Substitutional doping

[Inaoton]

Dear ATK team
                                  I want to dope a particular atom in a crystal by some fraction. And I cannot do so in the unit cell because there is only one atom (the one I want to replace)  in the unit cell. In order to do so, I have to create a super  cell. My question is:
                                 1. Should I optimize the pristine crystal, create super cell  , dope  and then optimize it?
                                                                   "OR"
                                 2. Create a super cell and dope it, then optimize it?

[Petr Khomyakov]

The #1 seems to be the most natural approach.

[Inaoton]

Thanks Petr

[Inaoton]

hello again Petr
           If I substitute an atom in the structure with another atom of different Oxidation/valence state, what things I have to consider?
           1. Does the whole system needs to be neutrally charged for DFT calculations?
           2. Or Can I run the system by changing calculator settings?

[Petr Khomyakov]

If you mean global charge neutrality, any system modeled in QuantumATK is charged neutral, even if you introduce a charge.  In the latter case, there is an automatically added compensation charge distribution. As a matter of fact, if you adopt periodic boundary conditions, the charge neutrality must be imposed on the system to allow for numerical solution of the problem.

I did not  get the second question. You always do calculations either by using calculator default settings or  adjusting them for particular calculation needs.

[Inaoton]

So it means that if the global charge of the system is positive because I have substituted a +2 oxidation state atom with +3 oxidation atom, the calculation is still valid??

[Petr Khomyakov]

There are 2 scenarios:

1. When you substitute an atom in the Builder, this atom is treated by default as a neutral atom (i.e., the number of electrons = Z).  After doing a DFT calculation, this atom may, e.g., loose an electron, donating it to other atoms in the system. The entire system stays neutral whatever charge transfer takes place during the self-consistent calculation of the charge distribution.

2. If you want to study a charged defect, this is somewhat different story because you need to introduce an extra charge into the system. This can be done through the Calculator, Charge setting parameter. In this case, QuantumATK will automatically add a compensation charge to preserve the global charge neutrality. 

I do not know which of the two scenarios you are actually considering for doing your calculations.

Of course, if you are considering an isolated system, e.g., a molecule, then you may avoid using periodic boundary conditions and adopt a multigrid method  to impose Dirichlet or Neumann boundary conditions.  In this case, the compensation charge is not needed for charge systems indeed.

[Inaoton]

Thanks Petr again . I understood

[Inaoton]

Hello 
 I have replace X atoms in the optimized pristine structure with 0.25% of  Y atoms, and then optimized it.
 Can I use the resultant optimized structure ( with 0.25% of Y)  as initial structure for 0.50% substitution by adding more  Y atoms?

[Petr Khomyakov]

You are free to do it. But does it make sense for random alloy?

[Inaoton]

  The reason why I asked the question is that the system under consideration consists of 96 atoms and so it takes a lot of computational time during optimization of the system which has substituted atoms if I start from the beginning (pristine) each time. I was just guessing  if it could work that way..

[Petr Khomyakov]

  ... the system under consideration consists of 96 atoms and so it takes a lot of computational time during optimization of the system which has substituted atoms ...

If you run the DFT calculation for a system with 96 atoms on a laptop, this takes time for sure. DFT calculations usually require the use of computer clusters.  Then you must be able to do optimization much faster.