Make queue-executed ASE (UMA/fairchem) jobs runnable on a cluster

[alongd]

What

Make queue-executed ASEAdapter jobs actually run on a remote cluster. The ASE adapter had only ever been exercised incore; its queue path was latent and broke on the first real submission. This lets ASE-backed calculators (e.g. UMA / fairchem MLIPs) run hindered-rotor and other scans as ordinary PBS/Slurm jobs.

Why

Running a real ARC job that delegates its hindered-rotor scans to an ASE calculator on a cluster queue crashed the moment the first scan job was dispatched:

arc.exceptions.InputError: Cannot upload a non-existing file.
Check why file in path .../directed_scan_a2781/submit.sh is missing.

Two independent defects in the queue path, both masked because ASE had only ever run incore:

1. Files were never written. JobAdapter.execute() calls upload_files() before execute_queue(), and _initialize_adapter() calls set_files() while the job is constructed. The Gaussian/Orca/xTB adapters write submit.sh / input inside set_files(); ASEAdapter.set_files() only appended their names to files_to_upload and never wrote them, so the calcs dir was empty when ssh.upload_file() ran its os.path.isfile pre-flight.
2. Submission was dead code. ASEAdapter.execute_queue() guarded on self.server_adapter, an attribute nothing in ARC sets (hasattr → False), so even with the files present the job would never submit — the write fix alone just moves the crash one line down to an AttributeError.

Changes (confined to the ASE adapter)

• set_files() now writes submit.sh and input.yml for non-incore jobs, mirroring the other adapters. Incore is unchanged — it still writes its input in execute_incore().
• execute_queue() now delegates to the shared legacy_queue_execution() that every other adapter uses (which also records job_status / job_id), replacing the bespoke never-reached block.
• write_submit_script()'s non-queue branch falls back to local_path when remote_path is None (a server-less job), fixing a latent crash surfaced by writing at construction time.
• Adds test_set_files_writes_the_files_of_a_queue_job (red against the pre-fix adapter).

Verification

• New/updated unit tests: pytest arc/job/adapters/ase_test.py -q -n0 → 10 passed (the file requires serial -n0, a pre-existing xdist setUpClass race unrelated to this change).
• Incore path unregressed: full execute() → execute_incore() → ase_script.py → parse_results() reproduces the prior geometry/energy to 5 decimals.
• Live cluster run: an ARC job (DFT opt/freq/sp on the queue, hindered-rotor scans via a UMA/ASE calculator) now runs end-to-end — the DFT stage completes and the rotor jobs are written with their submit.sh + input.yml and submitted to the queue, where the pre-fix run crashed.

The diff is limited to arc/job/adapters/ase_adapter.py, arc/job/adapters/ase_test.py, and a 1-indexed→0-indexed constraint fix in arc/job/adapters/scripts/ase_script.py (ASE FixInternals is 0-indexed; ARC constraints are 1-indexed). No other adapter's submit path is touched.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 64.17%. Comparing base (9f41176) to head (366c5d0).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #985      +/-   ##
==========================================
- Coverage   64.17%   64.17%   -0.01%     
==========================================
  Files         119      119              
  Lines       39554    39584      +30     
  Branches    10264    10269       +5     
==========================================
+ Hits        25385    25403      +18     
- Misses      11199    11204       +5     
- Partials     2970     2977       +7     

Flag	Coverage Δ
functionaltests	64.17% <ø> (-0.01%)	⬇️
unittests	64.17% <ø> (-0.01%)	⬇️

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[Copilot]

Pull request overview

This PR fixes the previously-latent “queue execution” path for ASEAdapter so ASE-backed calculators (e.g., UMA/fairchem MLIPs) can run as real cluster jobs, including rotor/directed-scan workloads that ARC dispatches via the scheduler.

Changes:

• Write submit + input.yml during adapter construction for non-incore ASE jobs so upload_files() succeeds.
• Replace ASE’s bespoke queue submission logic with the shared legacy_queue_execution() flow.
• Correct ASE internal constraint indexing by translating ARC’s 1-indexed constraints to ASE FixInternals’ 0-indexed expectations.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
arc/job/adapters/ase_adapter.py	Writes queue job files in set_files(), adds directed-scan constraints translation, and delegates queue submission to legacy_queue_execution().
arc/job/adapters/ase_test.py	Adds unit coverage asserting queue-job construction writes/uploadables exist on disk (and that incore does not).
arc/job/adapters/scripts/ase_script.py	Converts constraint atom indices from ARC’s 1-indexing to ASE’s 0-indexing before applying FixInternals.

Suppressed comments (1)

arc/job/adapters/ase_adapter.py:415

• This method always writes the submit script to submit.sh. On Slurm, ARC submits submit.sl (see settings['submit_filenames']), so Slurm jobs will still error unless the script is written under the Slurm filename.

        with open(os.path.join(self.local_path, 'submit.sh'), 'w') as f:
            f.write(content)

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[alongd]

Added a third commit (dc23057): fix a stale directed-scan parser call site — check_directed_scan_job called parser.parse_e_elect(path=...) but the refactored API is log_file_path= (as every other call site uses). Without it, ARC crashes assembling V(φ) the moment a directed-scan job's energy is parsed. Verified by parsing a real UMA rotor output (−500058.16 kJ/mol). This is needed for ASE/UMA rotor scans to run end-to-end.