Vibrational Modes
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Dialog Box - called from: Input1 Menu

See the Import File dialog for general aspects of importing atomic-structure data files.

This dialog controls.MOT vibrational displacement files (see Import VIBRAT (.MOT) files and Coordinating ATOMS and VIBRATZ) written by the VIBRATZ program (or the original VIBRAT - Dowty, Phys Chem Minerals (1987) 14:67). When these files are read in the infomation is converted into a standard ATOMS data file, and also a special.MDT modes file which contains the atomic displacements and other information for each vibrational mode. When you re-read the.STR file, the.MDT file is read in also; if this fails, you can read it in using one of the options in the Modes file group in this dialog. The title of the.MDS file should already be present in the edit box so you can edit it and click the Read Named File button, or use the Browse button to find it.

The Read.MOT file for motions only button will read the atomic motions, but will ignore other information in the.MOT file. This allows you to set up the drawing once in terms of atom sizes, colors, etc., and retain all this if you decide to recalculate the vibrational modes in VIBRAT.

The mode which is in the.STR file and which is displayed when you first read and calculate the file is the one which was selected when the.STR file was last saved.

After selecting a new mode, you will need to recalculate the structure (Calculate command in the File menu, or the Dialog Bar), not simply replot, since new vectors involve generating new pseudo-atoms and pseudo-bonds.

To see on the screen or output which vibrational mode is being displayed, select the Print title on plot option in the Title/Axes dialog in the Input1 menu.

.MOT files from versions of VIBRAT previous to 1997 do not transmit the lattice-type information which is necessary for display of the unit cell. Insert the correct Bravais-lattice symbol if necessary with the Lattice combo box. This does not affect the atoms, bonds and displacements.

VIBRATZ data for a crystal can be imported in either of two ways; showing the atoms in the primitive unit cell as a molecule; or using the normal ATOMS boundary options for crystals (see Import VIBRAT (.MOT) files).

VIBRATZ uses two types of atoms for crystals or infinite polymers: primary atoms, which are just those in the primitive unit cell; and secondary atoms, which are those required to complete the bonds and angles of the complete set of internal coordinates (i.e. force constants). Molecules do not require secondary atoms. For a crystal, the atoms of the primitive (not Bravais) unit cell are listed in the.MOT file, but the coordinates are given in the standard Bravais cell..

If you have imported the.MOT file as a molecule, not a crystal, this distincion is preserved. The structure is treated as a molecule, that is there is no symmetry and no lattice translations. Sometimes there may be more secondary than primary atoms. You have the option to show the secondary atoms in just the same way as the primary atoms; to mark the secondary atoms with a triangle; or to omit the secondary atoms altogether. If you omit the secondary atoms, the bonds to them will also be omitted.

If you have imported the.MOT file as a crystal, there are no secondary atoms. If the unit cell is non-primitive the Bravais cell is filled out (i.e. you do not see only the atoms in the primitive cell), and all atoms which are translationally equivalent are displayed in the same way.

To specify the details of the vectors which represent the atomic displacements, including the scale factor, go to the Atomic Vectors dialog in the Input1 menu.

Animate Motions. This section controls animated display of the vibrational motions.

The Screen button will produce an animated display in the current Graphics window. Clicking the mouse or hitting any key will terminate the animation. In Windows, the Full-Screen mode can also be animated with CTRL-A.

Frames/cycle applies to screen display only - it controls the speed, larger values giving slower speed.

The Movie button will bring up the Movie dialog and allow writing of "video" files, .AVI for Windows or .MOV for Macintosh and .SWF (Flash) for all.