In wrfinput and wrfout files, you can find
float PH(Time, bottom_top_stag, south_north, west_east) ;
PH:FieldType = 104 ;
PH:MemoryOrder = "XYZ" ;
PH:description = "perturbation geopotential" ;
PH:units = "m2 s-2" ;
PH:stagger = "Z" ;
PH:coordinates = "XLONG XLAT XTIME" ;
float PHB(Time, bottom_top_stag, south_north, west_east) ;
PHB:FieldType = 104 ;
PHB:MemoryOrder = "XYZ" ;
PHB:description = "base-state geopotential" ;
PHB:units = "m2 s-2" ;
PHB:stagger = "Z" ;
PHB:coordinates = "XLONG XLAT XTIME" ;
PH + PHB is geopotential at each model level, which can be used to derive the layer depth. Is this what you are looking for?