GaussView Basics

The main GaussView interface consists of several windows, in addition to other dialogs which appear in the course of working. Figure 1 illustrates a simple session in which the user has just started to build a molecule.

Figure 1. GaussView on the Desktop
Several GaussView features are visible here: beginning at the upper left and moving clockwise, we see the main GaussView control panel, containing the menu bar, a variety toolbars, and the Current Fragment window. Next, we see the palettes used to select functional groups and individual atoms for addition to a molecule (note that these can function in a modal or amodal mode, according to user preference). Finally, we see the active view window containing the molecule being built.

The GaussView interface consists of these main components:

• The control panel containing the menu bar and Current Fragment display.
• Various toolbars. By default, these are placed below the menu bar in the control panel, but they may also be detached if desired (see Figure 3). They may also be rearranged within the control panel as desired (so your window may differ from the illustration in Figure 1).
• One or more molecule view windows.
• Dialogs corresponding to the various GaussView features.
• Preferences which control various aspects of the program’s functioning.

The toolbars that appear by default under the menu bar in the GaussView control panel are illustrated individually in Figure 2. The Builder toolbar can also appear as it does in the illustration on the right, when selected with View=>Builder. You can detach an individual  toolbar from the main toolbar by  grabbing the handle and dragging it out of the toolbar area. To reattach a standalone toolbar, either drag it back into main toolbar or double click it.

Figure 2. Toolbar Context Menu

If you right click in the grey area within any toolbar, you will bring up the Toolbar context menu.  The first section of the list are the names of the toolbars that are available in that window. Selecting one of the toolbar names from the list will toggle it between its visible and hidden states. The Line Up option cause the toolbars to move to eliminate empty space between them, and the Default option restores the default configuration for that toolbar (when applicable).

    
Figure 3. GaussView Toolbars in Standalone Mode
The Builder palette on the right is revealed with the View=>Builder menu path.

Molecules, Molecule Groups and Views

GaussView uses these constructs to organize the many molecules which may be being worked with at any given time:

• A molecule is most often a single molecule being worked on in isolation from other ones that may also be open. A molecule generally corresponds to a single file stored on disk. These are also sometimes referred to as models. Note that a molecule in this sense may contain more than one chemical species (i.e., “molecules” in the usual chemical sense).
• If there is more than one window open for the same molecule, the various different ones are referred to as views. Thus, a view window displays a molecule, and different views can show different orientations of and properties of the same molecule.
• A molecule group is a collection of one or more molecules that are worked on as unit. Molecule groups containing more than one molecule display each one in a separate subwindow of a combination view window (see Figure 4). Molecule groups are also referred to as model groups.

For molecule groups containing more than one molecule, there are two display modes. Single view mode displays a single molecule at a time. The current molecule number appears in the toolbar.

Clicking the single/multiview icon brings up multiview mode in which several molecules can be viewed at one time.  The molecules are laid out side-by-side like frames in a film strip. The molecule number is shown just below the individual molecule frame. The currently active molecule is shown with a slightly lighter background to distinguish it from the other molecules and is the one involved in atom selections or in the dialogs. Clicking on one of the individual molecule windows that is not the active molecule window will cause it to become the active molecule. In the event that not all of the individual molecules can fit in the view window, a scroll bar will at the bottom of the view window allows one to move between the different the different molecules.

If the view window is expanded in the horizontal direction, more and more of the molecules will be shown until all of them are visible.  After all of the molecules are visible, if the user continues to expand the window in the horizontal direction then empty space will be shown. If the view window is expanded in the vertical direction, then each individual molecule window is expanded in the vertical direction to match the window and correspondingly expanded in the horizontal direction. Thus, the vertical direction can be used to control the relative sizes of the individuals molecules.

Figure 4. A Molecule Group Containing 20 Molecules
The controls in the toolbar appear only when there is >1 molecule in a molecule group. The single/multiple view icon toggles between single window (left) and multi-window view (right).

The title bar of each view window displays information about the current molecule group, molecule and view:  each distinct molecule group is identified by an icon whose color is uniquely associated with it.  Figure 5 shows the color icons from three different view windows (each corresponding to a different molecule group).  All dialogs that are directly associated with that molecule group will use the same color icon to visually associate themselves with their parent molecule group (including new views created using View=>Add View).  This color icon is also used to identify the molecule group in the Windows menu.

Figure 5. Color Icons from 2 Different Views
The icon on the left corresponds to the 4th molecule in the 1st molecule group, while the one on the right is the 2nd view of the 1st molecule in the second molecule group. This same color icon will appear in all dialogs associated with that molecule. For some operating systems, the color icon is located in the status bar.

In addition to its color icon, each view window is uniquely identified by its group/molecule/view identifier.  This identifier consists of the molecule group (G), the molecule number (M), and the view number (V). Each of the molecules in a molecule group are numbered sequentially starting at 1. If a molecule in the group is deleted, the molecules are renumbered to maintain a continuous sequence.

Note that dialogs corresponding to molecule editing function are molecule-specific. If you activate a different view window with, say,  the Atom List Editor open, its context does not follow. Examine the header label of a dialog in order to determine the corresponding view window.

For molecule groups containing more than one molecule, a special toolbar will be present just below the header.  Clicking on the green run button will cause the view window to show each molecule in the group sequentially and continue to cycle through the full list until stopped.  This has the effect of visually animating the sequence of molecules like a movie. This can be particularly useful for animating a series of related geometries, such as a Reaction Path plot.  When the green run button is pressed, it turns into a red stop button, which will stop the animation.

The animation speed can controlled by the user. For an individual view window, the animation delay can be changed in the Display Format dialog’s Molecule tab. The default animation delay is set in the Display Format preferences.

Right clicking anywhere within a molecule window will bring up a context menu. The contents of the context menu duplicates much of the Builder, the menu bars, and the toolbars.  This is provided as a convenience for the user.

Figure 6. View Window Context Menu
Each of the options on the context menu brings up a submenu containing related items.

Using the Mouse

Interaction with molecules is designed around the movements of a three-button mouse. The functions of the mouse buttons are described in the following table:

Note that these mouse actions are active in any molecule display (including ones in GaussView dialogs).

Limiting Mouse Actions to One Fragment

If two items are not bonded to one another (not connected by visible chemical bonds on the screen), you can manipulate them individually on screen by holding down the Alt key and moving the cursor. When you use the Alt key, only the fragment closest to the cursor is affected.  Thus Alt-Shift allows you to drag only one fragment.

GaussView Menus

GaussView contains the following menus, which have the indicated general purposes:

• File: Creating, opening, printing and saving structures and movies, as well as setting GaussView preferences.
• Edit: Performing molecule building and configuration tasks.
• View: Managing and interacting with the display of molecules.
• Calculate: Setting up and submitting Gaussian calculations and viewing current GaussView-initiated jobs.
• Results: Examining calculation results, including surfaces, spectra, plots, and animations.
• Windows: Managing the various GaussView windows.
• Help: Viewing help files for GaussView and Gaussian, as well as GaussView tips.

Table of Icons and Menu Items

The following table lists the available icons and menu items along with their functions. Most items will be described in more detail in future sections of this book. Note that on Mac OS X systems, the Equivalent Key modifier is the Command key, not the Control key.

Icon and Button Name	Menu Path	Purpose	Equivalent Key
New	File=>New	Create a new molecule (per submenu selection).
	File=>New=>Create Mol. Group	Create a new (one-member) molecule group as an empty view window.	Ctrl-N
	File=>New=>Add to Mol. Group	Add a new molecule to the current molecule group.	Ctrl-Shift-N
Open	File=>Open	Open files supported by GaussView.	Ctrl-O
	File=>Recent Files	List of recently-opened files for easy reaccess.
	File=>Related Files	List of files related to the current molecule (e.g., input file, log file, checkpoint file, etc.).
	File=>Refresh	Reload current file in active view window.
Save	File=>Save	Save molecule(s) in the active molecule group to file(s).	Ctrl-S
	File=>Save Temp Files	Save any temporary files associated with Gaussian Quick Launch jobs.
Print	File=>Print	Print the contents of the active view window.	Ctrl-P
Save Image	File=>Save Image File	Produce a graphics file of current view window.
Save Movie	File=>Save Movie	Save movie file, movie frame files, or both.
Preferences	File=>Preferences	Specify defaults for aspects of GaussView’s behavior.
	File=>Exit	Close all Gaussview windows and exit application.
Undo	Edit=>Undo	Reverse the previous editing action and maintain a list of previous actions.	Ctrl-Z
Redo	Edit=>Redo	Reverse the previous Undo operation.	Ctrl-Y
Cut	Edit=>Cut	Cut the current selection to clipboard.	Ctrl-X
Copy	Edit=>Copy	Copy the current selection to clipboard.	Ctrl-C
Paste	Edit=>Paste	Copy clipboard contents to the current model(per submenu selection).
	Edit=>Paste=>Add to Molecule Group	Add the molecule on the clipboard as a new model within the current model group.
	Edit=>Paste=>Replace Molecule	Replace current molecule with clipboard contents.
	Edit=>Paste=>Append Molecule	Add molecule on the clipboard to the current model as a separate fragment.
Delete Molecule	Edit=>Delete Molecule	Remove the current selection.	Ctrl-Del
	Edit=>Image Capture	Copy the contents of the active view window to the clipboard.	Ctrl-I
Atom List Editor	Edit=>Atom List	Edit the molecule’s numerical coordinates/parameters.
Redundant Coord. Editor	Edit=>Redundant	Specify redundant internal coordinates for the Gaussian ModRedundant option.
Connection Editor	Edit=>Connection	Specify corresponding atoms in two related molecular structures (e.g., for QST2 or QST3 input).
Select Layer	Edit=>Select Layer	Assign atoms to layers graphically for ONIOM calculations.
	Edit=>Point Group	Specify/impose symmetry on the current model.
Crystal Editor	Edit=>PBC	Create and modify unit cells for periodic structures.
MO Editor	Edit=>MOs	View, reorder and modify occupancy for molecular orbitals.
Symmetrize	Edit=>Symmetrize	Apply point group symmetry to the current model.
	Edit=>Reorient	Restore canonical molecule orientation.
Rebond	Edit=>Rebond	Recompute the bound atoms, identifying bonded atoms based on a distance algorithm.
Clean	Edit=>Clean	Adjust molecular geometry according to a defined set of rules to more closely match chemical intuition.
	Edit=>Mirror Invert	Invert the molecule around the selected atom.
Add View	View=>Add View	adjustable view of the current molecule. Create a new view window, with an independently
Center	View=>Center	Center molecule in the view window (adjusts size).
	View=>Builder	Close or reopen the separate Builder palette.
	View=>Hydrogens	Control the display of hydrogens in view window.
	View=>Dummies	Control the display of dummy atoms in view window.
	View=>Labels	If selected, label each atom with its the sequence number in the list of atoms.
	View=>Symbols	If selected, display the chemical symbol for each atom in the view window.
	View=>Bonds	Controls the display of bonds in the view window.
	View=>Synchronize	Link views to synchronize mouse-based manipulations.
	View=>Cartesian Axes	Control the display of X,Y,Z axes in the view window.
	View=>Stereochemistry	Indicate molecule’s stereochemistry by labeling relevant atoms as R or S.
	View=>Positioning Tools	Display the positioning tools icons in the view window toolbar.
Display Format Editor	View=>Display Format...	Specify the display format for molecules and surfaces.	Ctrl-D
Calculation Setup	Calculate=>Gaussian Calculation Setup	Set up Gaussian input for the molecular structure in the current view window and optionally run the job.	Ctrl-G
Quick Launch	Calculate=>Gaussian Quick Launch	Run a Gaussian job for the curr. molecule, bypassing the setup dialog.
Scheme	Calculate=>Gaussian Calc. Scheme	Define and modify Gaussian calculation schemes.
Current Jobs	Calculate=>Current Jobs	Display currently running GaussView-initiated Gaussian jobs (including cubegen and freqchk).	Ctrl-J
	Results=>Summary	Provide summary data of the results of thecalculation after a results file is opened.
	Results=>Charge	Display partial charge density, as computed by various Gaussian methods.
	Results=>Surfaces/Contours	Create, load, save and display surfaces.
	Results=>Vibrations	Display calculated vibrational and other spectral data, including normal mode animation.
	Results=>NMR	Display calculated NMR spectra.
	Results=>UV-VIS	Display predicted UV/Visible spectra.
	Results=>Scan	Display plots of potential energy surface scans.
	Results=>IRC/Path	Display plots of predicted IRC paths.
	Results=>Trajectory	Display trajcectory plots from ADMP or BOMD calculations.
	Results=>Optimization	Display plots of geometry optimization results.
View File	Results=>View File	Start an editor session for the log file for the current molecule. Can also be used to view the Gaussian input file that was opened for the current molecule, provided that nothing has been modified.
Stream file	Results=>Stream File	Display output from a currently running Gaussian calculation as it becomes available.
	Windows=>Molecule Groups=>Show All	Display windows for all model groups.
	Windows=>Molecule Groups=>Show None	Hide windows for all model groups.
	Windows=>Molecule Groups=>Name	Display windows for the specified model group and make it the current view.
	Windows=>Minimize All	Minimize all view windows.
	Windows=>Restore	Raise active view window.
	Windows=>Restore All	Open all minimized view windows.
	Windows=>Close	Close the active view window.
	Windows=>Close All	Close all open view windows.
Previous	Windows=>Previous	Activate the previous view window in sequence.	PgUp
Next	Windows=>Next	Activate the next view window in sequence.	PgDown
Cascade	Windows=>Cascade	Arrange all view windows in an overlapped pile.
Tile	Windows=>Tile	Resize and rearrange view windows so that all are visible.
	Windows=>Name	Make the specified view window the active one.
Help	Help=>GaussView Help	Open the GaussView help file	Ctrl-H
	Help=>Gaussian Help	Access Gaussian help on the Internet.
	Help=>About GaussView	Display the GaussView copyright and version information.
	Help=>GaussViewTips	Display GaussView tips.
Elements		Open the elements palette.
Rings		Access a set of ring structures.
Functional Group		Summon a set of functional group fragments.
Biological Fragments		Summon amino acid and nucleoside fragments.
Custom Fragments		Access a custom fragment library.
Modify Bond		Access Bond Smartslide dialog after two atoms selected. Adjust bond type and/or interatomic distance.
Modify Angle		Access Angle Smartslide dialog after three atoms selected. Adjust bond angle.
Modify Dihedral		Access Dihedral  Smartslide dialog after four atoms selected. Adjust dihedral angle.
Inquire Mode		Examine structural data for the current molecule.
Add Valence		Add an additional hydrogen to the selected atom.
Delete Atom		Eliminate atoms and/or open valences (dangling half bonds).
Invert About Atom		Invert molecular structure about a selected atom.
Frag Placement		Open fragment placement options panels in control window.

Icons found in the Active Model View window:

Animate		Display all models within the molecule group in succession.
Stop Animation		Stop an animated display.
Single View		Display only one model within the molecule group.
Multi View		Display all models within the molecule group.

Icons found in the five Fragment Palette windows:

Tacked		Keep this palette open until explicitly closed (i.e., amodal operation).
Untacked		Close palette when a different one is opened (i.e., modal operation).

Icons related to various coordinate editing dialogs:

Z-matriz Coordinates		Display Z-matrix coordinates.
Cartesian Coordinates		Display Cartesian coordinates.
Fractional Coordinates		Display fractional coordinates for periodic systems.
ONIOM Layers		Display ONIOM layer assignments and related data.
MM Parameters		Display Molecular Mechanics atoms types and other data.
PDB info		Display residue and chain assignments from a PDB file.
Sort Ascending       Move Up		Atom List Editor: Sort items in ascending order.Redundant Coordinate Editor: Move item up in list.
Sort Descending        Move Down		Atom List Editor: Sort items in descending order. Redundant Coordinate Editor: Move item down in list.
Create New Coordinate		Add a new redundant coordinate in the Redundant Coordinate Editor.
Add Selected		Add the selected item to the list.
Add All		Add all items to the list.
Remove Selected		Remove the selected item from the list.
Remove All		Remove all items from the list.

Miscellaneous icon:

Browse

Select a file/directory via operating system browse function.

GaussView Preferences

Default settings for many GaussView features can be customized via the preferences, which are reached with the File=>Preferences menu path. The following preferences are available:

• Building: Set default settings for advanced fragment placement options for all three sets (Default, Old and Custom).
• Charge Distribution: Specify desired settings for displaying atomic charge and dipole moment data.
• Clean Controls: Set the adjustable parameters and controls for the structure cleaning function.
• Colors: Customize the coloring of various GaussView displays.
• Desktop: Define file associations for extensions associated with Gaussian and GaussView files (Windows version only).
• Display Format: Set the preferred Display Format dialog settings for view windows.
• File/Directory: Set preferred directory locations for various GaussView contexts.
• Gaussian Setup: Set the preferred Gaussian Calculation Setup dialog settings.
• Icons: Set default icon sizes in the user interface.
• Image: Set the preferred values for capturing images.
• Job Setup: Define execution procedures for Gaussian and related jobs.
• Movie: Specify preferences for animations created by GaussView.
• Print: Set the preferred values for printing images.
• Vibrations: Set the preferred Display Vibrations dialog settings.
• Window Behavior: Set the preferred behavior for dialogs.

All of the preferences dialogs contain several buttons: Ok (save current settings and exit), Cancel (exit and discard unsaved changes), Default (restore GaussView’s installation settings) and Help (obtain online help). When you use the Default button, the dialog in Figure 7 will appear.

Figure 7. Restoring Default Preferences
When you click the Defaults button in the Preferences, you are given the choice of restoring all default preferences or only the ones pertaining to the current dialog.

We will consider two of the preferences here. The others will be discussed along with the relevant features in the course of this manual.

Specifying GaussView Window Behavior and Default Icon Sizes

The Window Behavior preference, illustrated in Figure 8, controls how various GaussView window types behave.

Figure 8. Window Behavior Preferences
These settings allow you to force certain window types to remain uppermost, as well as whether an empty view window is automatically created when the program starts.

The Icons Preferences allow you to specify the icon sizes for various GaussView windows. It is illustrated in Figure 9.

Figure 9. Customizing Icon Sizes
You can select larger icons for various GaussView windows with this preference.

The controls in the dialog control the icons for menus, toolbars and the standalone Builder palette. The defaults are small icons for the first two items and large icons for the third one.

Displaying GaussView Tips

The Help=>GaussView Tips menu path opens the GaussView Tips window, which displays various tips for using the program effectively. You can also choose to have a tip displayed each time GaussView starts up using the checkbox at the bottom of the window (the default is unchecked).

Figure 9a. GaussView Tips
Click Show tips at startup to view a tip each time you start GaussView.