\(\newcommand{\AA}{\text{Å}}\)

Command-line utilities

\(\mathrm{LModeA\text{-}}\vec{\mathbf{k}}\) installs four command-line programs. Each utility has a separate section below so that analysis, plotting, visualisation, and CNM post-processing options are easier to find.

• Main analysis CLI: lmodea-k
  • Required
  • Core options
  • Special coordinate options
  • Workflow toggles
  • Outputs
  • Help
  • References
• Plotting CLI: lmodea-k-plot
  • Usage
  • Shared options
  • Colouring schemes
  • Data read by each plot
  • Required datasets
  • Palette files
  • Examples
  • Configuration
• Visualisation CLI: lmodea-k-vis
  • Usage
  • Options
  • Required datasets
• CNM post-processing CLI: lmodea-k-cnm
  • Usage
  • Options
  • Output datasets
  • Examples

Quick reference

lmodea-k

Run the local-mode analysis and write lmodea.h5.

lmodea-k-plot

Plot selected results from lmodea.h5. The plotting command now opens the HDF5 file lazily and reads only the datasets and slices required by the requested plot and colouring scheme.

lmodea-k-vis

Convert stored vectors and frequencies into .phonon and/or .json visualisation files.

lmodea-k-cnm

Post-process existing CNM amplitudes and append de-overlapped CNM datasets.