To get an accurate prediction of the geometry and electronic structure of two-dimensional materials, the use of functionals for the exchange-correlation and the van der Waals corrections are consequential. We present a more rigorous simulation procedure by adopting different exchange-correlation functionals for geometry relaxation and electronic structure calculation. As the results, by using Perdew-Burke-Ernzerhof (PBE) functional, the geometry and the bandgap of the bulk transition metals dichalcogenides can be satisfied in comparison with the experimental measurement. It should, however, incorporate the Heyd-Scuseria-Ernzerhof (HSE06) functional and DFT-D2 van der Waals correction at the same time to reproduce a close geometry and bandgap of bulk black phosphorus (BP). A large cell calculation for BP, such as contact engineering and doping engineering, can thus take the advantage of accuracy while remains time efficiency.