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To represent molecules and states making up the simulation, PGOPHER makes use of a hierarchy of objects. This works rather like a nested directory structure containing files except that each level can only contain certain types of object. These are no particular limits to the number of objects at each level, so that arbitrary combinations of spectra can be constructed, and multiple interacting (perturbing) states can be simulated. To view or edit any of these objects, use the tree view in the Constants window (View, Constants). The topmost object is a

Mixture which contains settings controlling details of the calculation, such as the units used. The name of the mixture is normally the filename, as it corresponds to a single .pgo file. A mixture contains one or more: Duplicate names for objects under any given object should be avoided; they can be used when setting up the calculation in the first place, but some operations may fail if duplicates are allowed to persist.

Overlays and Experimental Data

Experimental data used to overlay simulated spectra are also described by a similar, if simpler hierarchy of objects. These are not saved in the .pgo file, but can be saved separately in a .ovr file if required. These can be individually inspected using the tree view in the Overlays window (Overlays, Properties). The topmost object is:

Overlays, (corresponding to a .ovr file if saved) which can contain three types of plots:
To manipulate these see the File Menu, the Overlays Menu or the Overlays window. Some operations can also be carried out by right clicking on the overlay on the plot window, depending on the format of the plot.