Mixture

This is the topmost object in the hierarchy, and there will be only one of these objects for a simulation. It contains settings controlling details of the calculation, such as the units used. 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 and an optional Correlations object.

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:

None: no output
Default: Mainly for internal use, but as None
Minimal: Currently as None
CSV: Show line list in comma separated variable (.csv) format, suitable for import to spreadsheets or other programs.
Text: Show line list with the fields separated by tabs, suitable for import to spreadsheets or other programs.
Binary: Show line list in binary format, for quick import into other programs. See Binary Line List Format for how to do this.
Detail: Show symbolic matrix elements associated with each constant, where available.
LineList: As Detail, and show individual lines also
EigenVectors: As LineList, and show details of all calculated states, including eigenvector make up
Hamiltonian: As EigenVectors, and show all Hamiltonian matrices
Matrices: As Hamiltonian, and show (almost) all matrices, including transition matrices
All: All possible output; this setting 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.

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

Note that the definition of quantum numbers includes the rank and component of transition moments, so this setting is only recommended for use in input files for least squares fitting.

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.

AllowComplex

If set, calculations will be performed using complex wavefunctions if there are matrix elements that require it. Otherwise purely imaginary matrix elements are multiplied by -i to force them to be real. This often has no effect on the calculations, but there are circumstances where the calculation is wrong if the matrix elements are not allowed to be complex. Circumstances in which it is not significant include cases where the factor of -i is simply equivalent to a different phase choice for the basis states, or where the interaction involved is sufficiently small that second order perturbation theory gives a good result, as the energy shift essentially depends on the square modulus of the matrix element.

NoLineList

Disable the use of recorded line lists during simulations. This disables some features, such as the ability to right click on a line to identify it, but allows larger calculations to be performed. For example, the maximum J in a simple asymmetric top calculation is increased from about 200 to 500 with this setting.

ShowEstUnc

Show estimated uncertainties of line positions in the line list window and in line lists (use PrintLevel = LineList or Export a line list from the File menu).

ShowDerivatives

Show derivatives with respect to parameters in line lists.

SVDlimit

Number of contributions to show for each SVD vector; 0 for all.

Parameters

SVDThresh

In least squares fitting, discard singular value decomposition eigenvalues below this fraction of the largest eigenvalue. This stabilizes badly behaved fits, where little or no information is available about certain parameters, or combinations of them. The singular value decomposition is shown in the log window when some values are discarded.

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: None: no output Default: Mainly for internal use, but as None Minimal: Currently as None CSV: Show line list in comma separated variable (.csv) format, suitable for import to spreadsheets or other programs. Text: Show line list with the fields separated by tabs, suitable for import to spreadsheets or other programs. Binary: Show line list in binary format, for quick import into other programs. See Binary Line List Format for how to do this. Detail: Show symbolic matrix elements associated with each constant, where available. LineList: As Detail, and show individual lines also EigenVectors: As LineList, and show details of all calculated states, including eigenvector make up Hamiltonian: As EigenVectors, and show all Hamiltonian matrices Matrices: As Hamiltonian, and show (almost) all matrices, including transition matrices All: All possible output; this setting 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.
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 Note that the definition of quantum numbers includes the rank and component of transition moments, so this setting is only recommended for use in input files for least squares fitting.
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.
AllowComplex	If set, calculations will be performed using complex wavefunctions if there are matrix elements that require it. Otherwise purely imaginary matrix elements are multiplied by -i to force them to be real. This often has no effect on the calculations, but there are circumstances where the calculation is wrong if the matrix elements are not allowed to be complex. Circumstances in which it is not significant include cases where the factor of -i is simply equivalent to a different phase choice for the basis states, or where the interaction involved is sufficiently small that second order perturbation theory gives a good result, as the energy shift essentially depends on the square modulus of the matrix element.
NoLineList	Disable the use of recorded line lists during simulations. This disables some features, such as the ability to right click on a line to identify it, but allows larger calculations to be performed. For example, the maximum J in a simple asymmetric top calculation is increased from about 200 to 500 with this setting.
ShowEstUnc	Show estimated uncertainties of line positions in the line list window and in line lists (use PrintLevel = LineList or Export a line list from the File menu).
ShowDerivatives	Show derivatives with respect to parameters in line lists.
SVDlimit	Number of contributions to show for each SVD vector; 0 for all.

SVDThresh	In least squares fitting, discard singular value decomposition eigenvalues below this fraction of the largest eigenvalue. This stabilizes badly behaved fits, where little or no information is available about certain parameters, or combinations of them. The singular value decomposition is shown in the log window when some values are discarded.
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.