Basic Parameters
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Dialog Box: Basic Parameters [Settings menu]

The Force constants radio buttons determine the units of force constants and the way they are interpreted. Force constants for bonds are always in md/A (millidynes per Angstrom), but those involving angles may be expressed in either of two ways - in md-A (per radian squared) or in md/A. Published values may be given either way, and it is absolutely necessary to choose the appropriate option if such values are to be used or compared.

Using md-A is the more "natural" in terms of the calculations - to use md/A everywhere it is necessary during calculation to multiply the angle force constants entered by two bond lengths. In the case of 3-atom valence angles this is straightforward - the two bond lengths are simply the two legs of the angle. However, for tau and psi angles there are three bond lengths, and for interactions involving these angles as many as six bond lengths could be involved. Selection of two bond lengths from among all the possibilities would be arbitrary. Therefore the approach taken in VIBRATZ when the universal md/A option is chosen is to multiply together all n bond lengths in all angles involved, take the nth root, and multiply the s-vectors for the angle coordinate by this factor. When the internal coordinates are converted to Cartesian forces, these s-vectors are multiplied together. Thus the result is to multiply the entered force constants by the following factors:

f (angle) = square root ( d1 * d2 * d1 * d2 ) = d1 * d2


f (angle/angle) = square root ( d1 * d2 * d3 * d4 )


f (bond/angle) = square root ( d1 * d2 )


f (tau or psi) = cube root ( d1 * d2 * d3 * d1 * d2 * d3 ) = cube root ( d1^2 * d2^2 * d3^2 )

This gives the possibilities excluding interactions involving tau or psi, which are more complex. In the case of angle/angle interactions, one pair of distances may be the same if one leg is shared, or all four may be different. In bond/angle interactions the two bond lengths are those of the legs of the angle, and the length of the bond does not enter unless it is also a leg of the angle. Because force-constant specifications in VIBRATZ may involve more than one specific symmetry-unique bond or angle (internal coordinate), or combinations thereof in the case of interactions, it will not always be possible to use the above formulas to convert from one system of units to the other. However, by narrowing the specifications so that each applies to only one specific bond or angle (and its symmetry equivalents) an exact conversion should be possible. Bond lengths and angles may be examined with the Coordination option in the Input Atoms dialog (Input menu).

The units for kappa force constants in Urey-Bradley models are always md-A - this is unaffected by the units setting.

The following three settings in this dialog involve scaling of atomic motions, which influence the calculation of intensities and least-square adjustment - they have no effect on the calculation of frequencies.

Atomic displacements represent radio buttons. First, the eigenvectors of the normal equations are divided by the atomic masses, to give actual atomic motions; the square-root of the masses, to give mass-weighted normal coordinates; or not at all (raw eigenvectors). The first option is the normal one, the others being used only for special purposes.

Normalize photon energy to radio buttons. For comparison between compounds and among vibrations of a single compound, the motions are then scaled by apportioning the energy of a photon in either of two ways; to a constant number of atoms, nominally 100, or to the actual number of atoms in the molecule or unit cell.

Scale atomic displacements by factor. After normalization, the motions are multiplied by an arbitrary factor, entered in this edit box. The calculation of intensities, especially Raman, assume that atomic motions are small in relation to interatomic distances.

If the photon energy is normalized to 100 atoms, then this scale factor should be in the neighborhood of 0.1. Factors much larger than this may result in motions which violate the assumptions of the calculations (next paragraph), and factors much smaller may cause inaccuracy because the motions may become smaller than the gereral level of precision of atom locations and other factors. One way of checking the accuracy of the calculated atomic motions is by selecting least squares (Control window) and comparing the "Frequency recalculated from atomic motions" with that calculated directly from the secular equation (see Output).

When forces are very weak, atomic displacements may be large enough to cause inaccuracies. This is especially likely for modes that are due to or dominated by torsion forces. If the "frequency recalculated" for such modes is very different from the observed frequency it may be necessary to reduce the scaling factor.

Atomic motions shown in the Atoms window are scaled by a further factor, in the Atom Plot Parameters dialog (Setting menu) or in the Dialog Bar attached to the Atoms window itself. This factor has no effect on intensities. The "average" or non-polarized Raman intensity as shown in the output window as well as the Spectra window is also influenced by two additional parameters in the Spectra Plot Parameters dialog (Setting menu).

Initial rotation angle. The rotation angle in the Atoms window can be reset at will, but the initial or default value is set in this dialog.

Sort modes in final list. The final list of frequencies can be sorted in descending order of frequency either by species or including all modes together. When sorted by species the result is often, but not always, the same as standard numbering schemes as v1, v2, etc.

Sound at end of calculation. If this box is checked, a sound will be emitted at the end of the calculation.

-----Windows only -----------------

The.WAV file named in the Sound file edit box will be played. If the file cannot be found or the system does not support multimedia sounds, the system sound will be emitted. Some sample.wav files are in the \SOUNDS folder

-----Macintosh/Linux only -----------------

The system sound is emitted.

File name filtering in Open File dialogs (Macintosh). When you want to open a file, it is usually best if the Open File dialog shows only the type of file you want, rather than every single file in the current folder. Every Macintosh file other than an application or program file has two four-character keywords or signatures - the Creator and the Type, and it is standard practice for Macintosh programs to use these to filter the file names shown in the Open File dialogs. The main data files for Vibratz have Creator 'VIBR' and Type 'TEXT'.

If the "Main data files (.VBR) - show only Creator = 'VIBR'... " box is checked, Vibratz use the Creator to filter file names for the File/Open dialog. If you only use the Macintosh, this box can usually be kept checked. Files from the IBM-PC (DOS or Windows) versions of Vibratz normally have Creator 'dosa', so this will not work - the Vibratz data files will be invisible. If you use files created on the IBM-PC, you will need to uncheck this box.

Many other types of auxiliary data files are used by Vibratz (see Types of Files), and it is not practicable to assign a different Type and or Creator to each of these. Atom-coordinate data files may be imported from other systems, not just IBM-PC, and such files will not have distinguishable signatures. However, it is fairly standard in non-Macintosh systems to use a three character file-name extension to distinguish different types of files. Thus if the "Use extensions (.XXX) for import and other secondary data files " box is checked, only those files with the appropriate extension will be shown. If not, all Type = 'TEXT' files are shown. You can change the extension for each type of import file when you select import of that type of file in the File Menu.

-----End Windows/Macintosh only ---------------