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Manuscript Title: Hydrodynamic Forces Implemented into LAMMPS Through a Lattice-Boltzmann Fluid
Authors: F.E. Mackay, S.T.T Ollila, C. Denniston
Program title: fix_lb_fluid
Catalogue identifier: AEPH_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 184(2013)2021
Programming language: C++.
Computer: All.
Operating system: All.
Has the code been vectorised or parallelized?: Yes. Parallelized using MPI directives.
RAM: Depends on the problem
Supplementary material: The data file for the "confined_colloid" example can be downloaded here.
Keywords: Lattice-Boltzmann Algorithm, Molecular Dynamics, Hydrodynamics.
PACS: 47.11-j, 83.10.Rs, 82.70.Dd.
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 walls in the z-direction (x-y plane) only; the simulation domain is always assumed periodic along the x and y directions.

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.

References:
[1] S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995).
[2] Ollila, S.T.T., Denniston, C., Karttunen, M. and Ala-Nissila, T., J. Chem. Phys. 134 064902 (2011).
[3] Mackay, F.E. and Denniston, C., J. Comput. Phys. 237 289 (2013).