Command-Line Interface (CLI)

In addition to its Python library, VacHopPy provides a powerful Command-Line Interface (CLI) to perform key tasks directly from your terminal. This allows you to run analyses quickly without writing custom scripts.

The general command structure is:

vachoppy <command> [options]

Available Commands

To see a list of all available commands and their brief descriptions, use the -h or --help option:

vachoppy -h

Here is a summary of the main commands available:

Command	Description
`trajectory`	Identify and visualize vacancy trajectories from a single trajectory file.
`analyze`	Extract hopping parameters from an ensemble of trajectories.
`vibration`	Extract atomic vibration frequency from a single trajectory.
`distance`	Trace change in cosine distance from a reference structure over time.
`fingerprint`	Calculate and plot the fingerprint for a single static structure.
`msd`	Calculate diffusivity from mean squared displacement (Einstein relation).
`convert`	Convert various MD trajectory formats to the standard HDF5 format.
`concat`	Concatenate two successive HDF5 trajectory files into a new one.
`cut`	Cut a portion of a HDF5 file and saves it as a new file.
`show`	Display a metadata summary of a HDF5 trajectory file.

Getting Help for a Specific Command

Each command has its own set of specific options and arguments. You can view the detailed help for any command by adding -h after the command name.

For example, to see all options for the trajectory command, run:

vachoppy trajectory -h