dynasor—A Tool for Extracting Dynamical Structure Factors and Current Correlation Functions from Molecular Dynamics Simulations

Abstract

Perturbative treatments of the lattice dynamics are widely successful for many crystalline materials; however, their applicability is limited for strongly anharmonic systems, metastable crystal structures and liquids. The full dynamics of these systems can, however, be accessed via molecular dynamics (MD) simulations using correlation functions, which includes dynamical structure factors providing a direct bridge to experiment. To simplify the analysis of correlation functions, here the dynasor package is presented as a flexible and efficient tool that enables the calculation of static and dynamical structure factors, current correlation functions as well as their partial counterparts from MD trajectories. The dynasor code can handle input from several major open source MD packages and thanks to its C/Python structure can be readily extended to support additional codes. The utility of dynasor is demonstrated via examples for both solid and liquid single and multi‐component systems. In particular, the possibility to extract the full temperature dependence of phonon frequencies and lifetimes is emphasized.

Extremely anisotropic van der Waals thermal conductors

“…Next, we compared the dispersion of bulk MoS 2 to that calculated using MD simulations to verify the accuracy of our MD simulations for calculating the phonon dispersion of r-MoS 2 . For both bulk and r-MoS 2 , we extracted the phonon dispersions and lifetimes at 300 K by analysing the longitudinal and transverse current correlation functions generated by MD simulations in the microcanonical (NVE) ensemble using dynasor 67 . The MD simulations details were otherwise identical to the HNEMD simulations.…”

“…The MD simulations details were otherwise identical to the HNEMD simulations. The obtained correlation functions were Fourier transformed and fitted to peak shape functions corresponding to (over)damped harmonic oscillators using the full expressions given in the dynasor paper 67 to obtain phonon frequencies and lifetimes.…”

Efficient Calculation of the Lattice Thermal Conductivity by Atomistic Simulations with Ab Initio Accuracy

“…We also note that much more extensive analyses can be readily carried out on the basis of MD trajectories, such as free energy calculations and time correlation functions, for example, via codes such as dynasor . [ 38 ]…”

“…The output from these simulations typically consists of the LTC and, if requested, the spectral thermal conductivity or the (fully anharmonic) phonon density of states (PDOS). Additional information can be obtained by further analyzing the positions and velocities, yielding, for example, correlation functions and dynamical structure factors, [ 38 ] which provide in‐depth information concerning the dynamics of the material and can also establish a direct connection to inelastic neutron or X‐ray scattering experiments.…”

Dynamics & Spectroscopy with Neutrons—Recent Developments & Emerging Opportunities

“…Establishing the mechanism of stabilization of the perovskite phase (which from the outset stems from the softness of the iodoplumbate framework) can therefore facilitate the design of efficient routes for the further optimization of these solid solutions. In closing this discussion, we also note that to date a number of tools has been developed to support neutron scattering experiments with AIMD simulations, including calculations of the Vibrational Densities of States or VDOS (TRAVIS [ 182 ], MDANSE [ 183 ], OCLIMAX [ 184 ], DYNASOR [ 185 ]), as well as anharmonic phonon-dispersion relations at finite temperatures (DYNASOR [ 185 ], DynaPhoPy [ 186 ], phq [ 187 ]). Further discussion on the application of AIMD as a route to explore the vibrational dynamics of condensed matter is presented in Section 4 .…”