Command line interface

List of recipes

The list of the available xdatbus CLI recipes can be displayed by running the xdatbus command:

Following is the list of available CLI commands:

Command	Description
`xdc_aggregate`	Aggregate XDATCAR files from an AIMD simulation
`xdc_unwrap`	Unwrap the coordinates in the XDATCAR file (to xyz)
`thermal_report`	Generate a thermal report from the OSZICAR files
`xml2xyz`	Convert the vasprun.xml files to extended xyz files

Not all the functionalities are available in the CLI. For the detailed tutorials of the application, please refer to the examples directory of the GitHub repository.

Combine trajectories

Copy the XDATCAR files in sequence, naming as XDATCAR01, XDATCAR02, XDATCAR10 … or XDATCAR1, XDATCAR2, XDATCAR10…; both formats will work. In the same directory, run the command xdc_aggregate or use xdc_aggregate -h for help. The script will first wrap the coordinates within the cell and concatenate the trajectories using a naming sequence.

$ xdc_aggregate
 [13:45:19] sequence: ['XDATCAR0', 'XDATCAR1']
 [13:45:22] xdc_aggregate: wrapping XDATCAR0 | number of frames: 2000
 [13:45:25] xdc_aggregate: wrapping XDATCAR1 | number of frames: 2000
 [13:45:30] xdc_aggregate: initializing XDATBUS
 [13:45:36] xdc_aggregate: appending XDATCAR1

Unwrap trajectory

To unwrap the trajectory in the XDATCAR file, run the command xdc_unwrap or use xdc_unwrap -h for help.

$ xdc_unwrap
 [13:50:56] xdc_unwrap: Processing step 100
 [13:50:59] xdc_unwrap: Processing step 200
 [13:51:02] xdc_unwrap: Processing step 300
 [13:51:05] xdc_unwrap: Processing step 400
 [13:51:08] xdc_unwrap: Processing step 500

Check energies / temperatures

Copy the OSZICAR files in sequence, naming as OSZICAR01, OSZICAR02, OSZICAR10 … or OSZICAR1, OSZICAR2, OSZICAR10…; both formats will work. In the same directory, run the command thermal_report or use thermal_report -h for help. The script will export four-column .csv data with potential energy, kinetic energy, total energy, and temperature for each time step.

$ thermal_report
 [13:59:18] sequence: ['OSZICAR0', 'OSZICAR1']
            thermal_report: Processing OSZICAR0
            thermal_report: Processing OSZICAR1

Convert xml to xyz

To convert the vasprun.xml files to extended .xyz files, run the command xml2xyz or use xml2xyz -h for help.

$ xml2xyz --train_ratio 0.8
 [14:01:53] sequence: ['vasprun01', 'vasprun02']
            xml2xyz: processing vasprun01
 [14:01:54] xml2xyz: processing vasprun02