6.3.5.1. SETTING LINKS/BONDS BETWEEN ATOMS

next, previous Section / Table of Contents / Index Option [C] selected from the graphics option menu G, see Sec. 6.3.5, allows you to define links connecting atom pairs and shown in plots by straight lines or cylindrical sticks. This can be used to visualize chemical bonds or neighbor relationships inside the cluster. The link option menu GC of BALSAC/CLUSTER sessions reads == GRAPHICS OPTIONS =================================================== nl link(s) : Nuc1 Nuc2 Rmin Rmax Lcolor Lrad 1) nuc1 nuc2 rmin rmax lcol lrad 2) ... [N]ew [A]dd [E]rase [C]olrs [R]adii c[T]abl [D]ispla {[X]plot} [?,]esc ================================================================= 32 == where nl is the number of link constraints defined at present. Each constraint is given by one line where two different types can appear: For positive nuc1 and nuc2 the values refer to nuclear charges (values nuc1/2 = 0 are meaningful, see below) and are followed by a distance range [rmin, rmax], a line/stick color lcol, and a stick radius lrad. Here a link constraint means that any two atoms of the cluster will be connected by a line or cylindrical stick if one atom is of nuclear charge nuc1, the other of charge nuc2, and if the distance between the two atoms lies inside the distance range [rmin, rmax]. For negative nuc1 and nuc2 the values refer to atom numbers. The distances rmin, rmax are meaningless and set to zero while the line/stick color lcol, and the stick radius lrad are used. Here a link constraint means that only the two cluster atoms of numbers -nuc1 and -nuc2 will be connected by a line or cylindrical stick. For stick radii rad = 0 atom pairs will be connected by thin lines of color lcol while rad > 0 uses cylindrical sticks of finite thickness (radius rad) and of color lcol . With atoms shown as (shaded) balls lines/sticks will connect ball surfaces thus enhancing the 3-dimensional impression. Charge values nuc1/2 = 0 ignore the respective charge constraint. Thus, nuc1 = nuc2 = 0 connects any pair of atoms with a distance inside the prescribed range while for example nuc1 = 14, nuc2 = 0 connects all Si atoms with any other cluster atom A if the Si-A distance lies inside the distance range [rmin, rmax]. All options of the link option menu GC are identical to those of the BALSAC/LATTICE link option menu as discussed in detail discussed in Sec. 6.2.7.1. next, previous Section / Table of Contents / Index