The magnetohydrodynamics with embedded particle-in-cell (MHD-EPIC) model has been successfully applied to global magnetospheric simulations in recent years. However, the PIC region was restricted to be one or more static boxes, which is not always sufficient to cover the whole physical structure of interest efficiently. The FLexible Exascale Kinetic Simulator (FLEKS), which is a new PIC code and allows a dynamic PIC region of any shape, is designed to break this restriction. FLEKS is usually used as the PIC component of the MHD with adaptively embedded particle-in-cell (MHD-AEPIC) model. FLEKS supports dynamically activating or deactivating cells to fit the regions of interest during a simulation. An adaptive time-stepping scheme is also introduced to improve the accuracy and efficiency of a long simulation. The particle number per cell may increase or decrease significantly and lead to load imbalance and large statistical noise in the cells with fewer particles. A particle splitting scheme and a particle merging algorithm are designed to limit the change of the particle number and hence improve the accuracy of the simulation as well as load balancing. Both particle splitting and particle merging conserve the total mass, momentum, and energy. FLEKS also contains a test-particle module to enable tracking particle trajectories due to the time-dependent electromagnetic field that is obtained from a global simulation.