Vibrations

Use plot_vibs to inspect normal modes from FRUST frequency calculations. For transition states, the imaginary mode should match the intended reaction coordinate.

from frust.vis import plot_vibs

plot_vibs(df_ok, row_index=0, vId=0)

One imaginary frequency is not enough

A first-order saddle point should have one imaginary frequency, but the mode must also describe the intended bond formation, bond breaking, proton transfer, hydride transfer, or other reaction coordinate.

Multiple Rows

plot_vibs(
    df_ok,
    row_indices=[0, 1, 2, 3],
    viewergrid=(2, 2),
    linked=True,
)

Custom Coordinate Column

Use custom_coords_col_name when you want to inspect vibrations against a specific coordinate stage.

plot_vibs(
    df_ok,
    row_index=0,
    vId=0,
    custom_coords_col_name="UMA-OptTS-oc",
)

Export HTML

Use export_HTML to save an interactive viewer that can be embedded in the documentation or shared with collaborators.

Export an imaginary-mode viewer

plot_vibs(
    df_ok,
    row_index=0,
    vId=0,
    export_HTML="docs/assets/my-imaginary-mode.html",
)

Then embed it in a Markdown page:

<iframe
  src="../../assets/my-imaginary-mode.html"
  title="Imaginary-mode animation"
  width="100%"
  height="480"
  loading="lazy"
  style="border: 1px solid var(--md-default-fg-color--lightest); border-radius: 6px;"
></iframe>

Label comparison grids

When comparing rows, pass legends so each viewer cell is identified:

plot_vibs(
    df_ok,
    row_indices=[0, 1],
    legends=["lowest", "second-lowest"],
)