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

In this paper, a Lagrangian-Eulerian (LE) two-way coupling model is developed to numerically study the cavitation bubble cloud. In this model, the gas-liquid mixture is treated directly as a continuous and compressible fluid and the governing equations are solved by methods in Eulerian descriptions. An isobaric closure exhibiting better consistency properties is applied to evaluate the pressure of gas-liquid mixture. The dispersed gas/vapor bubbles are tracked in a Lagrangian fashion, and their compression and expansion are described by a modified Rayleigh-Plesset equation, which considers the close-by flow properties other than these of the infinity for each bubble. The performance of the present method is validated by a number of benchmark tests. Then, this model is applied to study how the bubble cloud affects the shape and propagation of a pressure wave when the pressure pulse travels through. In the end, a three-dimensional simulation of a vapor cloud’s Rayleigh collapse is carried out, and the induced extreme pressure is discussed in detail. The total bubble number’s influence on the extreme collapse pressure and the size distribution of bubbles during the collapse are also analyzed.

Modeling of Cavitation Bubble Cloud with Discrete Lagrangian Tracking

Experimental and Numerical Study of Heat Transfer at the Underbody of a Production Car

This work presents a detailed analysis of the aerodynamic characteristics for a helicopter fuselage including a skid-landing-gear and a rotating rotor head. Thereby, a special emphasis is set on the rotor head. The results are obtained through numerical simulations based on the incompressible URANS equations. The modelling of the rotating rotor head, including collective and cyclic pitch, is based on a sliding mesh interface in combination with mesh deformation. The numerical simulations are performed under the same conditions and at the same scale as for the existing wind tunnel data. Thus a detailed validation study based on the broad experimental data base could be performed. For this purpose the experimental data base was further extended by rotor phase locked stereo particle image velocimetry measurements.

Validation of a Flow Simulation for a Helicopter Fuselage Including a Rotating Rotor Head

Ignition and mixing in shock-bubble interaction with chemical reactions

We apply a standard nonequilibrium dynamics microscopic analysis of transport coefficients to the smoothed dissipative particle dynamics (SDPD) method of steady-shear flow conditions. Extending the research of Ellero et al. [Phys. Rev. E 82, 046702 (2010)PRESCM1539-375510.1103/PhysRevE.82.046702] for smoothed particle hydrodynamics (SPH), we focus, in particular, on velocity and acceleration statistics and on mean-density phenomena. Implicit and explicit fluctuations affect non-Gaussian statistics and effective viscosities whereas only explicit fluctuations affect large-scale dissipation through the fluctuation-dissipation relation. SDPD facilitates the simulation of mesoscopic systems as the resolution scale is defined by the scaling of the random fluctuations. In the kinetic regime, SDPD recovers the behavior of SPH. In the diffusive regime, non-Gaussian behavior occurs, in contrast to SPH. We observe the formation of isotropic randomly oriented structures with high density which are related to the magnitude of thermal fluctuations. It is demonstrated that SDPD produces non-Gaussian acceleration PDF corresponding to that of a turbulent flow field.

Nikolaus A. Adams

Papers

Modeling of Cavitation Bubble Cloud with Discrete Lagrangian Tracking

Experimental and Numerical Study of Heat Transfer at the Underbody of a Production Car

Validation of a Flow Simulation for a Helicopter Fuselage Including a Rotating Rotor Head

Ignition and mixing in shock-bubble interaction with chemical reactions

Implicit atomistic viscosities in smoothed dissipative particle dynamics.