Y Wang and JK Sigurdsson and PJ Atzberger, SIAM JOURNAL ON SCIENTIFIC COMPUTING, 38, S62-S77 (2016).

DOI: 10.1137/15M1026390

We introduce a software package integrated with the molecular dynamics software LAMMPS for fluctuating hydrodynamics simulations of fluid- structure interactions subject to thermal fluctuations. The package is motivated to provide dynamic thermostats to extend implicit-solvent coarse-grained (IS-CG) models by incorporating kinetic contributions from the solvent to facilitate their use in a wider range of applications. To capture the thermal and hydrodynamic contributions of the solvent to dynamics, we introduce momentum conserving thermostats and computational methods based on fluctuating hydrodynamics and the stochastic Eulerian Lagrangian method (SELM). SELM couples the coarse- grained microstructure degrees of freedom to continuum stochastic fields to capture both the relaxation of hydrodynamic modes and thermal fluctuations. Features of the SELM software include (i) numerical time- step integrators for SELM fluctuating hydrodynamics in inertial and quasi-steady regimes, (ii) Lees Edwards-style methods for imposing shear, (iii) a Java-based graphical user interface (GUI) for setting up models and simulations, (iv) standardized XML formats for parametrization and data output, and (v) standardized formats VTK for continuum fields and microstructures. The SELM software package facilitates for pre-established models in LAMMPS easy adoption of the SELM fluctuating hydrodynamics thermostats. We provide here an overview of the SELM software package, computational methods, and applications.

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