Ampac Calculation Setup
An Ampac Calculation Setup dialog is used to setup Ampac calculations for the current molecule (or molecule group in the case of Ampac Chain calculations) of its parent view window. It is also used for defining and saving Schemes for easy setups of future Ampac calculations. An Ampac calculation which uses the settings in the Ampac Calculation Setup dialog can be submitted from it after explicitly saving, and possibly editing, a corresponding Ampac input file. Alternatively, using Ampac Quick Launch, the same calculation can be run and the corresponding results automatically loaded, without explicitly saving an input file or opening an Ampac result file .
The Ampac Calculation Setup dialog for the active view window is opened and / or activated by selecting "Ampac Setup..." from the Calculate Menu of the main window or the context popup menu of the active view window, or by clicking on the "Ampac Setup" icon on the calculate tool bar of the main window.
Default settings for Ampac Calculation Setup dialogs can be specified in the Preferences dialog.
See the Ampac Manual for detailed help on the Ampac program itself.
The Title, Comment, and Keywords labels at the top of the dialog correspond exactly to the Title, Comment, and Keyword sections at the head of the Ampac input file which would be created from the current Ampac Calculation Setup dialog settings. The title and comment lines can be edited in the corresponding Title and Comment tab panels of the dialog and are restricted to 79 characters. The keyword line is automatically updated according to what other settings are specified in the dialog.
This field is used to specify the net charge of the molecule to use for the Ampac calculation. The default is 0 and the charge must be an integer. Changing the charge by an odd number will necessarily change the spin multiplicity.
This field specifies the spin multiplicity of the molecule to use for the Ampac calculation. It is meaningful only for UHF and CI calculations. RHF calculations always use the lowest possible spin multiplicity, i.e., Singlet for even electron systems and Doublet for odd-electron systems. For CI calculations, this field specifies the spin multiplicity of the primary CI eigenstate (the one followed during geometry optimizations, for example). Secondary CI eigenstates of other spin multiplicities may be calculated depending on how many CI eigenstates are requested.
This list box determines the basic type of Ampac calculation to do. Each of the job types is described below.
Do a single-point energy calculation, i.e., no geometry changes.
Do a geometry optimization, i.e., find a minimum or transition state geometry. All Z-Matrix coordinates whose corresponding optimization flags are set to "Yes" in the parent view window's Atom List Editor will be optimized. The "Minimize" listbox specifies whether the energy or the gradient of the energy should be minimized. The former should be used for finding minima. The latter should be useful for finding transition states or other non-minimum stationary points. The "Using" listbox specifies which geometry optimization algorithm to use. See the Ampac Manual for details on these algorithms. The default TRUST algorithm is usually the best choice. The Hessian algorithm can be useful for finding transition states and / or for very flat potential energy surfaces.
Do a frequency calculation. If the input geometry is not already a stationary point, Ampac will not perform the frequency calculation by default. The four options available when doing frequency calculations are self-explanatory. If the characterization of a stationary point as a minimum or transition state is all that is needed, then one of the last two options is recommended since they can drastically reduce the computation time compared to a full frequency calculation. Results from a Frequency calculation can be visualized in a Display Vibrations dialog.
Do a geometry optimization followed by a frequency calculation at the optimized geometry. If the geometry optimization fails to converge, then no frequency calculation is done. All of the options available for both the Optimization and the Frequency Job Types are available for this combined job type.
Do a series of geometry optimizations in which a single Z-Matrix coordinate (the "reaction coordinate") is fixed at a series of specified values. A "reaction coordinate" can be specified using an Atom List Editor. In the above example, the Z-Matrix dihedral coordinate involving atoms 14,12,3 and 2 is the reaction coordinate. Its current and starting value is -90 degrees and its final value will be 90 degrees. The values of the coordinate to use can be equally spaced or arbitrarily specified. Results from a Reaction Path calculation can be visualized in a Reaction Path Plot dialog.
Do an annealing calculation. See the Ampac Manual for details on Annealing calculations. Results from an Annealing calculation can be visualized in an Annealing Plot dialog.
Do an IRC calculation. See the Ampac Manual for details on IRC calculations. Results from an IRC calculation can be visualized in an IRC Plot dialog.
Do a Steepest Descent Path calculation. See the Ampac Manual for details on Steepest Descent Path calculations.
Do a Chain calculation using all of the molecules of the parent view window's molecule group as the input geometries. Chain calculations require at least two molecules in the group as well as a consistent atom ordering between the molecules. If this is not the case, the "Chain" Job Type menu item is disabled. See the Connection Editor for how to consistently order the atoms of a molecule group. Results from a Chain calculation can be visualized in a Chain Coordinate Plot dialog.
Do a series of geometry optimizations in which two Z-Matrix coordinates (the "reaction coordinates") are fixed at a series of specified values. The series of values can, of course, be different for the two coordinates. A "reaction coordinate" can be specified using an Atom List Editor. In the above example, the Z-Matrix dihedral coordinate involving atoms 13,11, 6 and 1 is the first coordinate, whose current value is -90 degrees and which will range from -118 degrees to -62 degrees during the calculations. The second reaction coordinate is a Z-Matrix bond coordinate involving atoms 22 and 3, whose current value is 1.54 Angstroms and which will range from 1.45 to 1.63 Angstroms during the calculations. A Reaction Grid calculation is similar to a Reaction Path calculation, except Reaction Path that it uses two reaction coordinates instead of one. In contrast to calculations, however, the series of values to use for reaction coordinates must be equally spaced for Reaction Grid calculations and the input geometry is always the central point. Results from a Reaction Grid calculation can be visualized in a Reaction Grid Plot dialog.
These fields specify the semi-empirical model and wavefunction type to use for the Ampac calculation.
See the Ampac Manual for a discussion of these models and which elements they are available for.
This field specifies the wavefunction type to use for the Ampac calculation. RHF and UHF refer to the usual single determinant SCF methods. "C.I." means do a CI calculation. The CI fields are shown below.
The above pictures show all of the controls for setting up a CI calculation in an Ampac Calculation Setup dialog. Usually the most important controls are the "CI-active MOs" controls. Often, the desired CI-active MOs will lie near the HOMO / LUMO energy level. In the above example, the four MOs bracketing this level have been chosen, i.e., MOs 42, 43, 44 and 45. The CI-active MOs should all or no members of a set of degenerate MOs. An MOs dialog can be used to visualize the MOs from an Ampac calculation and help select the desired CI-active MOs. See the Ampac Manual for more details on CI calculations. CI is recommended for open-shell systems and is necessary for excited states and ground state properties involving coupling with excited states, such as dynamic polarizabilities.
This field specifies the first line of the Ampac input file. It should be less than 80 characters in length.
This field specifies the second line of the Ampac input file. It should be less than 80 characters in length.
The Time Limit fields are used to control how long an Ampac calculation should run before it stops. The "Use default time limit" option means, let Ampac decide, which almost always means, until the job is complete. The "No time limit" option means the Ampac calculation will run until it is completed normally or until it is killed. The "Specify time limit..." option means the Ampac calculation will run until the calculation is completed normally or until the specified time elapses.
The RMS Gradient Norm Tolerance field is relevant for geometry optimization calculations. It determines at what point a geometry is considered optimized by Ampac. Higher numbers give less precisely optimized geometries, with the tradeoff that the optimization calculation is completed in less time. Lower numbers give more precise geometries but the calculation takes longer and the optimization may fail to converge to the specified threshold.
The Use Quadratically Convergent SCF box should only be checked if the SCF calculations are expected to have difficulty converging (a rare occurrence). See the Ampac Manual for details.
The Use Tight Convergence Criteria box should only be checked if the SCF calculations need to be very precise. See the Ampac Manual for details.
The Reduce Size of Visualization (.vis) File option prevents the writing of surface information (molecular orbitals, density, etc.) to the Visualization file thus greatly reducing its size. This option is primarily intended for very large jobs where the surface information takes up a large amount of space. When this option is used, the resulting Visualization file behaves identically to a regular Visualization file except that surface information cannot be displayed. See the Ampac Manual for details.
By default, all three types of Ampac result files (Archive, Output and Visualization) are produced when an Ampac calculation is run. Sometimes one or more of these file types is of no interest to the user. In such cases, checking the corresponding boxes will cause Ampac not to produce these files.
Checking any of these boxes will cause Ampac to calculate the corresponding properties at the final geometries. If a result file that contains Bond Orders is opened in GaussView, the bonding in the corresponding view window will correspond to those bond orders. If a result file that contains ESP charges is opened in GaussView, the charges can be displayed in a Display Atomic Charges dialog. The "Generate Output for Codessa" option will cause a number of different properties to be calculated by Ampac, including Bond Orders and polarizabilites.
The Solvent tab panel is used for running Ampac calculations with a solvation model. Ampac supports both COSMO and various SM5 solvation models. Use of the SM5 models requires a special license. See the Ampac Manual for more details about solvation calculations.
GaussView does not directly support all Ampac keywords, but any Ampac keywords can still be added to the keyword line of the Ampac input file by specifying them in this field. If a keyword is entered that is recognized by GaussView, then the other dialog settings will reflect that keyword and it will be removed from the Additional Keywords section. Selecting the Update button simply updates the dialog based on the Additional Keywords field
This list box shows the most recently used Schemes for Ampac calculations. The Ampac scheme which corresponds to the current Ampac Calculation Setup Dialog settings is selected. Selecting a different scheme from the list, or from the Ampac Calculation Schemes dialog, will change the dialog settings accordingly. Dialog settings which do not correspond to a named scheme are labeled "(Unnamed Scheme)", as in this example, and can be saved as a named Scheme using the Ampac Calculation Schemes dialog.
The Ampac Calculation Setup dialog's status bar appears below the Schemes control. It is empty unless their is an inconsistency in the dialog settings or between the dialog settings and the molecule. In the above example, the Job Type has been set to Reaction Path, but no reaction coordinate has been defined.
This button is used to run an Ampac calculation using the current molecule and current dialog settings. If the molecule has not already been loaded from or saved to an Ampac input file, or has since been modified, then the user is prompted to save an Ampac input file first. Once an Ampac calculation has been submitted, its status can be viewed in the Job Manager dialog. When the calculation is complete, the user will be prompted to open a corresponding Ampac result file.
This button causes the Ampac calculations can be submitted without explicitly saving a file using Ampac Quick Launch. Once the job has been launched, the Ampac Calculation Setup dialog automatically closes. The status of the Ampac calculation can be viewed in the Job Manager dialog. When the calculation is complete, the user will be prompted to open a corresponding Ampac result file. To save the Ampac input file and result files, use Save Temp Files, otherwise they will be removed once the molecule group is removed or GaussView exits.
Selecting this button cancels all changes made in the dialog since it was last opened.
Selecting this button is similar to selecting the Submit button, except that the user is prompted to either edit the file associated with molecule if a save is not need or save a new file. In either case, the file appears in an editor so that it can be inspected and possibly changed manually. Once the editor is closed, the file is re-loaded in the same molecule group (in case the file was edited) and the user is then prompted to submit the file to Ampac.
This button is used to close the dialog and save its current settings, but an Ampac input file is not saved or updated, nor is an Ampac calculation submitted. This is especially useful for later Ampac Quick Launch calculations using the "(Unnamed Scheme)" option.
Selecting this button (which is equivalent to selecting the "(Default)" Scheme) will change the dialog settings to the preferred settings for an Ampac Calculation Setup dialog, as defined in Preferences.
Selecting this button will open the GaussView Help dialog and set its current page to this Ampac Calculation Setup help page.