Objects

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:

• Species which contain one or more isotopomers or:
• Molecules These specify the settings such symmetry and statistical weight which are common to all the states within a molecule. There are four different types available, depending on the type of molecule: Linear, Symmetric Top, Asymmetric Top and Vibrating Molecules (for vibrational structure only). Molecules contain three types of object:
• Manifolds provide a way of grouping states together, allowing perturbations to be simulated. Manifolds contain two types of object:
• States which contain the band origin and rotational constants of a particular state. Again, these are specific to the type of molecule, with Linear, Symmetric Top, Asymmetric Top and Vibrating Molecule versions, depending on the Hamiltonian used. If nuclear hyperfine structure is to be simulated, then each state contains nNuclei:
• Nucleus which contains the hyperfine parameters for each nucleus for the parent state.
• Perturbation which describes an interaction or perturbation between two states. There is one of these for each perturbation parameter.
• Transition Moments which describe the spectroscopic transitions between or within manifolds. One of these objects is required for each pair of manifolds that have transitions between them. They contain one or more
• Transition Moment objects, which can be of various types, again depending on whether the molecule is a Linear Molecule, Symmetric Top, Asymmetric Top or Vibrating Molecule.
• Interpolated Partition Functions. This (optional) object can be used if the partition function is to be input externally, rather than automatically calculated.
• Simulation objects, which describe the experimental conditions. One of these will be generated automatically and relate to the main window, and additional simulation windows and the corresponding objects are created if additional plot windows are created from View, Another Plot.
• Polarization objects are optional, and only relevant if the effects of external static fields are to be simulated.
• Variables objects, which contain global parameters typically used to constrain fits.
• Table objects which contain tables of values for use in expressions.
  
• An optional Correlations object, which contains the correlation between parameters in the most recent least squares fit. It is automatically created and updated on every fit.

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, (corresponding to a .ovr file if saved) which can contain three types of plots: