Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid
FE Mackay and STT Ollila and C Denniston, COMPUTER PHYSICS COMMUNICATIONS, 184, 2021-2031 (2013).
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 summary Program title: fix_lb_fluid Catalogue identifier: AEPH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEPH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public license No. of lines in distributed program, including test data, etc.: 439446 No. of bytes in distributed program, including test data, etc.: 9579863 Distribution format: tar.gz Programming language: C++. Computer: All. Operating system: All. Has the code been vectorized or parallelized?: Yes. Parallelized using MPI directives. RAM: Depends on the problem Supplementary material: The data file for the "conflned_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. References: 1 S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys. 117 (1995) 1-19. 2 S.T.T. Ollila, C. Denniston, M. Karttunen, T. Ala-Nissila, J. Chem. Phys. 134 (2011) 064902. 3 F.E. Mackay, C. Denniston, J. Comput. Phys. 237 (2013) 289. (C) 2013 Elsevier B.V. All rights reserved.
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