Cluster Builder 1180


(Balsac/Cluster sessions only) Balsac offers a rather powerful tool to build clusters of atoms which includes free molecules of any size. Various options are available to modify all cluster parameters and will be discussed in detail in the following subsections.

List Cluster                                                           Modify Cluster

Add to Cluster                                                      Add Atom, from File

Build Nanoparticle

L-clicking the

opens the cluster builder window.

Clubuild

This window contains a menu bar at the top offering options to include additional atoms from files (entries “File | Replace cluster …”, “File | Add to cluster …”), to backup all parameters of the present cluster (entry “File | Backup”), to activate/deactivate the confirm option (entry “File | Confirm option”), and to quit Balsac altogether (entry “File | Exit”). Further, the “Title | Modify” option opens a separate input window to modify the title of the particle. In addition, the “Atoms” option allows to revive all hidden atoms of the list and the “Group” option allows to group/ungroup all cluster atoms.

Further, the title of the present session is shown in the input box next to “Title” where it can be changed.

Further, the line starting with “Atom centers” lists, in parentheses, the element composition of the present particle in a pseudo-chemical format “( E1n1E2n2… )” where Ei denote the elements appearing in the particle and ni refers to the corresponding number of atoms of the element type. As an example, Ni1O4C4, means that the particle contains 1 nickel, 4 oxygen and 4 hydrogen atoms.

The line below “Atom centers” reading

Total= Ntot (nh hidden)  |  group= ng (ngh hidden)

gives the present total number of atoms in the particle Ntot, the total number of hidden atoms nh, the number of atoms ng included in a group, and the number of hidden atoms ngh in the group.

The following atom list box shows all atoms of the cluster (only 12 atoms will be visible at a time, the complete listing may be obtained by moving the scroll bar at the left). Each line reading

i)     x     y     z     Rad     Znuc

refers to one atom showing its atom index i, its position in Cartesian coordinates (x, y, z) (in corresponding length units), its atom radius Rad, and its nuclear charge Znuc. While the list is useful to inspect atom properties in numerical detail it can also be used to modify /add and remove atoms. Further details are described separately.

At the bottom of the window there are four control buttons.

L-clicking the “Nano-P.” button opens the Nanoparticle Builder window which allows to build nanoparticles (NPs) of atoms forming sections of the ideal cubic lattices, simple, body centered, and face centered. The sections can be confined by (hkl) oriented layers forming symmetric polyhedral nanoparticles or by facets simulating the shape of spheres resulting in spherical nanoparticles. In addition, icosahedral NPs formed by sets of concentric icosahedral shells (Ih symmetry) can be built.

L-clicking the “Scratch” button resets all cluster definitions (including graphics parameters) to an internal default representing one hydrogen atom positioned at (0, 0, 0). The reset needs to be confirmed by L-clicking the “Yes” button of the message box reading

Balsac resets all cluster data, continue?

L-clicking “No” leaves all cluster definitions unchanged.

Note that this option is identical with the
reset option available by L-clicking the “Default” button below the atom list box except that the present option resets also all previously defined graphics parameters by their default values.

L-clicking the “Visualize” button opens the graphics window drawing the cluster defined at present. The cluster builder window is left open for further changes. The graphics window offers many options to modify the appearance of the cluster.

L-clicking the “Close” button closes the cluster builder window and returns to the graphics window redrawing the cluster.

If a cluster is built from scratch and as not been visualized before the “Hide” option is identical with the “Close” option discussed below.