mdFoam+: Advanced molecular dynamics in OpenFOAM

This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes

Openfoam-interactive (OFI): an innovative universal interface to control solvers in openfoam

We present a new method for coupling fluid and particle systems that works by directly manipulating the flow field variables, mimicking the presence of solid particles rather than adding additional force terms in the governing equations as, e.g., in the traditional immersed boundary method (IBM). We demonstrate an implementation based on the open source OpenFOAM [2] package. The OpenFOAM-Interactive (OFI) presented here gives access to all internal field variables of the governing equations. This ease and facilitates complex computational and seamless data exchange and manipulation of the field variable. OFI contributes to reducing the time needed in creating the initial geometry and enables readily recreating the geometry for the basic computational fluid dynamics (CFD) simulation steps. The presented methodology is verified for a reference simple problem (i) obstruction to flow with bluff bodies. The verified methodology is then applied as an example to demonstrate a realistic problem of heat transfer to a gas through particle bed [1]. The particle bed is created “on the fly” with OFI, this will facilitate studying fluid behavior over different particle configurations in particle beds (i.e. porosity variation) more efficiently in future

A generalised Landau-Lifshitz fluctuating hydrodynamics model for concurrent simulations of liquids at atomistic and continuum resolution

A new hybrid molecular dynamics-hydrodynamics method based on the analogy with two-phase flows is implemented that takes into account the feedback of molecular dynamics on hydrodynamics consistently. The consistency is achieved by deriving a discrete system of fluctuating hydrodynamic equations whose solution converges to the locally averaged molecular dynamics field exactly in terms of the locally averaged fields. The new equations can be viewed as a generalisation of the classical continuum Landau-Lifshitz fluctuating hydrodynamics model in statistical mechanics to include a smooth transition from large-scale continuum hydrodynamics that obeys a Gaussian statistics to all-atom molecular dynamics. Similar to the classical Landau-Lifshitz fluctuating hydrodynamics model, the suggested generalised Landau-Lifshitz fluctuating hydrodynamics equations are too complex for analytical solution; hence, a computational scheme for solving these equations is suggested. The scheme is implemented in a popular open-source molecular dynamics code GROMACS (GROningen MAchine for Chemical Simulations), and numerical examples are provided for liquid argon simulations under equilibrium conditions and under macroscopic flow effects.</p