To run WRF with urban physics scheme, you can simply turn on the urban physics option in namelist.input, i.e.,
sf_urban_physics = 1 (single layer urban canopy model)
= 2: Multi-layer, Building Environment Parameterization (BEP) scheme
(works only with YSU, MYJ and BouLac PBL)
= 3: Multi-layer, Building Environment Model (BEM) scheme
(works only with YSU, MYJ and BouLac PBL)