As an introduction to cloud-topped boundary layers taught at Utrecht University I have written a syllabus. It discusses the main thermodynamic quantities used in cloud research, as well as a short explanation of the physical processes that take place in stratocumulus and shallow cumulus.

Another syllabus briefly presents the global energy balance, some large-scale dynamics, turbulence and the dry convective boundary layer. These topics are part of the courses 'Physics of the Earth and Atmosphere', 'Water in the Atmosphere', and 'Environmental Physics'.

To get yourself acquainted with the Dutch Atmospheric Large Eddy Simulation model you may want to take a look at the manual belonging to the course 'From Field Observations to Modeling'.