Spectra Plotting Parameters
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Dialog Box: Spectra Plotting Parameters [Settings menu]

This dialog sets parameters for the Spectra window.

Gaussian line widths. Gaussian half-widths of infrared and Raman modes in plotted spectrum (default 25 cm-1 for infrared and 10 cm-1 for Raman).

Minimum transmission, infrared. (Default 1.0). This only applies when the Infrared mode (below) is Resonance down. A value of 1.0 will give an absorbance spectrum. A small value (0.1 or less) will mimic an optically dense sample and will accentuate weak peaks and truncate strong ones. This value affects only the shape of the IR spectrum; the maximum absorption is still normalized to the same value (that is, decreasing this value won't cause the spectrum to disappear).

Atomic motion scaling factor. This factor affects the calculated atomic motions before intensities are calculated. This factor also appears in the Basic Parameters dialog; see that dialog for other factors which affect the magnitude of atomic motions.

Raman intensity factors. These are the coefficients for the isotropic or spherical (alpha) and anisotropic (beta) components of the polarizability tensor, as described in WDC Ch. 3, p. 47; they are only used in spatially averaged Raman spectra. Default values are 45.0 and 0.1, which have been found to give a reasonable approximation to silicate glass and powdered crystal spectra.

Maximum intensities. These are the full-scale intensities for the plots of infrared and Raman spectra, respectively. If they are set to zero (or left blank), the plots will be scaled so that the maximum intensity is full scale. Full scale will be half the window or page height if both infrared and Raman spectra are shown, and full height if only one is selected. Note that absolute intensities depends on the atomic-motion scaling parameter above as well as the method of normalization selected in the Basic Parameters dialog in the Settings menu.

Infrared mode. If resonance is down, the spectrum mimics the usual absorption spectrum and the Minimum transmission parameter applies. If resonance is up, as for FTIR, simple gaussian lineshapes are used.

Horizontal scale factor. This is used only if the plot must have a fixed scale in wavenumbers per inch. If this value is zero, the plot will be scaled horizontally to fill the window.

The Minimum and Maximum wavenumber are the starting and ending values shown in the plot. The necessary maximum value may be very different depending on the compound; especially whether or not hydrogen is present.

If the Print title and/or Print species boxes are checked the relevant information will be printed at the top of the plot.

The components shown in the calculated spectra, whether polarized components or average, and whether an individual species or all species, are selected in the Dialog Bar which resides on the upper edge of the Spectra window itself.

NRVS Parameters. See Spectra Window for details of NRVS spectra.

Read Observed. With this you can read digital or digitized spectral data for display in the Spectra Window.

The PED curves section sets the FCONs which contribute to each curve in the PED (potential energy distriibution) section of the Window (if selected with the PED checkbox in the Spectra Window). The numbers which are entered in each edit box are the FCON numbers from the listings of the force in the various dialogs of the Forces menu, or from the Force List called from the Control Window. There may be up to 20 FCONs in each curve - the numbers may be separated by spaces, commas or semicolons.

The contributions from each FCON in each mode are those which appear in the printed Output, in the part label "Bnd En/Gp" and the like. These contributions are summed up during calculation, so if there are any changes in this dialog, the Calculation must be repeated. The contributions from each mode are given a Gaussian shape with the specified linewidth and summed up at each frequency.

The colors of the curves can also be set, by entering the red, green and blue components as numbers from 0 to 255. The curves are plotted in reverse order (4-3-2-1).

As selected in the Mode combo box, the energy distribution curves can be shown either as raw fractions (just as in the printed output), or multiplied by the calculated intensities for any of the spectra, infrared, Raman or NRVS. The raw fractions curves are applicable to all modes (in species selected in the Species dialog in the Input menu), whether they have significant intensity or not. This type of curve may be ambiguous when modes are very close together. The specified Line width is used for the raw fractions mode, but for the infrared, Raman or NRVS the respective linewidths for these individual spectra are used.

Contributions to the energy (frequency) from interactions may be negative which in turn means that the coefficient for even a single mode may be more than one (the contributions are fractions which sum to one for each mode in the raw fraction option). Generally the baseline (zero) will be obvious from the part of the spectrum where there are no modes.