected by this bug. However, this fix prevents future issues when users try odd grid sizes. Status: Both critical issues (#1 scipy import, #2 hyper_n=6 tests) AND the Nyquist bug are now resolved. |
PR Review: Hermite Cascade Validation (#48)SummaryThis PR successfully validates the Hermite moment cascade implementation by reproducing thesis Figure 3.3 (m^(-1/2) velocity-space spectrum). The work demonstrates a methodical scientific investigation with excellent documentation. Overall Assessment: ✅ APPROVE with minor suggestions Strengths1. Excellent Scientific Validation 🎯
2. Outstanding Documentation 📚
3. Robust Test Coverage ✅
4. Well-Designed Benchmark Scripts 🔧
5. Code Quality
Areas for Improvement1. Force Hermite Moments Implementation (forcing.py:500-650)Issue: The Observations:
Suggestion: def enforce_hermitian_symmetry_rfft(field: Array, Nx_full: int) -> Array:
"""Extract shared Hermitian symmetry enforcement logic."""
# Enforce kx=0 plane reality
field = field.at[:, :, 0].set(field[:, :, 0].real.astype(field.dtype))
# Enforce Nyquist plane reality if Nx is even
if Nx_full % 2 == 0:
nyquist_idx = field.shape[2] - 1
field = field.at[:, :, nyquist_idx].set(
field[:, :, nyquist_idx].real.astype(field.dtype)
)
return fieldImpact: Minor - this is a code quality improvement, not a bug. 2. Documentation Clarity (CLAUDE.md:186-220)Issue: The hyper-collision exponent description could be clearer about when m^n vs m^(2n) is used. Current text (line 188-190):
Suggestion: Add a brief physics explanation: **Why the difference?**
- Spatial dissipation: ∇^(2r) operator → k^(2r) (even power from differential operator)
- Moment collisions: Linear operator on index m → m^n (direct power, matching GANDALF convention)Impact: Very minor - improves clarity for future developers. 3. Parameter Discovery Documentation (HERMITE_CASCADE_INVESTIGATION.md:350-400)Missing Information:
Suggestion: Add a "Parameter Discovery Method" section: ## Parameter Discovery Method
The successful amplitude (0.0035) was found through:
1. Energy balance analysis: Monitored injection/dissipation ratio
2. Binary search between over-damped (0.15) and under-damped regimes
3. Target: ratio ≈ 1.0 with steady-state energy plateau
4. Final tuning: Adjusted ν to achieve exact m^(-1/2) slopeImpact: Minor - helps future users understand the methodology. 4. Test Naming Convention (test_config.py:134-143)Observation: Test names could be more descriptive. Current: def test_hyper_n_thesis_value_6(self):
def test_hyper_n_invalid_value_5(self):Suggestion: def test_hyper_n_accepts_thesis_figure_3_3_value(self):
def test_hyper_n_rejects_unsupported_value_with_clear_error(self):Impact: Very minor - improves test discoverability. 5. Potential Performance Issue (hermite_cascade_benchmark.py:200-250)Observation: The Line 247 (approx): for step in range(total_steps):
state = gandalf_step(...)
if step % diagnostic_interval == 0:
C_plus, C_minus, _ = compute_forward_backward_spectra(state) # Not JIT-compiledSuggestion: Consider adding Impact: Minor - could improve performance for large M values. Security & Safety✅ No security concerns identified
RecommendationsBefore Merge:
Future Work (separate PRs):
Testing ValidationI verified the test changes are comprehensive:
Physics ValidationThe key physics result is scientifically sound:
This validates the kinetic physics implementation in the solver. ConclusionThis is high-quality scientific software development with:
The minor suggestions above are for code quality and future maintainability, but do not block this PR. Recommendation: APPROVE and MERGE ✅ Additional NotesThe 476-line investigation document ( Great work on Issue #48! 🎉 |
Summary
Successfully reproduced thesis Figure 3.3 showing m^(-1/2) velocity-space spectrum through systematic parameter investigation. This validates the kinetic physics implementation in the KRMHD solver and closes #48.
Key Discovery
The thesis requires much lower forcing amplitude (0.0035) than initially guessed (0.15), combined with νm^6 hypercollision and moderate collision frequency (ν=0.25).
Successful Parameters
Results
Changes
1. New Benchmarks (examples/benchmarks/)
2. Infrastructure Improvements
3. Documentation
Quick Validation
examples/output/successful_fig_3.3.pngInvestigation Details
See
docs/HERMITE_CASCADE_INVESTIGATION.mdfor complete investigation including:Testing
All existing tests pass. New benchmarks validated against thesis Figure 3.3.
Closes #48