The slab model is computationally quite efficient. However, it might distort the molecule, and make it hard to re-align it with the right electrode. Also it's a multistep process and one needs to be careful with constraints etc, you one will need to re-insert the optimized coordinates into the original system.
Therefore, in ATK 11.2 we will introduce a fully automatic way to relax a two-probe system. You will build the central region (or indeed the entire two-probe model) and just push a button. Ideally - we'll see how it works in practice, but our tests show that it works very well. The point is that in addition to relaxing the internal arrangement of the atoms, it will also, automatically, relax the unit cell of the central region. This means, the distance from the molecule to the surface will be optimized too.
In earlier versions you can still relax a two-probe system, but since the unit cell of the central region is fixed, as you have noticed this means one cannot optimize the distance between the electrodes. This ultimately translates to the distance between the molecule and the surface, since the molecule will either be stretched to "fill" the distance, or if the molecule remains rather intact it will separate or approach the surface. Thus one will either have a good molecule and a bad distance, or opposite. With ATK 11.2, you will easily get both!
