The first step is to enter the basic structural data, which is in the dialogs of the Input menu, or buttons in the Startup Window. There are basically three ways to enter the data, through the New or Import buttons or options in the File menu; or by modifying an existing file.
The New option will step through the dialogs which are usually mandatory for input of new data. This process is described below.
The Import option will read data from a file of one sort or another. Crystallographic data files will usually provide most if not all of the information needed in the Input menu, but molecular files may provide only part of the necessary data, namely the atomic coordinates
If you want to enter data for a compound which is closely related to one you have already done, it may be easiest just to change only certain parts of the input, for example the atomic positions and/or symmetry, or perhaps just the atomic weights.
Molecules. All the Lattice translation boxes at the bottom of the dialog must be unchecked for a molecule. Normally the atomic coordinates for a molecule are on Cartesian axes, so axis lengths should be 1.0 and interaxial angles should be 90 degrees. One possible exception might be molecules with trigonal or hexagonal symmetry, for which an interaxial gamma angle of 120 degrees simplifies the symmetry matrices. VIBRATZ uses the gamma angle to distinguish between hexagonal and Cartesian axes and should use the correct symmetry matrices.
Crystals. All the Lattice translation boxes at the bottom of the dialog must all be checked for a crystal.
Although VIBRATZ will ultimately use only the atoms in the primitive unit cell, you must enter here the axes for the conventional Bravais cell, which may be non-primitive.
In the case of trigonal rhombohedral crystals you can choose either primitive axes or non-primitive hexagonal axes. If you choose rhombohedral axes, VIBRATZ will automatically derive the appropriate Pre-Calculation Rotations (below) to bring the 3-fold symmetry axis parallel to z, as required for proper symmetry analysis. The choice of rhombohedral/hexagonal axes should agree with the space-group setting in the Symmetry option. The axes for monoclinic crystals should be consistent with the atomic coordinates, but if the second setting is used (unique axis b), the axes, atoms and symmetry matrices must be rotated so that the unique axis is parallel to z. VIBRATZ detects this setting and automatically enters the correct rotations in the PreCalculation Rotations dialog (below).
Polymers. One or two of the Lattice translation boxes at the bottom of the dialog should be checked.
Molecules. Molecules should either have no symmetry or point-group symmetry (not space-group symmetry). The symmetry matrices supplied by VIBRATZ, whether in internal form for crystallographic point groups or in files for non-crystallographic groups, have orientation as follows. Any unique axis is parallel to z. If "horizontal" two-fold axes perpendicular to the unique (normally high-order) axis are present, one of them is parallel to the x-axis. If there are vertical mirror planes, but no horizontal 2-fold axes, one of the mirror planes is perpendicular to the x-axis. For icosahedral groups, one 5-fold axis is vertical and an adjacent 3-fold axis is in the x-z plane.
If the atomic coordinates for your molecule are not consistent with these orientations, there are two alternatives. First, the atomic coordinates may be rotated around the z-axis with an option in the Input Atoms dialog. Second, you could supply symmetry matrices consisent with your orientation, reading them in with the Symmetry from file option in the Point-Group Symmetry dialog. This might require different basis functions from the standard ones (see Making Symmetry Files), or rotations as in the next paragraphs.
Crystals. The normal choice of symmetry option is Space Group, but if you have imported a file the option may be Custom Symmetry.
Polymers. Polymers should normally use Space Group or Custom symmetry. Translations in one or two directions should be disabled in the Title/Axes dialog dialog. The chosen space group should not have screw-axis, glide-plane or centered-lattice translational components in a non-polymer direction.
This is intended primarily for space groups which do not have the standard orientation described above (see Space Group Symmetry); it rotates both the symmetry matrices and the atoms in order to make the orientation consistent with the basis functions used for symmetry analysis. The proper rotations should usually be determined automatically when space-group symmetry is specified, and this dialog does not normally appear in New input. It is not necessary for point groups unless a custom set of symmetry matrices with non-standard orientation is read in with the Symmetry from file option in the Point-Group Symmetry dialog, or if a non-standard orientation is used in the Custom Symmetry option.
Input Atoms dialog. VIBRATZ generates all the atoms in a molecule by applying the symmetry matrices to the input atom coordinates, so there is no need to enter all atoms. However, it is possible to enter all atoms, and VIBRATZ should identify those which are unnecessary and delete them with your permission. The Atom type for each input atoms is typically the atomic number. The Coordination option can be very valuable in identifying the bonds and angles which may be important as internal coordinates (see Forces below) - it lists the bond distances and angles.
The atom types list ties together the atom types assigned to the input atoms with the bond, angle and interaction specifications, and assigns atomic weights. The simplest way to do this in most cases is to use standard atomic numbers, and this is the default list. However, there are times when it may be necessary to assign different type numbers to input atoms of the same chemical species, for example when an element occurs in Urey-Bradley polyhedra with different coordination numbers.
Species dialog.
This dialog lists the species for the selected point/factor group, but before a calculation is made the number of modes in each species is not correct. If the checkbox for a species is not checked at this stage, that species will not be calculated and the number of modes will remain zero. Once a calculation has been made, these numbers are present and are saved in the data file.
For least-squares adjustment, and general evaluation of the calculation, observed wavenumbers can be entered for each species.
The sequence of dialogs in New input may be halted at this point, without entering forces. If this is done, a symmetry analysis may be carried out without entering forces by checking the Symmetry only box in the Control Window and clicking on the Calculate button. This gives the number of modes in each species only, without information about frequencies or atomic motions.
Forces. If the structure is not well known, it may be useful to use the Coordination option in the Input Atoms dialog. This can give not only the coordination of each atom, but a sorted list of bonds and angles. Generally the strongest forces involve the chemically strongest bonds, which are usually the shortest. However, some modes are dominated by forces other than bonds and 3-atom angles, and the longer-range forces of this type are not so readily identified. Possible long-range forces inclued tau torsion angles, psi bond-plane angles and second-nearest neighbor "bonds". It should first be considered whether these more complex forces cannot sometimes be avoided by use of 3-atom angle forces in the direction perpendicular to the plane of the bond (or in two directions for 180 degree angles) - see Angle Force List. Otherwise it may be a good idea to carry out a calculation using only the stronger short-range forces, that is ordinary valence bonds and 3-atom angles, to 1) see what symmetry species are affected by an insufficient number of forces, and 2) study the structure in the Atoms graphics window. No harm is done if there is an insufficient number of force constants (or internal coordinates) overall or for a particular species - some frequencies may simply be calculated as zero or much lower than the true values. It should also be clearly understood that there is no limit to the number of force constants or internal coordinates which may be used - since all forces are converted to Cartesian coordinates, and symmetry analysis and solution of the secular equation are done using the Cartesian coordinates, redundancies among the internal coordinates need not be explicitly considered (but superfluous force constants may cause problems in least-square adjustment).
For crystals, particularly those with a small unit cell, the geometric relationships which call for more complex forces such as tau and psi angles and/or second-nearest neighbor bonds may not always be apparent in the part of the structure (basically one unit cell) which can be shown in the Atoms graphics window. It may be advantageous to examine the structure in a program such as ATOMS which can show larger portions (many unit cells) of the structure.
Full Calculation. Having completed the mandatory input in the dialogs of the Input Menu, with at least some forces specified in the dialogs of the Forces Menu, clicking on the Calculate button with the Symmetry Only button unchecked will give a full calculation with output of frequencies and information about atomic motions and changes in the bonds and angles (depending somewhat on which output items are selected in the Listings dialog). In terms of adjusting force constants, the most informative part of the output is probably the parts labeled "En/grp", which is the fraction of the energy of the mode under consideration contributed by all the individual bonds, angle or interactions belonging to each input coordinate or force constant.
Least-Squares. In general, least-squares adjustment should not be attempted until the force model is complete, that is until the full number of force constants is specified. Even then, it may be necessary to limit refinement to only a few force constants at a time. The fastest way to change which force constants are refined is through the Forces List button in the Control Window - this gives a consolidated list of independent force constants.
Perhaps the main requirement of least-squares is that the assignment of calculated to observed modes be correct, that is the list of calculated modes in order of frequency within each species should correspond to the list of observed modes (of course the assignment of observed modes to species must also be correct). When the full number of modes in a species is not observed, the determination of which particular ones are absent (absent modes are signified in VIBRATZ by entering observed wavenumber 0.0) is extremely critical, especially if higher-frequency modes are absent. Correct assignment and correspondence of modes becomes more difficult, and requires more exact pre-adjustment of force constants, the more frequencies there are in a species and the fewer restrictions there are on the nature of the modes because of symmetry. This consideration being met (not a trivial requirement), the least-squares process is capable of adjusting force constants over a considerable range, especially if only one or a few are done at a time.
Some force constants may only appear in certain species, and both Species and force constants (most easily with the Forces List button in the Control Window ) may be omitted from a least-squares calculation to take advantage of such situations. The force constants or internal coordinates which participate in each species are not directly determined by the symmetry analysis in VIBRATZ (as they would be in a symmetry analysis based on internal coordinates), but the average contribution of each force constant to each species is given in the Output.