The complexity of charge trapping in novel semiconductor devices such as high-k MOSFETs is increasing as the devices themselves become more complicated. To facilitate the research on such charge trapping issues, here we propose an optimized simulation framework that is composed of density functional theory (DFT) for electronic structure calculation and Marcus theory for charge trapping rates calculation. The DFT simulations are either carried out or corrected by HSE hybrid functional. Using this framework, the hole trapping characteristics along multiple paths in Si/SiO2/HfO2 stacks are investigated, and the relative importance of each path is revealed by calculating its exact hole trapping rate. Besides the study on crystalline stacks, we also create an amorphous stack, which is more realistic compared to experiments and real devices, to reveal more active trapping centers and to study the statistical feature of charge trapping induced by structural disorder. In addition, to seek effective measures for relieving these charge trapping problems, the effects of hydrogen (H) and fluorine (F) passivations are discussed, and physical insights for improving the performance of high-k MOSFETs are provided.