Command line interface

Command-line utility to generate an input for chemiscope — the interactive structure-property explorer. Parses an input file containing atomic structures using the ASE I/O module, and converts it into a JSON file that can be loaded in chemiscope. Frame and environment properties must be written in the same file containing atomic structures: we recommend the extended xyz format, which is flexible and simple. In all cases, this utility will simply write to the JSON file anything that is readable by ASE. 

chemiscope-input [-h] [-o OUTPUT] [--properties PROPERTIES]
                 [--only-atoms | --only-structures] [--cutoff CUTOFF] [--name NAME]
                 [--description DESCRIPTION] [--authors [AUTHORS ...]]
                 [--references [REFERENCES ...]] [--settings SETTINGS]
                 input

positional arguments

  • input - input file containing the structures and properties (default: None)

options

  • -h, --help - show this help message and exit

  • -o OUTPUT, --output OUTPUT - chemiscope output file in JSON format (default: None)

  • --properties PROPERTIES - comma-separated list of properties that should be extracted. defaults to all

  • --only-atoms - only use per-atom properties from the input file

  • --only-structures - only use per-structure properties from the input file (default)

  • --cutoff CUTOFF - spherical cutoff radius that should be visualized around environments (default: 3.5)

  • --name NAME - name of the dataset (default: )

  • --description DESCRIPTION - description of the dataset (default: )

  • --authors AUTHORS - list of dataset authors (default: [])

  • --references REFERENCES - list of references for the dataset (default: [])

  • --settings SETTINGS - visualization settings, as a JSON string, following the chemiscope format (default: )