[alongd]

Summary

This PR supersedes/complements #855. It is #855's four commits (Added the ND Scan module, Added directed scan to xTB job adapter, Added ND scan functionalities to plotter, Adaptations to Scheduler) rebased onto current main (263 commits of drift since #855 was opened), plus two additional fixes:

• A fix for a finalization crash in finalize_directed_scan_results (see review comment on Refactor ND scan subsystem with adaptive sparse 2D sampling, surface validation, and coupling classification #855 for details).
• A fix for a pipe_planner initialization-order bug in Scheduler.__init__.

#855 should not be force-pushed or rebased in place — its branch (nd_scans) is currently checked out in a live, long-running working session with uncommitted local patches, and rewriting it there would destroy that work. This PR exists so the rebased/fixed history can be reviewed and landed without touching nd_scans.

Detailed review findings (conflict-resolution notes, two latent bugs found on main, the finalization-crash fix, and several design questions worth discussing) are posted as a comment on #855.

Closes/relates to #855.

Test plan

• CI green on this branch
• Review findings on Refactor ND scan subsystem with adaptive sparse 2D sampling, surface validation, and coupling classification #855 addressed or discussed
• Existing directed-scan / ND-scan unit tests pass, including the new regression test for the finalization-crash fix

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 67.73%. Comparing base (828e7a6) to head (17a740a).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #930      +/-   ##
==========================================
+ Coverage   67.18%   67.73%   +0.55%     
==========================================
  Files         123      124       +1     
  Lines       43674    44537     +863     
  Branches    11153    11312     +159     
==========================================
+ Hits        29342    30169     +827     
+ Misses      11194    11153      -41     
- Partials     3138     3215      +77     

Flag	Coverage Δ
functionaltests	67.73% <ø> (+0.55%)	⬆️
unittests	67.73% <ø> (+0.55%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.
see 15 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

This PR rebases and integrates the ND rotor-scan work (superseding #855) onto current main, adds an ESS finalization crash fix, fixes a pipe-mode initialization-order issue in Scheduler.__init__, and introduces adaptive sparse 2D scan support end-to-end (scan utilities, scheduler orchestration, plotting, and tests).

Changes:

• Added arc/species/nd_scan.py to centralize ND scan utilities and implement adaptive sparse 2D scanning, validation, coupling metrics, and classification.
• Updated arc/scheduler.py to use the new ND-scan utilities, fix ESS scan finalization, support adaptive batching, and fix pipe planner/coordinator initialization ordering.
• Added sparse/adaptive 2D plotting support in arc/plotter.py, plus extensive unit/functional tests and an xTB directed-scan --opt fix.

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 utility module including adaptive sparse 2D scanning, validation, and classification helpers.
arc/species/nd_scan_test.py	New unit tests covering dense/continuous/adaptive scan utilities, validation, and classification.
arc/scheduler.py	Integrates ND scan module, adds adaptive scan orchestration, fixes ESS finalization crash, and adjusts pipe init ordering.
arc/scheduler_test.py	Adds functional directed-scan tests (dense + adaptive) using xTB, and related helpers.
arc/plotter.py	Adds sparse/adaptive 2D plotting path (interpolation + overlays) and fixes axis limit setting bugs.
arc/plotter_test.py	Adds tests for sparse plotting helpers and non-crashing plot generation.
arc/job/adapters/xtb_adapter.py	Ensures directed_scan jobs that are optimization scans pass --opt to xTB.

---

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.

[Copilot]

🟡 Changes recommended

Unresolved critical and moderate correctness issues remain, including plotter import failure and scan limit, filtering, and scheduler bookkeeping bugs.

3 open issues

• Fix missing typing imports in plotter annotations · New
• Exclude non-isomorphic points from energy normalization · New
• Include failed and invalid points in max_points · New

2 resolved since last review

• number_of_running_jobs is decremented for brute-force directed-scan jobs even when the job is…
• Sparse 2D plotting currently includes energies from invalid (non-isomorphic) points in the…

_{Review effort: Lite}

[Copilot]

🟡 Changes recommended

Unresolved critical and moderate findings affect adaptive scan correctness, reachability, validation, and completion.

6 open issues

• Record failed adaptive points before batch completion · New
• Enforce max_points when selecting seed batches · New
• Exclude invalid points from sampled neighbor iteration · New
• Deduplicate periodic-edge validation checks · New
• Exclude non-isomorphic results from adaptive metrics · New
• Persist processed adaptive jobs across scheduler rounds · New

3 resolved since last review

• Fix missing typing imports in plotter annotations
• Include failed and invalid points in max_points
• Exclude non-isomorphic points from energy normalization

_{Review effort: Lite}