Mixture

This is the topmost object in the hierarchy, and there will be only one of these objects for a simulation. It contains the parameters and settings that are common to all molecules included in the simulation. The data files PGOPHER uses (.pgo) thus contain one mixture (and all contained objects) and the name of the mixture will normally be the name of the file.

Settings

Units Units for calculation of frequencies/energy - valid values are cm1 (cm-1), MHz, Kelvin and eV. The key change this makes is in calculating Boltzmann factors from temperature; the units are otherwise not significant.
IntensityUnits Units for intensity. Possible values are Arbitrary (fastest), Normalized (include partition function), Squared (square the calculated intensity), nm2MHzperMolecule (for absorption), cm2WavenumberperMolecule (for absorption) or HzperMolecule (for emission). For the last three, transition moments are assumed to be in Debye.
PrintLevel Controls the amount of printout in the Log window. Negative for no output, 0 for a line list, larger numbers for printouts of the Hamiltonian and transition matrices.
nDF Number of points (between Fmin and Fmax) to calculate the spectrum at. Note that if a peak width is less than 3*(Fmax-Fmin)./nDF, i.e. only a few points wide, then it is shown as a stick, rather than a peak.
WidthMult Multiple of linewidth to extend convolution over.
Precision Precision of printout (decimal places after the point).
LifeModel Model to use for state dependent lifetimes and linewidths. Valid values are lmNone, lmWidth, lmProduct, lmProductWidth, lmParent, lmParentWidth, lmGate, lmGateWidth.
BasisOrder How to order the basis states making up a basis. Valid values are: boDefault, boDiagonal and boStateDiagonal.
ShowSum Plot overall sum of individual spectra. This is toggled by the button.
ShowParts Plot individual spectra making up overall spectrum. The individual spectra are grouped by colour, so you will need to set colours to see something different to the sum. Colours can be set at the transition moment, state, molecule or species level. This is toggled by the button.
ShowFortrat Plot a Fortrat diagram, i.e. J against frequency, in the main window. This is toggled by the button.
UseUpper Set to use upper rather than lower state J and symmetry in the Fortrat diagram.
JAdjustSym If set, energy level plots and Fortrat diagrams will take account of the alternation in symmetry with J that is often found. For example in linear molecules an energy level will typically alternate between + and - parity with J (hence the e/f notation).
ShowSymmetry Show symmetry in fortrat plots.
ShowDeltaJ Show change in J in fortrat plots.
ScaleMarkSize Scale Mark Size with intensity in fortrat plots.
DoubleQnos If set (default) all quantum numbers are displayed as twice their actual values.
FitCycles Number of least squares fit cycles to do on each press of a "fit" button.
AutoReplot If false, automatic recalculation of the simulation is disabled in some circumstances. Use if the program is running slowly.
PlotUnits Units for the horizontal scale for spectrum plots. Possibilities are as for Units above (the calculation units) and also nmVac, nmAir, corresponding to nm in vacuum and air respectively.

Parameters

Several of these can be set from the toolbar in the main window.
Fmin Left edge of plot range in main window.
Fmax Right edge of plot range in main window.
Temperature Rotational temperature (Kelvin).
Gaussian Gaussian contribution to linewidth (full width half maximum). If both this and a Lorentzian width (below) is set the result is a convolution of the two, a Voigt profile.
Lorentzian Lorentzian contribution to linewidth (full width half maximum). This and the Gaussian width can also be set from the main window.
Foffset Frequency offset to simulation.
SMargin Relative Size of peak to ignore when convoluting for contour fitting.
OThreshold Ignore peaks smaller than this fraction of the maximum peak intensity.
RefWidth Reference width in linewidth (predissociation) calculations.
Tvib Vibrational Temperature (Kelvin); set to -1 (default) to use rotational temperature for all Boltzmann factors.
MinI Set the scaling of mark sizes in Fortrat plots.