39,511 research outputs found
Phase changes in 38 atom Lennard-Jones clusters. II: A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical
We study the 38-atom Lennard-Jones cluster with parallel tempering Monte
Carlo methods in the microcanonical and molecular dynamics ensembles. A new
Monte Carlo algorithm is presented that samples rigorously the molecular
dynamics ensemble for a system at constant total energy, linear and angular
momenta. By combining the parallel tempering technique with molecular dynamics
methods, we develop a hybrid method to overcome quasi-ergodicity and to extract
both equilibrium and dynamical properties from Monte Carlo and molecular
dynamics simulations. Several thermodynamic, structural and dynamical
properties are investigated for LJ, including the caloric curve, the
diffusion constant and the largest Lyapunov exponent. The importance of
insuring ergodicity in molecular dynamics simulations is illustrated by
comparing the results of ergodic simulations with earlier molecular dynamics
simulations.Comment: Journal of Chemical Physics, accepte
Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces
A new algorithm for calculating intermolecular pair forces in molecular dynamics (MD) simulations on a distributed parallel computer is presented. The arbitrary interacting cells algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh that has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid mechanics simulation by MD in complex geometries, and to provide the MD component of a hybrid MD/continuum simulation. The spatial relationship of the cells of the mesh is calculated at the start of the simulation and only the molecules contained in cells that have part of their surface closer than the cut-off radius of the intermolecular pair potential are required to interact. AICA has been implemented in the open source C++ code OpenFOAM, and its accuracy has been indirectly verified against a published MD code. The same system simulated in serial and in parallel on 12 and 32 processors gives the same results. Performance tests show that there is an optimal number of cells in a mesh for maximum speed of calculating intermolecular forces, and that having a large number of empty cells in the mesh does not add a significant computational overhead
Efficient swap algorithms for molecular dynamics simulations of equilibrium supercooled liquids
It was recently demonstrated that a simple Monte Carlo (MC) algorithm
involving the swap of particle pairs dramatically accelerates the equilibrium
sampling of simulated supercooled liquids. We propose two numerical schemes
integrating the efficiency of particle swaps into equilibrium molecular
dynamics (MD) simulations. We first develop a hybrid MD/MC scheme combining
molecular dynamics with the original swap Monte Carlo. We implement this hybrid
method in LAMMPS, a software package employed by a large community of users.
Secondly, we define a continuous time version of the swap algorithm where both
the positions and diameters of the particles evolve via Hamilton's equations of
motion. For both algorithms, we discuss in detail various technical issues as
well as the optimisation of simulation parameters. We compare the numerical
efficiency of all available swap algorithms and discuss their relative merits.Comment: 16 pages, 13 figure
Controllers for imposing continuum-to-molecular boundary conditions in arbitrary fluid flow geometries
We present a new parallelised controller for steering an arbitrary geometric region of a molecular dynamics (MD) simulation towards a desired thermodynamic and hydrodynamic state. We show that the controllers may be applied anywhere in the domain to set accurately an initial MD state, or solely at boundary regions to prescribe non-periodic boundary conditions (PBCs) in MD simulations. The mean molecular structure and velocity autocorrelation function remain unchanged (when sampled a few molecular diameters away from the constrained region) when compared with those distributions measured using PBCs. To demonstrate the capability of our new controllers, we apply them as non-PBCs in parallel to a complex MD mixing nano-channel and in a hybrid MD continuum simulation with a complex coupling region. The controller methodology is easily extendable to polyatomic MD fluids
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