mdse.cli.cli

Functions for parsing MDSE configuration files.

Functions

calc_isobaric_specific_heat(args)

calc_lindemann(args)

calc_msd(args)

calc_self_diff(args)

main()

Entry point for the MDSE CLI.

remove_all_traj(args)

Remove all .traj files from a specified directory.

simulate(args)

Run molecular dynamics simulations defined in a YAML configuration.

view_crystal(args)

Open one or more crystal structure files in the ASE GUI.
mdse.cli.cli.calc_isobaric_specific_heat(args)
mdse.cli.cli.calc_lindemann(args)
mdse.cli.cli.calc_msd(args)
mdse.cli.cli.calc_self_diff(args)
mdse.cli.cli.main()

Entry point for the MDSE CLI.

Provides the following subcommands:

  • simulate: Run simulations defined in a YAML file.

    Usage: mdse simulate -f config.yml

  • view: Open structure files with the ASE GUI.

    Usage: mdse view -f file1.traj file2.traj

  • clean: Remove all .traj files in a directory.

    Usage: mdse clean -f ./results

Notes

The selected subcommand is dispatched to the corresponding function via argparse’s set_defaults(func=…).

mdse.cli.cli.remove_all_traj(args)

Remove all .traj files from a specified directory.

Parameters:

  • args (argparse.Namespace) –

    Command-line arguments. Should contain: - filepath (str or None): Directory path where .traj files

    will be removed. If None, defaults to the current directory.

    • recursive (bool): If True, also search subdirectories.

  • Effects (Side)

  • ------------

  • file. (Deletes files from disk and prints status messages for each)

mdse.cli.cli.simulate(args)

Run molecular dynamics simulations defined in a YAML configuration.

Parameters:

args (argparse.Namespace) – Command-line arguments. Should contain: - filepath (str): Path to a YAML file describing simulation parameters.

Notes

Parses the input YAML using main_read, creates a RunManager, and executes all simulations sequentially.

mdse.cli.cli.view_crystal(args)

Open one or more crystal structure files in the ASE GUI.

Parameters:

args (argparse.Namespace) –

Command-line arguments. Should contain: - filepath (list[str] or None): Paths to files to view.

If None, opens all .traj files in the current directory.

Notes

Uses the ase gui command under the hood.