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At least 901 records · Page 50

Shape optimization of single- and two-element airfoils on multiblock grids

A multiblock, discrete sensitivity analysis method is used to couple a direct optimization method and a flow analysis method. The domain is divided into smaller subdomains for which the sensitivities are obtained separately. Then, an effective sensitivity equation is solved to complete the coupling of all the sensitivity information. The flow analysis is based on the thin-layer Navier-Stokes equations solved by an implicit, upwind-biased, finite-volume method. The method of feasible directions is used for the present gradient-based optimization approach. First, a transonic airfoil is optimized to investigate the behavior of the method in highly nonlinear flows as well as the effect of different blocking strategies on the procedure. A supercritical airfoil is produced from an initially symmetric airfoil with multiblocking affecting the path but not the final shape. Secondly, a two-element airfoil is shape optimized in subsonic flow to demonstrate the present method's capability of shaping aerodynamically interfering elements simultaneously. For a very low and a very high Reynolds number cases, the shape of the main airfoil and the flap are optimized to yield improved lift-to-drag ratios.

Lacasse, James M.↗

P1 Nonconforming Finite Element Method for the Solution of Radiation Transport Problems

The simulation of radiation transport in the optically thick flux-limited diffusion regime has been identified as one of the most time-consuming tasks within large simulation codes. Due to multimaterial complex geometry, the radiation transport system must often be solved on unstructured grids. In this paper, we investigate the behavior and the benefits of the unstructured P(sub 1) nonconforming finite element method, which has proven to be flexible and effective on related transport problems, in solving unsteady implicit nonlinear radiation diffusion problems using Newton and Picard linearization methods. Key words. nonconforrning finite elements, radiation transport, inexact Newton linearization, multigrid preconditioning

Kang, Kab S.↗

An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions

Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem of systematically determining a proper reaction coordinate (RC) for a specific process in terms of a set of putative CVs can be achieved using committor analysis (CA). Identifying essential degrees of freedom that govern such transitions using CA remains elusive because of the high dimensionality of the conformational space. Various schemes exist to leverage the power of machine learning (ML) to extract an RC from CA. Here, we extend these studies and compare the ability of 17 different ML schemes to identify accurate RCs associated with conformational transitions. We tested these methods on an alanine dipeptide in vacuum and on a sarcosine dipeptoid in an implicit solvent. Our comparison revealed that the light gradient boosting machine method outperforms other methods. In order to extract key features from the models, we employed Shapley Additive exPlanations analysis and compared its interpretation with the “feature importance” approach. For the alanine dipeptide, our methodology identifies ϕ and θ dihedrals as essential degrees of freedom in the C7ax to C7eq transition. For the sarcosine dipeptoid system, the dihedrals ψ and ω are the most important for the cisαD to transαD transition. We further argue that analysis of the full dynamical pathway, and not just endpoint states, is essential for identifying key degrees of freedom governing transitions.

Chemistry↗

A hybrid numerical technique for predicting the aerodynamic and acoustic fields of advanced turboprops

A hybrid numerical procedure is presented for the prediction of the aerodynamic and acoustic performance of advanced turboprops. A hybrid scheme is proposed which in principle leads to a consistent simultaneous prediction of both fields. In the inner flow a finite difference method, the Approximate-Factorization Alternating-Direction-Implicit (ADI) scheme, is used to solve the nonlinear Euler equations. In the outer flow the linearized acoustic equations are solved via a Boundary-Integral Equation (BIE) method. The two solutions are iteratively matched across a fictitious interface in the flow so as to maintain continuity. At convergence the resulting aerodynamic load prediction will automatically satisfy the appropriate free-field boundary conditions at the edge of the finite difference grid, while the acoustic predictions will reflect the back-reaction of the radiated field on the magnitude of the loading source terms, as well as refractive effects in the inner flow. The equations and logic needed to match the two solutions are developed and the computer program implementing the procedure is described. Unfortunately, no converged solutions were obtained, due to unexpectedly large running times. The reasons for this are discussed and several means to alleviate the situation are suggested.

Homicz, G. F.↗

CFD applications in pump flows

The objective of the proposed paper is to develop a computational procedure that solves incompressible Navier-Stokes equations for pump flows. The solution method is based on the pseudo-compressibility approach and uses an implicit-upwind differencing scheme together with the Gauss-Seidel line relaxation method. The equations are solved in steadily rotating reference frames and the centrifugal force and the Coriolis force are added to the equation of motion. As a benchmark problem, the flow through the Rocketdyne inducer is numerically simulated. A coarse grid solution is obtained with a single zone by using an algebraic turbulence model. In multi-zone fine grid computation, a one-equation Baldwin-Barth turbulence model is utilized. Numerical results are compared with experimental measurements and a good agreement is found between the two. The resulting computer code is then applied to the flow analysis inside a two-stage fuel pump impeller operating at 80 percent, 100 percent, and 120 percent of design flow.

Kiris, Cetin↗

Contour interpolated radial basis functions with spline boundary correction for fast 3D reconstruction of the human articular cartilage from MR images

Purpose: The aim of this work is to demonstrate a new image processing technique that can provide a “near real-time” 3D reconstruction of the articular cartilage of the human knee from MR images which is user friendly. This would serve as a point-of-care 3D visualization tool which would benefit a consultant radiologist in the visualization of the human articular cartilage. Methods: The authors introduce a novel fusion of an adaptation of the contour method known as “contour interpolation (CI)” with radial basis functions (RBFs) which they describe as “CI-RBFs.” The authors also present a spline boundary correction which further enhances volume estimation of the method. A subject cohort consisting of 17 right nonpathological knees (ten female and seven male) is assessed to validate the quality of the proposed method. The authors demonstrate how the CI-RBF method dramatically reduces the number of data points required for fitting an implicit surface to the entire cartilage, thus, significantly improving the speed of reconstruction over the comparable RBF reconstruction method of Carr. The authors compare the CI-RBF method volume estimation to a typical commercial package (3D DOCTOR), Carr’s RBF method, and a benchmark manual method for the reconstruction of the femoral, tibial, and patellar cartilages. Results: The authors demonstrate how the CI-RBF method significantly reduces the number of data points (p-value < 0.0001) required for fitting an implicit surface to the cartilage, by 48%, 31%, and 44% for the patellar, tibial, and femoral cartilages, respectively. Thus, significantly improving the speed of reconstruction (p-value < 0.0001) by 39%, 40%, and 44% for the patellar, tibial, and femoral cartilages over the comparable RBF model of Carr providing a near real-time reconstruction of 6.49, 8.88, and 9.43 min for the patellar, tibial, and femoral cartilages, respectively. In addition, it is demonstrated how the CI-RBF method matches the volume estimation of a typical commercial package (3D DOCTOR), Carr’s RBF method, and a benchmark manual method for the reconstruction of the femoral, tibial, and patellar cartilages. Furthermore, the performance of the segmentation method used for the extraction of the femoral, tibial, and patellar cartilages is assessed with a Dice similarity coefficient, sensitivity, and specificity measure providing high agreement to manual segmentation. Conclusions: The CI-RBF method provides a fast, accurate, and robust 3D model reconstruction that matches Carr’s RBF method, 3D DOCTOR, and a manual benchmark method in accuracy and significantly improves upon Carr’s RBF method in data requirement and computational speed. In addition, the visualization tool has been designed to quickly segment MR images requiring only four mouse clicks per MR image slice.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Development and Verification of the Charring, Ablating Thermal Protection Implicit System Simulator

The development and verification of the Charring Ablating Thermal Protection Implicit System Solver (CATPISS) is presented. This work concentrates on the derivation and verification of the stationary grid terms in the equations that govern three-dimensional heat and mass transfer for charring thermal protection systems including pyrolysis gas flow through the porous char layer. The governing equations are discretized according to the Galerkin finite element method (FEM) with first and second order fully implicit time integrators. The governing equations are fully coupled and are solved in parallel via Newton s method, while the linear system is solved via the Generalized Minimum Residual method (GMRES). Verification results from exact solutions and Method of Manufactured Solutions (MMS) are presented to show spatial and temporal orders of accuracy as well as nonlinear convergence rates.

Amar, Adam J.↗

A comparison of two methods for solving 3-D unsteady compressible viscous flows

Numerical solutions of 3D unsteady compressible flows for several steady and unsteady cases are obtained using two procedures - a noniterative Alternating Direction Implicit (ADI) scheme and a Generalized Minimal RESidual (GMRES) method. Results obtained are compared with each other and also with experimental data. It is found that the GMRES procedure can provide significant speedups compared to the noniterative ADI procedure.

Hixon, Ray↗

An FFT-based approach for Bloch wave analysis: application to polycrystals

A method based on the Fast Fourier Transform is proposed to obtain the dispersion relation of acoustic waves in heterogeneous periodic media with arbitrary microstructures. The microstructure is explicitly considered using a voxelized Representative Volume Element (RVE). The dispersion diagram is obtained solving an eigenvalue problem for Bloch waves in Fourier space. To this aim, two linear operators representing stiffness and mass are defined through the use of differential operators in Fourier space. The smallest eigenvalues are obtained using the implicitly restarted Lanczos and the subspace iteration methods, and the required inverse of the stiffness operator is done using the conjugate gradient with a preconditioner. The method is used to study the propagation of acoustic waves in elastic polycrystals, showing the strong effect of crystal anistropy and polycrystaline texture on the propagation. It is shown that the method combines the simplicity of classical Fourier series analysis with the versatility of Finite Elements to account for complex geometries proving an efficient and general approach which allows the use of large RVEs in 3D.

97 MATHEMATICS AND COMPUTING↗

Fractional Step and Pseudocompressibility Methods for the Solution of Incompressible Navier-Stokes Equations

The fractional step and the pseudocompressibility methods for the solution of the incompressible Navier-Stokes equations are outlined. The fractional step method is based on finite-volume formulation and uses the pressure and the volume fluxes across the faces of each cell as dependent variables. The momentum equations are solved implicitly and the Poisson equation for the pressure is solved by using the multigrid method. The pseudocompressibility approach uses an implicit-higher-order-upwind differencing scheme for the convective terms together with the Gauss-Seidel line relaxation method. The dependent variables in the pseudocompressibility approach are the pressure and the cartesian velocity components in unstaggered mesh orientation. The 90-degree square duct flow, the wing-tip vortex wake flow and unsteady turbulent flows over an oscillating NACA 0015 airfoil are computed using both the fractional step and the pseudocompressibility methods. The results obtained from two different schemes are compared against experimental measurements.

Kiris, Cetin↗

Considering computational speed vs. accuracy: Choosing appropriate mesoscale RVE boundary conditions

Modeling a material’s microstructure using continuum theories allows for inspection of the relationship between coarse scale and fine scale behaviors. Computational limits generally require selection of a sub-volume from a bulk sample in order to directly model the microstructure. Boundary conditions are applied to the sub-volume to mimic the excluded bulk material. Appropriate selection of boundary conditions helps effectively determine the appropriate spatial scale required of the sub-volume. Applicable boundary conditions include direct displacement, periodic, and uniform traction. While direct displacement and periodic boundary conditions are commonly used, uniform traction boundary conditions have seen limited use due to rigid body stability issues in simulations of compression or shear deformation. A new application of uniform traction boundary conditions was developed through linear constraint equations, similar to approaches employed by direct displacement and periodic boundary conditions, to quench rigid body motions with minimal interference of the relative deformation of the model. These boundary conditions were tested by compressing several synthetically generated periodic microstructures using the finite element method. Evaluating the effective stiffness along the compression axis, the direct displacement boundary condition produced the stiffest response, whereas the uniform traction boundary condition produced the most compliant. Periodic boundary conditions produced the same response for all volumes analyzed and both the direct displacement and uniform traction boundary conditions trended toward the periodic response as the domain volume increased. Computational performance was also evaluated for each boundary condition using implicit and explicit solvers. Direct displacement boundary conditions presented the lowest computational cost of all of the boundary conditions followed by periodic then uniform traction. The computational expense of periodic and uniform traction boundary conditions limited the viable spatial scale and mesh resolutions able to be simulated. Selection of appropriate boundary conditions for specific uses need to be a balance between allowable computational expense and accuracy of the method. Techniques for evaluating which boundary conditions to use are discussed.

42 ENGINEERING↗

Viscous analysis of three-dimensional rotor flows using a multigrid method

A three-dimensional code for rotating blade-row flow analysis was developed. The space discretization uses a cell-centered scheme with eigenvalues scaling for the artificial dissipation. The computational efficiency of a four-stage Runge-Kutta scheme is enhanced by using variable coefficients, implicit residual smoothing, and a full-multigrid method. An application is presented for the NASA rotor 67 transonic fan. Due to the blade stagger and twist, a zonal, non-periodic H-type grid is used to minimize the mesh skewness. The calculation is validated by comparing it with experiments in the range from the maximum flow rate to a near-stall condition. A detailed study of the flow structure near peak efficiency and near stall is presented by means of pressure distribution and particle traces inside boundary layers.

Arnone, A.↗

Time-marching methods for three-dimensional steady and unsteady viscous imcompressible flows

An implicit algorithm for the solution of three-dimensional, steady and unsteady, viscous, incompressible flows is presented. The algorithm is based on an upwind-relaxation finite-difference method. Steady-state solutions are carried out using a time-marching solution technique in combination with a local time-stepping strategy. To obtain time-accurate solutions, a subiterative procedure is employed at each physical time step using a global time step to ensure the divergence-free condition. Steady-state flows in several straight ducts and in a square duct with a 90-degree bend are computed and compared with analytical and experimental results. The classical problem of starting flow in a circular pipe is chosen to verify the time accuracy of the present scheme. Finally, the three-dimensional bubble-type vortex breakdown of a slender cylindrical vortex in an unbounded flow is investigated.

Hsu, C.-H.↗

Liquid Phase Modeling in Porous Media: Adsorption of Methanol and Ethanol in H-MFI in Condensed Water

Zeolites are used in the chemical and separation industries for their exceptional selectivity, adsorption capacity, regenerability, and stability in gas and liquid phase processing. Here, we developed an explicit solvation method for predicting solvent/condensed phase effects on adsorption free energies in microporous media such as zeolites based on the hybrid quantum mechanical/molecular mechanical free energy perturbation (QM/MM-FEP) technique. Our explicit solvation method for zeolite systems, called eSZS, aims to capture site-specific interactions during the adsorption process at the Brønsted acid sites of H-MFI zeolite while still considering the diverse configuration space of the solvent molecules. This strategy is ideal for chemical reactions or adsorbates that interact with the microporous medium in few distinct adsorbate/transition state configurations, i.e., the harmonic or similar approximations are acceptable for the adsorbate/transition state while such approximations break down for the solvent molecules that require extensive configuration space sampling. In this way, our approach effectively overcomes the limitations of implicit solvation models and classical force field methods for describing solvation effects on chemical reactions within porous materials such as zeolites. Specifically, in this study, we investigated various aspects of our hybrid QM/MM approach, including QM cluster size dependencies in a periodic electrostatically embedded cluster model (PEECM), rules for link atoms at the QM/MM boundary, and functional and basis set considerations for converged and reasonably accurate gas and aqueous phase methanol and ethanol adsorption free energy predictions in H-MFI. For gas phase adsorption of methanol and ethanol in H-MFI at a Brønsted acid site in T12 position, we compute adsorption free energies at 298 K of −0.61 and −0.75 eV, respectively, using a PEECM containing 50 Si and 1 Al atom with ωB97x-D/def2-TZVP level of theory. For solvent effect calculations, we sample the aqueous phase using grand canonical Monte Carlo (GCMC) simulations to (1) obtain a mean field of electrostatic interactions in the reaction system and (2) perform a rigorous free energy perturbation calculation. Similar to the experimentally and computationally observed endergonic solvation effects observed for hydrocarbon adsorption on metal surfaces, we also observe that a condensed aqueous environment destabilizes methanol and ethanol at these acid sites in H-MFI at 298 K. Specifically, the computed solvation free energies of adsorption (ΔΔG solv ) for methanol and ethanol are +0.44 and +0.54 eV, respectively. From this study, it is evident that adsorbates (methanol and ethanol) are competing with water for adsorption space inside the H-MFI zeolite, leading to an endergonic solvation effect. Here, we expect that the endergonic, aqueous solvent effect during adsorption in microporous zeolites is highly tunable by changing the pore size and hydrophobicity of the microporous material as this will affect the water density inside the pore structure.

Adsorption↗

High order finite difference and multigrid methods for spatially evolving instability in a planar channel

The fourth-order finite-difference scheme with fully implicit time-marching presently used to computationally study the spatial instability of planar Poiseuille flow incorporates a novel treatment for outflow boundary conditions that renders the buffer area as short as one wavelength. A semicoarsening multigrid method accelerates convergence for the implicit scheme at each time step; a line-distributive relaxation is developed as a robust fast solver that is efficient for anisotropic grids. Computational cost is no greater than that of explicit schemes, and excellent agreement with linear theory is obtained.

Liu, C.↗

Scalable edge clustering of dynamic graphs via weighted line graphs

Timestamped relational datasets consisting of records (or connections) between pairs of entities are ubiquitous in network science. For applications like peer-to-peer communication, email, various social network interactions, and computer network security, it is useful to organize these records into groups based on how and when they are occurring. Weighted line graphs offer a natural way to model how records are related in such datasets but for large real-world graph topologies, building and utilizing the line graph is prohibitively expensive. Here, we present the framework to cluster the edges of a dynamic graph via the associated line graph that contains two major contributions. The first is a method to work with the line graph implicitly and the second is a distributed scale implementation of an agglomerative hierarchical graph clustering algorithm. We outline a novel hierarchical dynamic graph edge clustering approach that efficiently breaks massive relational datasets into small sets of edges containing events at various timescales. This is in stark contrast to traditional graph clustering algorithms that prioritize highly connected (clique-like) community structures. Our approach relies on constructing a sufficient subgraph of a weighted line graph and applying a hierarchical agglomerative clustering. This approach is related to scalable techniques from spatial clustering, nonlinear-dimension reduction, topological data analysis, and draws particular inspiration from HDBSCAN. As an edge clustering, this method yields an overlapping node clustering. Our algorithm is parallelizable and we demonstrate efficient clustering of a billion-scale, real-world dynamic graph into small edge sets that correlate in topology and time. The entire clustering process for a graph with tens of billions of edges takes just a few minutes of run time on 256 nodes of a distributed compute environment. We argue how the output of the edge clustering is useful for a multitude of data visualization and powerful machine learning tasks, both involving the original massive dynamic graph data and metadata associated with the nodes and edges. Finally, we describe how this approach can be extended to dynamic hypergraphs and dynamic graphs/hypergraphs with unstructured data living on vertices and edges.

Data Analysis↗

Reducing the Spatial Discretization Error of Thermal Emission in Implicit Monte Carlo Simulations

Implicit Monte Carlo simulations of thermal radiative transport can exhibit what is known as teleportation error in problems with strong coupling between radiation and matter. Teleportation error occurs when energy deposited in a localized region of a spatial zone is emitted throughout the zone in the next time step. Teleportation error is commonly reduced by biasing the positions of photon thermal emission using a fit to the spatial distribution of temperature to the fourth power. The current work samples and stores locations along photon paths based on absorption probabilities. These locations are used as sites for emission in the subsequent time step. This method of teleportation correction is demonstrated in several sample problems, and is validated against an Implicit Monte Carlo Diffusion Method, which does not exhibit teleportation error. We report the new method reduces teleportation error relative to the source tilting method, and enables the use of lower spatial resolutions than would be required to mitigate teleportation error using the source tilting method.

97 MATHEMATICS AND COMPUTING↗

Schwarz-Based Algorithms for Compressible Flows

We investigate in this paper the application of Schwarz-based algorithms to compressible flows. First we study the combination of these methods with defect-correction procedures. We then study the effect on the Schwarz-based methods of replacing the explicit treatment of the boundary conditions by an implicit one. In the last part of this paper we study the combination of these methods with Newton-Krylov matrix-free methods. Numerical experiments that show the performance of our approaches are then presented.

Tidriri, M. D.↗