Here we present the numerical methods, applications, and comparisons with observations and previous studies. It includes numerical analyses of shallow water equations, Sun’s scheme, and nonlinear model simulations of a dam break, solitary Rossby wave, and hydraulic jump without smoothing. We reproduce the longitude and transverse cloud bands in the Equator; two-day mesoscale waves in Brazil; Ekman spirals in the atmosphere and oceans, and a resonance instability at 30° from the linearized equations. The Purdue Regional Climate Model (PRCM) reproduces the explosive severe winter storms in the Western USA; lee-vortices in Taiwan; deformation of the cold front by mountains in Taiwan; flooding and drought in the USA; flooding in Asia; and the Southeast Asia monsoons. The model can correct the small-scale errors if the synoptic systems are correct. Usually, large-scale systems are more important than small-scale disturbances, and the predictability of NWP is better than the simplified dynamics models. We discuss the difference between Boussinesq fluid and the compressible fluid. The Bernoulli function in compressible atmosphere conserving the total energy, is better than the convective available potential energy (CAPE) or the Froude number, because storms can develop without CAPE, and downslope wind can form against a positive buoyancy. We also present a new terrain following coordinate, a turbulence-diffusion model in the convective boundary layer (CBL), and a new backward-integration model including turbulence mixing in the atmosphere.