GV6 Help 1

The GaussView Interface

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

GaussView on the Desktop

Several GaussView features are visible here. At the top, we see the main GaussView control panel, containing the menu bar, a
variety of toolbars, and the Current Fragment area. Below this, on the right, are 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). At the bottom left is 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 Builder Fragment display area (grey background).

◦ Various toolbars. By default, these are placed below the menu bar in the control panel, but they may also be
detached if desired (see below). They may also be rearranged within the control panel as desired. This is why your
toolbar may differ from the illustration above.

◦ One or more molecule View window(s) (blue background by default).

◦ Dialogs corresponding to the various GaussView features.

◦ Preferences which control various aspects of the program’s functioning.

Molecules appear and can be modified in View windows. Do not confuse the Builder Fragment display area below the main
toolbar for a View window; it shows what item will be added to the current molecule at the next mouse click.
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GaussView Toolbars

The toolbars that appear by default under the menu bar in the GaussView control panel are illustrated individually below.
Descriptions of the various icons are provided here.

GaussView Toolbars in Standalone Mode

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GaussView Builder Palette

The Builder palette on the right is revealed with the View=>Builder menu path.
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You can detach an individual toolbar from the main toolbar by grabbing its handle and dragging it out of the toolbar area. To
reattach a standalone toolbar, either drag it back into the main toolbar or double click it.

The Builder toolbar can also appear as a standalone palette (as illustrated on the right above). You can open it with
View=>Builder.

Molecules, Molecule Groups, and Views

GaussView uses these constructs to organize the many molecules which are being utilized 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.
Accordingly, a View window displays a molecule, and different views—and View windows—can display different
orientations and properties of the same molecule.

◦ A molecule group is a collection of one or more molecules that are worked on as a 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.

View window title bars display 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. The figure below shows the color icons from two
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.

Color Icons from 2 Different Views

The icon on the left corresponds to the 4th molecule in the 1st molecule group (red), while the one on the right is the 2nd
view of the 1st molecule in the second molecule group (green). 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.

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.
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View Window Context Menu

Each of the options on the context menu brings up a submenu containing related items.

Working with MultiView Windows

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

In a single-view window, clicking the multiview icon brings up multiview mode, in which several molecules can be
viewed at one time (on the right below). Be aware that the multiview fields and controls in the toolbar appear only when there
is >1 molecule in the molecule group. The icon toggles between two forms, depending on the current view mode.
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A Molecule Group Containing 12 Molecules

Individual molecule views are contained within the larger multiview window. The molecule number is shown in the title bar
of each 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 allows you to move between the different molecules.

Clicking on the small triangle to the right of the multiview icon reveals the Multiview Display Mode context menu:

The Multiview Mode Content Menu

You can also open this menu by right clicking the title bar of the multiview display area. This menu controls the layout and
behavior of multiview display mode:

◦ Workspace Background Color: Modify the background color of the current window.
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◦ Options: Open the MultiView Options dialog (see below).

◦ Fit: Resize all individual molecule frames so all are visible in the window.

◦ Synchronize: Link all frames so that mouse actions in one affect all of them (e.g., rotations). By default, each view
is independent.

◦ Manually Resizable SubWindows: Allow the resizing the SubWindows manually by clicking and dragging on the
triangle in the lower right corner.

◦ Manually Movable SubWindows: Allow for the moving of the SubWindows manually by clicking and dragging on
the upper portion of the SubWindow.

Customizing MultiView Windows

The Multiview Options Dialog

The button labeled Less above closes the bottom part of the
dialog, and its label is More when the lower display is hidden.

The various controls in the MultiView Options dialog have the following uses:

◦ Visible Rows and Visible Columns: Number of rows and columns of individual frames initially appearing in a
multiview window.

◦ Scrolling: Placement of scroll bars.

◦ Auto Fit SubWindows: When unchecked, resizing the multiview window does not affect the size of the individual
frames, so more of them are typically visible when the window is made larger. When checked, individual frames
are resized whenever the main window is so the same number of frames are always visible (based on the row and
column values specified).

The following controls are visible when the More button has been pressed:

◦ Workspace Margin, Horizontal Spacing, and Vertical Spacing: Padding around the block of individual view
subwindows and between the individual columns and rows (respectively).

◦ Borders, Titles, Captions, and Numbers: When checked, Borders displays border on individual view frames.
Titles and Numbers control whether the job title and structure number appear in each frame title bar. Captions
controls all title-bar text as a whole, and unchecking it suppresses all text regardless of the settings of the other
items.
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Deleting Views from Molecule Groups

When you no longer need views within a molecule group, the Edit=>Delete menu path will delete the current molecule and
its View. The Delete button on the toolbar can perform the same function. Notat that if any atoms are currently selected in
the current View, then both of these delete functions will only delete those atoms, and leave the rest.

If you want to remove all of the atoms but keep the empty view within the molecule group, click on the Select All Atoms
button on the toolbar and then navigate to one of the two delete functions. This will clear the View window.

The Cut button and the Edit=>Cut offer the same functionality as the Delete function, except that it puts the molecule (or
atoms) on the clipboard for future use.

Animating Multiple Structures

Clicking on the green run button in the toolbar for a multiview molecule group 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. After the green run button has been pressed, it turns into a red stop button, which will stop the
animation.

Animation Playback Controls

The small triangle next to the animation button contains a small menu. The Repeats button allows the user to specify how
often the animation will play for. The Sequence button allows the user to specify how the animation will play. The Frame
Delay (msec) button indicates, in miliseconds, how long the delay is between each frame. The Endpoint Delay (msec) button
indicates, in miliseconds, how long the delay is between the endpoint of the animation and the next loop.
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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:

Mouse Button
1,2-Button
3-Button Equiv. Action Function
Left Left Click Insert atom/fragment, pick atom for modification, etc.
Click (C key pressed) Select or deselect by atom.
Drag (R key pressed) Select or deselect via marquee.
Drag (P key pressed) Select or deselect via brush.
Drag Left/Right Rotate about Y axis.
Drag Up/Down Rotate about X axis.
Center Shift-Left Drag Translate molecule.
Right Ctrl-Left Drag Left/Right Rotate about Z axis.
Drag Up/Down Zoom in and out.
Click in an open area Display context menu.
Shift-Click on atom Highlight corresponding row in Atom List Editor.

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 or Alt-Center mouse button will allow you to drag only the closest 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 configuration tasks on a structure as a whole.

◦ Tools: Specialized features for specific building tasks and calculation types.

◦ Builder: Creating and modifying molecular structures and structural parameters.

◦ 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.

A reference table listing all GaussView menu items and toolbar icons is available here.
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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: Specify default settings for advanced fragment placement options.

◦ 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.

◦ Custom Bonding Parameters: Specify data for identifying/assigning bond types.

◦ Desktop: Define file associations for extensions associated with Gaussian and GaussView files (Windows version
only).

◦ Display Format: This category is broken down into four seperate categories: General, Molecule, Surface, and Text.

◦ File/Directory: Set preferred directory locations for various GaussView contexts.

◦ Font: Specify the font used for the GaussView interface.

◦ 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, Animation: 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, a dialog similar to the one below will appear:

Restoring Default Preferences

When you click the Default button in the Preferences, you are given the choice of restoring all default
preferences or only the ones pertaining to the current dialog (here, the default preferences for Vibrations).
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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).

GaussView Tips
Click Show tips at startup to view a tip each time you start GaussView.
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How To: Set up Gaussian Jobs

This page discusses setting up Gaussian calculations with GaussView. It deals only with the mechanics of doing so. Consult
the Gaussian User’s Reference for detailed information about all Gaussian keywords and options.

The Gaussian Calculation Setup Window

Once the desired molecule is completed, you can use the Calculate=>Gaussian Calculation Setup menu path to open the
Gaussian Calculation Setup dialog. It is illustrated below:

The Gaussian Calculation Setup Dialog

This dialog allows you to set up virtually all types of Gaussian calculations and to submit them from GaussView. The route
section that GaussView is generating appears at the top of the dialog, and it is constantly updated as you make selections in
the dialog’s various panels.

The dialog contains the following panels:

◦ Job Type: The specified type of job appears in the top popup menu. The default is a single point energy calculation.
The remaining fields in the panel represent common options for the selected job type.

◦ Method: This panel specifies the quantum mechanical method to be used in a calculation. The factory default
method is a ground state, closed shell Hartree-Fock calculation using the 3-21G basis set, but you can modify this
with the Gaussian Setup Preferences.

◦ Title: This panel holds a field used for the Gaussian title section (designed to contain a brief description of the job).
Type your description into the text box.

◦ Link 0: This panel is used for entering Link 0 commands for the job.

◦ General: This panel allows you to select commonly used general calculation options.

◦ Guess: This panel contains settings related to the initial guess. Consult the discussion of the Guess keyword in
the Gaussian User’s Reference for full details on these options.
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◦ Pop: This panel is used to select NBO analysis at the conclusion of the Gaussian job.

◦ PBC: This panel is used to specify options to the Gaussian PBC keyword.

◦ Preview: Preview the generated input file.

◦ Solvation: This panel allows you to specify that the calculation is to be performed in solution rather than in the gas
phase.

◦ Additional Input Panel: The final panel in the Gaussian Calculation Setup dialog is labeled Add. Inp. It may be
used to enter any additional input section(s) required by the calculation you plan to run.

The Additional Keywords field below the panel area is used to enter any desired Gaussian keyword and/or option. Note that
you must include the keyword for every option in this field even if it already appears in the route section as a result of panel
item selection.

Below the panel area is the Calculation Scheme area. The controls have the following uses:

◦ Scheme popup menu: Select and apply a calculation scheme.

◦ (Schemes button): Open the Gaussian Calculation Schemes editor. This can also be accessed with the
More Schemes selection from the Scheme menu.

◦ Assign to Molecule Group: Apply the current settings to all members of the current molecule group. Saving
multiple files is explained here. Submitting multiple jobs is explained here.

The buttons at the bottom of the dialog have the following effects:

◦ Submit: Starts a Gaussian calculation using the current input file. You will be prompted to save the input file if you
have not already done so.

◦ Quick Launch: Launches a Gaussian job without further ado (more information here).

◦ Cancel: Closes the dialog box and returns all selections to their default values.

◦ Edit: Allows direct access to the input file with an external text editor. The input file is not available for editing until
it has been saved with GaussView.

◦ Retain: Closes the dialog box. Current selections are retained, but the input file is not created/updated, and no
Gaussian job is submitted.

◦ Defaults: Returns all items to their default values.

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The Job Type Panel

The Job Type panel appears below.

The Job Type Panel

This dialog illustrates adding an option via the Additional Keywords field.

The top dropdown menu selects the job type. The default is a single point energy calculation. The remaining fields in the panel
represent common options for the selected job type.

The available job types are:

◦ Energy: Performs a single point energy calculation.

◦ Optimization: Performs a geometry optimization until a stationary point on the potential energy surface is found.
More information...

◦ Frequency: Computes Vibrational frequencies and intensities. More information...

◦ Opt+Freq: Performs a geometry optimization and then analyzes frequencies.

◦ IRC: Specifies that a reaction path be followed by integrating the intrinsic reaction coordinate. More information...

◦ Scan: Perfoms a potential energy surface scan. More information...

◦ Stability: Performs a calculation to test the stability of the Hartree-Fock or DFT wavefunction. More information...

◦ NMR: Predits NMR shielding tensors and magnetic susceptibilities. More information...

◦ blank: In order to select a job type other than those listed in the popup menu, select the blank menu item at the
bottom of the list, and then type the appropriate Gaussian keyword into the Additional Keywords field in the lower
section of the dialog.
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You can also use the Additional Keywords field to add any desired Gaussian keyword and/or option. GaussView will merge
all options for the same keyword within the generated route section. Note that you must include the keyword with any options
appearing in this field even if it already appears in the route section. For example, in the dialog above, we’ve added the Phase
option to the IRC keyword, while other options has been generated with the various popup and checkbox selections.

The Additional Keywords field is designed only for adding keywords to the route section. Use the Edit button for creating
complex input files.

See here for a list of equivalent G16 Keywords for Gaussian Calc. Setup selections.
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The Method Panel

The Method panel specifies the quantum mechanical method to be used in a calculation. The default method is a ground
state, closed shell Hartree-Fock calculation using the 3-21G basis set. This panel is illustrated below.

The Method Panel

The fields in the Method line specify the following items:

◦ Whether the calculation is for a ground state (the default) or an excited state. If the latter, then the desired excited
state method should be selected.

◦ The theoretical method. For some choices, a fourth field will appear. It is used to select the specific method of the
given type. For example, in the figure above, the method field is set to DFT, and the fourth field selects the B3LYP
functional.

◦ The wavefunction type (closed shell vs. open shell). The default is an unspecified type. The Restricted,
Unrestricted, and Restricted-Open selections prepend R, U, and RO to the method keyword (respectively).

The Custom item on the second menu from the left—the theoretical method menu—can be used to specify a method other
than those available via the menu(s). Place the desired method keyword in the text area that appears.

The Basis Set menus allow the selection of the basis set to be used in the calculation. Polarization functions and diffuse
functions may be added to the basis set, using the corresponding menus in this line. Select the Custom item at the bottom of
the basis set menu to select a basis set other than those that can be constructed via the controls in this area. You may enter
any basis set keyword in the name field.
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Entering a Custom Basis Set Keyword

The Charge and Spin fields specify the molecule’s charge and spin multiplicity. GaussView will select values for these fields
based on the molecular structure. They may be modified as needed.

The Empirical dispersion popup allows you to specify that empirical dispersion should be included in a DFT calculation.

The If defined selection will use whatever dispersion treatment is available for the selected functional. You can also select
a particular dispersion scheme via one of the menu options. Finally, the None option will prevent the use of empirical
dispersion.

See here for a list of equivalent G16 Keywords for Gaussian Calc. Setup selections.
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The Title Panel

The Title panel holds a field used for the Gaussian title section (designed to contain a brief description of the job). Type your
description into the text box.
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The Link 0 Panel

The Link 0 panel is used for entering Link 0 commands for the job. It has three subpanels.

The Link 0 Panel

This panel specifies a name for the checkpoint file, old checkpoint file and the read-write file, the amount of memory to use
for this job, the number of shared memory processors, and/or the locations of Linda workers.

The Options Subpanel

You can specify the various settings via controls in the Options subpanel. The items on the various popup menus have the
following meanings (the default choice is starred):

Item
Link 0 Command Selections
Memory Limit *Don't use: Do not include %Mem in the input file.
%Mem value: Use the selected value (in megawords).
Specify: Use the specified value and units (see the example above).
Shared Processors *Don't use: Do not include %NProcShared in the input file.
%NProcShared value: Use the selected number of processors.
Specify: Use the value specified in the text field that appears with the option.
Chkpoint File *Default name: Include %Chk with a name derived from the input filename.
%Chk Specify: Use the name specified in the input field. Use the ... button to navigate to a file.
Don't save: Do not include %Chk in the input file. See the note below.
OldChk File *No: Do not include %OldChk in the input file
%OldChk Default name: Include %OldChk with a name derived from the input filename.
Specify: Use the name specified in the input field. Use the ... button to navigate to a file.
Read-write File *Don't save: Do not include %RWF in the input file.
%RW Default name: Include %RWF with a name derived from the input filename.
Specify: Use the name specified in the input field. Use the ... button to navigate to a file.
Linda Workers *Don't use: Do not include %LindaWorkers in the input file.
%LindaWorkers Specify: Use the value specified in the text field.
Kill Job No: Run job normally.
%KJob Lnnn: Stop after the specified link completes.
Specify: Enter the desired link into the test field.
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Note: If you remove the specification for the name and location of the checkpoint file, you will not be able to visualize output
automatically from this job.

The Full Path checkboxes control whether an absolute path (checked) or relative path (unchecked) is placed into the %Chk
or %OldChk Link 0 command. However, the full path will not appear in the Edit subpanel even when the box is checked.
The ... buttons allow you to select a specific file by navigating it it.

The Edit Subpanel

The Edit subpanel allows you to edit the Link 0 commands directly.

The Link 0 Commands Editing Panel

The Default Route Subpanel

The Default Route subpanel shows the contents of the Default.Route file in use. The path to the file is indicated at the top of
the panel.

Viewing the Default.Route File

This display is informational only; the file cannot be edited.

See here for a list of equivalent G16 Keywords for Gaussian Calc. Setup selections.
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The Guess Panel

The Guess panel contains settings related to the initial guess. It is illustrated below. Consult the discussion of the Guess
keyword in the Gaussian User’s Reference for full details on these options.

The Guess Method popup specifies the type of initial guess to use. It has the following options:

◦ Default: Uses the default Harris initial guess.

◦ Core Hamiltonian: Uses the Gaussian 98 default initial guess (Guess=INDO). Generally, we do not recomment its
use except when recommended by Gaussian, Inc. technical support staff.

◦ Extended Huckel: Uses the Huckel guess (Guess=Huckel).

◦ Read checkpoint file: Retrieves the initial guess from the checkpoint file (Guess=Read).

◦ Read checkpoint if possible; otherwise generate: Check checkpoint file for the initial guess; generate if not present
(Guess=TCheck).

◦ Read input checkpoint file: Read the guess from the checkpoint file whose name is specified in the input stream
(Guess=Input).

Gaussian Initial Guess Options

The checkboxes in this panel have the following meanings:

Option Default Keyword

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Gaussian Calculation Setup Preview Panel

This panel presents a preview of the Gaussian input file that GaussView will create when a save or job submit operation is
requested:

Gaussian Calculation Setup Preview Panel

The text is read-only. Use the Edit button to modify it directly.

The Runtestrt button runs the testrt utility to verify the job's route section. The utility's output will appear in a separate
window.

Gaussian Context Menu

The context menu for this panel's display area contains the following items: