Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

Molecular Simulation

Volumn 33, Issue 15, 2007, Pages 1199-1212

  Macpherson, G B ^a   Borg, M K ^a   Reese, J M ^a  

^a UNIVERSITY OF STRATHCLYDE   (United Kingdom)

Author keywords

Molecular dynamics; Molecular geometry definition; Nano fluidics; OpenFOAM; Parallel computing

Indexed keywords

COMPUTATIONAL GEOMETRY; COMPUTATIONAL METHODS; COMPUTER SIMULATION; CRYSTAL STRUCTURE; NANOFLUIDICS; PARALLEL PROCESSING SYSTEMS; SINGLE CRYSTALS;

ARBITRARY GEOMETRIES; CRYSTAL UNIT CELLS; SINGLE CRYSTAL LATTICES; SINGLE PROCESSOR;

MOLECULAR DYNAMICS;

EID: 36949027146     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020701730724     Document Type: Article

References (12)

1. OpenFOAM, The Open Source CFD Toolbox, http://www.openfoam.org
2. G.B. Macpherson, J.M. Reese. Molecular dynamics in arbitrary geometries: parallel evaluation of pair forces. Mol. Simul., Submitted (2007).
3. J.G. Powles, S. Murad, P.V. Ravi. A new model for permeable micropores. Chem. Phys. Lett., 188, 21 (1992).
4. K.P Travis, B.D. Todd, DJ. Evans. Departure from Navier-Stokes hydrodynamics in confined liquids. Phys. Rev E, 55(4), 4288 (1997).
5. H. Goldstein. Classical Mechanics, 2nd ed., Addison-Wesley, Readng, MA (1980).
6. D.C. Rapaport. The Art of Molecular Dynamics Simulation, 2nd ed., Cambridge University Press, Cambridge (2004).
7. M.P. Allen, D.J. Tildesley. Computer Simulation of Liquids, Oxford University Press, Oxford (1987).
8. G. Karypis, V. Kumar. METIS. A software package for partitioning unstructured graphs, partitioning meshes and computing fill-reducing orderings of sparse matrices, Version 4.0. University of Minnesota, http://glaros.dtc.umn. edu/gkhome/views/metis
9. ParaView: parallel visualization application, http://www.paraview.org
10. L.D. Landau, E.M. Lifshitz. Statistical Physics Part 1 (Course of Theoretical Physics v.5), 3rd ed., Pergamon, Oxford (1980).
11. T. Werder, J.H. Walther, P. Koumoutsakos. Hybrid atomistic-continuum method for the simulation of dense fluid flows. J. Comput. Phys., 205(1), 373 (2005).
12. C. Kittel. Introduction to Solid State Physics, 8th ed., Wiley, NY (2005).