Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

In this review the theory and application of Smoothed particle hydrodynamics (SPH) since its inception in 1977 are discussed. Emphasis is placed on the strengths and weaknesses, the analogy with particle dynamics and the numerous areas where SPH has been successfully applied.

https://iopscience.iop.org/article/10.1088/0034-4885/68/8/R01/pdf

Smoothed particle hydrodynamics

to be done in this area. Face recognition is a problem that scarcely clamoured for attention before the computer age but, having surfaced, has involved a wide range of techniques and has attracted the attention of some fine minds (David Mumford was a Fields Medallist in 1974). This singular application of mathematical modelling to a messy applied problem of obvious utility and importance but with no unique solution is a pretty one to share with students: perhaps, returning to the source of our opening quotation, we may invert Duncan's earlier observation, 'There is an art to find the mind's construction in the face!'.

Linear and nonlinear waves, by G. B. Whitham. Pp.636. £50. 1999. ISBN 0 471 35942 4 (Wiley).

In these lecture notes we describe the construction, analysis, and application of ENO (Essentially Non-Oscillatory) and WENO (Weighted Essentially Non-Oscillatory) schemes for hyperbolic conservation laws and related Hamilton-Jacobi equations. ENO and WENO schemes are high order accurate finite difference schemes designed for problems with piecewise smooth solutions containing discontinuities. The key idea lies at the approximation level, where a nonlinear adaptive procedure is used to automatically choose the locally smoothest stencil, hence avoiding crossing discontinuities in the interpolation procedure as much as possible. ENO and WENO schemes have been quite successful in applications, especially for problems containing both shocks and complicated smooth solution structures, such as compressible turbulence simulations and aeroacoustics.

https://www3.nd.edu/~zxu2/acms60790S13/Shu-WENO-notes.pdf

Essentially Non-Oscillatory and Weighted Essentially Non-Oscillatory Schemes for Hyperbolic Conservation Laws

An alternative approach to large-eddy simulation based on approximate deconvolution (ADM) is developed. The main ingredient is an approximation of the nonfiltered field by truncated series expansion of the inverse filter operator. A posteriori tests for decaying compressible isotropic turbulence show excellent agreement with direct numerical simulation. The computational overhead of ADM is similar to that of a scale-similarity model and considerably less than for dynamic models.

An approximate deconvolution procedure for large-eddy simulation

http://xiangyu-hu.userweb.mwn.de/papers/2006-jcp.pdf

A multi-phase SPH method for macroscopic and mesoscopic flows

A generalized wall boundary condition for smoothed particle hydrodynamics

The approximate deconvolution model (ADM) for the large-eddy simulation of incompressible flows is detailed and applied to turbulent channel flow. With this approach an approximation of the unfiltered solution is obtained by repeated filtering. Given a good approximation of the unfiltered solution, the nonlinear terms of the filtered Navier–Stokes equations can be computed directly. The effect of nonrepresented scales is modeled by a relaxation regularization involving a secondary filter operation. Large-eddy simulations are performed for incompressible channel flow at Reynolds numbers based on the friction velocity and the channel half-width of Reτ=180 and Reτ=590. Both simulations compare well with direct numerical simulation (DNS) data and show a significant improvement over results obtained with classical subgrid scale models such as the standard or the dynamic Smagorinsky model. The computational cost of ADM is lower than that of dynamic models or the velocity estimation model.

Nikolaus A. Adams

Papers

An approximate deconvolution procedure for large-eddy simulation

A multi-phase SPH method for macroscopic and mesoscopic flows

A generalized wall boundary condition for smoothed particle hydrodynamics

An approximate deconvolution model for large-eddy simulation with application to incompressible wall-bounded flows

A High-Resolution Hybrid Compact-ENO Scheme for Shock-Turbulence Interaction Problems