```6.2.7.1.  SETTING LINKS/BONDS BETWEEN ATOMS

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

== GRAPHICS OPTIONS ===================================================
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
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
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

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 the existing set. The prompt

asks for a set of four numbers nuc1, nuc2, rmin, rmax defining a
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

>   [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

>   [C]  selected from submenu GC allows you to define line/stick colors of
all nl existing link constraint. The prompt

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

each of the nl existing link constraints. All sticks referring to a
given constraint will be drawn with the same thickness defined by
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

>   [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

>   [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.