PES Analysis

Analysis > PES Analysis shows the energy data of scans, NEB paths, energy refinements and other jobs that store energies with their trajectory: a 1D energy profile and, for two-dimensional scans, a 2D energy surface (Figure 1).

Data

• Coordinates: the object (trajectory) to analyze; only objects with energy data attached are listed.

• Dataset: the energy dataset (scan or profile) of that object.

2D surface tools (enabled with the checkbox)

• Color map, Threshold (kJ/mol) (energies above this value, relative to the minimum, get the same color), Smooth image and Show contours with the number of levels.

• RC label type: label the axes by frame number or by the reaction-coordinate value (Å). Colors... changes the background, axis and frame colors.

• Picking a path: left-click points on the surface to build a path; with Interpolate clicks the intermediate grid points are filled automatically. The 1D profile then shows the energy along the picked path.

Path and energy

• Energy: kJ/mol or kcal/mol. Profile x: point index or reaction coordinate.

• Lowest-barrier path: on a 2D surface, finds the path whose highest point is as low as possible (the route through the lowest saddle point), between the first and the last picked points, or between the two lowest minima when fewer than two points are picked.

• Mark minima and saddle points: circles on the local minima of the grid and diamonds on its saddle points.

• Clear path, Save table... (the points of the profile as CSV: i, j, RC1, RC2, energy, frame) and Export path (a new trajectory object containing only the picked points, for example to start a NEB or an umbrella sampling).

The status line below the profile gives the barrier (with the point of the maximum) and the reaction energy. The slider moves through the points of the profile and shows the corresponding structure in the 3D view. Export PNG saves each plot at high resolution; Side by side / Stacked arrange the two plots and Hide tools gives them the whole window.