Integrate Atomic Simulation Environment (ASE) as a Job Adapter

.gitignore

@@ -75,3 +75,10 @@ build/*
 
 # AI Agent files
 AGENTS.md
+spec.md
+
+# Other AI things
+.agents
+ARC.egg*
+uv*
+*graphify*

arc/constants.py

@@ -25,7 +25,7 @@
 pi (float): Pi, 3.14159...
 """
 
-import math
+from math import pi
 
 #: The Hartree energy :math:`E_\mathrm{h}` in :math:`\mathrm{J}`
 E_h = 4.35974434e-18
@@ -47,7 +47,7 @@
 amu = 1.660538921e-27
 
 #: The speed of light in a vacuum :math:`c` in :math:`\mathrm{m/s}`
-c = 299792458
+c = 299792458.0
 
 #: The elementary charge :math:`e` in :math:`\mathrm{C}`
 e = 1.602176565e-19
@@ -71,7 +71,7 @@
 m_p = 1.672621777e-27
 
 #: :math:`\pi = 3.14159 \ldots`
-pi = float(math.pi)
+pi = float(pi)
 
 #: Faradays Constant F in C/mol
 F = 96485.3321233100184

arc/job/adapter.py

@@ -92,6 +92,7 @@ class JobEnum(str, Enum):
             - gan  # Generative adversarial networks, https://doi.org/10.1063/5.0055094
     """
     # ESS
+    ase = 'ase'
     cfour = 'cfour'
     gaussian = 'gaussian'
     mockter = 'mockter'

arc/job/adapters/__init__.py

@@ -1,4 +1,5 @@
 import arc.job.adapters.common
+import arc.job.adapters.ase_adapter
 import arc.job.adapters.cfour
 import arc.job.adapters.gaussian
 import arc.job.adapters.mockter

arc/job/adapters/ase_adapter.py

@@ -0,0 +1,241 @@
+"""
+An adapter for executing ASE (Atomic Simulation Environment) jobs
+"""
+
+import datetime
+import os
+import subprocess
+from typing import TYPE_CHECKING, List, Optional, Tuple, Union
+
+from arc.common import get_logger, read_yaml_file, save_yaml_file
+from arc.job.adapter import JobAdapter
+from arc.job.adapters.common import _initialize_adapter
+from arc.job.factory import register_job_adapter
+from arc.imports import settings
+from arc.settings.settings import ARC_PYTHON, find_executable
+
+if TYPE_CHECKING:
+    from arc.level import Level
+    from arc.species.species import ARCSpecies
+    from arc.reaction import ARCReaction
+
+logger = get_logger()
+
+# Default mapping if not yet fully defined in settings.py
+DEFAULT_ASE_ENV = {
+    'torchani': 'TANI_PYTHON',
+    'xtb': 'XTB_PYTHON',
+}
+
+class ASEAdapter(JobAdapter):
+    """
+    A generic adapter for ASE (Atomic Simulation Environment) jobs.
+    Supports multiple calculators and environments.
+    """
+    def __init__(self,
+                 project: str,
+                 project_directory: str,
+                 job_type: Union[List[str], str],
+                 args: Optional[dict] = None,
+                 bath_gas: Optional[str] = None,
+                 checkfile: Optional[str] = None,
+                 conformer: Optional[int] = None,
+                 constraints: Optional[List[Tuple[List[int], float]]] = None,
+                 cpu_cores: Optional[str] = None,
+                 dihedral_increment: Optional[float] = None,
+                 dihedrals: Optional[List[float]] = None,
+                 directed_scan_type: Optional[str] = None,
+                 ess_settings: Optional[dict] = None,
+                 ess_trsh_methods: Optional[List[str]] = None,
+                 execution_type: Optional[str] = None,
+                 fine: bool = False,
+                 initial_time: Optional[Union[datetime.datetime, str]] = None,
+                 irc_direction: Optional[str] = None,
+                 job_id: Optional[int] = None,
+                 job_memory_gb: float = 14.0,
+                 job_name: Optional[str] = None,
+                 job_num: Optional[int] = None,
+                 job_server_name: Optional[str] = None,
+                 job_status: Optional[List[Union[dict, str]]] = None,
+                 level: Optional['Level'] = None,
+                 max_job_time: Optional[float] = None,
+                 run_multi_species: bool = False,
+                 reactions: Optional[List['ARCReaction']] = None,
+                 rotor_index: Optional[int] = None,
+                 server: Optional[str] = None,
+                 server_nodes: Optional[list] = None,
+                 queue: Optional[str] = None,
+                 attempted_queues: Optional[List[str]] = None,
+                 species: Optional[List['ARCSpecies']] = None,
+                 testing: bool = False,
+                 times_rerun: int = 0,
+                 torsions: Optional[List[List[int]]] = None,
+                 tsg: Optional[int] = None,
+                 xyz: Optional[dict] = None,
+                 ):
+
+        self.job_adapter = 'ase'
+        self.execution_type = execution_type or 'incore'
+        self.incore_capacity = 100
+
+        self.sp = None
+        self.opt_xyz = None
+        self.freqs = None
+
+        self.args = args or dict()
+        self.python_executable = self.get_python_executable()
+        self.script_path = os.path.join(os.path.dirname(__file__), 'scripts', 'ase_script.py')
+
+        _initialize_adapter(obj=self,
+                            is_ts=False,
+                            project=project,
+                            project_directory=project_directory,
+                            job_type=job_type,
+                            args=args,
+                            bath_gas=bath_gas,
+                            checkfile=checkfile,
+                            conformer=conformer,
+                            constraints=constraints,
+                            cpu_cores=cpu_cores,
+                            dihedral_increment=dihedral_increment,
+                            dihedrals=dihedrals,
+                            directed_scan_type=directed_scan_type,
+                            ess_settings=ess_settings,
+                            ess_trsh_methods=ess_trsh_methods,
+                            fine=fine,
+                            initial_time=initial_time,
+                            irc_direction=irc_direction,
+                            job_id=job_id,
+                            job_memory_gb=job_memory_gb,
+                            job_name=job_name,
+                            job_num=job_num,
+                            job_server_name=job_server_name,
+                            job_status=job_status,
+                            level=level,
+                            max_job_time=max_job_time,
+                            run_multi_species=run_multi_species,
+                            reactions=reactions,
+                            rotor_index=rotor_index,
+                            server=server,
+                            server_nodes=server_nodes,
+                            queue=queue,
+                            attempted_queues=attempted_queues,
+                            species=species,
+                            testing=testing,
+                            times_rerun=times_rerun,
+                            torsions=torsions,
+                            tsg=tsg,
+                            xyz=xyz,
+                            )
+
+    def get_python_executable(self) -> str:
+        """
+        Identify the correct Python executable based on the calculator.
+        """
+        calc = self.args.get('keyword', {}).get('calculator', '').lower()
+        env_mapping = settings.get('ASE_CALCULATORS_ENV', DEFAULT_ASE_ENV)
+        env_var_name = env_mapping.get(calc)
+
+        if env_var_name and env_var_name in settings:
+            exe = settings[env_var_name]
+            if exe:
+                return exe
+
+        # Fallback to calculator-specific env if it exists
+        found_exe = find_executable(f'{calc}_env')
+        if found_exe:
+            return found_exe
+
+        return ARC_PYTHON or 'python'
+
+    def write_input_file(self) -> None:
+        """
+        Write the input file for ase_script.py.
+        """
+        input_dict = {
+            'job_type': self.job_type,
+            'xyz': self.xyz,
+            'charge': self.charge,
+            'multiplicity': self.multiplicity,
+            'constraints': self.constraints,
+            'settings': self.args.get('keyword', {}),
+        }
+        save_yaml_file(os.path.join(self.local_path, 'input.yml'), input_dict)
+
+    def execute_incore(self) -> None:
+        """
+        Execute the job incore.
+        """
+        self.write_input_file()
+        cmd = [self.python_executable, self.script_path, '--yml_path', self.local_path]
+        process = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
+        if process.returncode != 0:
+            logger.error(f"ASE job failed incore:\n{process.stderr}")
+        self.parse_results()
+
+    def execute_queue(self) -> None:
+        """
+        Execute a job to the server's queue.
+        """
+        self.write_input_file()
+        self.write_submit_script()
+        self.set_files()
+        if self.server_adapter is not None:
+            for file_dict in self.files_to_upload:
+                self.server_adapter.upload_file(remote_path=file_dict['remote'],
+                                               local_path=file_dict['local'])
+            self.server_adapter.submit_job(self.remote_path)
+
+    def set_files(self) -> None:
+        """
+        Set files to be uploaded and downloaded.
+        """
+        # 1. Upload
+        if self.execution_type != 'incore':
+            self.files_to_upload.append(self.get_file_property_dictionary(file_name='submit.sh'))
+            self.files_to_upload.append(self.get_file_property_dictionary(file_name='input.yml'))
+            self.files_to_upload.append(self.get_file_property_dictionary(file_name='ase_script.py',
+                                                                         local=self.script_path))
+        # 2. Download
+        self.files_to_download.append(self.get_file_property_dictionary(file_name='output.yml'))
+
+    def set_additional_file_paths(self) -> None:
+        """
+        Set additional file paths specific for the adapter.
+        """
+        pass
+
+    def set_input_file_memory(self) -> None:
+        """
+        Set the input_file_memory attribute.
+        """
+        pass
+
+    def write_submit_script(self) -> None:
+        """
+        Write the submission script.
+        """
+        remote_script_path = os.path.join(self.remote_path, 'ase_script.py')
+        command = f"{self.python_executable} {remote_script_path} --yml_path {self.remote_path}"
+        content = f"#!/bin/bash\n\n{command}\n"
+        with open(os.path.join(self.local_path, 'submit.sh'), 'w') as f:
+            f.write(content)
+
+    def parse_results(self) -> None:
+        """
+        Parse the output.yml generated by ase_script.py.
+        """
+        out_path = os.path.join(self.local_path, 'output.yml')
+        if os.path.isfile(out_path):
+            results = read_yaml_file(out_path)
+            self.electronic_energy = results.get('sp')
+            self.xyz_out = results.get('opt_xyz') or results.get('xyz')
+            self.frequencies = results.get('freqs')
+            self.hessian = results.get('hessian')
+            self.normal_modes = results.get('modes')
+            self.reduced_masses = results.get('reduced_masses')
+            self.force_constants = results.get('force_constants')
+            if 'error' in results:
+                logger.error(f"ASE job error: {results['error']}")
+
+register_job_adapter('ase', ASEAdapter)