Dialog Box: Atom Types [Input menu]
This lists the atom types which are used in the definitions of force constants (Forces menu). The atom type list also specifies the atomic weights, which must be accurate for proper calculation of frequencies. The data for each type 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 Type number is the number which is used in the bond and angle specifications (Forces menu). It is typically the atomic number, but see below.
The Mass is the atomic weight - see below under ELEMENTS.DAT file for different default values.
The Charge is used to calculate the dipole moment, changes in which determine the infrared intensities.
If the Use (charge) button is not checked, this atom type is assigned the charge necessary to neutralize the molecule or unit cell. This assumes that at least some other atoms are assigned charges. This option is intended for radicals, such as CO3, SiO4, etc.
The Radius is optionally used in the Coordinates option (called from the Input Atoms dialog, Input menu), to help in screening bond lengths. It is not used in the Atoms graphics window, where all atoms have a constant radius (Atom Plot Parameters).
The Color, which is shown on the button, is selected graphically with a standard system color dialog which comes up when the button is clicked.
Shade. Gray shades, which are used in black-and-white display, printing and other output, are numbers ranging from 0 (white) to 15 (black).
Used. After a calculation, this column will indicate whether each type is actually used by the current data set. When saving a data set, if not all atom types are used by the Input Atoms you are given the option of deleting the unused types.
The Clear button entirely removes the current list. The Defaults button restores the standard atomic numbers and atomic weights. The default atom type list contains standard atomic numbers and mean atomic weights for the natural isotope mixture of each element, which is adequate for many purposes. Of course if the compound under consideration has isotopic substitution, you must correct the atomic weight. See below under ELEMENTS.DAT file.
Type numbers. It may be necessary to use more than one type for a given element, in order to more easily differentiate bond and angle force constants. The main alternative to using standard atomic numbers, or in other words chemical species, as type numbers is to use symmetrically distinct input atoms. This may be necessary in some cases, for example when using Urey-Bradley forces involving a single element in different coordinations, but generally should be avoided as it often leads to an excessive number of force constants. Defining bonds and angles using chemical species (atomic numbers) and bond-length and angle limits allows easy transferrence of specifications from one compound to another. In fact, files containing such specifications may be written and read (Read and Write file options in the Forces menu). When assigning different type numbers to the same chemical element, 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.
If you are studying compounds which are isostructural or even very similar, it may be advantageous to retain all the force specifications using constant type numbers, and just change the atomic weights. Certainly isotopic substitutions can be handled this way, if the substitution is complete. Also, for example, substitution of one transition metal for another, or one rare-earth element for another, may not require any changes in the force constant specifications, and even the force constant values may be close enough for initial trials.
ELEMENTS.DAT file. See Types of Files. The default data for atom types are in this file, which can be modified with a word processor. On each line are listed the atomic number; the standard chemical symbol; the effective (covalent) radius; the red, green and blue components of the color on a scale of 1-255; the gray-scale "color" (for black-and-white output) on a scale of 0 for white to 15 for black; the atomic weight; and the normal ionic charge. The standard version of this file has the atomic weight for the most abundant isotope (if this is known - otherwise the average natural weight is used). An alternate version of the file, called ELEMAV.DAT, has the average natural atomic weight. If you prefer to use this version, it should be renamed ELEMENTS.DAT. The backup for the most-common-isotope version is called ELEMAIN.DAT.