How should I compute the amount of energy of an EM wave absorbed by a material? Can I just use the divergence of the Poynting vector?
There is another possible approach. You can calculate the flux of the Poynting vector over the boundary of the absorbing volume (http://ocw.mit.edu/resources/res-6-001-electromagnetic-fields-and-energy-spring-2008/chapter-11/11.pdf , 11.1, eq. (1)). I used this approach to calculate the power absorbed in a thin cylinder heated by a broad electromagnetic beam (http://arxiv.org/abs/physics/0405091 , http://arxiv.org/abs/physics/0611169 ). The results were later confirmed in experiments (http://arxiv.org/abs/1109.1626 , http://arxiv.org/abs/1208.0066)
Yes you can, as the thread in the lumerical knowledge base mentioned. https://kb.lumerical.com/en/layout_analysis_pabs_simple.html There is another method included in that thread. Hope that can help too.
The related material is listed as follows: The absorption per unit volume can be calculated from the divergence of the Poynting vector,
It is possible to calculate the absorption directly from this formula (see the Divergence of Poynting vector section), but divergence calculations tend to be very sensitive to numerical problems. Fortunately, there is a more numerically stable form. It can be shown that the above formula is equivalent to
Pabs=-0.5real(iwvec_Evec_D) (w is the radian frequency)
With a little more work, we get the desired result
To calculate the absorption as a function of space and frequency, we only need to know the electric field intensity and the imaginary part of the permittivity. Both quantities are easy to measure in an FDTD simulation.