Control Window
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This window controls the overall operation of VIBRATZ. It is similar to a dialog with standard controls, but it cannot be dismissed without closing the current data set. It is present whenever there is a data set in memory. If no Control Window is present, go to the File menu and select New, Open or Import File.

See the complete list of Menu options

Save, SaveAs, Open, Close buttons. These buttons duplicate some of the standard functions in the File menu. However, these buttons may be more convenient and safer to use than selecting the functions in the File menu. If the Output Window or another of the Text windows (see Operation - Windows, Menus, Dialogs) is active, the commands in the File menu pertain to that text file, not to the VIBRATZ data set and thus it is quite possible to Save (for example) a text file when you really mean to Save the current VIBRATZ data set. If you click on the Save button in the Control Window, it is always the VIBRATZ data set which is saved.

Calculate button. This carries out a normal-coordinate calculation, using the data input through the dialogs in the Input and Forces menus. This always causes the Output file (below) to be rewritten. If no bond and/or angle forces have been entered (Forces menu), the calculation will be carried out as if the Symmetry only box (below) were checked.

Open button. This will open an existing .VIB or .VBR data file. Since VIBRATZ only does one problem at a time, the current file will be closed (if changes have been made you are asked if you want to save them).

Output File. VIBRATZ always writes the results of the calculation to an Output File, named infile.VBD, where infile.VBR is the name of the data file. This is a standard ASCII text file, which may be read and modified with any word processor. If the Window radio button is checked the contents of this file are shown on screen in a Text window, which has its own menu bar with editing options. The Listings button brings up the Listings dialog, allowing selection of what parts of the output are written to the file.

Symmetry only. If this box is checked, VIBRATZ does not actually calculate frequencies, but only determines the number of normal modes in each symmetry species. The results are printed in the Output file, and will also be shown in the Species Data dialog in the Input menu. If the Atoms plot box is checked, the atoms (only) will also appear in the Atoms Window.

Frequencies only. If this box is checked the calculations of atomic displacements, changes in internal coordinates and intensities are omitted. This can speed up the calculation considerably, especially for smaller structures. However, the time required for these calculations tends to be linearly proportional to the number of modes, whereas the time required for the actual solution for frequencies is proportional to a higher power of the number of modes in each species.

Spectrum plot. If this is checked, sythetic spectra will be drawn in the Spectra Window. The Parameters button brings up the Spectra Plotting Parameters dialog in which the various parameters can be set. The selection of infrared and/or Raman components which are shown in the spectra is made with the controls in the Dialog Bar of the Spectra Window itself after it appears.

Atoms plot. If this is checked, the atomic structure will be drawn in the Atoms Window, with vectors representing the atomic motions in the particular normal mode selected. The Parameters button brings up the Atoms Plotting Parameters dialog in which the various parameters can be set. The Atoms Window itself has a Dialog Bar which allows simple rotations and selection of the particular mode which is shown. The mode may also be selected in the Select Mode dialog in the Settings menu.

You can see the atomic structure before forces are entered by clicking on Calculate, after checking the Symmetry only box (above). If fact, if there are no bond or angle forces specified the calculation will be carried out as symmetry only, and there will be no atomic displacement or mode information in the plot.

Motion file (.mot). If this is checked, a file is written with the atomic displacements in all modes, for use in other programs, such as ATOMS, which can plot the structure in more elaborate ways than VIBRATZ.

NRVS check box. This enables the special features of VIBRATZ for Nuclear Resonance Vibrational Spectroscopy. If you do not have NRVS data or wish to model an NRVS spectrum, uncheck this box.

NRVS Parameters button. This calls up the NRVS parameters dialog.

Spectrum file (.spc). If this is checked, a file is written with the calculated intensities of all modes. This includes the individual components (x, y and z for infrared and the six cross-products or combinations thereof for Raman) and the spatial averages.

Cartesian forces. VIBRATZ may optionally use Cartesian atomic forces instead of valence forces or internal coordinates. In this case a matrix of Cartesian atomic forces is read in, and any forces entered in the dialogs of the Forces menu are ignored. The input file is specified in the Cartesian Atomic Forces from File dialog, called up with the Cartesian Forces button.

The Units for angle forces option, formerly in this dialog, has been moved to the Angle Forces dialog.

Forces List. Once the specifications for the forces or internal coordinates have been entered in the dialogs of the Forces menu, the easiest way to change the force-constant values or select which ones are subject to least-squares adjustment is through the Forces List button. This gives a single list of all the current force constants.

Mean-Squares button. This will compute the mean-square changes in interatomic distances, for use in calculating EXAFS

Isotopes button. This controls isotope substitution in up to two configurations beyond the base or non-substituted configuration - see Isotope Configurations

Least-squares iteration. VIBRATZ can do least-squares adjustment of the force constants in three different ways, analytical refinement on frequencies, step-by-step refinement on frequencies, or step-by-step refinement on intensities for NRVS spectra (and also step-by-step refinement on both frequencies and NRVS intensities). Different parameters appear at the bottom of the Control Window depending on which option is selected.

Note that entire species may be omitted from the calculation, and from least-squares, with the Species dialog in the Input menu. Also, individual modes may be omitted, using the settings in the Observed dialog in the Input menu.

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1) Least-Squares - Analytical method. This assumes that the calculated atomic motions for each mode are correct, and calculates the change in the force constants required to make the calculated potential energy agree with observed (see Theory and Implementation). This method is not supported for Isotope Configurations.

Parameters. The End criterion determines when the cycles are terminated. For frequency refinement only, if the improvement in the average squared deviation in wavenumber for all modes is smaller than this value the adjustment is terminated, keeping the new adjusted values. If the average deviation worsens, the interation is terminated and the force constants revert to their values before the current cycle. This can usually be set quite small, 0.01 or less, unless computation time is a problem. However, if it is too small in comparison to either the Reduction factor or the step-by-step Increment, the refinement may terminate prematurely. The Reduction factor multiplies the calculated change in each force constant - a value less than 1.0 will potentially reduce overshoot, but will give slower conversion.

The observed wavenumbers are entered in the Observed dialog in the Input menu. The modes must be entered in decreasing order of wavenumber for each species. If a mode is not observed, it is given a wavenumber of zero.

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2) Least-Squares - The step-by-step method (on mode frequencies) simply varies each selected force constant by the given increment until there is no longer any improvement in the squared deviations.

Parameters. The Fcon Increment is simply added and/or subtracted from the last value of each force constant until there is no improvement. If the Order is up-down the increment will be first added, and if there is no improvment the value of the force constant will revert to the original and the increment will be subtracted. If the order is down-up the process with start with subtraction. It may be a good idea to refine from the original values one way, then re-read the file and try the other way. The End criterion of earlier versions is no longer used - the increment is added or subtracted until either the sum of squares increases, or the Maximum change in each fcon is reached (this condition will be noted in the refinement output).

The step-by-step method does not require that the number of force constants be less than or equal to the number of observations. The force constants will be adjusted in the order given in the Forces menu, or the Forces List in this dialog, and thus any redundant or correlated force constants at the bottom of the list will tend to be adjusted less than those at the top. For example, there is a strong correlation between polyhedron angles and the corresponding Urey-Bradley X-X repulsion forces, and the order in the list dictates that angles will be refined first. If it is desired to refine primarily on the X-X forces the angles should be deselected from refinement in preliminary cycles.

Additional Isotope Configurations may be included using the Isotopes button.

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3) Least-Squares - NRVS intensity. See Spectra Window for details of NRVS spectra. This uses the same step-by-step method of varying force constants as the step-by-step method on mode frequencies, but the quantity minimized is the average sum of squared deviations between calculated and observed NRVS intensity for the specified wavelength limits.

Parameters. The Increment, Maximum change and Order are the same as for Step-by-Step (frequencies). The Low frequency limit and High frequency limit are the same as in the NRVS Parameters dialog, where detailed parameters of the NRVS spectra are set. The Refine box determines whether the refinement is on isotopes using the spatial average spectra, or on orientations using the base isotope configuration (see the NRVS Parameters dialog).

The individual NRVS frequencies used are those of the input data - frequency intervals can no longer be set.

If the Use frequency deviations also box is checked, the refinement will be on the sum of a) the average squared NRVS intensity deviations, plus b) the average squared deviation of observed and calculated wavelengths:

Sum of squared deviations = F(nrvs) * sum[ Dev(nrvs)^2 ] / N(nrvs) + F(frequency) * sum[ Dev(freq)^2 ] / N(freq)

Here the F factors are the Factor for NRVS deviations and the Factor for frequency deviations. VIBRATZ stores the NRVS spectra in units of cm-1 for frequency and cm for intensity, so the Factor for NRVS deviations should be on the order of 1000 to get results in the single-digit range - the factor for frequency deviations can be around 1.


Additional Isotope Configurations may be included using the Isotopes button.

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Recommendations for least-squares refinement on frequencies. For frequency refinement, the step-by-step method, added to VIBRATZ after the analytical method had been in use for some time, seems to be much more powerful. In fact the analytical method may be dropped if it is not found to give better results in at least some cases. With either method least-squares adjustment is not likely to be successful unless the average deviation between calculated and observed at the start is less than the average frequency difference between modes in each species - your model of the forces must be essentially correct (see Theory and Implementation).

Errors and Correlations

After Step-by-Step refinement, VIBRATZ can provide some information about the reliability of the calculation. If the Do Errors box is checked, each fcon is stepped away from the minimum until the total deviation is increased by the specified fraction.

If the Do correlations box is checked, to get the correlation between two fcons, one fcon is moved away from its value at the minimum and then the second fcon is adjusted to re-minimize the sum of squared deviations.

These calculations involve repeated complete solutions of the normal equations, so they can be very time-consuming.