Simulation

There is one of these objects for each simulation. The first one is for the main window, with others for each plot window. The settings can all be adjusted from the Constants window, and some can also be adjusted from menus in the main window and text boxes in the main window and plot windows.

Settings

IntensityUnits

Units for intensity. These are described in detail under Intensity Formulae. Possible values are:

Arbitrary - fastest, as it does not include the partition function, but can give misleading results (see below).
Normalized - default, and recommended for most cases unless absolute intensities are required.
Squared - square the calculated intensity
HonlLondon - The line strength factors, essentially the transition dipole moment summed over all the degenerate M levels and squared. The value displayed is actually 3S_pol, which is correct for one photon transitions, but see the discussion under Line Strengths for possible caveats for other types of transition.
OscillatorStrength - The oscillator strength calculated from the line strength divided by the lower state degeneracy.
EinsteinASum - The Einstein A coefficient for each transition summed over upper and lower state M levels, with population factors excluded. This was EinsteinASum up to version 6.0.228.
EinsteinA - The Einstein A coefficient for each transition summed over lower state M levels, with population factors excluded. This corresponds to the radiative rate from the upper state.
nm2MHzperMolecule - for normal absorption
cm2WavenumberperMolecule - for normal absorption
HzperMolecule - for emission. This is the rate of emission of photons by one molecule on each transition, including the Boltzmann factor and partition function. See also Emission Spectra for a discussion of fluorescence.
WperMolecule - as HzperMolecule, but scaled by hν to give power rather than photons/second.
PopDist - Plots an energy diagram, rather than a spectrum, with intensities just the level population. This is intended for modeling a time of flight spectrum or similar experiment where energy levels are observed directly, rather than transitions.
NormPopDist - as for PopDist, but include partition function.

For the five with units (EinsteinA, nm2MHzperMolecule, nm2MHzperMolecule, HzperMolecule and WperMolecule) and OscillatorStrength, transition moments are assumed to be in Debye for electric dipole transitions and Bohr or nuclear magnetons for magnetic dipole transitions.

Misleading results can be obtained for a setting of Arbitrary when simulating isotopologues or isotopomers with different symmetry or statistical weights together, such as ³⁵Cl₂ and ³⁵Cl³⁷Cl. The calculation is "correct", in that the partition function is necessary to give the correct relative intensities, but is excluded by design for this setting.

LifeModel

Model to use for state dependent lifetimes and linewidths. Valid values are lmNone, lmWidth, lmProduct, lmProductWidth, lmParent, lmParentWidth, lmGate, lmGateWidth. See Widths and Lifetime Effects for how this setting works.

PlotUnits

Units for the horizontal scale for spectrum plots. Possibilities are standard energy units (cm1, MHz, Kelvin and eV) as in the Mixture object and also:

sqrtcm1 - Velocity in units of cm^-1/2
nmVac - Wavelength in vacuum in nm
nmAir - Wavelength in air in nm
angVac - Wavelength in vacuum in Å
angAir - Wavelength in air in Å

The correction between air and vacuum wavelengths is made using the formula for the dispersion of air given in B Edlen, Metrologica, 2, 71 (1966).

Fluorescence

Set to always discard lower state population; see Emission Spectra for further discussion of this flag.

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 line width to extend convolution over.

AutoMin

If set (the default), Ymin is automatically updated to minimum point in plot range

AutoMax

If set (the default), Ymax is automatically updated to maximum point in plot range

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.

ShowSymmetry

Show symmetry in Fortrat plots.

ShowDeltaJ

Show change in J in Fortrat plots.

ScaleMarkSize

Scale Mark Size with intensity in Fortrat plots.

UseSymmetry

If true, show different symmetries in separate Fortrat plots.

UseStateNumber

If true, show different state numbers in separate Fortrat plots.

FortratQno

Select quantum number to use in Fortrat plots.

PreserveArea

If set, then changing the PlotUnits changes the vertical scale, giving a constant area to peaks. This implies the units of the vertical scale depend on the horizontal scale. For example, if units of cm2WavenumberperMolecule are selected for IntensityUnits and the PlotUnits are MHz the vertical scale units are actually cm²wavenumber/molecule/MHz to give integrated peak areas (calculated from the numerical values plotted) of cm²wavenumber/molecule independent of the PlotUnits. Versions of PGOPHER before 10.1 did this by default.
The default in newer versions is to not set this parameter, and thus always plot the same quantity for intensity. Changing the PlotUnits thus does not change the vertical scale, which is less confusing when comparing to experimental spectra or doing contour fits.

SeparateScales

When showing multiple plots, scale plots separately, rather than requiring the same scale factor for each.

LogScale

Take ln of vertical axis on plots. (Initial implementation.)

Show2DPlot

(Future Use)

Auto2DY

(Future Use)

Parameters

Fmin

Left edge of plot range in main window.

Fmax

Right edge of plot range in main window.

Ymin

          

Lower end of current plot range; overwritten with lowest value in current range if AutoMin set

Ymax

Upper end of current plot range; overwritten with lowest value in current range if AutoMin set

Temperature

Rotational temperature (Kelvin). Setting this < 0 will force the use of numerical populations for all manifolds, as described in Non-Boltzmann Populations.

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. Note that this is in PlotUnits, and is taken to be constant over the plot range, which may be a concern if the plot range is large, as a width that is constant in wavelength will not be constant in frequency.

Lorentzian

Lorentzian contribution to linewidth (full width half maximum). This and the Gaussian width can also be set from the main window. Note that this is in PlotUnits, and is taken to be constant over the plot range, which may be a concern if the plot range is large, as a width that is constant in wavelength will not be constant in frequency.

Foffset

Frequency offset to simulation.

SMargin

This setting controls the number of extra points to calculate at each end of the spectrum. (These points are not plotted, but may be required to avoid artefacts in the convoluted spectrum):
If > 0: Number of extra points to calculate at each end
If < 0: Number of points is |SMargin|*WidthMult*(Gaussian+Lorentzian)

OThreshold

Ignore peaks smaller than this fraction of the maximum peak intensity in selected simulations. In line listings, lines with an intensity less than this are excluded from the printout; in this case the value is absolute, rather than a fraction of the strongest. Note that line lists produced by File, Export, Line List use a separate value that is a fraction of the maximum intensity.

RefWidth

Reference width in linewidth (predissociation) calculations; see LifeModel

Tvib

Vibrational Temperature (Kelvin); set to -1 (default) to use rotational temperature for all Boltzmann factors.

MinI

Discard lines weaker then this fraction of the strongest in Fortrat plots. Note that the default for this increased from 0 to 0.01 in 10.0.31.

Saturation

Zero for normal calculation; positive values progressively switch strength to population only by replacing the line strength, S by:

S = (1-exp(-S*Saturation/g))*g

where g = Min(2J'+1, 2J"+1)*Statistical Weight. This is appropriate for saturation by z polarized light. Values of, say, 1 to 10 will wash out the differences between allowed branches and much higher values will bring out transitions that are only allowed by some weak mixing.

Tspin

Spin temperature (Kelvin); set to -1 (default) to assume equilibrated nuclear spin states. If set >=0 then the fraction of molecules with each particular nuclear spin species (ortho/para for diatomics) is fixed at the fractions found at T = Tspin. This is often appropriate for molecular beams, where the nuclear spin states do not relax during the expansion. There are two limitations in the current implementation, which may lead to incorrect results:

If hyperfine structure is included for equivalent nuclei
For asymmetric tops if the statistical weight for two different spin species is the same

IScale

Scale all simulated intensities by this value. (The default is 1.)

EField

Static electric field, V/m; see External Fields - The Zeeman and Stark Effects

BField

Static magnetic field in Tesla (= 10⁴ Gauss); see External Fields - The Zeeman and Stark Effects

Doppler

Plot each transition as two peaks, split by 2*Doppler*Centre Frequency. This gives the double peak structure often seen in Fourier transform microwave spectroscopy.

PlotSplit

Fraction of plot area to use for the simulation where simulation and overlay plots are separated. The possible range is -1..1, with 0.5 the default. Negative values put the simulation, rather than the overlay, at the top.

Ymin2D

(Future Use)

Ymax2D

(Future Use)

Operations

Right click on the item in the constants window for the following operations in addition to the standard ones:

Temperature Table

Print a table in the log window of the intensity at the central frequency/wavelength of the simulation. You are prompted for the temperature step size, and the values tabulated will be from 0 to the temperature of the simulation.

IntensityUnits	Units for intensity. These are described in detail under Intensity Formulae. Possible values are: Arbitrary - fastest, as it does not include the partition function, but can give misleading results (see below). Normalized - default, and recommended for most cases unless absolute intensities are required. Squared - square the calculated intensity HonlLondon - The line strength factors, essentially the transition dipole moment summed over all the degenerate M levels and squared. The value displayed is actually 3S_pol, which is correct for one photon transitions, but see the discussion under Line Strengths for possible caveats for other types of transition. `OscillatorStrength` - The oscillator strength calculated from the line strength divided by the lower state degeneracy. EinsteinASum - The Einstein A coefficient for each transition summed over upper and lower state M levels, with population factors excluded. This was EinsteinASum up to version 6.0.228. EinsteinA - The Einstein A coefficient for each transition summed over lower state M levels, with population factors excluded. This corresponds to the radiative rate from the upper state. nm2MHzperMolecule - for normal absorption cm2WavenumberperMolecule - for normal absorption HzperMolecule - for emission. This is the rate of emission of photons by one molecule on each transition, including the Boltzmann factor and partition function. See also Emission Spectra for a discussion of fluorescence. `WperMolecule` - as HzperMolecule, but scaled by hν to give power rather than photons/second. PopDist - Plots an energy diagram, rather than a spectrum, with intensities just the level population. This is intended for modeling a time of flight spectrum or similar experiment where energy levels are observed directly, rather than transitions. NormPopDist - as for PopDist, but include partition function. For the five with units (EinsteinA, nm2MHzperMolecule, nm2MHzperMolecule, HzperMolecule and `WperMolecule`) and `OscillatorStrength`, transition moments are assumed to be in Debye for electric dipole transitions and Bohr or nuclear magnetons for magnetic dipole transitions. Misleading results can be obtained for a setting of Arbitrary when simulating isotopologues or isotopomers with different symmetry or statistical weights together, such as ³⁵Cl₂ and ³⁵Cl³⁷Cl. The calculation is "correct", in that the partition function is necessary to give the correct relative intensities, but is excluded by design for this setting.
LifeModel	Model to use for state dependent lifetimes and linewidths. Valid values are lmNone, lmWidth, lmProduct, lmProductWidth, lmParent, lmParentWidth, lmGate, lmGateWidth. See Widths and Lifetime Effects for how this setting works.
PlotUnits	Units for the horizontal scale for spectrum plots. Possibilities are standard energy units (`cm1`, `MHz`, `Kelvin` and `eV`) as in the Mixture object and also: sqrtcm1 - Velocity in units of cm^-1/2 nmVac - Wavelength in vacuum in nm nmAir - Wavelength in air in nm angVac - Wavelength in vacuum in Å angAir - Wavelength in air in Å The correction between air and vacuum wavelengths is made using the formula for the dispersion of air given in B Edlen, Metrologica, 2, 71 (1966).
Fluorescence	Set to always discard lower state population; see Emission Spectra for further discussion of this flag.
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 line width to extend convolution over.
`AutoMin`	If set (the default), Ymin is automatically updated to minimum point in plot range
`AutoMax`	If set (the default), Ymax is automatically updated to maximum point in plot range
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.
ShowSymmetry	Show symmetry in Fortrat plots.
ShowDeltaJ	Show change in J in Fortrat plots.
ScaleMarkSize	Scale Mark Size with intensity in Fortrat plots.
UseSymmetry	If true, show different symmetries in separate Fortrat plots.
UseStateNumber	If true, show different state numbers in separate Fortrat plots.
FortratQno	Select quantum number to use in Fortrat plots.
`PreserveArea`	If set, then changing the `PlotUnits` changes the vertical scale, giving a constant area to peaks. This implies the units of the vertical scale depend on the horizontal scale. For example, if units of cm2WavenumberperMolecule are selected for `IntensityUnits` and the `PlotUnits` are MHz the vertical scale units are actually cm²wavenumber/molecule/MHz to give integrated peak areas (calculated from the numerical values plotted) of cm²wavenumber/molecule independent of the `PlotUnits`. Versions of PGOPHER before 10.1 did this by default. The default in newer versions is to not set this parameter, and thus always plot the same quantity for intensity. Changing the `PlotUnits` thus does not change the vertical scale, which is less confusing when comparing to experimental spectra or doing contour fits.
`SeparateScales`	When showing multiple plots, scale plots separately, rather than requiring the same scale factor for each.
`LogScale`	Take ln of vertical axis on plots. (Initial implementation.)
`Show2DPlot`	(Future Use)
`Auto2DY`	(Future Use)

Fmin	Left edge of plot range in main window.
Fmax	Right edge of plot range in main window.
Ymin	Lower end of current plot range; overwritten with lowest value in current range if AutoMin set
Ymax	Upper end of current plot range; overwritten with lowest value in current range if AutoMin set
Temperature	Rotational temperature (Kelvin). Setting this < 0 will force the use of numerical populations for all manifolds, as described in Non-Boltzmann Populations.
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. Note that this is in `PlotUnits`, and is taken to be constant over the plot range, which may be a concern if the plot range is large, as a width that is constant in wavelength will not be constant in frequency.
Lorentzian	Lorentzian contribution to linewidth (full width half maximum). This and the Gaussian width can also be set from the main window. Note that this is in `PlotUnits`, and is taken to be constant over the plot range, which may be a concern if the plot range is large, as a width that is constant in wavelength will not be constant in frequency.
Foffset	Frequency offset to simulation.
SMargin	This setting controls the number of extra points to calculate at each end of the spectrum. (These points are not plotted, but may be required to avoid artefacts in the convoluted spectrum): If > 0: Number of extra points to calculate at each end If < 0: Number of points is \|`SMargin`\|`WidthMult`(`Gaussian`+`Lorentzian`)
OThreshold	Ignore peaks smaller than this fraction of the maximum peak intensity in selected simulations. In line listings, lines with an intensity less than this are excluded from the printout; in this case the value is absolute, rather than a fraction of the strongest. Note that line lists produced by File, Export, Line List use a separate value that is a fraction of the maximum intensity.
RefWidth	Reference width in linewidth (predissociation) calculations; see LifeModel
Tvib	Vibrational Temperature (Kelvin); set to -1 (default) to use rotational temperature for all Boltzmann factors.
MinI	Discard lines weaker then this fraction of the strongest in Fortrat plots. Note that the default for this increased from 0 to 0.01 in 10.0.31.
Saturation	Zero for normal calculation; positive values progressively switch strength to population only by replacing the line strength, S by: S = (1-exp(-SSaturation/g))g where g = Min(2J'+1, 2J"+1)*Statistical Weight. This is appropriate for saturation by z polarized light. Values of, say, 1 to 10 will wash out the differences between allowed branches and much higher values will bring out transitions that are only allowed by some weak mixing.
Tspin	Spin temperature (Kelvin); set to -1 (default) to assume equilibrated nuclear spin states. If set >=0 then the fraction of molecules with each particular nuclear spin species (ortho/para for diatomics) is fixed at the fractions found at T = Tspin. This is often appropriate for molecular beams, where the nuclear spin states do not relax during the expansion. There are two limitations in the current implementation, which may lead to incorrect results: If hyperfine structure is included for equivalent nuclei For asymmetric tops if the statistical weight for two different spin species is the same
`IScale`	Scale all simulated intensities by this value. (The default is 1.)
EField	Static electric field, V/m; see External Fields - The Zeeman and Stark Effects
BField	Static magnetic field in Tesla (= 10⁴ Gauss); see External Fields - The Zeeman and Stark Effects
Doppler	Plot each transition as two peaks, split by 2DopplerCentre Frequency. This gives the double peak structure often seen in Fourier transform microwave spectroscopy.
`PlotSplit`	Fraction of plot area to use for the simulation where simulation and overlay plots are separated. The possible range is -1..1, with 0.5 the default. Negative values put the simulation, rather than the overlay, at the top.
`Ymin2D`	(Future Use)
`Ymax2D`	(Future Use)