Gaussian Geometry Optimization10/31/2021
If the selected item is not present in the file, the item is dimmed in the menu.When interfaced to Gaussian or GAMESS, the NBO program makes it possible to. This menu opens a series of dialog boxes that allow you to examine the results of calculations from Gaussian output files. This section describes the Results menu and the options available through it. In order to make GaussView also able to visualize optimization trajectory, monitor geometry convergence status as well as examine vibrational modes for ORCA, the OfakeG is developed, which can convert output file of 'opt', 'freq' and 'opt freq' tasks of ORCA to. GaussView is a nice visualization tool, however it only formally supports Gaussian.This tool manages the display of partial charge density as computed by various methods in Gaussian. Summary of a Gaussian CalculationThis window summarizes the results of a B3LYP/6-31G(d) frequency calculation.The Results=>View File menu item and the View File button can both be used to open the Gaussian log file associated with the Gaussian calculation (if applicable).The Results=>Stream Output File menu item and the Stream Output button can both be used to view the Gaussian log file associated with the current Gaussian calculation continuously as the job runs.Displaying Atomic Charges Computed in GaussianThe Results=>Charge Distribution menu item opens the Display Atomic Charges dialog (see Figure 84). It is displayed in Figure 83.Figure 83. Of QM simulation such as geometry optimizations and freqency calculations.The Results=>Summary menu item displays summary data about the results of the Gaussian calculation (available when a Gaussian log file or checkpoint file is opened). These procedures are discussed in the final part of this section of the manual.Currently only Gaussian is supported but future versions will also support.Symmetric Color Range: Forces the positive and negative limits of the charge range to have the same absolute magnitude (regardless of the actual range of the atomic charge values). Color Atoms by Charge: Recolor each atom by atomic charge according to the specifications of the Color Range fields and the Force Symmetric Charge Range checkbox. Show Numbers: Place atomic charge values next to each atom. The range can also be adjusted manually by entering values into the Charge Range fields.The remaining checkboxes in the top portion of this dialog have the following meanings: The window in the middle shows the numeric charge numbers display, and the one on the right shows the atoms colored by charge (reflecting the settings in the dialog on the left), as well as the dipole moment vector.By default, the color spectrum for charge display is set by reading the maximum charge computed for the molecule and setting the range to match the charge. The Charge Type menu lists the available choices.The dialog on the left is used to control what charges are shown and how they are displayed.
Gaussian Geometry Optimization Series Of DialogCharge Distribution PreferencesThis preference panel specifies how atomic charge results are visualized, using the same options as in the Charge Distribution dialog.The Results=>Surfaces/Contours menu item opens the GaussView Surfaces and Contours dialog (see Figure 86). Clicking Close will cause the atomic charges display to be retained, while clicking Cancel will return the View window to its normal state.Defaults for the items in the Display Atomic Charges dialog can be set with the Charge Distribution Preferences panel (see Figure 85).Figure 85. When the vector is displayed, you can specify the scaling factor for the vector’s length (the default is about 1.0) as well as its origin.The buttons at the bottom of the Display Charge Distribution dialog control whether the display persists after the dialog is closed. This range is set to -1.0 to 1.0 by default, and it can be modified in the Charge Distribution Preferences.The Dipole Moment area of the dialog controls whether a vector representing the dipole moment is included in the display. Cubes Available: Shows data that is currently available for display by GaussView. The Surfaces and Contours DialogThis dialog allows you to select cubes for display as surfaces and/or contours and also to manipulate currently displayed surfaces and contours.The following items in the Surfaces and Contours dialog relate to cubes: Generating the actual surface for display.Figure 86. Obtaining a cube by generating it or reading it in. Note that there are two steps involved in actually displaying a surface: The surface data may be generated from a Gaussian checkpoint file or be read in from a cube file. For most selections, additional fields will appear to further specify the desired data. GaussView automatically invokes the CubeGen utility.The Type popup selects the molecular property for which to generate a cube. It is used to generate new cubes from the electron density and other data in the checkpoint file. Cube Actions: Allows you to generate a new cube ( New Cube), load a cube from an external file ( Load Cube), save the current cube to an external file ( Save Cube), and remove the current item from the Cubes Available list ( Remove Cube).The New Cube selection on the Cube Action button’s menu brings up the dialog in Figure 87. Generally, the default setting of Coarse is adequate for most visualization purposes, Medium is adequate for most printing and presentation purposes. Increased density brings increased computational requirements. Here, we are generating a cube of the electrostatic potential computed from the SCF electron density (frozen core by default).The Grid field is used to specify the density of the cube. Similarly, for molecular orbitals, the specific orbital(s) to generate are indicated via additional fields.This dialog will generate the type of cube specified in the Type field. Mikuni carb tuningFor example, if you wanted to display a difference density, you can load in the two cube files (e.g., the densities computed in the gas phase and in solution). Note: Cubes generated on the fly in this manner are not saved to disk unless you do so explicitly otherwise, they will be lost when GaussView terminates.There are several items in the Type popup that allow you to transform one or more cubes: you can scale and square cubes and add or subtract two cubes. You can view the job via the Calculate=>Current Jobs menu item or the equivalent Current Jobs button. The new cube will appear in the Cubes Available list when the calculation finishes. Use the Custom item to specify a different value.Clicking the Ok button will generate the cube (as a background calculation) and exit the dialog. Add views for new surfaces: If checked, a new View window is opened to display the new surface. Isodensity for new surfaces: Specifies the isodensity value used for generating new surfaces. Surfaces Available: Displays a list of generated surfaces. Creating a Cube as the Difference of Two DensitiesThis dialog creates a new cube that is the difference between corresponding values in the two source cubes.The following items in the Surfaces and Contours dialog relate to surfaces: Both are for formaldehyde.Note that surfaces cannot be saved as data (only cubes can). Remove Surface: Discard this surface, removing it from its View window and from the Surfaces Available list.These windows display the HOMO molecular orbital surface (left, displayed in transparent mode) and an electron density surface (right, displayed in solid mode). Hide Surface: Hide this surface in its View window, but retain it for possible later redisplay. Show Surface: Make this surface visible in its View window. New Mapped Surface: Create a new property-mapped surface (see below). Select the desired surface from the list that is present when this item is selected.This dialog allows you to create a surface in which the coloring is determined by the values of a second property. Use an existing cube: Use one of the current cubes as the colorization data. This will bring up the dialog illustrated in Figure 90.The fields in this dialog have the following purposes: This is accomplished by selecting the New Mapped Surface item from the Surface Actions button’s menu. Images of surfaces can also be saved as image files for use in other contexts.GaussView also allows you to map the values of one property on an isosurface of a different property.
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