  We propose a method for efficiently coupling the finite element method with
atomistic simulations, while using molecular dynamics or kinetic Monte Carlo
techniques. Our method can dynamically build an optimized unstructured mesh
that follows the geometry defined by atomistic data. On this mesh, different
multiphysics problems can be solved to obtain distributions of physical
quantities of interest, which can be fed back to the atomistic system. The
simulation flow is optimized to maximize computational efficiency while
maintaining good accuracy. This is achieved by providing the modules for a)
optimization of the density of the generated mesh according to requirements of
a specific geometry and b) efficient extension of the finite element domain
without a need to extend the atomistic one. Our method is organized as an
open-source C++ code. In the current implementation, an efficient Laplace
equation solver for calculation of electric field distribution near rough
atomistic surface demonstrates the capability of the suggested approach.
