Dialog Box: Input Atoms [Input menu]
This gives a list of input atoms. The data for each one is in a single line in the scrolling list or spreadsheet. To add a new entry, press the down arrow key while the focus is on the last row, or click the Add button.
The Label may be up to 6 characters. There should be no embedded blanks.
The Type refers to the Atom Types list. By default, type numbers are standard atomic numbers, although it is also possible to assign different type numbers to particular atoms to assist in defining bonds and angles. In fact, it is frequently necessary to assign different type numbers to specific input atoms to differentiate bonds and angles. It is usually best to use atomic numbers modulo 100, for example 6, 106, 206, etc. for carbon atoms, as the structure display program ATOMS, which can animate the vibrational motions, will read these all as type 6 (carbon) when importing VIBRATZ files.
In the x, y and z boxes, enter the coordinates, fractional in the case of crystals, or absolute in the case of molecules. For polymers, coordinates could be part fractional and part absolute. Coordinates should be given to the 5th decimal place where necessary - for example, a coordinate which is 2/3 by symmetry should be entered as 0.66667, not 0.667.
Note. If Urey-Bradley forces are used, and if an element occurs as central atom in CXn polyhedra in different coordinations (that is, if n is not always the same), each occurrence must be given a different type number.
VIBRATZ expects to use the specified symmetry on the entered atoms to generate all the atoms in the unit cell or molecule. However, it is possible to enter all the atoms, including some or all symmetry equivalents. VIBRATZ will then identify those which are redundant, and will delete them with your permission.
The Read Atoms from File button calls the Read Atom List from File dialog, to read a text file containing atom labels and coordinates.
The Coordination button calls up the Coordination of Atoms dialog which shows the bonding environment (bonds and angles) of any or all atoms. This option can give sorted lists of bonds and angles which can be an important aid in assigning force constants.
Z-Matrix. This allows construction of a molecule from a z-matrix or table of bond lengths and angles instead of using Cartesian coordinates.
Rotate all input atoms on axis. This option is primarily for molecules, in case the atomic coordinates are for a setting of the symmetry elements which is different from that used by VIBRATZ. The standard VIBRATZ orientation is as follows: In Cnv groups a vertical mirror plane is perpendicular to the x axis (not the y axis if there is a difference). In groups which have horizontal 2-fold axes with or without vertical mirror planes, a 2-fold axis is oriented parallel to the x axis and mirror planes are oriented accordingly. The icosahedral groups are oriented with a 5-fold axis parallel to z, and an adjacent 3-fold axis in the x-z plane.
The rotation is permanent, but can be reversed by entering the negative of the angle (see Orientation)