Integrate Atomic Simulation Environment (ASE) as a Job Adapter by kfir4444 · Pull Request #836 · ReactionMechanismGenerator/ARC

kfir4444 · 2026-03-16T17:12:36Z

Summary

This PR introduces a new job adapter that allows ARC to utilize the Atomic Simulation Environment (ASE) as a backend engine. By integrating ASE, ARC can now run single-point energy calculations, geometry optimizations, and vibrational (frequency) analyses using any ASE-compatible calculator.

Key Changes

ASE Adapter Interface: Added the main ASEAdapter class (arc/job/adapters/ase.py) and registered it in the adapter factory (arc/job/adapters/common.py and init.py).
Standalone Execution Script: Introduced arc/job/adapters/scripts/ase_script.py, a standalone Python script designed to standardise the execution of ASE tasks in a robust, isolated
environment.
Multi-Calculator Support: The script natively supports initializing calculators such as TorchANI (with options for ANI1x, ANI1ccx, ANI2x), xTB, and MOPAC, with fallbacks for
generic ASE calculators.
Flexible Geometry Optimization: Enables geometry optimizations via various engines, including Sella, BFGS, LBFGS, and GPMin. Allows defining constraints (e.g., fixing internal
coordinates).
Robust Vibrational Analysis: Implemented a pure NumPy vibrational analysis function that reliably calculates frequencies, normal modes (Mass Deweighted Normalized), reduced
masses, and force constants directly from the Hessian, matching physical constants and standards used by TorchANI/ASE.

Impact

This integration significantly broadens ARC's computational capabilities by tapping directly into the ASE ecosystem, making it trivial to incorporate Machine Learning Potentials (like TorchANI) and any method that interacts with ASE very easily.

arc/job/adapters/scripts/ase_script.py

+import sys
+import yaml
+import numpy as np
+from typing import Optional, Union


To fix unused imports, remove the specific unused names from the import statement (or delete the whole import if none of its names are used). This reduces unnecessary dependencies and clarifies which types or modules are actually required.

In this file, from typing import Optional, Union appears on line 15, and neither Optional nor Union is referenced in the displayed code. The minimal, behavior-preserving fix is to remove this import line entirely. No additional methods, definitions, or imports are needed, and no other lines must be modified.

Concretely: in arc/job/adapters/scripts/ase_script.py, delete the line from typing import Optional, Union (currently line 15). Leave all surrounding imports unchanged.

arc/job/adapters/scripts/ase_script.py

+from ase import Atoms
+from ase.constraints import FixInternals
+from ase.optimize import BFGS, LBFGS, GPMin
+from ase.optimize.sciopt import Converged, OptimizerConvergenceError, SciPyFminBFGS, SciPyFminCG


In general, the correct fix for unused imports is to remove only the unused names from the import statement, leaving in place any names that are actually used. This reduces unnecessary dependencies and clarifies which external APIs the file relies on.

Here, the import line

from ase.optimize.sciopt import Converged, OptimizerConvergenceError, SciPyFminBFGS, SciPyFminCG

should be edited to drop Converged and OptimizerConvergenceError, while keeping SciPyFminBFGS and SciPyFminCG intact (since we cannot see whether they are used elsewhere). This change affects only arc/job/adapters/scripts/ase_script.py at line 20, and no additional methods, imports, or definitions are needed.

Copilot

Pull request overview

Adds support for running calculations via ASE (Atomic Simulation Environment) as a new ARC job adapter, along with YAML parsing adjustments to consume ASE-produced YAML outputs.

Changes:

Register a new ase job adapter and supporting standalone execution script (ase_script.py) producing YAML outputs.
Extend settings to recognize ASE as supported ESS and define ASE-specific filenames/options/environment mappings.
Update YAML parsing and XYZ-from-file fallback to better handle .yml/.yaml inputs.

Reviewed changes

Copilot reviewed 8 out of 9 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
arc/settings/settings.py	Adds ASE to supported ESS + filenames/options; updates cluster delete command and ASE env mapping.
arc/parser/parser.py	Adds `.yml/.yaml` path in `parse_xyz_from_file()` to parse geometry via YAML adapter.
arc/parser/adapters/yaml.py	Expands supported YAML keys; modifies energy parsing logic.
arc/level.py	Changes `deduce_software()` control flow to return early when software is already set.
arc/job/adapters/scripts/ase_script.py	New standalone runner for ASE jobs (SP/opt/freq) producing `output.yml`.
arc/job/adapters/ase.py	New `ASEAdapter` integrating ASE script into ARC job execution (incore/queue).
arc/job/adapters/init.py	Imports/registers the new ASE adapter module.
arc/job/adapter.py	Adds `ase` to `JobEnum`.
.gitignore	Ignores `spec.md`.

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arc/settings/settings.py

                  }

-delete_command = {'OGE': 'export SGE_ROOT=/opt/sge; /opt/sge/bin/lx24-amd64/qdel',
+delete_command = {'OGE': 'export SGE_ROOT=/opt/sge; /opt/sge/bin/scancel',


arc/settings/settings.py

+ASE_CALCULATORS_ENV = {'torchani': 'TANI_PYTHON',
+                       'xtb': 'SELLA_PYTHON',


arc/parser/adapters/yaml.py

+        if energy is not None:
+            # If the value is very small, it might already be in kJ/mol (unlikely for E_elect),
+            # but standard internal representation is Hartree.
+            if abs(energy) < 1e6: # Arbitrary threshold to detect Hartree vs kJ/mol
+                return energy * E_h_kJmol
+            return energy


arc/level.py

        Args:
            job_type (str, optional): An ARC job type, assists in determining the software.
        """
+        if self.software is not None:


arc/job/adapters/scripts/ase_script.py

+    if job_type in ['sp', 'opt', 'conf_opt', 'freq', 'optfreq', 'directed_scan']:
+        output['sp'] = to_hartree(atoms.get_potential_energy())
+
+    if job_type in ['opt', 'conf_opt', 'optfreq', 'directed_scan']:
+        fmax = float(settings.get('fmax', 0.001))
+        steps = int(settings.get('steps', 1000))
+        engine_name = settings.get('optimizer', 'BFGS').lower()
+
+        engine_dict = {
+            'bfgs': BFGS, 'lbfgs': LBFGS, 'gpmin': GPMin,
+            'scipyfminbfgs': SciPyFminBFGS, 'scipyfmincg': SciPyFminCG,
+            'sella': None,
+        }
+        if engine_name == 'sella':
+            from sella import Sella
+            opt_class = Sella
+        else:
+            opt_class = engine_dict.get(engine_name, BFGS)
+        opt = opt_class(atoms, logfile=os.path.join(os.path.dirname(input_path), 'opt.log'))
+
+        try:
+            opt.run(fmax=fmax, steps=steps)
+            save_current_geometry(output, atoms, xyz)
+            output['sp'] = to_hartree(atoms.get_potential_energy())
+        except Exception as exc:


arc/job/adapters/scripts/ase_script.py

+    job_type = input_dict.get('job_type')
+    xyz = input_dict.get('xyz')
+    settings = input_dict.get('settings', {})
+
+    atoms = Atoms(symbols=xyz['symbols'], positions=xyz['coords'])
+    calc = get_calculator(settings)
+    atoms.calc = calc
+
+    apply_constraints(atoms, input_dict.get('constraints'))


arc/job/adapters/ase.py

+# Default mapping if not yet fully defined in settings.py
+DEFAULT_ASE_ENV = {
+    'torchani': 'TANI_PYTHON',
+    'xtb': 'XTB_PYTHON',


arc/job/adapters/ase.py

+class ASEAdapter(JobAdapter):
+    """
+    A generic adapter for ASE (Atomic Simulation Environment) jobs.
+    Supports multiple calculators and environments.
+    """
+    def __init__(self,


kfir4444 added 9 commits March 16, 2026 18:54

added ase to job adapter

41c871e

added ase to job adapter init

d29cb3a

Better management of deduce_software when software is given

2b9d785

added ase to settings

098f0c8

Better treatment of yml files in parse_xyz_from_file

31bb7b8

added to parsing from yaml file

8af5782

added ase adapter

fbaebe2

added ase script for running incore

193e6ed

added spec.md to gitignore (for SDD)

4b7a6fa

github-advanced-security bot found potential problems Mar 16, 2026

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alongd requested a review from Copilot March 16, 2026 17:20

Copilot started reviewing on behalf of alongd March 16, 2026 17:21 View session

Copilot AI reviewed Mar 16, 2026

View reviewed changes

kfir4444 changed the title ~~Title: Integrate Atomic Simulation Environment (ASE) as a Job Adapter~~ Integrate Atomic Simulation Environment (ASE) as a Job Adapter Mar 16, 2026

kfir4444 added 3 commits March 16, 2026 22:15

added ase to adapters common

15fe0b9

Test: ase

a601ea2

!f ase

465b726

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Integrate Atomic Simulation Environment (ASE) as a Job Adapter#836

Integrate Atomic Simulation Environment (ASE) as a Job Adapter#836
kfir4444 wants to merge 12 commits intomainfrom
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		ASE_CALCULATORS_ENV = {'torchani': 'TANI_PYTHON',
		'xtb': 'SELLA_PYTHON',

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