Frequency Visualizer program overview

Frequency Visualizer reads Gaussian03 output files and displays the calculated infrared or Raman 
vibrational spectrum.  In addition, the molecule is displayed and can rotate or animate frequencies.

Spectra for multiple molecules can be shown on the plot at the same time.

There are three main regions of the user interface: the Menus, the Spectra Plot and the Molecule
Display Area.  Specific help for each area is given below.

Interacting with the Spectra Plot:
	The calculated spectrum for a molecule is displayed both as a series of vertical frequency 
	lines representing the computed frequencies, and as a spectrum calculated by placing a
	Lorentzian curve at each frequency with an peak area proportional to the intensity of the
	frequency.

	Right-clicking on a frequency line will animate that frequency in the molecule display.

	Left-clicking on a frequency line or the spectrum will allow the user to change the
	properties of that line.  If the color of the spectrum is changed, the frequency lines can
	all be made the same color by turning the frequency lines off and then on again using the
	Preferences menu item "Frequency Lines".

	Clicking on a plot axis brings up a dialog box that allows the user to change the properties
	and scale of the axis.

Interacting with the Molecule Display Area:
	The molecule can be rotated by dragging with the left mouse button through the Molecule 
	Display Area.

	The Molecule Display Area can be moved around the Spectra Plot by dragging it with the right
	mouse button.

	Animations can be stopped by clicking on the red stop sign in the Molecule Display Region.

	Only one molecule can be displayed at a time.  To display a different molecule, right click
	on the spectrum curve for that molecule.

	To animate a vibration, right click on any verticle frequency line.

Interacting with the Menu items:
	File Menu

		Open Gaussian Output
			Allows the user to choose a Gaussian output file to open

		Save XY Data
			Saves the X & Y data for a spectrum in a tab-delimited text file.

		Remove Spectrum
			Removes one of the spectra (spectrum and frequency lines) from the plot and 
			the molecule from the Molecule Display Area.

	Edit Menu

		Copy Plot
			Copies the Spectrum Plot and Molecule Display Area to the clipboard

		Add Text
			Choose this menu item and then click anywhere in the Spectrum Plot to add
			some text to the plot.  After adding the text, it can be moved by dragging
			it with the left mouse button, and deleted by right-clicking on it.

	Preferences Menu

		Bandwidth
			Change the bandwidth used in the Lorentzian curve calculation that converts
			calculated frequencies to a spectrum.

		Frequency Type
			Choose from IR or Raman frequencies

		Vibration Amplitude
			How far to displace the atoms when animating a frequency

		Vibration Speed
			How fast to displace the atoms when animating a frequency

		Molecule Size
			The size of the Molecule Display Area

		Frequency Lines
			Whether to display the vertical frequency lines or not.  If the color of a 
			spectrum line is changed, the frequency lines can be set to the same color 
			by turning this option on and off again.