Objects  <Prev Next> 
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 of the parameters were moved into the Simulation object in version 5.2.
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:

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:

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).
This requires the standard deviations and correlation matrix
from a fit to be present in the file, typically from a
preceding fit. Note also that this can considerably slow
down the calculation. 
ShowDerivatives  Show derivatives with respect
to parameters in line lists. 
SVDlimit  Number of contributions to show for each SVD
vector; 0 for all. 
ShowSubBasis 
Include subbasis labels in quantum number
display. These are shown enclosed in {}. 
AllowZeroI 
Set to allow lines with zero calculated
intensity are permitted when fitting to intensities 
ScaledParameters 
Scale parameters when fitting using
derivatives. If this is False then SVDThresh
is likely to need adjustment. 
FixTransitionPhase 
Set for a more consistent phase definition for transition moments; see the discussion at the end of Transition Moments and Line Strengths for more details. 
OldHyperfineOrder  This controls the order of J and F values within a given basis, and is only likely to be useful for compatibility with older versions. The default order from version 10.0.502 has the quantum numbers in increasing order; set this True to force a decreasing order, which was the only possibility in earlier versions. In most cases this will make no difference, but the newer default can provide better quantum number assignments under some circumstances. For this to have any possibility of an effect hyperfine structure must be present, and BasisOrder must be boDefault. 
OldColourOrder  Set to use the older algorithm (before
10.1.160) for determining colours for transitions, where the
state/manifold ordering was determined by the order in the
constants window, rather than energy order. See Determining Colours and J
ranges. 
SVDThresh  In least squares fitting, discard singular values below
the given value. 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. The default (10^{6}) is chosen to
catch obvious errors, such as floating both upper and lower
state origins of a transition, but may need adjustment. If ScaledParameters is False then the cut off is SVDThresh times the largest singular value, and SVDThresh values around 10^{15} are more likely to be appropriate. (ScaledParameters was introduced in version 8.0.390, and previous versions did not do the parameter scaling, and the default for SVDThresh was 10^{15}.) A negative value here implies an alternative least squares method is used, specifically a QR factorisation using the LAPACK routine DGELS. 
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. 
SmallE 
Matrix elements smaller than this are
discarded. 
Robust  If not zero, adjust estimated errors using
σ_{i} = (σ_{i}^{2}+Robust*((Obs_{i}Calc_{i})/σ)^{2})^{½},
giving less weight to larger errors. σ is the root
mean square weighted error before adjusting the
weights. 