Refactor ND scan subsystem with adaptive sparse 2D sampling, surface validation, and coupling classification

[alongd]

• New module arc/species/nd_scan.py: Extracts ND scan logic from scheduler.py into a dedicated subsystem with clean interfaces for grid generation, continuous scan state, adaptive sparse 2D sampling, surface validation, coupling metrics, and rotor classification
• Adaptive sparse 2D scans: For eligible brute_force_sp/brute_force_opt 2D rotors, ARC can now run batched adaptive sampling instead of the full Cartesian grid, controlled by a sampling_policy field on the rotor — no new directed_scan_type values are introduced
• Surface validation: Neighbor-edge continuity checks, periodic boundary consistency, and branch-jump detection diagnose PES discontinuities without blocking finalization
• Coupling analysis and classification: Separable-fit residual analysis classifies each adaptive 2D rotor as separable, coupled, or unreliable with an explicit recommended action
• Sparse-aware 2D plotting: plot_2d_rotor_scan dispatches to an interpolation-based sparse contour path for adaptive scans, with sampled/failed/invalid point overlays
• xTB directed_scan fix: The xTB adapter now correctly runs --opt for brute_force_opt directed scan jobs (was silently running SP)
• Bug fix: Corrected parse_e_elect(path=...) → parse_e_elect(log_file_path=...) kwarg in check_directed_scan_job

[Copilot]

Pull request overview

Refactors ARC’s N-dimensional (ND) directed-rotor scan logic into a dedicated arc/species/nd_scan.py subsystem, adds an adaptive sparse 2D sampling path with surface validation + coupling classification, and updates the scheduler/plotter/xTB adapter to support the new flow.

Changes:

• Extracted ND scan utilities from scheduler.py into arc/species/nd_scan.py and updated scheduler call sites accordingly.
• Added adaptive sparse 2D scan execution (batch selection, bookkeeping, surface validation, coupling metrics, and rotor classification) with new unit/functional tests.
• Updated 2D plotting to support sparse/adaptive scans via interpolation-based contours with overlays; fixed xTB directed-scan opt behavior.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
arc/species/nd_scan.py	New ND scan subsystem incl. adaptive sparse 2D sampling, validation, coupling metrics, and classification.
arc/species/nd_scan_test.py	Unit tests covering dense/continuous helpers and the new adaptive/validation/classification logic.
arc/scheduler.py	Integrates nd_scan helpers; adds adaptive batch spawning and refactors directed-scan finalization/recording.
arc/scheduler_test.py	Functional xTB-backed tests for dense + adaptive 2D directed scans.
arc/plotter.py	Adds sparse/adaptive 2D plotting path (interpolation + overlays) and dispatch logic.
arc/plotter_test.py	Tests for sparse plotting helpers and interpolation behavior.
arc/job/adapters/xtb_adapter.py	Ensures --opt is used for directed_scan jobs whose directed-scan type implies optimization.

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 5 comments.

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 60.30%. Comparing base (1e374ec) to head (e8f8a8f).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #855      +/-   ##
==========================================
+ Coverage   59.24%   60.30%   +1.06%     
==========================================
  Files          98       99       +1     
  Lines       30023    30856     +833     
  Branches     7929     8082     +153     
==========================================
+ Hits        17786    18609     +823     
+ Misses       9985     9926      -59     
- Partials     2252     2321      +69     

Flag	Coverage Δ
functionaltests	60.30% <ø> (+1.06%)	⬆️
unittests	60.30% <ø> (+1.06%)	⬆️

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

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