Molecular dynamics (MD) simulation has been developed to investigate molecular properties in many areas . In this simulation, atoms are typically modelled as points and their movements are calculated by solving the Newton equation. This typically limits time steps allowed in simulation to femtosecond (fs) scales, and a tremendous simulation loop is needed to treat longer time scale phenomena. Recently, new modelling of MD is proposed from materials science named phase-field crystal modelling . In this modelling, a crystal lattice is modelled as a periodic field such as a plane wave which corresponds with the probability density of an atom. This atomistic phase-field modelling has made it possible to employ diffusive equations to calculate the dynamics of atoms, enabling us to use a much longer time step. As a result, a phase-field modelling of an atom is expected to be a strong strategy to clarify longer time scale phenomena that is difficult for conventional MD simulations.