What is the eggbox-effect in DFT calculations? How can I make this effect to disappear in a SIESTA calculation?

Siesta uses a finite 3D grid for the calculation of some integrals and the representation of charge densities and potentials. Its fineness is determined by its plane-wave cutoff, as given by the MeshCutoff option.

The existence of the grid causes the breaking of translational symmetry (the **egg-box effect**, due to the fact that the density and potential do have plane wave components above the MeshCutOff).

This symmetry breaking is clear when moving one single atom in an otherwise empty simulation cell. The total energy and the forces oscillate with the grid periodicity when the atom is moved, as if the atom were moving on an eggbox. In the limit of infinitely fine grid (infinite MeshCutOff) this effect disappears.

For reasonable values of the mesh cutoff, the effect of the eggbox on the total energy or on the relaxed structure usually is unimportant. However, it can affect substantially the process of relaxation, by increasing the number of steps considerably and can also spoil the calculation of vibrations, usually much more demanding than relaxations.

Here you can find a very helpful tutorial.

Look at point 4 “Convergence of the calculation with respect the MeshCutoff. The eggbox effect” you will find a brief explanation of Eggbox effect in SIESTA.