This chapter discusses setting up and running Gaussian calculations with GaussView. It deals only with the mechanics of doing so. Consult the Gaussian 03 User’s Reference for detailed information about all Gaussian 03 keywords and options.
The first step in producing a Gaussian input file is to build the desired molecule. The bond lengths, bond angles, and dihedral angles for the molecule will be used by GaussView to write a molecular structure for the calculation. Once this is completed, you can use the Calculate=>Gaussian Calculation Setup menu path to open the Gaussian Calculation Setup dialog. It is illustrated in Figure 60.
Figure 60. 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.
The Gaussian Calculation Setup (dialog contains several panels, described individually below. The buttons at the bottom of the dialog have the following effects:
The Job Type panel appears in Figures 60 and 61. The top popup 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 figure shows the ones for an Opt Freq calculation).
In order to select a different job type 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 section in the lower section of the dialog.
You can also use this field to add any desired Gaussian keyword and/or option. In the latter case, you must repeat the keyword within this field even if it already appears in the route section. GaussView will merge all options for the same keyword within the route section (see Figure 61 for an example). Note that this area is designed only for adding keywords to the route section. Use the Edit button for creating complex input files.
Figure 61. Adding an Option via the Additional Keywords Field
This window illustrates GaussView’s ability to merge options from dialog controls and ones typed into the Additional Keywords field. Here, we’ve added the Internal option to the IRC keyword, while another option has been generated with the Calculate Force Constants popup selection.
The Scheme field at the bottom of the dialog is used to quickly retrieve a stored set of keywords and options. This feature is described later in this chapter.
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 in Figure 62.
The fields in the Method line specify the following items:
Figure 62. The Method Panel
The Method panel is where the model chemistry for the calculation is specified.
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 blank 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 Additional Keywords area.
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 Title panel holds a field used for the Gaussian title section (designed to contains a brief description of the job). Type your description into the text box.
The Link 0 panel is used for entering Link 0 commands for the job (see Figure 63). Be sure to name the checkpoint file if you intend to visualize output from this job.
Figure 63. The Link 0 Panel
This panel specifies a name for the checkpoint file and also the amount of memory to use for this job. You can specify the various settings using the controls in the Options subpanel. Alternatively, you can edit the Link 0 commands directly using the Edit subpanel.
The General panel allows you to select some commonly used general calculation options. It is illustrated in Figure 64.
Figure 64. Selecting General Gaussian Options
This panel contains a set of commonly used options. This window illustrates the defaults.
The following table indicates the Gaussian keywords corresponding to these items:
Option Default Keyword
Use Quadratically Convergent SCF Off SCF=QC
Use Modified Redundant Coordinates On Geom=ModRedundant
Ignore Symmetry Off NoSymm
Use MaxDisk= Off MaxDisk
Additional Print Off #P
Write Connectivity On Geom=Connectivity
The Use Modified Redundant Coordinates item is enabled only if you have set up redundant coordinates with the Redundant Coordinate Editor. If not, the item is ignored (despite its default value).
The Write Connectivity option also includes the appropriate additional input section(s) within the Gaussian input file.
Note: The default SCF algorithm has changed with Gaussian 03, and we have new recommendations for the few remaining problem cases (SCF=QC is not always the best next choice). Consult the discussion of the SCF keyword in the Gaussian 03 User’s Reference for details.
Th Guess panel contains settings related to the initial guess. It is illustrated in Figure 65. Consult the discussion of the Guess keyword in the Gaussian 03 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:
Figure 65. Gaussian Initial Guess Options
This window shows the default settings for the initial guess.
The options in this panel have the following meanings:
Option Default Keyword
Mix HOMO & LUMO in initial guess Off Guess=Mix
Only do guess (no SCF) Off Guess=Only
Save orbitals to checkpoint file Off Guess=Save
Always generate guess in optimizations Off Guess=Always
Localize orbitals Off Guess=Local
Permute orbitals from MOs Dialog On Guess=Permute
The Permute orbitals for MOs Dialog is disabled unless you have specified an alternate orbital ordering with the MO Editor. If enabled, it is on by default.
The NBO panel is used to select NBO analysis at the conclusion of the Gaussian job. It is illustrated in Figure 66. The Type menu specifies the kind of NBO analysis to perform. The Checkpoint Save field allows you to save NBOs in the checkpoint file for later visualization (the default is Don’t Save).
Figure 66. The NBO Panel
The panel specifies the type of NBO analysis and which NBOs to save in the checkpoint file. The selection in this window is often a useful one when you will use them to generate an active space for a CASSCF calculation.
The Solvation panel allows you to specify that the calculation is to be performed in solution rather than in the gas phase. It is illustrated in Figure 67. The Model field allows you to specify a specific solvation model (the default is PCM, which itself defaults to IEFPCM). You can also specify the solvent by selecting it from the corresponding popup menu. Use the Other selection to select a solvent other than those on the list; you will need to specify within the route section manually (e.g., placing SCRF(EPS=value) within the Additional Keywords field).
Figure 67. The Solvation Panel
This panel specifies the SCRF model to use for solvent effects. The Default selection corresponds to the Gaussian default of SCRF=PCM.
Note that some solvation models may present different/additional fields for their required parameters. You may use the Read additional input box to generate the SCRF=Read option; additional input must be entered by editing the Gaussian input file manually.
The PBC panel is used to specify options to the Gaussian PBC keyword (see Figure 68). Checking the Use PBC box causes the translation vectors to be added to the molecule specification. This is the default when a unit cell has been defined with the Crystal Editor. The panel is disabled for non-periodic systems.
Figure 68. The PBC Panel
The Use PBC checkbox causes the translation vectors to be placed in the molecule specification. After you select the option above, an additional field for specifying the number of K-points will appear.
This section summarizes information about setting up various Gaussian job types for which some special steps are required All GaussView features mentioned are discussed in detail earlier in this book.
Gaussian STQN-based transition structure optimizations require two or three structures as input. To set up these jobs, you must create a molecule group containing the required number of structures. If you plan on running an Opt=QST3 job, then the transition structure initial guess should be molecule 3.
Once you have done so, the TS (QST2) and TS (QST3) options will be enabled in the Optimize to a field for the Optimization job type in the Job panel of the Gaussian Calculation Setup dialog.
In most cases, GaussView will automatically identify the corresponding atoms in the multiple structures for these transition state optimizations. However, you can verify this using the Connection Editor, accessed via the Connection Editor button on the toolbar or the Edit=>Connection Editor menu item.
You can set up jobs for Gaussian’s Periodic Boundary Conditions facility using the Crystal Editor (reached via the Crystal Editor button or the Edit=>PBC menu path). Once you have defined a unit cell, GaussView automatically sets up PBC jobs for this structure by including the translation vectors within the molecule specification. This is indicated by the enabling of the PBC panel in the Gaussian Calculation Setup dialog, and the checked Use PBC item. Note that for normal cases, you do not need to access this panel at all and can proceed directly to setting up Gaussian input in the normal manner.
GaussView contains several features for setting up ONIOM calculations.
The Layer Editor allows you to graphically assign atoms to various ONIOM layers. It is accessed via the toolbar’s Select Layer button or via the Edit=>Select Layer menu item.
GaussView will assign Molecular Mechanics atoms types for UFF, Dreiding and Amber (including Amber charges) to all atoms in the molecule automatically. You can view and modify these using the Atom List Editor (reached via the Atom List Editor button on the toolbar or the Edit=>Atom List menu path).
GaussView will automatically assign minimal link atom information for the appropriate atoms in an ONIOM calculation. However, all link atoms are always handled in the same way, and they may require modification for your purposes. Link atoms generated by GaussView are always hydrogens (using the H_ UFF and Dreiding atom types and the HR Amber atom type, where R is the element of the linked-to atom). The only other link atom parameters which is included is the linked-to atom (the atom in the higher layer to which the current atom is bonded); all other parameters are left blank.
Once you have prepared the structure and specified all necessary parameters, you can set up an ONIOM calculation via the Method panel of the Gaussian Calculation Setup dialog. The Multilayer ONIOM Model checkbox indicates that this will be an ONIOM calculation (see Figure 69).
Figure 69. Setting Up a Gaussian Input File for an ONIOM Job
This example is preparing an input file for a two-layer ONIOM calculation. When Multilayer ONIOM Model is checked, the additional tabs appear in the Method panel. Each of them allows you to specify the theoretical method and basis set for the corresponding layer. In this case, we are using the Amber Molecular Mechanics method for the Low layer.
GaussView can make it easy to specify CASSCF active space. The MOs dialog allows you to generate, view, select and reorder the starting orbitals. It is reached with the Edit=>MO Editor menu path and via the MO Editor button on the toolbar.
You can specify additions and other modifications to redundant internal coordinates for geometry optimizations and other jobs by using the Redundant Coordinate Editor, reached via the Redundant Coordinate Editor button on the toolbar or the Edit=>Redundant Coordinates menu path.
The Gaussian Setup preferences may be used to specify defaults for the Gaussian Calculation Setup dialog. Click the Calculation button, and then specify the desired settings for future Gaussian calculations. These will be applied to future job setup operations.
Modifying the Gaussian Setup preferences as described in the preceding paragraph has the effect of modifying the Gaussian calculation scheme named “Default.” Schemes are named sets of calculation keywords and options, and this feature has been generalized in the current release of GaussView to enable you to save as many sets as you want to. You can view the calculation scheme in effect at the bottom of the Gaussian Calculation Setup dialog and in the scheme popup in the toolbar, and in the Calculate=>Gaussian Calculation Scheme submenu. You can apply a scheme to the current molecule using any of these controls as well.
For new molecules, the Default scheme is initially applied. When you open a new molecule from a file, the scheme will be set to the scheme that matches its settings (if any) or to “Unnamed Scheme.”
You can view and modify the properties of the various defined schemes using the Schemes button or by selecting More Schemes from any scheme list. The resulting dialog appears in Figure 70.
Figure 70. Viewing and Modifying Calculation Schemes
This dialog shows four schemes organized into two groups.
Any field within a scheme can be edited by clicking on it. Right clicking on a scheme produces a context menu, allowing you to add groups and schemes, cut and paste between fields, delete schemes. You can also save schemes to an external file and load ones saved in this way back into GaussView. Note that neither the Default scheme nor the Main group may be renamed or deleted.
Currently, there are two limitations on what can be included within calculation schemes. First, only Link 0 commands corresponding to the items on the Link 0 panel’s Options subpanel are accepted. Second, custom methods may not be included.
The traditional way to run a Gaussian job from GaussView is to open the Gaussian Calculation Setup, set the correct job options, click the Submit button, and specify the name and location for the input file. The Quick Launch feature greatly simplifies this common task. A job can be launched using the Quick Launch toolbar button, the Quick Launch button in the Gaussian Calculation Setup dialog or the Calculate=>Gaussian Quick Launch menu path.
Clicking on the button in the Gaussian Calculation Setup dialog or on the portion of the toolbar icon to the left of the small arrow will immediately launch a Gaussian job using the current calculation scheme and temporary files. The toolbar icon arrow and the Calculate menu item both lead to a submenu. Its Temp File item will also result in a job started from a temporary input file. The Save File option will prompt you to save an input file and submit that file as a Gaussian job afterwards.
When you start a new calculation using Quick Launch a new view window is opened corresponding to it. While the job is running, a text message identifying the job, a stop button, and a stream output file button are placed in the status bar of the view window. Once the job finishes successfully, the results file is opened automatically in the same view window. When more than one results file is produced by a calculation—e.g., both a log file and a checkpoint file are created—then you will be prompted to select the file to open.
You can save the files generated from a Quick Launch operation to temporary files using the File=>Save Temp Files menu item. This item replaces the usual Related Files option under these circumstances.
The Calculate=>Current Jobs menu path opens the Job Manager dialog (shown in Figure 71); the Job Manager button on the toolbar performs the same function.
This window displays all the jobs started by GaussView that are currently running. Note that only jobs started during the current session of GaussView can be displayed. Examples of jobs that may be displayed are Gaussian jobs submitted from the Gaussian dialog box, Gaussian input file edit sessions launched from GaussView, cubegen processes for building surfaces for display, and/or processes from other Gaussian utilities.
Figure 71. The Job Manager Dialog
This dialog allows you to view and control Gaussian jobs as well as jobs running Gaussian utilities like cubegen. You can terminate a job using the Kill button.
Clicking on the Jobs Log button displays the current GaussView job log containing system messages associated with the execution of GaussView external processes. Note that it does not display the log file associated with a running Gaussian job. The latter is accomplished by the Stream Output File button for Gaussian calculations. Note that selecting this button when for job types (e.g., cube generation jobs) will display whatever file GaussView can find that is associated with the job (often the Gaussian input file).
Individual jobs may be aborted using the Kill button. The Clean button removes old jobs from the list.
The Job Setup preferences dialog allows you to examine and customize how Gaussian and its utilities are launched from within GaussView. It is illustrated in Figure 72.
The Application field selects which type of external job the settings apply to, and the Priority field specifies the relative priority level at which such jobs will run.
Figure 72. Job Setup Preferences
These settings are used to specify how various external jobs get initiated by GaussView.
For each job type, there are three launch choices:
GaussView provides the following scripts in its bin subdirectory:
Menu Item UNIX Windows Mac OS X
Gaussian gv_gxx.csh gv_gxx.bat gv_gxx.csh
Cubegen gv_cubegen.csh gv_cubegen.bat gv_cubegen.csh
Cubman gv_cubman.csh gv_cubman.bat gv_cubman.csh
FormChk gv_formchk.csh gv_formchk.bat gv_formchk.csh
FreqChk gv_freqchk.csh gv_freqchk.bat gv_freqchk.csh
Gaussian Help gv_gaussianhelp.csh gv_gaussianhelp.bat gv_gaussianhelp_mac.csh
File Editor gv_fileeditor.csh gv_fileeditor.bat gv_fileeditor_mac.csh
Each script’s usage is documented in comments at the beginning of the file. Prudence dictates making a backup copy of any script before modifying it in any way. Note that all standard UNIX scripts are also provided on Mac OS X systems for your convenience.
You can also specify a custom command line for external jobs using the third choice in the Job Setup preferences dialog. Successfully using this feature depends on a clear understanding of the command line invocation of Gaussian and its utilities under the current operating system. Consult the Gaussian 03 User’s Reference for details.
The following GaussView internal variables can be used within commands (note that they are not operating system environment variables, despite their resemblance to them).
Parameter Meaning
$GEXE Path to the Gaussian executable (UNIX)
$GEXE_WIN Path to Gaussian executable (Windows)
$CUBEGEN Path to the cubegen executable
$FORMCHK Path to the formchk executable
$FREQCHK Path to the freqchk executable
$MM Path the Gaussian mm executable
$WORDPAD Path to Wordpad (Windows)
$NEDIT Path to UNIX editor
$GHELP Path to the ghelp executable
$something_SCRIPT Path to the script for the specified utility
$INFILE Gaussian input file
$OUTFILE Gaussian or utility output file
$KIND Type of cube for cubegen
$NPTS Cube density for cubegen
$HEADER cubegen header flag