LAMMPS lb/fluid fix version 2: Improved hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

The first version of this code (Mackay et al., 2013) [10] implemented long-range hydrodynamic interactions into the open-source molecular dynamics package LAMMPS. This was done through the creation of a fix, lb/fluid which was subsequently included as a user-package in the main LAMMPS distribution. Here we substantially update this package by making improvements to its accuracy, adding significant new features, and by simplifying the use of the package. A new two-pass interpolation and spreading scheme is introduced which results in the improved accuracy and numerical stability. New features include new output options, several added computes, and mesh geometry option suitable for micro- and nano-fluidic device simulations. The original package could require fairly careful calibration to obtain accurate thermostating and accurate reproduction of properties related to the hydrodynamic size of objects such as colloids. This process has now been largely automated so that the default settings should suffice for most applications. Program title: fix lb/fluid CPC Library link to program files: https://doi.org/10.17632/2289cnrdtz.1 Licensing provisions: GPLv3 Programming language: C++ Journal reference of previous version: Comput. Phys. Commun. 184 (2013) 2021–2031. Does the new version supersede the previous version?: Yes Reasons for the new version: The new version improves accuracy, adds new features, and simplifies the use of the package. Summary of revisions: A new two-pass interpolation and spreading scheme is introduced to relate properties on the fluid mesh to off-lattice particle properties. New features include output options, several added computes, and mesh geometry suitable for micro- and nano-fluidic device simulations. Calibration processes have been largely automated so that the default settings should suffice for most applications. Nature of problem: The inclusion of long-range hydrodynamic effects into molecular dynamics simulations requires the presence of an explicit solvent. Prior to the implementation of this fix, the only option for incorporating such a solvent into a LAMMPS [1] simulation is the explicit inclusion of each of the individual solvent molecules. This is obviously quite computationally intensive, and for large system sizes can quickly become impractical. Solution method: As an alternative, we have implemented a coarse-grained model for the fluid, simplifying the problem, while retaining the solvent degrees of freedom. We use a thermal lattice-Boltzmann model for the fluid, which is coupled to the molecular dynamics particles at each fluid time step. S. Plimpton, J. Comput. Phys. 117 (1995) 1–19.