Usually when passivating the slab's bottom side with pseudohydrogen, I would optimize the structure of the bulk, cut the bulk and get the slab model, then I would add the pseudohydrogen at the midpoint of the bond between the bottom atom and the atom from the neighbor unit cell. Do I have to put the pseudohydrogen at the midpoint?
No, you don't have to put the pseudohydrogen at the mid-point of the bond. Putting it at the mid-point is an attempt to put it close to its optimal location, on the assumption that any X-H bond will be short (for a generic element X), and half of the X-X bond length is a good approximation. A simple alternative is to estimate how long the X-H bond would be, convert that to a fraction of the X-X bond, and place the pseudohydrogen that far along.
There is a significant potential problem with placing the pseudohydrogen exactly along the X-X bond: it preserves the symmetry of the bulk X-X. Most simulation programs will preserve input symmetry, either by explicitly enforcing it, or simply because the computed force will be symmetric, and hence have zero component in any symmetry-breaking direction. If you are not interested at all in the passivated face, then this may be acceptable; however, be aware that if the actual ground state of the X-H face does not have the same symmetry, then the symmetric face may be mechanically unstable. This means that if you compute phonon properties, for example, there would be large negative phonon frequencies arising from these unstable pseudohydrogen faces.
A simple method to avoiding any such symmetry issues is to add a small amount of random noise to the pseudohydrogens after you have placed them. The noise needn't be large, perhaps up to 0.05 Angstroms; just enough to break the symmetry. If the system's ground state does have the symmetry, then the forces will act to restore the symmetric geometry; if, however, the symmetric position is unstable, then the forces should be large enough to push the atoms further away and, eventually, to the correct locations.
Whatever your choice of initial positions, it is usually wise to constrain all but the surface X and H for the initial geometry optimisation, at least if the optimisation is in absolute coordinates. If you don't do this, the optimisation will create a phonon-like displacement wave which travels through the slab at a rate of one atomic layer per geometry iteration, meaning that thick slabs can take an extremely large number of iterations to converge. (This problem should not be present in optimisers using delocalised internal coordinates, or similar relational coordinates.)
$\begingroup$ According to your answer, it seems that you are assuming the pseudohydorgen's position would be changed during the structure optimization. But When calculating the electronic structure of a slab, I assume the bottom side should be the bulk phase, so I put the pseudohydrogen at the bottom side of the slab, keeping the pseudohydorgen's position and the bottom 2 layers of the original atom's positions fixed. $\endgroup$ Jan 5, 2022 at 5:34
$\begingroup$ May I ask if I calculate the structure optimization as I describe above, what is the optimal position of the pseudohydrogen? After all, the purpose of pseudohydrogen is to simulate the situation of a real X-X bond. So I assume keeping the X-PH bond along the original X-X direction should be right. $\endgroup$ Jan 5, 2022 at 5:34
$\begingroup$ Do you mean that firstly I should optimize the pseudohydrogen and bottom atom's position, keeping all the other fixed so that I could find the optimal position of pseudohydrogen? And then I do the structure optimization as I said above by keeping the pseudohydrogen and bottom 2 layers of bulk atoms' position fixed. $\endgroup$ Jan 5, 2022 at 5:57
$\begingroup$ If you're only interested in the electronic properties, then you're correct that you don't need to find the ground state of the passivated surface - in fact, it is probably advantageous to maintain the bulk symmetry. However, you should still optimise the bond length, otherwise the surface may not be passivated at all! $\endgroup$ Jan 5, 2022 at 9:13
$\begingroup$ Thanks, that does make sense. However, I also find some papers don't use pseudohydrogen at all. I open another thread. Here is the link. mattermodeling.stackexchange.com/questions/8480/… $\endgroup$ Jan 5, 2022 at 9:47