ADFmovie

The ADFmovie module of the GUI is used mainly to visualize molecular geometries, and graphs related to it. For exampe, follow the progress of a geometry optimization, the trajectory of an MD run, or visualize the Potential Energy Surface.

Additionally scalar atomic data (like names, charges, atomic temperature, etc) and vector atomic data (forces, gradients, velocities) may be visualized when available.

Geometries

When opening a results file, ADFmovie will show the current geometry of the system. If multiple geometries are available, there will be a slider and buttons that allow you to play a movie, and to move to a specific frame.

If the calculation is a PES (Linear Transit) calculation, there may be many unconverged geometries as well as converged geometries. In the View menu you can toggle if you want to see all geometries, or just the converged geometries.

Scalar Atomic Properties

If atomic properties are available for a geometry, you can show them using the View menu:

  • Atom Info: show the selected property as a text label
  • Color Atoms By: use the selected property to color the atoms
  • Atom Radius From: use the selected property to scale the atoms

Properties may be things like Name, AtomType, Charge (actually many different kinds of charges), ...

Atomic Vectors

If atomic vectors are available for a geometry, you can show them using the View menu: use the Vectors command in the View menu to select which vectors to show.

Examples of atomic vectors: gradient, force, velocity

When doing a geometry optimization via AMS, or an MD calculation via AMS or ReaxFF these may be present.

With the Scale Vectors menu command in the View menu you can make the vectors bigger or smaller (often needed to see very small vectors at all).

Graphs

ADFmovie can also make graphs of many properties (like energy, temperature, selected distances, angles etc) that change with the geometry. Check the tutorials for many examples.

Note that you can have multiple curves in one graph, and you can have multiple graphs.

You can save the graph in many different formats, and you can export the graph data.

Trajectory Analysis

ADFmovie also provides an interface to some tools to analyze MD trajectories, apart from the graphs.

  • Histograms
  • Radial Distribution Function
  • Molecule Fractions: make graphs of specific molecules detected
  • ChemTraYzer: use the Reaction Event Detection command in the Properties menu to analyze reactions happening