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, with all other objects contained within it, and the name of the mixture will normally be the name of the file. The Mixture object contains one or more Species and Simulation objects. Note that many or the parameters were moved into the Simulation object in version 5.2.

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 and for selected intensity units; the units are otherwise not significant.

PrintLevel

Controls the amount of printout in the Log window. Possible values, in order of increasing amount of output are:

plNone: no output
plDefault: Mainly for internal use, but as plNone
plMinimal: Currently as plNone
plBasic: Show constants
plDetail: Show symbolic matrix elements associated with each constant, where available.
plLineList: Show lines
plEigenVectors: Show details of all calculated states, including eigenvector make up
plHamiltonian: Show all Hamiltonian matrices
plMatrices: Show (almost) all matrices, including transition matrices
plAll: All possible output; can force more output while fitting.

Precision

Precision of printout (decimal places after the point).

BasisOrder

How to order the basis states making up a basis. Valid values are: boDefault, boDiagonal and boStateDiagonal.

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).

QuantumNumberFormat

Controls how quantum numbers are read and displayed.Possible values are:

J: Values are displayed as integer or integer + 0.5, such as 2 and 3.5. On input, strings contain /2 are also accepted, such as 7/2 (=3.5)
2J: All quantum numbers are doubled, and always display and must be read as integers. This was the default for versions before 5.2
2J+1/2: The value displayed is the quantum number + 0.5, but otherwise as for J
2J-1/2: The value displayed is the quantum number - 0.5, but otherwise as for J

FitCycles

Number of least squares fit cycles to do on each press of a "fit" button.

FitDetails

      

If true, display more information following a fit, currently a singular value decomposition of the parameters.

AutoReplot

If false, automatic recalculation of the simulation is disabled in some circumstances. Use if the program is running slowly.

ContourFile

If set, read an observation file when contour fitting, typically to set constraints

AllowComplex

If set, calculations will be performed using complex wavefunctions if there are matrix elements that require it. Otherwise purely imaginary matrix elements are forced to be real.

Parameters

SVDThresh

In least squares fitting, discard singular value decomposition eigenvalues below this value

ScaleChanges

In least squares fitting, scale proposed changes in parameters by this; the default is 1, but smaller values may help fits with convergence problems.

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 and for selected intensity units; the units are otherwise not significant.
PrintLevel	Controls the amount of printout in the Log window. Possible values, in order of increasing amount of output are: plNone: no output plDefault: Mainly for internal use, but as plNone plMinimal: Currently as plNone plBasic: Show constants plDetail: Show symbolic matrix elements associated with each constant, where available. plLineList: Show lines plEigenVectors: Show details of all calculated states, including eigenvector make up plHamiltonian: Show all Hamiltonian matrices plMatrices: Show (almost) all matrices, including transition matrices plAll: All possible output; can force more output while fitting.
Precision	Precision of printout (decimal places after the point).
BasisOrder	How to order the basis states making up a basis. Valid values are: boDefault, boDiagonal and boStateDiagonal.
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).
QuantumNumberFormat	Controls how quantum numbers are read and displayed.Possible values are: J: Values are displayed as integer or integer + 0.5, such as 2 and 3.5. On input, strings contain /2 are also accepted, such as 7/2 (=3.5) 2J: All quantum numbers are doubled, and always display and must be read as integers. This was the default for versions before 5.2 2J+1/2: The value displayed is the quantum number + 0.5, but otherwise as for J 2J-1/2: The value displayed is the quantum number - 0.5, but otherwise as for J
FitCycles	Number of least squares fit cycles to do on each press of a "fit" button.
FitDetails	If true, display more information following a fit, currently a singular value decomposition of the parameters.
AutoReplot	If false, automatic recalculation of the simulation is disabled in some circumstances. Use if the program is running slowly.
ContourFile	If set, read an observation file when contour fitting, typically to set constraints
AllowComplex	If set, calculations will be performed using complex wavefunctions if there are matrix elements that require it. Otherwise purely imaginary matrix elements are forced to be real.

SVDThresh	In least squares fitting, discard singular value decomposition eigenvalues below this value
ScaleChanges	In least squares fitting, scale proposed changes in parameters by this; the default is 1, but smaller values may help fits with convergence problems.