Hi Daniel,
From SAM's Help system, the physical trough model is described as:
The physical trough model calculates the electricity delivered to the grid by a parabolic trough solar field that delivers thermal energy to a power block for electricity generation, with an optional thermal energy storage system. The physical trough model characterizes many of the system components from first principles of heat transfer and thermodynamics, rather than from empirical measurements as in the empirical trough system model. While the physical trough model is more flexible than the empirical trough model, it adds more uncertainty to performance predictions than the empirical model.
And the empirical trough model:
The empirical trough model models the same type of parabolic trough system as the physical trough model, but uses a set of curve-fit equations derived from regression analysis of data measured from the SEGS projects in the southwestern United States, so you are limited to modeling systems composed of components for which there is measured data. The model is based on Excelergy, originally developed for internal use at at the National Renewable Energy Laboratory.
In general the physical trough model is the best choice. The empirical trough model is based on older designs, but is suitable when you need faster simulations.
For a thermal application like a desalination plant, you may want to consider using the Parabolic Trough - Heat model, which is similar to the physical trough model, but without the power cycle.
Best regards,
Paul.