Displaying Vibrational Frequency Results
Related Information:
This dialog displays a table of all computed spectra from frequency calculations. These can include vibrational frequencies, infrared intensities, Raman intensities and/or VCD rotational strengths (depending on the specific calculation performed). The window’s
button is used to access graphical representations of the predicted spectra.
The Display Vibrations Window
The items in the top row of the dialog allow you to select which isotopologue’s data is displayed (the Active Data popup menu). The button opens the Run FreqChk dialog, and the button opens the Atom List Editor. Note that these items are not visible when you have opened the frequency data from a .LOG file.
The highlighted row in the list area indicates which vibration is currently selected for dynamic display. You can start this display by selecting the
button and halt it by clicking on it again, now labeled . During animation, a cyclical display shows the nuclear motions corresponding to the vibration selected. You can select a different mode by clicking on the desired mode in the scrolling list. You can select a new mode without halting the previous one. You can also rotate and move the vibrating molecule, using the normal mouse buttons.The two slide bars below the Vibrations Preferences panel (as well as for the displacement and dipole derivative unit vector discussed below).
button adjust the speed and magnitude of the motion. Default values for these settings may be specified in theThe animation can also be saved as a movie and/or as individual frames using the
button. The controls in the line below this button specify characteristics of the resulting movie.The
menu offers several different options for the animation of the molecule. The numbers represent how many cycles will be displayed when you press the button. Selecting means the animation will not end until you press the button. The menu allows you to specify how many frames should be present in each cycle. You can specify any number of frames between 4 and 120. The more frames that it takes to complete a cycle makes the resulting animation smoother. The menu allows you to modify the length of time between each frame. Increasing this number allows for a slower animation.The
slider allows you to specify the magnitude of the displacement of the atoms when animating a vibrational mode. This will determine how extreme the vibrations will appear in the animiation. Increasing the displacement by dragging the slider to the right will make the vibrations more pronounced, while decreasing it--dragging the slider towards the left--will make them more subtle.The
area can be used to scale frequency values by a uniform amount. When the popup menu is set to , you can enter the scaling factor into the field at the right.The two vector-related checkboxes in the lower section of the dialog have the following meanings (see figure below for examples):
Displaying the Displacement Vector and Dipole Derivative Unit Vector
By default, the displacement vectors are blue,
and the dipole derivative vector is orange.
The various displacement vectors are displayed in blue, and the dipole derivative unit vector is the orange arrow on the left.
You can specify defaults for this dialog using the Vibrations Preference. You can change the colors of the vectors using the panel of the Colors Preference.
The Manual Displacement box allows you to set a displacement from the equilibrium geometry. When it is checked, animation of the vibration will be turned off. When checked, the slider, number box, and button become active. In this mode, changing the slider or the corresponding number box will cause the molecule to be statically displaced along the currently active normal mode. The center value of the slider, or zero in the text box, corresponds to no displacement. Moving the slider to the right or entering a positive value in the text box will displace the atoms along the currently active normal mode. Moving to the left or entering a negative value will displace the atoms in the direction opposite of the currently active normal mode. The range of values allowed in the text box ranges from -1 to +1. Clicking on will cause a new molecule window to appear with a geometry exactly corresponding to the displaced structure.
The primary use of this tool is to help eliminate spurious negative eigenvalues. When one is searching for a transition state, it is not uncommon to end up with a structure containing two (or more) negative eigenvalues instead. These spurious negative eigenvalues are generally small but must be eliminated to isolate the true transition state. For these cases, select the normal mode corresponding to the spurious negative eigenvalue, and then select Manual Displacement. Adjust the slider to the right (or enter a positive number in the text box), and then select to create a new molecule with the displaced geometry, which you can then reoptimize. If a positive displacement fails to eliminate the spurious negative eigenvalue, follow the same procedure with a displacement in the negative direction. You can also try varying the magnitude of the displacement.
A second purpose of manual displacement is to generate pictures of a molecule in the midst of a vibration. Thus, it can be used to effectively freeze the animation of the vibration at a specific point.