Command Line Interface

WeasWidget provides a command-line interface (CLI) for visualizing atomic structures, molecules, trajectories, and volumetric data using WEAS.

Usage

Run weas <filename> to visualize structures:

weas <filename> [OPTIONS]

Examples

  1. Visualizing a crystal structure (CIF file):

    weas Li2Mn3NiO8.cif

  2. Visualizing a molecular dynamics trajectory (XYZ file):

    weas deca_ala_md.xyz

  3. Phonon mode visualization:

    weas graphene.cif --phonon --eigenvectors '[ [[-0.31, 0.47], [-0.16, -0.38], [0, 0]], [[0.54, -0.15], [-0.31, -0.27], [0, 0]] ]'

  4. Loading a saved WEAS state:

    weas weas-state.json

Options

  • –style <int> : Model style (0 = ball, 1 = ball+stick, 2 = polyhedra).

  • –color-type <str> : Atom color scheme (CPK, VESTA).

  • –boundary <str> : Periodic boundary conditions (JSON format).

  • –phonon : Enable phonon visualization.

  • –eigenvectors <json> : Phonon eigenvectors in JSON format.

  • –kpoint <json> : K-point for phonon mode.

  • –amplitude <float> : Phonon amplitude (default: 2).

  • –nframes <int> : Number of animation frames (default: 50).

Note

When the input file is a WEAS state snapshot (.json), the viewer loads the saved state directly and ignores –style, –color-type, and –boundary unless explicitly overridden in the snapshot itself.

Running on a Remote Computer

If you are running weas on a remote server, you can access the visualization locally using SSH port forwarding.

  1. Start the visualization on the remote machine:

    weas structure.cif --use-server

    The command will print a message like:

    Serving at http://localhost:8000
Open this URL in your browser to access the visualization.

  2. Forward the port to your local machine:

    On your local machine, run:

    ssh -L 8000:localhost:8000 your_remote_user@your_remote_host

    Then, open http://localhost:8000 in your browser.

Note

If you are using Visual Studio Code with Remote SSH, port forwarding is handled automatically. When you start the server with –use-server, VS Code will detect the port and provide a clickable link in the terminal.