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At least 1,459 records · Page 81

A fast platform for simulating semi-flexible fiber suspensions applied to cell mechanics

We present a novel platform for the large-scale simulation of three-dimensional fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space in three dimensions. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular assemblies of flexible fibers. We use non-local slender body theory to compute the fluid–structure interactions of the fibers and a second-kind boundary integral formulation for other rigid bodies and the confining boundary. A kernel-independent implementation of the fast multipole method is utilized for efficient evaluation of HIs. The deformation of the fibers is described by nonlinear Euler–Bernoulli beam theory and their polymerization is modeled by the reparametrization of the dynamic equations in the appropriate non-Lagrangian frame. We use a pseudo-spectral representation of fiber positions and implicit time-stepping to resolve large fiber deformations, and to allow time-steps not excessively constrained by temporal stiffness or fiber–fiber interactions. The entire computational scheme is parallelized, which enables simulating assemblies of thousands of fibers. We use our method to investigate two important questions in the mechanics of cell division: (i) the effect of confinement on the hydrodynamic mobility of microtubule asters; and (ii) the dynamics of the positioning of mitotic spindle in complex cell geometries. Finally to demonstrate the general applicability of the method, we simulate the sedimentation of a cloud of semi-flexible fibers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Space-Dependent Wielandt Shift Methods for Multigroup Diffusion Eigenvalue Problems

In the calculation of neutronic eigenfunctions and eigenvalues, it is often desirable to approximate the neutron transport equation by a diffusion equation that requires significantly less computational resources to solve. Even when a full transport solution is needed, the solution of the diffusion system can be used to accelerate iterative methods for calculating the transport eigenfunction and eigenvalue. The convergence rate of the basic power iteration method for eigenvalue problems is governed by the dominance ratio; realistic reactor core problems often have high dominance ratios and the power iteration method can converge slowly as a result. A common technique for accelerating the convergence of power iteration is the Wielandt shift (WS) method, which reduces the dominance ratio by 'shifting' the eigenvalue spectrum using an estimate of the desired eigenvalue. WS provides a significant speedup over power iteration if the eigenvalue estimate is close to the true eigenvalue, but it can be difficult to obtain such an estimate. In practice, the shift in the WS method can be dynamically updated in the iteration scheme, in a way that depends on the eigenvalue estimates from the most recent iterations. We present a physically-motivated Space-Dependent Wielandt Shift (SDWS) for solving multigroup diffusion eigenvalue problems. The space-dependence of the eigenvalue shift in SDWS enables a more effective acceleration of the power iteration scheme than WS at the beginning of the iteration scheme, when the current estimate of the eigenvalue is not close to the actual eigenvalue. Several variants of SDWS are discussed here, including an SDWS method that combines the strengths of SDWS (in the early iterations) with those of standard WS (in the later iterations). Numerical results from a 1-D multigroup diffusion problem demonstrate an order of magnitude speedup over power iteration and a 41% speedup over a standard WS technique. This speedup is problem-dependent and appears to be greater for 'more difficult' problems. In this summary, the term 'speedup' refers to a reduction in the number of iterations required to converge to the correct eigenvalue and eigenfunction. Because the scattering is treated fully implicitly (i.e., it is part of the left-hand side of the diffusion system and directly inverted), the computational cost of a single iteration does not vary significantly among the methods discussed in this summary. The number of iterations is therefore representative of the total computational cost for a method. We acknowledge that certain iterative solvers for linear systems (e.g., GMRES) require more computational time to converge when the system is nearly singular (i.e., when a very aggressive Wielandt shift is applied). Nonetheless, when using SDWS in the manner described in this summary, we have seen that the reduction in computational time from reducing the number of power iterations generally outweighs the extra computational time required by iterative solvers such as GMRES. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Numerical Solution of Incompressible Navier-Stokes Equations Using a Fractional-Step Approach

A fractional step method for the solution of steady and unsteady incompressible Navier-Stokes equations is outlined. The method is based on a finite volume formulation and uses the pressure in the cell center and the mass fluxes across the faces of each cell as dependent variables. Implicit treatment of convective and viscous terms in the momentum equations enables the numerical stability restrictions to be relaxed. The linearization error in the implicit solution of momentum equations is reduced by using three subiterations in order to achieve second order temporal accuracy for time-accurate calculations. In spatial discretizations of the momentum equations, a high-order (3rd and 5th) flux-difference splitting for the convective terms and a second-order central difference for the viscous terms are used. The resulting algebraic equations are solved with a line-relaxation scheme which allows the use of large time step. A four color ZEBRA scheme is employed after the line-relaxation procedure in the solution of the Poisson equation for pressure. This procedure is applied to a Couette flow problem using a distorted computational grid to show that the method minimizes grid effects. Additional benchmark cases include the unsteady laminar flow over a circular cylinder for Reynolds Numbers of 200, and a 3-D, steady, turbulent wingtip vortex wake propagation study. The solution algorithm does a very good job in resolving the vortex core when 5th-order upwind differencing and a modified production term in the Baldwin-Barth one-equation turbulence model are used with adequate grid resolution.

Kiris, Cetin↗

High-order solution methods for grey discrete ordinates thermal radiative transfer

This work presents a solution methodology for solving the grey radiative transfer equations that is both spatially and temporally more accurate than the canonical radiative transfer solution technique of linear discontinuous finite element discretization in space with implicit Euler integration in time. We solve the grey radiative transfer equations by fully converging the nonlinear temperature dependence of the material specific heat, material opacities, and Planck function. The grey radiative transfer equations are discretized in space using arbitrary-order self-lumping discontinuous finite elements and integrated in time with arbitrary-order diagonally implicit Runge–Kutta time integration techniques. Iterative convergence of the radiation equation is accelerated using a modified interior penalty diffusion operator to precondition the full discrete ordinates transport operator.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Sonic Boom Prediction and Minimization of the Douglas Reference OPT5 Configuration

Conventional CFD methods and grids do not yield adequate resolution of the complex shock flow pattern generated by a real aircraft geometry. As a result, a unique grid topology and supersonic flow solver was developed at Northrop Grumman based on the characteristic behavior of supersonic wave patterns emanating from the aircraft. Using this approach, it was possible to compute flow fields with adequate resolution several body lengths below the aircraft. In this region, three-dimensional effects are diminished and conventional two-dimensional modified linear theory (MLT) can be applied to estimate ground pressure signatures or sonic booms. To accommodate real aircraft geometries and alleviate the burdensome grid generation task, an implicit marching multi-block, multi-grid finite-volume Euler code was developed as the basis for the sonic boom prediction methodology. The Thomas two-dimensional extrapolation method is built into the Euler code so that ground signatures can be obtained quickly and efficiently with minimum computational effort suitable to the aircraft design environment. The loudness levels of these signatures can then be determined using a NASA generated noise code. Since the Euler code is a three-dimensional flow field solver, the complete circumferential region below the aircraft is computed. The extrapolation of all this field data from a cylinder of constant radius leads to the definition of the entire boom corridor occurring directly below and off to the side of the aircraft's flight path yielding an estimate for the entire noise "annoyance" corridor in miles as well as its magnitude. An automated multidisciplinary sonic boom design optimization software system was developed during the latter part of HSR Phase 1. Using this system, it was found that sonic boom signatures could be reduced through optimization of a variety of geometric aircraft parameters. This system uses a gradient based nonlinear optimizer as the driver in conjunction with a computationally efficient Euler CFD solver (NIIM3DSB) for computing the three-dimensional near-field characteristics of the aircraft. The intent of the design system is to identify and optimize geometric design variables that have a beneficial impact on the ground sonic boom. The system uses a simple wave drag data format to specify the aircraft geometry. The geometry is internally enhanced and analytic methods are used to generate marching grids suitable for the multi-block Euler solver. The Thomas extrapolation method is integrated into this system, and hence, the aircraft's centerline ground sonic boom signature is also automatically computed for a specified cruise altitude and yields the parameters necessary to evaluate the design function. The entire design system has been automated since the gradient based optimization software requires many flow analyses in order to obtain the required sensitivity derivatives for each design variable in order to converge on an optimal solution. Hence, once the problem is defined which includes defining the objective function and geometric and aerodynamic constraints, the system will automatically regenerate the perturbed geometry, the necessary grids, the Euler solution, and finally the ground sonic boom signature at the request of the optimizer.

Siclari, Michael J.↗

Numerical method for predicting flow characteristics and performance of nonaxisymmetric nozzles, theory

The theoretical foundation and formulation of a numerical method for predicting the viscous flowfield in and about isolated three dimensional nozzles of geometrically complex configuration are presented. High Reynolds number turbulent flows are of primary interest for any combination of subsonic, transonic, and supersonic flow conditions inside or outside the nozzle. An alternating-direction implicit (ADI) numerical technique is employed to integrate the unsteady Navier-Stokes equations until an asymptotic steady-state solution is reached. Boundary conditions are computed with an implicit technique compatible with the ADI technique employed at interior points of the flow region. The equations are formulated and solved in a boundary-conforming curvilinear coordinate system. The curvilinear coordinate system and computational grid is generated numerically as the solution to an elliptic boundary value problem. A method is developed that automatically adjusts the elliptic system so that the interior grid spacing is controlled directly by the a priori selection of the grid spacing on the boundaries of the flow region.

Thomas, P. D.↗

A Simple, Scalable Large Deformation Solid Mechanics Implementation in the MOOSE Framework

This article describes a large deformation solid mechanics solver implemented as part of the freely available and open source MOOSE finite element simulation framework. The article documents the choices made in developing the solid mechanics framework and describes novel formulations for the gradient operator and constitutive modeling framework made to simplify implementations of different coordinate systems, stabilized gradient operators, and different constitutive model inputs and outputs. In the process, the article describes a new formulation that casts objective integration of the Cauchy stress as a linear transformation of the small stress rate. Finally, the article presents key implementation details and examines the parallel efficiency of the solid mechanics solver implemented in MOOSE. The implementation retains a good weak scaling efficiency beyond 1,000 parallel processes. The article includes a discussion of the factors limiting the parallel efficiency of implicit, large deformation solid mechanics codes on current high-performance computers, with the main current limitation being the scalability of the algebraic multigrid methods used to solve the linearized equilibrium equations.

Applied computing → Computer-aided design↗

Inference-Engine v0.1.0

Given a pre-trained neural network, Inference-Engine performs maps network inputs to outputs by executing the forward pass through the provided network. Although the predominant programming language for machine-learning is Python, most high-performance computing (HPC) applications are written in Fortran, C, or C++. Inference-Engine aims to support HPC programs and is written in Fortran, a language with a large feature set supporting interoperability with C. This software exposes concurrency in a portable way by using standard language features that some modern Fortran compilers can exploit with various optimizations, including offloading computation to a Graphics Processing Unit (GPU). In particular, this software makes extensive use of Fortran's "do concurrent" parallel loop construct, implicitly parallel array statements, and pure procedures that can be invoked inside "do concurrent" blocks. Inference-Engine also supports dynamic choice of inference methods at runtime. Two current options include one method that uses Fortran's "dot_product" intrinsic function inside "do concurrent" blocks and another method that instead uses Fortran' "matmul" array intrinsic function. We plan to investigate automatic compiler offloading of "do concurrent" calculations to GPUs and compile-time substitution of optimized libraries such as the Basic Linear Algebra Library (BLAS) for "matmul" invocations. We also envision the potential for the choice of which method to use could happen at program launch based on in situ performance measurements on any given platform.

Rouson, Damian↗

On the Preconditioning of a Newton-Krylov Solver for a High-Order reconstructed Discontinuous Galerkin Discretization of All-Speed Compressible Flow with Phase Change for Application in Laser-Based Additive Manufacturing

This dissertation focuses on the development of a fully-implicit, high-order compressible ow solver with phase change. The work is motivated by laser-induced phase change applications, particularly by the need to develop large-scale multi-physics simulations of the selective laser melting (SLM) process in metal additive manufacturing (3D printing). Simulations of the SLM process require precise tracking of multi-material solid-liquid-gas interfaces, due to laser-induced melting/ solidi cation and evaporation/condensation of metal powder in an ambient gas. These rapid density variations and phase change processes tightly couple the governing equations, requiring a fully compressible framework to robustly capture the rapid density variations of the ambient gas and the melting/evaporation of the metal powder. For non-isothermal phase change, the velocity is gradually suppressed through the mushy region by a variable viscosity and Darcy source term model. The governing equations are discretized up to 4th-order accuracy with our reconstructed Discontinuous Galerkin spatial discretization scheme and up to 5th-order accuracy with L-stable fully implicit time discretization schemes (BDF2 and ESDIRK3-5). The resulting set of non-linear equations is solved using a robust Newton-Krylov method, with the Jacobian-free version of the GMRES solver for linear iterations. Due to the sti nes associated with the acoustic waves and thermal and viscous/material strength e ects, preconditioning the GMRES solver is essential. A robust and scalable approximate block factorization preconditioner was developed, which utilizes the velocity-pressure (vP) and velocity-temperature (vT) Schur complement systems. This multigrid block reduction preconditioning technique converges for high CFL/Fourier numbers and exhibits excellent parallel and algorithmic scalability on classic benchmark problems in uid dynamics (lid-driven cavity ow and natural convection heat transfer) as well as for laser-induced phase change problems in 2D and 3D.

42 ENGINEERING↗

Implicit approximate-factorization schemes for the efficient solution of steady transonic flow problems

Implicit approximate-factorization algorithms (AF) are developed for the solution of steady-state transonic flow problems. The performance of the AF solution method is evaluated relative to that of the standard solution method for transonic flow problems, successive line over-relaxation (SLOR). Both methods are applied to the solution of the nonlinear, two-dimensional transonic small-disturbance equation. Results indicate that the AF method requires substantially less computer time than SLOR to solve the nonlinear finite-difference matrix equation for a transonic flow field. This increase in computational efficiency is achieved with no appreciable increase in computer storage or coding complexity.

Ballhaus, W. F.↗

A modified dodge algorithm for the parabolized Navier-Stokes equations and compressible duct flows

A revised version of a split-velocity method for numerical calculation of compressible duct flow was developed. The revision incorporates balancing of mass flow rates on each marching step in order to maintain front-to-back continuity during the calculation. The (checkerboard) zebra algorithm is applied to solution of the three-dimensional continuity equation in conservative form. A second-order A-stable linear multistep method is employed in effecting a marching solution of the parabolized momentum equations. A checkerboard successive overrelaxation iteration is used to solve the resulting implicit nonlinear systems of finite-difference equations which govern stepwise transition.

Cooke, C. H.↗

An LU implicity scheme for high speed inlet analysis

A numerical method is developed to analyze the inviscid flowfield of a high speed inlet by the solution of the Euler equations. The lower-upper implicit scheme in conjunction with adaptive dissipation proves to be an efficient and robust nonoscillatory shock capturing technique for high Mach number flows as well as for transonic flows.

Yoon, S.↗

An upwind approach to unsteady flowfield simulation

A numerical method to determine unsteady solutions of the laminar, perfect gas Navier-Stokes equations has been developed. The structured finite-volume, approximately factored implicit scheme uses Newton subiterations to obtain the spatially and temporally second-order accurate time history of the interaction of blast-waves with stationary targets. The inviscid flux is evaluated using either of two upwind techniques, while the viscous terms are computed by central differencing. Comparisons of numerical, analytical, and experimental results are made in two and three dimensions. The results show accurate wave speed resolution and nonoscillatory discontinuity capturing.

Atwood, Christopher A.↗

Parallel computing strategies for block multigrid implicit solution of the Euler equations

A multigrid diagonal implicit algorithm has been developed to solve the three-dimensional Euler equations of inviscid compressible flow on block-structured grids. An improved method of advancing the multigrid cycle has been examined with respect to convergence rates, accuracy, and efficiency. In this method, the multigrid cycle is advanced independently in each of the blocks, and the information exchange between the blocks is done using buffer arrays, allowing for the asynchronous updating of interface boundary conditions. This updating scheme is used to eliminate the convergence problems found in a previous implementation of the algorithm while retaining its potential for efficient parallel execution. Results are computed for transonic flows past wings and include pressure distributions to verify the accuracy of the scheme and convergence histories to demonstrate the efficiency of the method. Efficiencies that were obtained using a modest number of processors in parallel are also presented and discussed.

Yadlin, Yoram↗

Development of an efficient analysis for high Reynolds number inviscid/viscid interactions in cascades

An efficient steady analysis for predicting strong inviscid/viscid interaction phenomena such as viscous-layer separation, shock/boundary-layer interaction, and trailing-edge/near-wake interaction in turbomachinery blade passages is described. It uses an inviscid/viscid interaction approach, wherein the flow in the outer inviscid region is assumed to be potential, and that in the inner or viscous-layer region is governed by Prandtl's equations. The inviscid solution is determined using an implicit, least-squares, finite-difference approximation. The viscous-layer solution is obtained using an inverse, finite-difference, space-marching method which is applied along the blade surfaces and the wake streamline. A semiinverse global iteration procedure permits the prediction of boundary-layer separation and other strong-interaction phenomena. Results are presented for two cascades where a range of inlet flow conditions was considered for one of them including conditions leading to large-scale flow separation.

Barnett, M.↗

On the Conservative Interface Treatment for Multi-Block Viscous Flow Computations

A pressure-based multi-block computational method is developed for solving the incompressible Navier-Stokes equations in general curvilinear grid systems. The scheme is based on the semi-implicit type flow solver with the staggered grid. Issues concerning the mass and momentum flux treatments at the discontinuous grid interface are addressed. Systematic numerical experiments for different interface treatments involving (1) straightforward interpolation, (2) globally conservative scheme, and (3) locally conservative scheme have been conducted. It is demonstrated that mass conservation has to be maintained locally, at the grid interface, with accuracy compatible with that of the scheme used in interior domain. Direct interpolation or globally conservative interface treatment of mass flux can not yield solutions with desirable accuracy.

Liu, J.↗

Probabilistic Risk Assessment Procedures Guide for NASA Managers and Practitioners (Second Edition)

Probabilistic Risk Assessment (PRA) is a comprehensive, structured, and logical analysis method aimed at identifying and assessing risks in complex technological systems for the purpose of cost-effectively improving their safety and performance. NASA's objective is to better understand and effectively manage risk, and thus more effectively ensure mission and programmatic success, and to achieve and maintain high safety standards at NASA. NASA intends to use risk assessment in its programs and projects to support optimal management decision making for the improvement of safety and program performance. In addition to using quantitative/probabilistic risk assessment to improve safety and enhance the safety decision process, NASA has incorporated quantitative risk assessment into its system safety assessment process, which until now has relied primarily on a qualitative representation of risk. Also, NASA has recently adopted the Risk-Informed Decision Making (RIDM) process [1-1] as a valuable addition to supplement existing deterministic and experience-based engineering methods and tools. Over the years, NASA has been a leader in most of the technologies it has employed in its programs. One would think that PRA should be no exception. In fact, it would be natural for NASA to be a leader in PRA because, as a technology pioneer, NASA uses risk assessment and management implicitly or explicitly on a daily basis. NASA has probabilistic safety requirements (thresholds and goals) for crew transportation system missions to the International Space Station (ISS) [1-2]. NASA intends to have probabilistic requirements for any new human spaceflight transportation system acquisition. Methods to perform risk and reliability assessment in the early 1960s originated in U.S. aerospace and missile programs. Fault tree analysis (FTA) is an example. It would have been a reasonable extrapolation to expect that NASA would also become the world leader in the application of PRA. That was, however, not to happen. Early in the Apollo program, estimates of the probability for a successful roundtrip human mission to the moon yielded disappointingly low (and suspect) values and NASA became discouraged from further performing quantitative risk analyses until some two decades later when the methods were more refined, rigorous, and repeatable. Instead, NASA decided to rely primarily on the Hazard Analysis (HA) and Failure Modes and Effects Analysis (FMEA) methods for system safety assessment.

Stamatelatos,Michael↗

A Simplified FANG Cell-Centered Finite-Volume Method and Comparison with Other Methods for Trouble-Prone Grids

We propose a simplication of the face-averaged nodal-gradient (FANG) method for a cell-centered finite-volume Euler/Navier-Stokes solver on arbitrary grids, and compare it with other gradient methods for trouble-prone grids in two dimensions. The implementation of the FANG method is simplified by adding the face-neighbor cells of the cells around a node to a least-squares gradient stencil. The resulting method is stable for both triangular and quadrilateral grids. Although it increases the residual stencil for triangular grids, it allows the solver to work seamlessly for mixed grids and greatly simplifies the implementation, especially in three dimensions. For comparison, only explicit weighted/unweighted least-squares cell-centered and nodal gradient methods are considered. These gradients are used in both inviscid and viscous schemes, and we investigate their impact on the iterative convergence of an implicit defect-correction solver on difficult grids such as highly-curved-and-thin grids and highly distorted anisotropic grids. Finally, we will also consider a face-stencil-based limiter and compare it with a conventional cell-stencil-based limiter.

Hiroaki Nishikawa↗