The command run runs the simulation for a given number of steps, 10000000 in this example. Naturally, after each run changes may be made to the scenerio, followed by more runs.
The command min_style determines the algorithm used to perform energy minimization. In this example, conjugate gradient is used.
The command minimize iteratively adjusting atom coordinates, minimizing the energy of the system. This brings the system to a critical point. This does not guarantee the point to be a minimum, and even if it is, the point is more likely to be a local minimum rather than a global. Nonetheless, it is advisable to use the command before applying any post-simulation analysis, such as RDF compilation. In this example, the stopping tolerance for energy is 1e-6, the stopping tolerance for force is 1e-6, the maximum number of iterations used is 5000 and the maximum number of force/energy evaluations is 10000.
The command unfix deletes a previously defined fix. In this example, it deletes the fix named 'dynamics'.
The command undump deletes a previously defined dump. In this example, it deletes the dump 'diamond'.