Fix wall_hit_cart/xend_cart inconsistency when from_cart fails

[krystophny]

Summary

Fix inconsistency between xend_cart and wall_hit_cart for STL wall hits.

Root cause: For STL wall intersections detected by CGAL, xend_cart was computed from zend via forward chartmap transformation. When the earlier from_cart() inverse transformation failed (in ill-conditioned chartmap regions), zend contained incorrect reference coordinates, causing xend_cart to be displaced from the true wall intersection.

Fix (2 commits):

1. simple_main.f90: Add linear interpolation fallback for zend when from_cart() fails
2. netcdf_results_output.f90: Use wall_hit_cart directly for xend_cart on STL hits (the clean fix)

The second fix is the definitive solution - xend_cart now equals wall_hit_cart exactly for all STL wall hits, regardless of whether from_cart() succeeds. The first fix improves zend for angle-space analysis.

Also: Update CGAL 5.6.1 -> 6.0.1 for GCC compatibility, and set xend_cart to zero (not xstart_cart) for untraced particles.

Related

• GECKO PR: https://github.com/itpplasma/GECKO/pull/6 - adds wall_mesh_from_chartmap() to create STL exactly matching chartmap boundary

Test plan

• CI build passes
• Manual verification with STL wall runs

[krystophny]

Visual Evidence

The histogram compares position differences between wall_hit_cart (true CGAL intersection) and xend_cart (computed from reference coordinates) before and after this fix.

Key improvements:

• Excellent agreement (<1 cm): 65.2% -> 78.6%
• Severe discrepancy (>500 cm): 22.3% -> 0%

Test configuration: SQUID stellarator, 1ms simulation, 1024 particles starting at s=0.6, using CGAL-embedded STL chartmap.

[qodo-code-review]

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PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
⚪	Supply chain integrity Description: The build fetches and builds a third-party dependency (CGAL) directly from a remote URL via FetchContent_Declare(URL ...) without any pinned integrity verification (e.g., URL_HASH/checksum or signature verification), which creates a software supply-chain risk if the downloaded archive is tampered with or replaced upstream. CMakeLists.txt [209-223] Referred Code include(FetchContent) FetchContent_Declare( cgal URL https://github.com/CGAL/cgal/releases/download/v6.0.1/CGAL-6.0.1.tar.xz DOWNLOAD_EXTRACT_TIMESTAMP TRUE ) FetchContent_GetProperties(cgal) if(NOT cgal_POPULATED) FetchContent_Populate(cgal) endif() # CGAL 6.x is header-only, just add include path set(CGAL_INCLUDE_DIR "${cgal_SOURCE_DIR}/include") message(STATUS "CGAL enabled via FetchContent: 6.0.1 (header-only)") message(STATUS "CGAL include dir: ${CGAL_INCLUDE_DIR}") add_compile_definitions(SIMPLE_ENABLE_CGAL)
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	Generic: Meaningful Naming and Self-Documenting Code Objective: Ensure all identifiers clearly express their purpose and intent, making code self-documenting Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
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	Generic: Security-First Input Validation and Data Handling Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent vulnerabilities Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
🔴	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Fallback edge case: The new interpolation fallback silently does nothing when segment_length is zero, leaving z(1:3) potentially unupdated after from_cart() failure and risking the same inconsistency the fix aims to address. Referred Code segment_length = sqrt(sum((x_cur_m - x_prev_m)**2)) if (segment_length > 0.0_dp) then hit_distance = sqrt(sum((x_hit_m - x_prev_m)**2)) t_frac = hit_distance / segment_length u_ref_hit = u_ref_prev + t_frac * (u_ref_cur - u_ref_prev) call ref_to_integ(u_ref_hit, z(1:3)) end if Learn more about managing compliance generic rules or creating your own custom rules
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[krystophny]

Update: The visual evidence histogram is available locally at /tmp/cgal_fix_comparison.png showing:

Position Discrepancy    Before Fix    After Fix
-------------------------------------------
< 1 cm (excellent)       65.2%         78.6%
> 100 cm (large)         32.1%          3.6%
> 500 cm (severe)        22.3%            0%

The fix significantly improves consistency between the CGAL-reported wall intersection (wall_hit_cart) and the position computed from reference coordinates (xend_cart).

[qodo-code-review]

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Handle zero-length segment case Add an else branch to handle the zero-length segment case by setting u_ref_hit to u_ref_prev, resetting ierr_from_cart, and calling ref_to_integ to prevent an uninitialized state. src/simple_main.f90 [634-639] if (segment_length > 0.0_dp) then hit_distance = sqrt(sum((x_hit_m - x_prev_m)**2)) t_frac = hit_distance / segment_length u_ref_hit = u_ref_prev + t_frac * (u_ref_cur - u_ref_prev) + ierr_from_cart = 0 + call ref_to_integ(u_ref_hit, z(1:3)) +else + u_ref_hit = u_ref_prev + ierr_from_cart = 0 call ref_to_integ(u_ref_hit, z(1:3)) end if Apply / Chat Suggestion importance[1-10]: 8 __ Why: The suggestion correctly identifies a bug in the new fallback logic where a zero-length segment would leave the particle state un-updated and the error flag set, leading to incorrect behavior. The proposed fix is comprehensive and correct.	Medium
General	Clamp interpolation fraction Clamp the interpolation fraction t_frac to the [0, 1] range to guard against numerical errors and prevent extrapolation. src/simple_main.f90 [636] -t_frac = hit_distance / segment_length +t_frac = min(1.0_dp, max(0.0_dp, hit_distance / segment_length)) Apply / Chat Suggestion importance[1-10]: 6 __ Why: This suggestion correctly identifies a potential numerical instability where hit_distance could be slightly larger than segment_length, leading to extrapolation. Clamping t_frac makes the interpolation more robust against floating-point inaccuracies.	Low
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