Vibrations Panel

This panel provides controls for the display of vibrational modes of the structures in the Workspace.

To open this panel, double-click the V button for the entry in the Entry List. If the entry is not already in the Workspace, it is included and other (non-fixed) entries are excluded.

This panel is docked into the Workspace by default, so you can easily switch focus from the panel to the Workspace. You can undock the panel if you want to place it somewhere else. To dock or undock the panel, use the docking button in the title bar (left of the Close button) .

  • Using
  • Features
  • Additional Resources

Using the Vibrations Panel

This panel controls the display of the vibrational motion of the atoms in the Workspace in a particular normal mode. There are two representations of the vibrational mode available:

  • Animation, in which the atoms oscillate along the directions specified by the normal mode, with a displacement proportional to the contribution of the atom's displacement to the normal mode.
  • Arrows on each atom, whose direction and amplitude are given by the components of the normal mode for the atom.

To display the arrows, change the amplitude of the displayed motion for either animation or arrows, or change the speed of the animation, click the Settings button .

The vibrational animation displays a harmonic oscillation of the atoms in the Workspace for a single vibrational mode. There is no information about anharmonicity or curvature of the coordinates in this display, so you should beware of drawing any structural inferences from large amplitude motions.

You can switch to a new mode and you can interact with the Workspace (e.g. to rotate the molecule) while the animation is occurring. You can stop animation by clicking the pause button or by pressing ESC, and you can step through the series of displaced structures generated for the animation.

The structure whose animation is displayed in the Workspace is a temporary structure: the source entry itself is not altered. When you stop the animation, the structure displayed is that of the current frame. When you close the panel, the temporary structure is replaced by the source entry structure.

You can save single structures from any frame of the animation as new project entries. You can also save an MPEG(.mpeg), AV1 (.mp4) or GIF movie of the selected vibrational mode.

In addition to the structure selected for vibrational animation, you can fix other entries in the Workspace, for example to examine interactions with the vibrating structure. (These other entries are not saved or exported with the vibrating structure.)

The vibrational data come from a Jaguar frequency calculation or a Quantum Espresso phonon calculation, and are read from a .vib file, which contains the normal modes and frequencies. The .vib file is automatically incorporated into the project at the end of the calculation, and a V button is added to the Title column in the Entry List/Project Table for the incorporated entry.

If you import a structure into Maestro for which a frequency calculation was performed, you can also import the data: in the Project Table panel, choose Data → Import → Vibrational Data. If the structure that you imported came from a Jaguar frequency calculation but does not have an associated .vib file, you can import the frequency data from the Jaguar output file.

Vibrations Panel Features

Workspace entry option menu

This option menu lists the entries in the Workspace that have vibrational data by entry ID and title. The entry chosen for vibrational animation (by clicking the V button) is selected by default. You can choose a different entry for display of vibrational modes.

Vibration table

This table lists the frequencies in cm−1 of the entry selected from the Workspace entry option menu, along with ir intensities, Raman activities and intensities. You can select a single frequency in the table to display, and you can select a new frequency while animation is in progress. The table is refreshed if you select a different entry for animation or include a different entry in the Workspace.

Play controls

These standard play controls allow you to start and stop the animation of vibrational modes, step through the frames, or jump to the first or last frames.

Settings button

Change settings for the display of vibrational modes. Changes to settings take effect immediately. Opens a pane with the following controls:

Speed slider

This slider allows you to adjust the speed of the animation.

Amplitude text box

This text box specifies the scaling factor for the amplitude of the vibrational motion that is used in the animation or is represented by the arrows.

Show displacement vectors option

Show the selected vibrational mode as arrows on each atom. The arrows show the relative magnitude and direction of displacement of each atom in the normal mode. The scaling of the arrow lengths can be changed by changing the value in the Amplitude text box. When arrows are shown, they move along with the atoms they are attached to in the animation.

Frame slider and text box

This slider allows you to step through the frames of the animation, or select a particular frame by entering the number in the text box. There are 24 frames used in the animation. The position of the slider updates during play.

Save Structure button

Save the structure from the current frame as a project entry. The new entry is named entry-name - Mode # - Frame #.

Export Mode button

Export the animation of the selected vibrational mode as a 10-second movie in MPEG, AV1 or GIF format. Opens a file selector so you can choose a location and name the file. The default base name is entry-name_mode#_frequencycm-1, with the extension .mpeg, .mp4 or .gif. The frequency is rounded to the nearest integer.

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