CLI References.

November 4, 2024 ยท View on GitHub

This documentation briefly introduces SOMD's command line interface (CLI).

Table of Contents

  1. Execution modes of the somd command.
  2. Keywords of the run mode.
  3. Keywords of the select mode.

Execution modes of the somd command.

After installing the SOMD package, the command somd will be available. You could type somd -v to check the package version, and somd -h for the help messages.

In order to execute a SOMD operation through the CLI, you will need to specify the require execution mode and the corresponding keywords through command:

somd [mode] --keyword_1 --keyword_2 ...

The [mode] string has two valid options, which are run and select. The run mode reads reads a TOML file and does the dynamics, and the select model selects structures for the active learning task.

Keywords of the run mode.

This mode taks the following keywords.

  • -i/--input

    If Mandatory: yes

    Type: str

    Number of Required Parameters: 1

    Default Value: None

    Descriptions: Name of the input TOML file.

Keywords of the select mode.

This mode taks the following keywords.

  • -t/--trajectories

    If Mandatory: yes

    Type: List[str] (delimited by white spaces)

    Number of Required Parameters: more than 1

    Default Value: None

    Descriptions: Paths to the input HDF5 trajectories, with forces recorded.

  • -o/--output

    If Mandatory: yes

    Type: str

    Number of Required Parameters: 1

    Default Value: None

    Descriptions: Name of the output trajectory file.

  • --msd_f_min

    If Mandatory: no

    Type: float

    Number of Required Parameters: 1

    Default Value: 50.0

    Descriptions: The lower boundary of the force MSD used for identifying candidate structures. In unit of (kJ/mol/nm).

  • --msd_f_max

    If Mandatory: no

    Type: float

    Number of Required Parameters: 1

    Default Value: 250.0

    Descriptions: The upper boundary of the force MSD used for identifying candidate structures. In unit of (kJ/mol/nm).

  • --n_max

    If Mandatory: no

    Type: int

    Number of Required Parameters: 1

    Default Value: inf

    Descriptions: The max number of structures to select (default: inf).

  • --log_file

    If Mandatory: no

    Type: str

    Number of Required Parameters: 1

    Default Value: somd_selection.json

    Descriptions: The name of the log file that contains the selection information.

  • --shuffle

    If Mandatory: no

    Number of Required Parameters: 0

    Default Value: True

    Descriptions: If perform randomly selection if the number of candidate structures is larger than n_max.