For many condensed matter problems, atomic type orbitals offer good computational efficiency. We have studied the clean surface of silicon using the program ${\mathrm{DMOL}}^{3}$ and obtain results in excellent agreement with well converged plane-wave calculations. We then proceed to study the effect of Ni on the diffusion of dimer vacancies (DVs). In the absence of certain impurities, DVs on the (001) surface of Si can be annealed away. Adding Ni, even in tiny amounts, can stabilize the vacancies. Both the local density approximation and generalized gradient corrections approximations (GGA) were used. Use of GGA does not change any of the qualitative conclusions, although it does modify the details slightly (notably, bond lengths, surface dimer buckling, and the binding of the Ni atom to the DV site are increased). The calculations show that Ni binds very strongly to DVs, from which we infer that a DV with a Ni attached can no longer diffuse. Thus, a pair of Ni atoms on a single dimer row can trap those DVs that lie between them, leading to the stabilization of the DVs.