Juan,
Your canopy becomes sparse after harvest and there lies one of your problems.
You may want to have a look at the following paper for one method of handling sparse canopies.
Kustas, W.P & Norma JM (1999) Evaluation of soil and vegetation heat flux predictions using a simple two-source model with radiometric temperatures fro partial canopy cover. Agricultural and Forest Meteorology, 94, 13-29.
Then you have to include some kind of a switch in your program to know when your canopy becomes sparce so that a different subroutine with a modified version of the Monsi-Saeki's Beer-Lambert equation takes over.
Hope this helps.
Dear Mohamadu
Thanks for your suggestions. I am taking a look to INTERCOM, but I seem very complicated, because when my soybeans start to grow the wheat is harveted, and the soybean has only two leaves, so they captures source during a very short time.
Regards.
Juan