Working with Plots
You can click on the various points in the plot, and the corresponding structure will appear in the View window.
All plots can be manipulated for viewing in a variety of ways:
Zooming In on a Plot
The Plots Menu
This menu is found in all plot and spectra windows. This particular example comes from the plots window displayed for an IRC calculation. Currently, all available plots are visible.
This menu also offers options for Printing and Saving the plot, Saving a picture of the plot, and modifying the properties of the plot.
You can create additional plots of various properties for these job types. This is done by selecting the
menu item in the plot window. This results in the dialog seen below.
Creating An Additional Plot
In this example, we are adding a plot displaying the C-C bond distance for atoms 1 and 2 over the course of the geometry optimization. The dialog at the left displays the various items that may be plotted.
The items available for plotting vary by the job type. Once generated, the new plot appears below the standard ones in the plots window.
When data is read in for a multi-geometry plot, the values along the X-axis should form a single continuous ascending set. In some occasions, a user may include molecules from two or more different files within the same molecule group. This is sometimes useful for comparison purposes or to extend the output from a previous run. When this occurs, the X-axis values will no longer form a single continuous ascending set, resulting in a jagged appearance in the resulting plot. When this situation is detected, an informational message is displayed.
The
menu item may be used to correct such plots. When this feature is used, the words “(Modified)” are added to the title of the plot to remind the user that the data in the plot has been modified and so should be viewed with caution.The menu on the left appears when you right click within a plot or spectrum.
Right clicking in the plot or spectrum, including the gray section containing the title and axis labels, will bring up a context menu for that specific plot/spectrum. The options in the menu generally apply only to the current item. The context menu is illustrated above. The items have the following meanings:
The context menu for plots contains the
item. Data from plots of geometry optimizations, IRC calculations, and the like can be saved in the same way. Here is some example data from an IRC calculation:# Total Energy along IRC # X-Axis: Intrinsic Reaction Coordinate # Y-Axis: Total Energy (Hartree) # X Y -0.5999778220 -289.5812430000 -0.4999857200 -289.5768190000 -0.3999923250 -289.5728940000 ...