In this work the effect of the geometric phase on time evolution of the density matrix was evaluated during nonadiabatic radiofrequency (RF) pulses with Sine amplitude modulation (AM) and Cosine frequency modulation (FM) functions of the RAFF (Relaxations Along a Fictitious Field) family, and the polarization between two energy level ½ spin system coupled by dipolar interaction was evaluated during the application of RF irradiation. The dependencies of the diagonal density matrix elements and the polarization on the rotational correlation times and the time during RF pulses were evaluated. The general treatment of the density matrix elements along with the polarization generated during RF pulses was unavailable thus far, and for the first time was here derived for the nonadiabatic case of the RAFF pulses. The current formalism could be extended to other AM and FM RF waveforms, including the adiabatic RF pulses which are widely used in magnetic resonance (MR). We demonstrate that the sub-geometric phases (SGP) influence the density matrix elements and thus the polarization generated during the application of RF AM and FM pulses. The corrections to describe the SGP influence of the density matrix elements developed in this work could be essential for determination of MR fundamental parameters necessary for evaluation of tissue contrasts in vivo in MRI and for protein dynamics characterization in high resolution NMR, where AM and FM RF pulses are frequently utilized.