Adapter Engine Utility

Adapt LAMMPS logs/dumps into ReaxKit canonical domain data models.

This adapter resolves LAMMPS run files, parses dump/log content through shared handlers, and maps extracted arrays/tables into engine-agnostic models. It focuses on ingestion/export wiring rather than analysis logic.

Usage context

• Engine resolution: Registered under "lammps" for adapter detection.
• Data ingestion: Builds trajectory and simulation models from dump/log files.
• Export fallback: Writes canonical trajectories to XYZ files.

Class: LAMMPSAdapter

Bases: EngineAdapter

Adapter scaffold for LAMMPS trajectory formats.

Method: detect

Score whether a path likely refers to a LAMMPS run location.

Parameters:

Name	Type	Description	Default
path	str | Path	Candidate file or directory path.	required

Returns:

Type	Description
float	Detection score in [0.0, 1.0].

Examples:

score = LAMMPSAdapter().detect("dump.lammpstrj")

Method: required_input_files

Return likely LAMMPS input files for a requested target data type.

Parameters:

Name	Type	Description	Default
data_type	type	Requested canonical data-model class.	required
args	dict	Adapter runtime arguments (unused in this mapping).	required

Returns:

Type	Description
tuple[str, ...] | None	Candidate file names or None if unconstrained.

Examples:

files = adapter.required_input_files(TrajectoryData, {})

Method: load_trajectory

Load trajectory coordinates/types from a LAMMPS dump file.

Parameters:

Name	Type	Description	Default
args	dict	Adapter arguments used to resolve dump file location.	required
reporter	callable | None	Progress callback passed to dump handler.	None

Returns:

Type	Description
TrajectoryData	Canonical trajectory payload with positions, labels, and iterations.

Examples:

traj = LAMMPSAdapter().load_trajectory({"dump": "dump.lammpstrj"})

Method: load_simulation

Load simulation thermo series from log.lammps content.

Parameters:

Name	Type	Description	Default
args	dict	Adapter arguments used to resolve log and optional dump paths.	required
reporter	callable | None	Reserved for interface consistency (unused here).	None

Returns:

Type	Description
SimulationData	Canonical simulation-level thermo and scalar time-series payload.

Examples:

sim = LAMMPSAdapter().load_simulation({"log": "log.lammps"})

Method: load_connectivity

Load connectivity payload for LAMMPS runs.

Parameters:

Name	Type	Description	Default
args	dict	Adapter runtime arguments.	required
reporter	callable | None	Progress callback placeholder.	None

Returns:

Type	Description
ConnectivityData	Placeholder empty connectivity matrix for current scaffold behavior.

Examples:

conn = LAMMPSAdapter().load_connectivity({})

Method: load_connectivity_trajectory

Load connectivity and trajectory together as one composite object.

Parameters:

Name	Type	Description	Default
args	dict	Adapter arguments forwarded to component loaders.	required
reporter	callable | None	Progress callback forwarded to component loaders.	None

Returns:

Type	Description
ConnectivityTrajectoryData	Composite payload containing connectivity and trajectory models.

Examples:

combo = LAMMPSAdapter().load_connectivity_trajectory({"dump": "dump.xyz"})

Method: write_trajectory

Write trajectory data to multi-frame XYZ using shared generator.

Parameters:

Name	Type	Description	Default
data	TrajectoryData	Canonical trajectory payload to export.	required
out_path	str | Path	Destination XYZ file path.	required
args	dict | None	Optional settings; supports precision.	None

Returns:

Type	Description
Any	Return value from write_xyz_trajectory.

Examples:

adapter.write_trajectory(traj, "traj.xyz", {"precision": 8})