SurfaceInitialConditions contains an example script to generate the initial conditions of a distorted lattice.
RMSD contains the scripts employed to calculate the RMSD for the various surface equilibration runs. 
Files like AIMDSurf01CarAndVel_2x2_5L_PBE.dat contain the positions and the velocities employed for the molecule-surface dynamics. The format is: X,Y,Z of the first atom, X,Y,Z of the second atom, ..., Vx,Vy,Vz of the first atom, Vx,Vy,Vz of the second atom , ... (one set per each time-step).