The vibrational-analysis program VIBRATZ and the structure-display program ATOMS are designed to work together. The structure-display capabilities of ATOMS, which has 3-D display and animation of vibrational motions, among many other things, are much greater than those of VIBRATZ.
Communication between the two programs is through the modes (.MDS) binary files, which can be written by either program. These files contain the detailed data for each mode, including atomic motions. These files are designed for quick access to the data for each individual mode, so all the data for all modes does not have to be in memory at the same time.
ATOMS can import the .MOT ascii (text) files written by VIBRATZ. These also contain detailed data for each mode. As ATOMS imports a .MOT file, it writes a .MDS (binary) file - this should be the same as the .MDS file written by VIBRATZ. Why bother with two different types of file? Because the binary .MDS files are not portable between platforms (e.g. Intel vs. Motorola processor).
ATOMS can also import the main VIBRATZ .VBR data files. The information in these files is not the same as in the .MOT files - the .VBR data files, like ATOMS .STR files, contain complete symmetry information and only the symmetry-unique input atoms, while .MOT files contain all atoms in the molecule or unit cell, without symmetry. The atomic motions in .MDS and .MOT files must refer to all atoms in the molecule or unit cell. Thus, **do not** import .VBR files into ATOMS if you want to display atomic motions.
When importing either type of VIBRATZ file, ATOMS will read the type numbers modulo 100 - for example, atom types number 6, 106, 206 etc. will all be converted to 6 (carbon).
Recommended procedure for using ATOMS to show vibrational motions.
1) If you import an ATOMS (.STR) file into VIBRATZ, it is a good idea to use two different names, for example myfile_orig.STR for the original ATOMS files, and myfile.VBR for the VIBRATZ file. This is because you will use another .STR file, without symmetry, to display the motions.
2) In VIBRATZ, check the .MOT file box in the Control window so that a .MOT file is written during calculation. This will be myfile.MOT.
3) In ATOMS, import the myfile.MOT file. This will rewrite myfile.MDS. The new ATOMS file will be by default myfile.STR. Set up the boundary (for crystals), display parameters, vectors, etc. as desired. Most parameters dealing specifically with motion display are in the Vectors and Vibrational Modes dialogs in the Input1 menu. The bonds are just those specified in VIBRATZ.
4) If you return to VIBRATZ to recalculate with changed forces, it will rewrite myfile.MDS, which can be read by ATOMS, so ATOMS will remain up to date with the latest VIBRATZ calculations. On the other hand, if you want to preserve the motions for a particular calculation, you can rename the .MDS file, e.g. myfile_1.MDS (you must do this in the operating system). You can switch between different .MDS files in the Vibrational Modes dialog in the Input1 menu. You can also reread the .MOT file, for atomic motions only, in the Vibrational Modes dialog.
5) Starting a new problem. Once you have the parameters in ATOMS set up to your liking, before importing a new .MOT file, just read an old ATOMS file with the appropriate settings. When you import a .MOT file, the new ATOMS .STR file will have the same name as the .MOT file. Or, save the desired parameters by selecting Save Defaults in the Settings menu in ATOMS. These parameters can be reread during import, or later through the Settings menu.
6) Transferring problems across platforms. The binary .MDS files may be incompatible between platforms (Macintosh and Windows computers write the bytes of numbers in opposite order). Thus you should transfer the ascii (text) files myfile_orig.STR, myfile.VBR and myfile.MOT. When you open the myfile.STR file in ATOMS for display of atomic motions, use the option in the Vibrational Modes dialog in the Input1 menu to read in the .MOT file for atomic-motion parameters only. This will cause writing of a new myfile.MDS. Rerunning VIBRATZ should also rewrite the .MDS file.
Display parameters in ATOMS. The atomic radii are controlled during import with the choice between covalent and ionic radii, and by the factor which may be applied - for displaying motions the factor should normally be well under 0.5. You can later change radii globally with the Atoms-Global option in the Input1 menu. You can change the default radii and atom colors for import by editing the ELEMENTS.ION and ELEMENTS.COV files. (The file RADII contains a universal table for automatic bond generation - this should not be modified unless there are problems with automatic bond generation). Bond parameters may be set during import, or reset with automatic bond generation (Bonds dialog in the Input1 menu).
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 the values of the first bond when defaults were last saved.