Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aeph_v1_0.tar.gz(9355 Kbytes)|
|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++.|
|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.|
External routines: LAMMPS  (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  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.
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]).
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.
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.
|||S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995).|
|||Ollila, S.T.T., Denniston, C., Karttunen, M. and Ala-Nissila, T., J. Chem. Phys. 134 064902 (2011).|
|||Mackay, F.E. and Denniston, C., J. Comput. Phys. 237 289 (2013).|
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