Looking at the atoms

  The simplest--at least conceptually--kind of ``probe'' that we can apply to our system to understand what is going on is ``looking at it''. One can assign a radius to the atoms (for instance corresponding to half the distance at which the pair potential between two atoms becomes strongly repulsive), represent the atoms as balls having that radius, and have a plotting program construct a ``photograph'' of the system from a certain point of observation. The resulting image can be observed on a graphic screen or printed.

Programs capable of doing this are commonly available. One of them, called BallRoom , has been written by the author and its source code is freely available. Among other things, this program allows to map properties attached to individual atoms (for instance, diffusion, potential energy, coordination, etc) to colors, providing a vivid representation of the spatial distribution of these properties. In some cases, such as in the analysis of complex structural arrangements of atoms, visual inspection is an invaluable tool. In other cases, however, it gives little information, and useful data must be extracted by processing atomic coordinates and/or velocities, obtaining for instance correlation functions, as discussed in the following.