6.2.7.1. SETTING LINKS/BONDS BETWEEN ATOMS

next, previous Section / Table of Contents / Index Option [C] selected from the graphics option menu G, see Sec. 6.2.7, allows you to define links connecting atoms and shown in plots by straight lines or cylindrical sticks. This can be used to visualize chemical bonds or neighbor relationships inside the lattice section. The link option menu GC of BALSAC/LATTICE 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 lattice section 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 lattice 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 atom A of the lattice section if the Si-A distance lies inside the distance range [rmin, rmax]. Note that in layer-by-layer display mode only atoms of the same layer will be connected by lines or sticks while for atom-by-atom mode every two atoms of the complete section may be connected. Further, in layer-by-layer display mode links between selected atoms (nuc1 < 0, nuc2 < 0) refer to atoms of the same layer and will be repeated for each layer due to the internal atom numbering scheme. This may result in unwanted visual effects. > [N] selected from submenu GC allows you to define link constraints from scratch overriding any existing constraints. The prompt No. of links NL (0-nmax, -1=esc): asks for a (new) number nl of link constraints to be given in the following where nmax gives the largest number (nmax = 20 at present). Dummy input nl = -1 leave all existing link definitions unchanged while nl = 0 erases all definitions and returns to submenu GC. For nl > 0 the prompts Input nl link(s) : 1) NUC1,NUC2,RMIN,RMAX : ... nl) NUC1,NUC2,RMIN,RMAX : ask for nl sets of four numbers nuc1, nuc2, rmin, rmax defining the new link constraints as discussed above. Note that for values nuc1, nuc2 < 0 (second constraint type) parameters rmin, rmax will not be used and are set to zero in the listing. For each constraint a default stick radius, rad = 0.0, and a default line/stick color, lcol = ICLBD (default line connect color, see Secs. 6.2.15, 6.4.10), will be assumed but can be redefined later on, see below. After input of all link constraints BALSAC returns to submenu GC. > [A] selected from submenu GC allows you to add another link constraint to the existing set. The prompt Add link NUC1,NUC2,RMIN,RMAX : asks for a set of four numbers nuc1, nuc2, rmin, rmax defining a link constraint as discussed above to be added to the existing ones. (Note that for nuc1 < nuc2 the nuclear charges will be swapped internally such that nuc1 > nuc2.) For values nuc1, nuc2 < 0 (second constraint type) parameters rmin, rmax will not be used and are set to zero in the listing. For the constraint a default stick radius, rad = 0.0, and a default line/stick color, lcol = ICLBD (default line connect color, see Secs. 6.2.15, 6.4.10), will be assumed but can be redefined later on, see below. After input of all link constraints BALSAC returns to submenu GC. > [E] selected from submenu GC allows you to erase link constraint from the existing set. The prompt Erase link no. N (1 - nl, 0=esc) : asks for a number n denoting the n-th constraint of the list shown in submenu GC to be removed from the set of constraints. Here n = 0 ignores the erase option while 0 < n <= nl removes the respective link constraint after which BALSAC returns to submenu GC. > [C] selected from submenu GC allows you to define line/stick colors of all nl existing link constraint. The prompt Input nl link color(s) : asks for nl integers lcol(i), i= 1,... nl denoting code numbers of the color table (nctot colors, see Sec. 5.4) for each of the nl existing link constraints. All lines/sticks referring to a given constraint will be drawn with the same color lcol. This allows you to distinguish between different constraints in a plot. Possible colors can be inspected by the color table display, option [T], see below. After complete input BALSAC returns to submenu GC. > [R] selected from submenu GC allows you to define stick radii of all nl existing link constraint. The prompt Input nl link radii ( rlmin / rlmax ) : asks for nl values rad(i), i= 1,... nl denoting stick radii for each of the nl existing link constraints. All sticks referring to a given constraint will be drawn with the same thickness defined by radius radi. This allows you to distinguish between different constraints. Parameters rlmin, rlmax shown in the above prompt are minimum and maximum values of all atom radii of the lattice section helping to choose reasonable stick radii. No stick should be thicker than 70% of the diameter of the largest ball in the plot. Note that the use of sticks of finite thickness is meaningful only if atoms are represented by balls. After complete input BALSAC returns to submenu GC. > [T] selected from submenu GC displays a color test table (in a separate graphics window, Unix) showing all color definitions together with color numbers available inside BALSAC. The table is described in detail in the graphics option, see Sec. 6.2.7. > [D] selected from submenu GC shows up to 10 lines of the most recent output generated by the graphic analysis option, see Sec. 6.2.14.2, by ============ Latest Graphics Output ================== 1: Xyz,R,Id( n1)= x y z rad nuc ... ====================================================== This allows you to look up and use numerical output from the analysis for input within submenu GC. After the listing BALSAC returns to submenu GC. > [X] selected from submenu GC (if available) plots the lattice section (switching to graphics mode (DOS) or opening a graphics window (Unix)) or lists its atom coordinates depending on the plot/list mode defined in the graphics option, see Sec. 6.2.7. > [,] selected from submenu GC returns to the graphics option menu G, see Sec. 6.2.7. next, previous Section / Table of Contents / Index