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At least 163 records · Page 9

A numerical comparison of discrete Kalman filtering algorithms: An orbit determination case study

The numerical stability and accuracy of various Kalman filter algorithms are thoroughly studied. Numerical results and conclusions are based on a realistic planetary approach orbit determination study. The case study results of this report highlight the numerical instability of the conventional and stabilized Kalman algorithms. Numerical errors associated with these algorithms can be so large as to obscure important mismodeling effects and thus give misleading estimates of filter accuracy. The positive result of this study is that the Bierman-Thornton U-D covariance factorization algorithm is computationally efficient, with CPU costs that differ negligibly from the conventional Kalman costs. In addition, accuracy of the U-D filter using single-precision arithmetic consistently matches the double-precision reference results. Numerical stability of the U-D filter is further demonstrated by its insensitivity of variations in the a priori statistics.

Thornton, C. L.↗

Evaluating Model Performance of an Ensemble-based Chemical Data Assimilation System During INTEX-B Field Mission

We present a global chemical data assimilation system using a global atmosphere model, the Community Atmosphere Model (CAM3) with simplified chemistry and the Data Assimilation Research Testbed (DART) assimilation package. DART is a community software facility for assimilation studies using the ensemble Kalman filter approach. Here, we apply the assimilation system to constrain global tropospheric carbon monoxide (CO) by assimilating meteorological observations of temperature and horizontal wind velocity and satellite CO retrievals from the Measurement of Pollution in the Troposphere (MOPITT) satellite instrument. We verify the system performance using independent CO observations taken on board the NSFINCAR C-130 and NASA DC-8 aircrafts during the April 2006 part of the Intercontinental Chemical Transport Experiment (INTEX-B). Our evaluations show that MOPITT data assimilation provides significant improvements in terms of capturing the observed CO variability relative to no MOPITT assimilation (i.e. the correlation improves from 0.62 to 0.71, significant at 99% confidence). The assimilation provides evidence of median CO loading of about 150 ppbv at 700 hPa over the NE Pacific during April 2006. This is marginally higher than the modeled CO with no MOPITT assimilation (-140 ppbv). Our ensemble-based estimates of model uncertainty also show model overprediction over the source region (i.e. China) and underprediction over the NE Pacific, suggesting model errors that cannot be readily explained by emissions alone. These results have important implications for improving regional chemical forecasts and for inverse modeling of CO sources and further demonstrate the utility of the assimilation system in comparing non-coincident measurements, e.g. comparing satellite retrievals of CO with in-situ aircraft measurements. The work described above also brought to light several short-comings of the data assimilation approach for CO profiles. Because of the limited vertical resolution of the measurement, the retrievals at different altitudes are correlated which can lead to problems with numerical error and overall efficiency. This has resulted in a manuscript that is about to be submitted to JGR:

Arellano, A. F., Jr.↗

Numerical Issues Associated with Compensating and Competing Processes in Climate Models: an Example from ECHAM-HAM

The purpose of this paper is to draw attention to the need for appropriate numerical techniques to represent process interactions in climate models. In two versions of the ECHAM-HAM model, different time integration methods are used to solve the sulfuric acid (H2SO4) gas evolution equation, which lead to substantially different results in the H2SO4 gas concentration and the aerosol nucleation rate. Using convergence tests and sensitivity simulations performed with various time stepping schemes, it is confirmed that numerical errors in the second model version are significantly smaller than those in version one. The use of sequential operator splitting in combination with long time step is identified as the main reason for the large systematic biases in the old model. The remaining errors in version two in the nucleation rate, related to the competition between condensation and nucleation, have a clear impact on the simulated concentration of cloud condensation nuclei in the lower troposphere. These errors can be significantly reduced by employing an implicit solver that handles production, condensation and nucleation at the same time. Lessons learned in this work underline the need for more caution when treating multi-time-scale problems involving compensating and competing processes, a common occurrence in current climate models.

climate↗

Experimental and theoretical study of energy transfer in a chromophore triad: What makes modeling dynamics successful?

Simulation of electronic dynamics in realistically large molecular systems is a demanding task that has not yet achieved the same level of quantitative prediction already realized for its static counterpart. This is particularly true for processes occurring beyond the Born–Oppenheimer regime. Non-adiabatic molecular dynamics (NAMD) simulations suffer from two convoluted sources of error: numerical algorithms for dynamics and electronic structure calculations. While the former has gained increasing attention, particularly addressing the validity of ad hoc methodologies, the effect of the latter remains relatively unexplored. Indeed, the required accuracy for electronic structure calculations to reach quantitative agreement with experiment in dynamics may be even more strict than that required for static simulations. In this study, we address this issue by modeling the electronic energy transfer in a donor–acceptor–donor (D–A–D) molecular light harvesting system using fewest switches surface hopping NAMD simulations. In the studied system, time-resolved experimental measurements deliver complete information on spectra and energy transfer rates. Subsequent modeling shows that the calculated electronic transition energies are “sufficiently good” to reproduce experimental spectra but produce over an order of magnitude error in simulated dynamical rates. We further perform simulations using artificially shifted energy gaps to investigate the complex relationship between transition energies and modeled dynamics to understand factors affecting non-radiative relaxation and energy transfer rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fully-relativistic full-potential multiple scattering theory: A pathology-free scheme

The Green function plays an essential role in the Korringa–Kohn–Rostoker(KKR) multiple scattering method. In practice, it is constructed from the regular and irregular solutions of the local Kohn–Sham equation and robust methods exist for spherical potentials. However, when applied to a non-spherical potential, numerical errors from the irregular solutions give rise to pathological behaviors of the charge density at small radius. Here we present a full-potential implementation of the fully-relativistic KKR method to perform ab initio self-consistent calculation by directly solving the Dirac differential equations using the generalized variable phase (sine and cosine matrices) formalism Liu et al. (2016). The pathology around the origin is completely eliminated by carrying out the energy integration of the single-site Green function along the real axis. Here, by using an efficient pole-searching technique to identify the zeros of the well-behaved Jost matrices, we demonstrated that this scheme is numerically stable and computationally efficient, with speed comparable to the conventional contour energy integration method, while free of the pathology problem of the charge density. As an application, this method is utilized to investigate the crystal structures of polonium and their bulk properties, which is challenging for a conventional real-energy scheme. The noble metals are also calculated, both as a test of our method and to study the relativistic effects.

36 MATERIALS SCIENCE↗

Entropy Splitting for High Order Numerical Simulation of Vortex Sound at Low Mach Numbers

A method of minimizing numerical errors, and improving nonlinear stability and accuracy associated with low Mach number computational aeroacoustics (CAA) is proposed. The method consists of two levels. From the governing equation level, we condition the Euler equations in two steps. The first step is to split the inviscid flux derivatives into a conservative and a non-conservative portion that satisfies a so called generalized energy estimate. This involves the symmetrization of the Euler equations via a transformation of variables that are functions of the physical entropy. Owing to the large disparity of acoustic and stagnation quantities in low Mach number aeroacoustics, the second step is to reformulate the split Euler equations in perturbation form with the new unknowns as the small changes of the conservative variables with respect to their large stagnation values. From the numerical scheme level, a stable sixth-order central interior scheme with a third-order boundary schemes that satisfies the discrete analogue of the integration-by-parts procedure used in the continuous energy estimate (summation-by-parts property) is employed.

Mueller, B.↗

Large deformation and brittle failure calculated using the dual-domain material point method

The dual domain material point (DDMP) method is explored as a candidate to be implemented in a general purpose code to perform simulations of materials with complex geometry that undergo large history-dependent deformation and failure. To test its candidacy, we study its mesh convergence, its sensitivity to mesh orientation, and its ability to handle softening and failure of a material. Simulations of large deformation and simulations of mechanical failure are performed using both DDMP and the material point method (MPM). When cell-crossing of material points is not an issue and when there are a sufficient number of material points in each computation cell, the numerical error decreases with the square of the cell size as expected for both MPM and DDMP. DDMP has reduced error compared with MPM when there are many instances of material points crossing cell boundaries due to the continuous nature of the modified gradient of the shape functions. Simulations of a specimen under tension are also performed where the background mesh is aligned and misaligned with the tension direction. MPM displays a significant mesh-dependent stress field, DDMP shows negligible mesh dependency. Despite a mesh orientation-dependent stress field from MPM, the critical tension and failure mode from both MPM and DDMP calculations have negligible mesh dependency when using a non-local failure model. If only the failure mode is important (i.e., local stresses are unimportant), MPM with a non-local failure model is a suitable method for modeling failure with small deformations. However, if local stresses are also important or if there are large deformations with many cell-crossings before failure, DDMP should be the method that is used. A needed improvement for DDMP is identified from our numerical simulations.

36 MATERIALS SCIENCE↗

Experiments with explicit filtering for LES using a finite-difference method

The equations for large-eddy simulation (LES) are derived formally by applying a spatial filter to the Navier-Stokes equations. The filter width as well as the details of the filter shape are free parameters in LES, and these can be used both to control the effective resolution of the simulation and to establish the relative importance of different portions of the resolved spectrum. An analogous, but less well justified, approach to filtering is more or less universally used in conjunction with LES using finite-difference methods. In this approach, the finite support provided by the computational mesh as well as the wavenumber-dependent truncation errors associated with the finite-difference operators are assumed to define the filter operation. This approach has the advantage that it is also 'automatic' in the sense that no explicit filtering: operations need to be performed. While it is certainly convenient to avoid the explicit filtering operation, there are some practical considerations associated with finite-difference methods that favor the use of an explicit filter. Foremost among these considerations is the issue of truncation error. All finite-difference approximations have an associated truncation error that increases with increasing wavenumber. These errors can be quite severe for the smallest resolved scales, and these errors will interfere with the dynamics of the small eddies if no corrective action is taken. Years of experience at CTR with a second-order finite-difference scheme for high Reynolds number LES has repeatedly indicated that truncation errors must be minimized in order to obtain acceptable simulation results. While the potential advantages of explicit filtering are rather clear, there is a significant cost associated with its implementation. In particular, explicit filtering reduces the effective resolution of the simulation compared with that afforded by the mesh. The resolution requirements for LES are usually set by the need to capture most of the energy-containing eddies, and if explicit filtering is used, the mesh must be enlarged so that these motions are passed by the filter. Given the high cost of explicit filtering, the following interesting question arises. Since the mesh must be expanded in order to perform the explicit filter, might it be better to take advantage of the increased resolution and simply perform an unfiltered simulation on the larger mesh? The cost of the two approaches is roughly the same, but the philosophy is rather different. In the filtered simulation, resolution is sacrificed in order to minimize the various forms of numerical error. In the unfiltered simulation, the errors are left intact, but they are concentrated at very small scales that could be dynamically unimportant from a LES perspective. Very little is known about this tradeoff and the objective of this work is to study this relationship in high Reynolds number channel flow simulations using a second-order finite-difference method.

Lund, T. S.↗

Numerical Simulations of High Enthalpy Pulse Facilities

Axisymmetric flows within shock tubes and expansion tubes are simulated including the effects of finite rate chemistry and both laminar and turbulent boundary layers. The simulations demonstrate the usefulness of computational fluid dynamics for characterizing the flows in high enthalpy pulse facilities. The modeling and numerical requirements necessary to simulate these flows accurately are also discussed. Although there is a large body of analysis which explains and quantifies the boundary layer growth between the shock and the interface in a shock tube, there is a need for more detailed solutions. Phenomena such as thermochemical nonequilibrium. or turbulent transition behind the shock are excluded in the assumptions of Mirels' analysis. Additionally there is inadequate capability to predict the influence of the boundary layer on the expanded gas behind the interface. Quantifying the gas in this region is particularly important in expansion tubes because it is the location of the test gas. Unsteady simulations of the viscous flow in shock tubes are computationally expensive because they must follow features such as a shock wave over the length of the facility and simultaneously resolve the small length scales within the boundary layer. As a result, efficient numerical algorithms are required. The numerical approach of the present work is to solve the axisymmetric gas dynamic equations using an finite-volume formulation where the inviscid fluxes are computed with a upwind TVD scheme. Multiple species equations are included in the formulation so that finite-rate chemistry can be modeled. The simulations cluster grid points at the shock and interface and translate this clustered grid with these features to minimize numerical errors. The solutions are advanced at a CFL number of less than one based on the inviscid gas dynamics. To avoid limitations on the time step due to the viscous terms, these terms are treated implicitly. This requires a block tri-diagonal matrix inversion along each line of cells normal to the wall. The cost of this inversion is more than offset by the larger allowable time step. The source terms representing the finite-rate chemical kinetics are also treated implicitly. An algebraic turbulence model for compressible flow is used. The flow in a low pressure shock tube is computed and the results are compared with Mirels'analysis. The driven gas is nitrogen at 70 Pa, and the incident shock speed is approximately 2.9 km/sec so that there is little dissociation. The simulations include a laminar boundary layer and are run until the limiting flow regime is achieved. At this limit, the shock and interface travel at the same velocity because the amount of driven gas between these two features remains the same: the mass flow across the shock is equal to the mass of gas being entrained at the interface by the boundary layer. Simulations with several grids are presented to establish the grid independence of the solution, Good agreement is achieved between Mirels' correlations and the computations. This is expected since the flow conditions are chosen to be consistent with the assumptions used in Mirels' analysis. This comparison adds credibility to the numerical approach and highlights some of the differences between the theory and the detailed simulations. In addition, simulations of the HYPULSE expansion tube are presented for two operating conditions and the computations are compared to experimental data. The operating gas for both cases is nitrogen. One test condition is at a total enthalpy of 15.2 MJ/Kg and a relatively low pressure of 2 kPa. This case is characterized by a laminar boundary layer and significant chemical nonequilibrium. in the acceleration gas. The second test condition is at a total enthalpy of 10.2 MJ/Kg and a pressure of 38 kPa and is characterized by a turbulent boundary layer. The simulations compare well with experiment and reveal that the nonuniformity in pressure observed during the test time is related to variations in the boundary layer displacement thickness.

Wilson, Gregory J.↗

Large-Eddy Simulation over Complex Terrain Using an Improved Immersed Boundary Method in the Weather Research and Forecasting Model

Abstract The Weather Research and Forecasting (WRF) Model is increasingly being used for higher-resolution atmospheric simulations over complex terrain. With increased resolution, resolved terrain slopes become steeper, and the native terrain-following coordinates used in WRF result in numerical errors and instability. The immersed boundary method (IBM) uses a nonconformal grid with the terrain surface represented through interpolated forcing terms. Lundquist et al.’s WRF-IBM implementation eliminates the limitations of WRF’s terrain-following coordinate and was previously validated with a no-slip boundary condition for urban simulations and idealized terrain. This paper describes the implementation of a log-law boundary condition into WRF-IBM to extend its applicability to general atmospheric complex terrain simulations. The implementation of the improved WRF-IBM boundary condition is validated for neutral flow over flat terrain and the complex terrain cases of Askervein Hill, Scotland, and Bolund Hill, Denmark. First, comparisons are made to similarity theory and standard WRF results for the flat terrain case. Then, simulations of flow over the moderately sloped Askervein Hill are used to demonstrate agreement between the IBM and terrain-following WRF results, as well as agreement with observations. Finally, Bolund Hill simulations show that WRF-IBM can handle steep topography (standard WRF fails) and compares well to observations. Overall, the new WRF-IBM boundary condition shows improved performance, though the leeside representation of the flow can be potentially further improved.

54 ENVIRONMENTAL SCIENCES↗

Conservative finite‐volume schemes for the quasi‐geostrophic equation on coastal‐conforming unstructured primal–dual meshes

In this article we propose finite‐volume schemes for solving the inviscid and viscous quasi‐geostrophic equations on coastal‐conforming unstructured primal–dual meshes. Several approaches for enforcing the boundary conditions are also explored along with these schemes. The pure transport parts in these schemes are shown to conserve the potential vorticity along fluid paths in an averaged sense, and conserve the potential enstrophy up to the time truncation errors. Numerical tests based on the centroidal Voronoi–Delaunay meshes are performed to confirm these properties, and to distinguish the dynamical behaviours of these schemes. Finally some potential applications of these schemes in different situations are discussed.

Chen, Qingshan↗

Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer

Molecular dynamics (MD) simulations must take very small (femtosecond) integration steps in simulation-time to avoid numerical errors. Efficient use of parallel programming models and accelerators in state-of-the art MD programs now is pushing Moore’s limit for time-per-MD step. As a result, directly simulating timescales beyond milliseconds will not be attainable directly, even at exascale. However, concepts from statistical physics can be used to combine many parallel simulations to provide information about longer timescales and to adequately sample the simulation space, while preserving details about the dynamics of the system. Implementing such an approach requires a workflow program that allows adaptable steering of task assignments based on extensive statistical analysis of intermediate results. Here we report the implementation of such an adaptable workflow program to drive simulations on the Summit IBM Power System AC922, a pre-exascale supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). We compare to experiences on Titan, Summit’s predecessor, report the performance of the workflow and its components, and describe the porting process. We find that using a workflow program managed by a Mongo database can provide the fault tolerance, scalable performance, task dispatch rate, and reconfigurability required for robust and portable implementation of ensemble simulations such as are used in enhanced-sampling molecular dynamics. This type of workflow generator can also be used to provide adaptive steering of ensemble simulations for other applications in addition to MD.

Ossyra, John R.↗

Voronoi Meshing to Accurately Capture Geological Structure in Subsurface Simulations

Mesh generation lies at the interface of geological modeling and reservoir simulation. Highly skewed or very small grid cells may be necessary to accurately capture the geometry of geological features, but the resulting poorly scaled or small grid cells can have a substantial negative impact on simulator accuracy and speed. One way to minimize numerical errors caused by gridding complex structures is to simulate on high-quality Voronoi meshes, which reduce grid orientation effects in fluid flow. This work presents a complete methodology to create Voronoi simulation grids, model fluid flow in complex geological systems, and visualize the results. A recently developed Voronoi meshing method that can automatically generate provably good unstructured meshes that conform to input surfaces creating closed volumes is used. Initially an analytical benchmark simulation is presented to validate the quality of the meshes and simulation results and demonstrate the superiority of simulation results using Voronoi meshes over flexed-hexahedral meshes on a domain with internal features. Next, meshes are created for test structures representing four of the most common geological features in the subsurface: layering, pinch-out, an interior lens that tapers to zero thickness on all sides and a fault with offset. Two benchmark flow simulations are run for each test structure. Finally, a realistic geological example for CO 2 injection into an anticline is simulated. Three realizations of the Voronoi mesh at the same resolution are generated for the simulations. Each mesh is highly refined near the injection wells and coarse in areas of less interest. These three meshes are used to model the CO 2 plume in the subsurface as it migrates to the top of the structure and then fills downward. Simulations on the meshes with randomly generated elements inside the input volumes each give slightly different fingering patterns for the viscous-unstable buoyant gas flow. The results presented in this work show a promising step towards utilizing fully automated Voronoi meshing for subsurface flow simulations in complex geology.

58 GEOSCIENCES↗

Phase field benchmark problems targeting fluid flow and electrochemistry

Here, we continue our development of phase field model benchmark problems with the addition of a third set, complimenting our previously developed problems for diffusion, precipitation, dendritic growth and linear elasticity. These benchmark problems are being jointly developed by the Center for Hierarchical Materials Design (CHiMaD) and the National Institute of Standards and Technology (NIST) along with input from the phase field community. The first problem in this third set targets Stokes flow, with a particular emphasis on flow around an obstruction placed asymmetrically in the domain. While Stokes flow is not traditionally in the canon of phase field problems, it is a class of problems gaining importance in areas such as filtration and water purification. The second problem deals with coupled Cahn-Hilliard diffusion and electrostatic forces, which is an important area in energy storage and battery sciences. We present our own solutions and discuss sources of numerical errors for the Stokes problem as well as simple checks to avoid fundamental issues in the coupled diffusion-electrostatics problem. The latter problem contains some subtleties that we expand on in an Appendix.

36 MATERIALS SCIENCE↗

Non-orthogonal computational grids for studying dislocation motion in phase field approaches

In this work, new non-orthogonal computational grids are implemented into a phase field model called Phase Field Dislocation Dynamics (PFDD). We demonstrate that the new non-orthogonal grid can accommodate multiple slip planes in either the face centered cubic (FCC) or body centered cubic (BCC) crystallographic systems. Here, we show that they avoid numerical errors induced when modeling glide on inclined slip planes in an orthogonal grid. The Gibbs effect that arises in the orthogonal or rotated orthogonal grids is substantially diminished when a non-orthogonal grid is employed. A few test cases demonstrate the effectiveness of using non-orthogonal grids in solving systems with multiple non-planar slip systems.

36 MATERIALS SCIENCE↗

Discrete event cellular automata: A new approach to cellular automata for computational material science

Here, we explore the computational advantages of discrete event simulation for cellular automata models of grain growth. These benefits include a reduction in execution time by up to an order of magnitude and the elimination of numerical errors that stem from overshooting grain capture events and approximating a Poisson process with a Bernoulli process. The fundamental mechanisms speeding up the discrete event simulation are uncovered, and with these we create a speedup model that explains our experimental outcomes.

36 MATERIALS SCIENCE↗

A coupled ALE-AMR method for shock hydrodynamics

We present a numerical method combining adaptive mesh refinement (AMR) with arbitrary Lagrangian-Eulerian (ALE) mesh motion for the simulation of shock hydrodynamics on unstructured grids. The primary goal of the coupled method is to use AMR to reduce numerical error in ALE simulations at reduced computational expense relative to uniform fine mesh calculations, in the same manner that AMR has been used in Eulerian simulations. We also identify deficiencies with ALE methods that AMR is able to mitigate, and discuss the unique coupling challenges. The coupled method is demonstrated using three-dimensional unstructured meshes of up to O(10 7 ) tetrahedral cells. Convergence of ALE-AMR solutions towards both uniform fine mesh ALE results and analytic solutions is demonstrated. Speed-ups of 5-10× for a given level of error are observed relative to uniform fine mesh calculations.

42 ENGINEERING↗

A high-order adaptive algorithm for multispecies gaseous flows on mapped domains

We report a fourth-order accurate finite-volume method is developed and verified for solving strongly nonlinear, time-dependent, compressible, thermally perfect, and multispecies gaseous flows on mapped grids that are adaptively refined in space and time. The algorithm introduces a new scheme for numerical flux calculations in order to cope with the nonlinear, spatially and temporally varying thermodynamic and transport properties of the gaseous mixture. The fourth-order numerical error convergence and solution accuracy are verified using Couette flow, species mass diffusion bubble, and vortex convection and diffusion problem. The thermally perfect, multispecies functionality is validated using a one-dimensional shock tube and two-dimensional shock box problem. Results are obtained for the Mach reflection problem where a strong shock propagates in the multispecies gaseous flow along a ramp and are compared to the solution of the shock propagation in a single species, calorically perfect, gaseous flow over the same ramp. The validated algorithm is then applied to simulate a relatively complex flow configuration to examine the secondary flow mixing due to the double air jets along with the main inlet where a premixed fuel mixture flows in. Future investigations will focus on three-dimensional configurations.

42 ENGINEERING↗