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

The purpose of this paper is to provide a comprehensive presentation and interpretation of the Ensemble Kalman Filter (EnKF) and its numerical implementation. The EnKF has a large user group, and numerous publications have discussed applications and theoretical aspects of it. This paper reviews the important results from these studies and also presents new ideas and alternative interpretations which further explain the success of the EnKF. In addition to providing the theoretical framework needed for using the EnKF, there is also a focus on the algorithmic formulation and optimal numerical implementation. A program listing is given for some of the key subroutines. The paper also touches upon specific issues such as the use of nonlinear measurements, in situ profiles of temperature and salinity, and data which are available with high frequency in time. An ensemble based optimal interpolation (EnOI) scheme is presented as a cost-effective approach which may serve as an alternative to the EnKF in some applications. A fairly extensive discussion is devoted to the use of time correlated model errors and the estimation of model bias.

The Ensemble Kalman Filter: Theoretical formulation and practical implementation

Detached-eddy simulation (DES) is well understood in thin boundary layers, with the turbulence model in its Reynolds-averaged Navier–Stokes (RANS) mode and flattened grid cells, and in regions of massive separation, with the turbulence model in its large-eddy simulation (LES) mode and grid cells close to isotropic. However its initial formulation, denoted DES97 from here on, can exhibit an incorrect behavior in thick boundary layers and shallow separation regions. This behavior begins when the grid spacing parallel to the wall Δ∥ becomes less than the boundary-layer thickness δ, either through grid refinement or boundary-layer thickening. The grid spacing is then fine enough for the DES length scale to follow the LES branch (and therefore lower the eddy viscosity below the RANS level), but resolved Reynolds stresses deriving from velocity fluctuations (“LES content”) have not replaced the modeled Reynolds stresses. LES content may be lacking because the resolution is not fine enough to fully support it, and/or because of delays in its generation by instabilities. The depleted stresses reduce the skin friction, which can lead to premature separation.

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A new version of detached-eddy simulation, resistant to ambiguous grid densities

1. Place animal in induction chamber and anesthetize the mouse and ensure sedation. 2. Once the animal is sedated, move it to a nose cone for hair removal using cream. Only apply cream to the area of the chest that will be utilized for imaging. Once the hair is removed, wipe area with wet gauze to ensure all hair is removed. 3. Move the animal to the imaging platform and tape its paws to the ECG lead plates and insert rectal probe. Body temperature should be maintained at 36-37°C. During imaging, reduce anesthesia to maintain proper heart rate. If the animal shows signs of being awake, use a higher concentration of anesthetic.

人唾液天疱疮抗原的纯化

A hybrid RANS-LES approach with delayed-DES and wall-modelled LES capabilities

A new subgrid scale model is proposed for Large Eddy Simulations in complex geometries. This model which is based on the square of the velocity gradient tensor accounts for the effects of both the strain and the rotation rate of the smallest resolved turbulent fluctuations. Moreover it recovers the proper y
3 near-wall scaling for the eddy viscosity without requiring dynamic procedure. It is also shown from a periodic turbulent pipe flow computation that the model can handle transition.

/pdf/subgrid-scale-stress-modelling-based-on-the-square-of-the-e05h19jine.pdf

Subgrid-scale stress modelling based on the square of the velocity gradient tensor

Large-Eddy Simulation of the Shock/Turbulence Interaction

An eddy-viscosity based, subgrid-scale model for large eddy simulations is derived from the analysis of the singular values of the resolved velocity gradient tensor. The proposed σ-model has, by construction, the property to automatically vanish as soon as the resolved field is either two-dimensional or two-component, including the pure shear and solid rotation cases. In addition, the model generates no subgrid-scale viscosity when the resolved scales are in pure axisymmetric or isotropic contraction/expansion. At last, it is shown analytically that it has the appropriate cubic behavior in the vicinity of solid boundaries without requiring any ad-hoc treatment. Results for two classical test cases (decaying isotropic turbulence and periodic channel flow) obtained from three different solvers with a variety of numerics (finite elements, finite differences, or spectral methods) are presented to illustrate the potential of this model. The results obtained with the proposed model are systematically equivalent or slightly better than the results from the Dynamic Smagorinsky model. Still, the σ-model has a low computational cost, is easy to implement, and does not require any homogeneous direction in space or time. It is thus anticipated that it has a high potential for the computation of non-homogeneous, wall-bounded flows.

/pdf/using-singular-values-to-build-a-subgrid-scale-model-for-4pzhmm2pkk.pdf

Using singular values to build a subgrid-scale model for large eddy simulations

Channel flow with friction Reynolds number Reτ as high as 80 000 is treated by large-eddy simulation at a moderate cost, using the subgrid-scale model designed for detached-eddy simulations. It includes wall modeling, and was not adjusted for this flow. The grid count scales with the logarithm of the Reynolds number. Three independent codes are in fair agreement with each other. Reynolds-number variations and grid refinement cause trades between viscous, modeled, and resolved shear stresses. The skin-friction coefficient is too low, on the order of 15%. The velocity profiles contain a “modeled” logarithmic layer near the wall and some suggest a “resolved” logarithmic layer farther up, but the two layers have a mismatch of several units in U+.

An approach to wall modeling in large-eddy simulations

two approaches for solving the corresponding nonlinear eigenvalue problem are proposed. The first one is based on an asymptotic expansion of the solution, the baseline being the acoustic modes and frequencies for a steady (or passive) flame and appropriate boundary conditions. This method allows a quick assessment of any acoustic mode stabilitybutisvalidonlyforcaseswherethecouplingbetweenthe flameandtheacousticwavesissmallinamplitude. The second approach is based on an iterative algorithm where a quadratic eigenvalue problem is solved at each subiteration. It is more central processing unit demanding but remains valid even in cases where the response of the flametoacousticperturbationsislarge.Frequency-dependentboundaryimpedancesareaccountedforinbothcases. A parallel implementation of the Arnoldi iterative method is used to solve the large eigenvalue problem that arises fromthespacediscretization ofthe Helmholtzequation.Several academicandindustrial testcasesareconsideredto illustrate the potential of the method.

/pdf/acoustic-modes-in-combustors-with-complex-impedances-and-3zf4qk5jt2.pdf

Franck Nicoud

Papers

Subgrid-scale stress modelling based on the square of the velocity gradient tensor

Large-Eddy Simulation of the Shock/Turbulence Interaction

Using singular values to build a subgrid-scale model for large eddy simulations

An approach to wall modeling in large-eddy simulations

Acoustic modes in combustors with complex impedances and multidimensional active flames