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Equation‐free methods for molecular dynamics: a lifting procedure
Author(s) -
Frederix Yves,
Samaey Giovanni,
Vandekerckhove Christophe,
Roose Dirk
Publication year - 2007
Publication title -
pamm
Language(s) - English
Resource type - Journals
ISSN - 1617-7061
DOI - 10.1002/pamm.200700025
Subject(s) - initialization , molecular dynamics , curse of dimensionality , kernel (algebra) , representation (politics) , point (geometry) , context (archaeology) , kernel density estimation , grid , computer science , statistical physics , mathematics , physics , computational chemistry , chemistry , geometry , artificial intelligence , paleontology , statistics , combinatorics , estimator , politics , political science , law , biology , programming language
We present a lifting procedure for the initialization of molecular dynamics simulations of dense fluids in the context of equation‐free computing. As the macroscopic system description we use a smooth representation of the density and velocity profile using a kernel density estimation, of which the dimensionality is reduced via a spline fit. The proposed initialization procedure generates initial atom positions on a grid, as well as initial velocities, such that the desired macroscopic density and velocity profiles are well approximated. We illustrate the approach on a model problem, and point out some inherent caveats in the design of good lifting operators for molecular dynamics. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)