Atom Bonds Window 1267


L-clicking the “Settings | Atom bonds | Modify bonds …” entry opens the Atom Bonds Window which allows inspecting, changing, adding, and removing bond and vector definitions. Bond definitions can be used to visualize chemical bonds or atom neighbor relationships while vector definitions allow to visualize additional vectors describing 3-dimensional (vector) quantities, such as forces inside the particle.

For bond definitions the atom bonds window looks as follows

This bonds window shows below “nb bond definition(s)” (nb denoting to total number of bond definitions) the bond definition box listing all existing bond definitions by their parameters and allowing selection of a definition for modification or removal.

Each bond definition in the bond definition box is shown by a line

n:   Z1   Z2     Dmin   Dmax   Thick

or

n:   -n1   Z2     Dmin   Dmax   Thick

or

n:   -n1   -n2     0.00000   0.00000   Thick

where n is the definition index. The line refers to atom pairs A (of nuclear charge Z1, atom count n1=-Z1) and B (of nuclear charge Z2, atom count n2=-Z2) being connected if

Note that in both definitions atom counts n1, n2 are shown by their negative values to be distinguished from nuclear charges.

The atoms are connected by a thin line if Thick = 0 or by a cylindrical stick of thickness Thick > 0 (equal to the stick radius in units of the atom coordinates, see below). Lengths Dmin, Dmax, Thick are always given in units of the atom coordinates.

Nuclear charge values Z1 = 0 and/or Z2 = 0 (combined with names “??” on the element buttons) ignore the corresponding charge constraint and apply to all atoms. Thus, Z1 = Z2 = 0 connects any pair of atoms with a distance inside the prescribed range, while, for example, Z1 = 14, Z2 = 0 connects all Si atoms with any other atom A of the particle if the Si-A distance lies inside the distance range [Dmin, Dmax].

Atom count values n1, n2 in selected bond (atom pair) definitions (combined with names “Atm” on the element buttons) ignore the corresponding distance constraint and values Dmin = Dmax = 0.0 are shown instead.

Each bond definition includes a bond color, shown in the box next to “Color =”, which is assigned to bonds / sticks in the graphics window and in PostScript graphics output. Further, the check box next to “Bi-color” allows an automatic two-color painting (indicated by a hook inside the button) of bonds connecting two atom balls where the two colors refer to the corresponding ball colors. In addition, the check box next to “Outline” allows to outline bond sticks by thin black lines (default) or prevent outlining, see Modify Bonds/Vectors in Window.

For vector definitions the bonds window differs somewhat from that for bond definitions, see entry in its bond definition box and layout of the definition frame, and looks as follows

Each Vector definition in the bond definition box is shown by a line

n:   -nn   999     Rx   Ry   Rz         

where n is the definition index (the title in the bond definition box shows “Z1   Z2   Rx   Ry   Rz” while quantity Thick is not shown). The line refers to an atom A (atom count nn) and a vector given in Cartesian coordinates (Rx, Ry, Rz). This displays a vector inside the graphics window as a cone (triangle, Z2 = 999) or a cylinder (rectangle, Z2 = 998) starting at atom A and pointing along (Rx, Ry, Rz) where the cone/clyinder base (at atom A) is defined by a width = Thick.

Note that in both definitions atom counts n1, n2 are shown by their negative values to be distinguished from nuclear charges.

L-clicking a line in the bond definition box selects the corresponding bond or vector definition # nb (indicated by a blue background behind the line) and copies all bond/vector parameters to the corresponding input boxes inside the definition frame entitled “Modify bond definition # nb” in the lower part of the bonds window. This allows modifying the corresponding bond/vector definition #nb. Further, buttons to the right of the bonds window allow adding and removing bond/vector definitions.

L-clicking the “Analysis …” entry of the option menu at the top of the window opens the Bond List Window giving additional information about the bond sticks/lines evaluated with the present bond constraints.

Further details of the different options are explained in the following sections

Modify Bonds/Vectors in Window

Add Bonds in Window

Add Vectors in Window

Remove Bonds/Vectors in Window

L-clicking the “Visualize” button inside the bonds window redraws the particle in the graphics window with the present bond settings but leaves the bonds window open for further changes.

L-clicking the “Close” button inside the bonds window closes the window and redraws the particle in the graphics window using the present bond settings.