It requires to determine first what do we mean saying "overall size or shape of an individual atom". Actually, the answer is not trivial one, because the term "boundaries of the atom" (despite either it is free or is bound in a compound) is quite conventional.

Dear Bannikov, there exists electron density in the atom. This density is asimmetrical if atom is in electrostatic field as a result of polarization.

Thank you for your responses. I am thinking about how they fit the problem I am working on.

You should put your atom into cell with corresponding distribution of inner surface charge.