Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

Abstract

Long-range hydrodynamic interactions have been implemented into the open-source molecular dynamics package, LAMMPS, though the creation of a fix, lb_fluid. These interactions are treated by interpolating the MD particle density onto a discrete lattice, which is then coupled to the fluid. A thermal lattice-Boltzmann algorithm is used to model the fluid, which includes mass and momentum conserving noise, providing a thermostat for both the particles and the fluid. Program summaryProgram title: fix_lb_fluidCatalogue identifier: AEPH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public licenseNo. of lines in distributed program, including test data, etc.: 439446No. of bytes in distributed program, including test data, etc.: 9579863Distribution format: tar.gzProgramming language: C++.Computer: All.Operating system: All.Has the code been vectorized or parallelized?: Yes.Parallelized using MPI directives.RAM: Depends on the problemSupplementary material: The data file for the “confined_colloid” example can be downloaded here.Classification: 7.7.External routines: LAMMPS [1] (http://lammps.sandia.gov)Nature of problem:The inclusion of long-range hydrodynamic effects into molecular dynamics simulations requires the presence of an explicit solvent. Currently, 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 [2,3].Restrictions:While LAMMPS supports non-orthogonal simulation boxes, this particular fix can only be performed using a three-dimensional, orthogonal simulation domain. In addition, this fix allows for external walls in the z-direction (x–y plane) only; the simulation domain is always assumed to be periodic along the x and y directions. However, immersed boundaries can be added anywhere by the user.Running time:The run time for fix_lb_fluid varies from minutes to days depending on the system size, the number of lattice mesh points, and the number of processors used.