Import VIBRATZ Files
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Import.MOT or .VBR (VIBRATZ) Files [ File menu (Startup) or File menu (Graphics)]

Both the.VBR main data files and the.MOT vibrational displacement files from VIBRATZ can be imported. The.VBR files simply contain standard crystallographic information. The remainder of this topic pertains to the .MOT files. See the topic Coordinating ATOMS and VIBRATZ in the Reference section for more information.

When importing either type of VIBRATZ file, ATOMS will read the type numbers modulo 100 - that is, atom types number 6, 106, 206 etc. will all be converted to 6 (carbon).

The.MOT vibrational displacement files are written by the VIBRAT program (Dowty, Phys Chem Minerals, 1987, 14:67) or the Windows version VIBRATZ (available from Shape Software). ATOMS converts the infomation in the.MOT file into a standard.STR ATOMS data file, and also a special.MDT file which contains the atomic displacements and other information for each vibrational mode. When the.MOT file is imported, the first vibrational mode in the list is selected and displayed (after calculation). When you re-read the.STR file, it will contain the information for the vibrational mode in the list which was selected when the file was saved. To see other modes, you must select the Vibrational Modes option in the Input1 menu. You must recalculate after changing the mode, since new pseudo-atoms and bonds representing vectors need to be generated.

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.

The atoms will be given the default colors specified in the ELEMENTS file, as for other types of import file. However, you have the choice of using radii in the ELEMENTS file (or some fraction thereof - see the Preferences dialog in the Settings menu), or of using constant radii.

Bonds.
When importing a .MOT file, bond specifications are taken directly from the VIBRATZ data. If there is a structure in memory, and if there are bonds (Bonds dialog in the Input1 menu), the radius and colors of all the new bonds are taken from the first old bond - if there are no bonds, radius and colors of the bonds derived from the .MOT file will be standard (radius 0.0, black rim, white fill), or from the values of the first bond the last time defaults were saved (Save Defaults in Settings menu).

Crystal import mode. VIBRATZ.MOT data for a crystal can be displayed 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. If the choice is a "molecule", there will usually be both primary and secondary atoms (next paragraph). Lattice translation will be disabled. If the choice is to show as a crystal, there will be no secondary atoms, and every translationally equivalent atom will be the same - they will all have the same motion vector. The boundary option will be Unit Cell, current default, but this can later be changed. The atom list (Atoms in the Input1 menu) will include all atoms in the Bravais (not primitive) unit cell. With either option, there will be no non-translational symmetry, that is all atoms in the unit cell will be in the atom list.

Secondary atoms (applicable only to crystals imported in molecule mode). VIBRAT 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 (force constants). Often there are more secondary than primary atoms. If you choose to show the structure as a molecule (last paragraph), 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. Molecules do not require secondary atoms.

The Vector button calls up the Atomic Vectors dialog (Input1 menu), for specification of the details of the vectors which represent the atomic displacements, including the scale factor.