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At least 559 records · Page 31

A unified hp-HDG framework for Friedrichs' PDE systems

Here, this work proposes a unified hp-adaptivity framework for hybridized discontinuous Galerkin (HDG) method for a large class of partial differential equations (PDEs) of Friedrichs' type. In particular, we present unified hp-HDG formulations for abstract one-field and two-field structures and prove their well-posedness. In order to handle non-conforming interfaces we simply take advantage of HDG built-in mortar structures. With split-type mortars and the approximation space of trace, a numerical flux can be derived via Godunov approach and be naturally employed without any additional treatment. As a consequence, the proposed formulations are parameter-free. We perform several numerical experiments for time-independent and linear PDEs including elliptic, hyperbolic, and mixed-type to verify the proposed unified hp-formulations and demonstrate the effectiveness of hp-adaptation. Two adaptivity criteria are considered: one is based on a simple and fast error indicator, while the other is rigorous but more expensive using an adjoint-based error estimate. The numerical results show that these two approaches are comparable in terms of convergence rate even for problems with strong gradients, discontinuities, and singularities.

97 MATHEMATICS AND COMPUTING↗

Analysis of the weighted shifted boundary method for the Poisson and Stokes problems

The Shifted Boundary Method (SBM) belongs to the class of unfitted (or immersed, or embedded) finite element methods, and relies on reformulating the original boundary value problem over a surrogate (approximate) computational domain. Accuracy is maintained by properly shifting the location and values of the boundary conditions. This avoids integration over cut cells and the associated implementation issues. Recently, the Weighted SBM (WSBM) was proposed for the Navier-Stokes equations with free surfaces and the Stokes flow with moving boundaries. The attribute “weighted” in the name WSBM stems from the fact that its variational form is weighted with the elemental volume fraction of active fluid. The motivation for the development of the WSBM was the preservation of the volume of active fluid to a higher degree of accuracy, which in turn resulted in improved stability and robustness characteristics in moving-boundary, time-dependent simulations. In this article, we present the numerical analysis of the WSBM formulations for the Poisson and Stokes problems. We give mathematical conditions under which the bilinear forms defining the discrete variational formulations are uniformly coercive (Poisson problem) or inf-sup stable (Stokes problem). By these results, stability and optimal convergence is proven in the natural norm; L2-error estimates can also be derived.

Approximate domain boundaries↗

An embedded variable step IMEX scheme for the incompressible Navier–Stokes equations

This report presents a series of implicit–explicit (IMEX) variable stepsize algorithms for the incompressible Navier–Stokes equations (NSE). Here, IMEX means the nonlinear term is treated fully explicitly while the remaining terms are treated implicitly. With the advent of new computer architectures there has been growing demand for low memory solvers of this type. The addition of time adaptivity improves the accuracy and greatly enhances the efficiency of the algorithm. We prove energy stability of an embedded first–second order IMEX pair. For the first order member of the pair, we prove stability for variable stepsizes, and analyze convergence. We believe this to be the first proof of this type for a variable stepsize IMEX scheme for the incompressible NSE. We then define and test a variable stepsize, variable order IMEX scheme using these methods. Our work contributes several firsts for IMEX NSE schemes, including an energy argument and error analysis of a two-step, variable stepsize method, and embedded error estimation for an IMEX multi-step method.

42 ENGINEERING↗

A comprehensive and fair comparison of two neural operators (with practical extensions) based on $\mathrm{FAIR}$ data

Neural operators can learn nonlinear mappings between function spaces and offer a new simulation paradigm for real-time prediction of complex dynamics for realistic diverse applications as well as for system identification in science and engineering. Herein, we investigate the performance of two neural operators, which have shown promising results so far, and we develop new practical extensions that will make them more accurate and robust and importantly more suitable for industrial-complexity applications. The first neural operator, DeepONet, was published in 2019 (Lu et al., 2019), and its original architecture was based on the universal approximation theorem of Chen & Chen (1995). The second one, named Fourier Neural Operator or FNO, was published in 2020, and it is based on parameterizing the integral kernel in the Fourier space. DeepONet is represented by a summation of products of neural networks (NNs), corresponding to the branch NN for the input function and the trunk NN for the output function; both NNs are general architectures, e.g., the branch NN can be replaced with a CNN or a ResNet. According to Kovachki et al. (2021), FNO in its continuous form can be viewed conceptually as a DeepONet with a specific architecture of the branch NN and a trunk NN represented by a trigonometric basis. In order to compare FNO with DeepONet computationally for realistic setups, we develop several extensions of FNO that can deal with complex geometric domains as well as mappings where the input and output function spaces are of different dimensions. We also develop an extended DeepONet with special features that provide inductive bias and accelerate training, and we present a faster implementation of DeepONet with cost comparable to the computational cost of FNO, which is based on the Fast Fourier Transform. Here we consider 16 different benchmarks to demonstrate the relative performance of the two neural operators, including instability wave analysis in hypersonic boundary layers, prediction of the vorticity field of a flapping airfoil, porous media simulations in complex-geometry domains, etc. We follow the guiding principles of FAIR (Findability, Accessibility, Interoperability, and Reusability) for scientific data management and stewardship. The performance of DeepONet and FNO is comparable for relatively simple settings, but for complex geometries the performance of FNO deteriorates greatly. We also compare theoretically the two neural operators and obtain similar error estimates for DeepONet and FNO under the same regularity assumptions.

42 ENGINEERING↗

A fast and accurate domain decomposition nonlinear manifold reduced order model

Here, this paper integrates nonlinear-manifold reduced order models (NM-ROMs) with domain decomposition (DD). NM ROMs approximate the full order model (FOM) state in a nonlinear-manifold by training a shallow, sparse autoencoder using FOM snapshot data. These NM-ROMs can be advantageous over linear-subspace ROMs (LS-ROMs) for problems with slowly decaying Kolmogorov n-width. However, the number of NM-ROM parameters that need to be trained scales with the size of the FOM. Moreover, for “extreme-scale” problems, the storage of high-dimensional FOM snapshots alone can make ROM training expensive. To alleviate the training cost, this paper applies DD to the FOM, computes NM-ROMs on each subdomain, and couples them to obtain a global NM-ROM. This approach has several advantages: Subdomain NM-ROMs can be trained in parallel, involve fewer parameters to be trained than global NM-ROMs, require smaller subdomain FOM dimensional training data, and can be tailored to subdomain specific features of the FOM. The shallow, sparse architecture of the autoencoder used in each subdomain NM-ROM allows application of hyper-reduction (HR), reducing the complexity caused by nonlinearity and yielding computational speedup of the NM-ROM. This paper provides the first application of NM-ROM (with HR) to a DD problem. In particular, this paper details an algebraic DD reformulation of the FOM, training a NM-ROM with HR for each sub domain, and a sequential quadratic programming (SQP) solver to evaluate the coupled global NM-ROM. Theoretical convergence results for the SQP method and a priori and a posteriori error estimates for the DD NM-ROM with HR are provided. The proposed DD NM-ROM with HR approach is numerically compared to a DD LS-ROM with HR on the 2D steady-state Burgers’ equation, showing an order of magnitude improvement in accuracy of the proposed DD NM-ROM over the DD LS-ROM.

97 MATHEMATICS AND COMPUTING↗

Data-driven reduced-order models for port-Hamiltonian systems with operator inference

Hamiltonian operator inference has been developed in Sharma et al. (2022) to learn structure-preserving reduced-order models (ROMs) for Hamiltonian systems. The method constructs a low-dimensional model using only data and knowledge of the functional form of the Hamiltonian. The resulting ROMs preserve the intrinsic structure of the system, ensuring that the mechanical and physical properties of the system are maintained. In this work, we extend this approach to port-Hamiltonian systems, which generalize Hamiltonian systems by including energy dissipation, external input, and output. Based on snapshots of the system’s state and output, together with the information about the functional form of the Hamiltonian, reduced operators are inferred through optimization and are then used to construct data-driven ROMs. To further alleviate the complexity of evaluating nonlinear terms in the ROMs, a hyper-reduction method via discrete empirical interpolation is applied. Accordingly, we derive error estimates for the ROM approximations of the state and output. Lastly, we demonstrate the structure preservation, as well as the accuracy of the proposed port-Hamiltonian operator inference framework, through numerical experiments on a linear mass–spring-damper problem and a nonlinear Toda lattice problem.

97 MATHEMATICS AND COMPUTING↗

Simulation-driven optimization of high-order meshes in ALE hydrodynamics

Here we propose tools for high-order mesh optimization and demonstrate their benefits in the context of multi-material Arbitrary Lagrangian-Eulerian (ALE) compressible shock hydrodynamic applications. The mesh optimization process is driven by information provided by the simulation which uses the optimized mesh, such as shock positions, material regions, known error estimates, etc. These simulation features are usually represented discretely, for instance, as finite element functions on the Lagrangian mesh. The discrete nature of the input is critical for the practical applicability of the algorithms we propose and distinguishes this work from approaches that strictly require analytical information. Our methods are based on node movement through a high-order extension of the Target-Matrix Optimization Paradigm (TMOP). The proposed formulation is fully algebraic and relies only on local Jacobian matrices, so it is applicable to all types of mesh elements, in 2D and 3D, and any order of the mesh. We discuss the notions of constructing adaptive target matrices and obtaining their derivatives, reconstructing discrete data in intermediate meshes, node limiting that enables improvement of global mesh quality while preserving space-dependent local mesh features, and appropriate normalization of the objective function. The adaptivity methods are combined with automatic ALE triggers that can provide robustness of the mesh evolution and avoid excessive remap procedures. The benefits of the new high-order TMOP technology are illustrated on several simulations performed in the high-order ALE application BLAST.

97 MATHEMATICS AND COMPUTING↗

Revisiting a minimally destructive analytic approach for determining electrochemical kinetic parameters: Measuring aluminum corrosion across a wide pH range based on the Butler-Volmer equation

Here, this study revisits the three-point sampling of the simplified Butler-Volmer equation to address the limitations of strong potentiodynamic polarization, which can introduce irreversible damage and uncertainty in corrosion analysis. The method extracts electrochemical kinetic parameters while minimizing polarization effects, evaluates noise sensitivity relative to overpotential, and accounts for errors from signal noise, OCP drift, ohmic resistance, and mass-transfer constraints. Verified against the Tafel extrapolation method for aluminum corrosion across a wide pH range, this low-polarization approach enables accurate evaluations with specific error estimates, offering a robust alternative to linear polarization resistance methods that assume constant Tafel slopes.

36 MATERIALS SCIENCE↗

Magnus method for electronic structure calculations at extreme conditions

We present the application of Magnus based methods to the solution of first order coupled ordinary differential equations in High Energy Density (HED) physics applications. Our focus is on the application to quantum mechanical methods, specifically on the solution of the radial Dirac equation for real and complex energies. HED applications require accurate solutions across a wide range of spatial and energy domains, including regimes where the solutions exhibit pronounced oscillatory behavior. Such cases pose significant computational challenges. We demonstrate that Magnus-based integrators can efficiently and accurately address these challenges. We discuss the implementation of the Magnus method for the solution of the radial Dirac equation, including practical considerations such as the evaluation of matrix exponentials, numerical integration, error estimation, and adaptive step size control. We also discuss the application of these methods to complex energy Green’s function techniques and the efficient approximation of integrals of the solutions relevant to HED electronic structure calculations. Here, we demonstrate the accuracy and robustness of the resulting method in applications to the free-particle case, for which analytic solutions are available for comparison, as well as the challenging case of gold at HED conditions.

general physics↗

Moment-based adaptive time integration for thermal radiation transport

Here, in this paper we develop a framework for moment-based adaptive time integration of deterministic multifrequency thermal radiation transpot (TRT). We generalize our recent semi-implicit-explicit (IMEX) integration framework for gray TRT to multifrequency TRT, and also introduce a semi-implicit variation that facilitates higher-order integration of TRT, where each stage is implicit in all components except opacities. To appeal to the broad literature on adaptivity with Runge–Kutta methods, we derive new embedded methods for four asymptotic preserving IMEX Runge–Kutta schemes we have found to be robust in our previous work on TRT and radiation hydrodynamics. We then use a moment-based high-order-low-order representation of the transport equations. Due to the high dimensionality, memory is always a concern in simulating TRT. We form error estimates and adaptivity in time purely based on temperature and radiation energy, for a trivial overhead in computational cost and memory usage compared with the base second order integrators. We then test the adaptivity in time on the tophat and Larsen problem, demonstrating the ability of the adaptive algorithm to naturally vary the timestep across 4–5 orders of magnitude, ranging from the dynamical timescales of the streaming regime to the thick diffusion limit.

97 MATHEMATICS AND COMPUTING↗

Thermodynamic properties and superconductivity of natural carrollite (CuCo 2 S 4 )

The thermodynamic properties of natural carrollite with a formula Cu 0.92 Co 2.07 S 4 are studied using low temperature heat capacity and high temperature oxidative solution calorimetry. The standard thermodynamic functions at 298.15 K are: C p,m °, S m °, H m °, and Φ m ° are 158.48 J∙K −1 ∙mol −1 , 176.33 J∙K −1 ∙mol −1 , 28.40 kJ∙mol −1 , and 81.07 kJ∙mol −1 with an estimated error of 1%. The enthalpies (Δ f H), entropies (Δ f S), and Gibbs energies of formation (Δ f G) from elements at 298.15 K are: −344.46 ± 12.87 kJ∙mol −1 , −45.22 ± 1.81 J∙K −1 ∙mol −1 , and −331.14 ± 1.89 J∙K −1 ∙mol −1 . The stability of carrollite relative to the elements is demonstrated with a negative Gibbs energy (ΔG r °) of formation for several temperatures between 0 and 300 K. Furthermore, a superconductivity transition, which has been observed previously for synthetic carrollite, is confirmed by both the low temperature heat capacity and magnetization measurements.

Chemistry↗

Temperature Effects on Interdiffusion of Al and U-Mo under Irradiation

A high-energy Xe ion irradiation experiment was conducted to investigate the temperature dependence of interdiffusion in bilayer Al-UMo samples under irradiation. The amount of interdiffusion achieved at a fixed dose with the increase of temperature showed a clear transition at 175 degrees C (with an estimated error in the range of ± 10 degrees C) from temperature-independent to temperature-dependent behavior. The activation energy derived from the curve of interdiffusion quantity vs. irradiation temperature is 0.77 ± 0.16 eV. This information has been utilized to understand the temperature effect on the interdiffusion process that occurred at the interfaces of U-Mo particles and the Al matrix in U-Mo/Al dispersion fuels, whose magnitude significantly impacts the fuel's performance. Although this temperature effect was deemed important, it cannot be examined directly using in-pile irradiation data, as fuel temperatures cannot be measured in reactor irradiation and are highly correlated with fission rate and thermal conductivity evolution. To connect the knowledge accumulated from ion irradiation with in-pile irradiation data, simulation of a full-sized U-Mo/Al dispersion fuel plate irradiated in the FUTURE test in the BR2 reactor was performed with the Dispersion Analysis Research Tool (DART), a dispersion fuel performance code. DART is equipped with an interaction or interdiffusion layer (IL) growth correlation formulated to describe the temperature dependence of ion mixing results. The agreement between calculated and measured fuel meat constituent volume fractions and swelling data demonstrated that the temperature effect on in-pile Al-UMo interdiffusion is well captured with the correlation. In this case, the fitted activation energy is 0.70 eV. Considering the uncertainties associated with the ion irradiation data, the activation energy obtained from in-pile data fitting is in accord with that from ion irradiation results.

36 MATERIALS SCIENCE↗

Heat pulse testing at monitoring wells to estimate subsurface fluid velocities in geological CO 2 storage

Monitoring the injected CO 2 during geological CO 2 storage (GCS) is essential to assure containment and identify CO 2 leakage. Here in this work, a new approach is introduced to estimate the evolution of the downhole fluid velocity at a monitoring well and identify CO 2 arrival time using in-well heat pulse/tracer test. The proposed technique involves using a downhole heater to generate a series of heat pulses and measuring their corresponding temperature response. The surface temperature of the downhole heater is controlled by the supplied electrical power and the heat loss by convection to the surroundings. Convective heat transfer is well described using Newton's law of cooling in which the temperature difference between the heater and the surrounding fluids drives the heat transfer, for which the convection heat transfer coefficient (h) controls the magnitude of heat loss. Among various factors that control h, it depends on the type of the flowing fluid and its velocity. Through analyzing the measured temperature at different heat pulses, the changes in h - due to mobilization of the in-situ brine or CO 2 arrival - can be estimated. Consequently, the velocity of the flowing fluid across the heater can be obtained. Since heat transfer by convection is sensitive to the type of the surrounding fluid, intrusion of CO 2 can be detected from the relatively higher surface temperature obtained at CO 2 arrival. Churchill and Bernstein (1977)'s correlation is adopted to estimate the change of fluid velocity in terms of the change in h. To demonstrate the validity of the proposed technique, the results are applied and validated against those of COMSOL Multiphysics simulation tool for single-phase brine (before CO 2 arrival) and single-phase CO 2 (after CO 2 arrival). The observed temperature heating is sensitive to the flowing fluid velocity and fluid type. The temperature signal observed at CO 2 arrival is large and easily detectable using temperature monitoring tool which provides reliable indication for tracking CO 2 arrival at monitoring wells compared with passive temperature monitoring. The results obtained using the proposed technique agree very well with the numerical results obtained from the simulation tool with a maximum estimation error of 7 percent.

02 PETROLEUM↗

Improved accuracy in degenerate variational integrators for guiding centre and magnetic field line flow

First-order-accurate degenerate variational integration (DVI) was introduced in Ellison et al. ( Phys. Plasmas , vol. 25, 2018, 052502) for systems with a degenerate Lagrangian, i.e. one in which the velocity-space Hessian is singular. In this paper we introduce second-order-accurate DVI schemes, both with and without non-uniform time stepping. We show that it is not in general possible to construct a second-order scheme with a preserved two-form by composing a first-order scheme with its adjoint, and discuss the conditions under which such a composition is possible. We build two classes of second-order-accurate DVI schemes. We test these second-order schemes numerically on two systems having non-canonical variables, namely the magnetic field line and guiding centre systems. Variational integration for Hamiltonian systems with non-uniform time steps, in terms of an extended phase space Hamiltonian, is generalized to non-canonical variables. It is shown that preservation of proper degeneracy leads to single-step (one-step) methods without parasitic modes, i.e. to non-uniform time step DVIs. This extension applies to second-order-accurate as well as first-order schemes, and can be applied to adapt the time stepping to an error estimate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Heterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II

Photosystem II (PSII) is a homodimeric protein complex that catalyzes water oxidation at the oxygen-evolving complex (OEC), a heterocubanoid calcium-tetra-manganese cluster. Here, we analyze the omit electron-density peaks of the OEC’s metal ions in five X-ray free-electron laser PSII structures at a resolution between 2.15 Å and 1.95 Å. The omit peaks can be described by the total number of electrons and approximated by the variance of electron density distribution when the distributions are spherically symmetric. We show that the number of electrons of metal centers are different in the two OECs of PSII dimers, implying that either the oxidation states and/or occupancies of individual metal ions are different in the two monomers. In either case, we find that the two OECs of dark-adapted PSII dimers in crystals are not fully synchronized in the same expected S 1 state. Differences in redox states of the OEC in PSII only partially account for the observation that the electron densities integrate to a smaller number of electrons than expected. Differences between the determined and expected relative electron numbers are much larger than the estimated errors, indicating heterogeneity in the OEC composition. Here, the reported findings suggest that two OECs of dark-adapted PSII crystals are typically not fully synchronized in the S 1 state and likely generate heterogeneity in the crystallographical data of PSII intermediate structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hetero-site Double Core Ionization Energies with Sub-electronvolt Accuracy from Delta-Coupled-Cluster Calculations

Benchmark scalar-relativistic delta-coupled-cluster calculations of hetero-site double core ionization energies of small molecules containing second-row elements are reported. The present study has focused on the high-spin triplet components of two-site double core-ionized states, which are single reference in character and consistent with the use of standard coupledcluster methods. Contributions to computed double core ionization energies from electron-correlation and basis-set effects as well as corrections to the core-valence separation approximation have been analyzed. Furthermore, on the basis of systematic convergence of computational results with respect to these effects, delta-coupled-cluster calculations have been shown to be capable of providing accurate double core ionization energies with remaining errors estimated to be below 0.3 eV, and thus they are recommended for use to facilitate experimental studies of two-site double core-ionized states that are involved in X-ray pump/X-ray probe studies of electronic and molecular dynamics following inner shell ionization or excitation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bond Dissociation Energies and Electronic Calculations on the Actinide Halides ThX and UX (X = Cl, Br, I)

Resonant two-photon ionization spectroscopy has been used to locate predissociation thresholds in the spectra of the actinide halides ThX and UX, where X = Cl, Br, and I. These predissociation thresholds are identified as the bond dissociation energies (BDEs) of the molecules. The resulting values show very similar BDEs for the corresponding ThX and UX species, with the thorium molecules being slightly more strongly bound: D 0 (ThCl) = 5.077(6) eV, D 0 (ThBr) = 4.391(4) eV, D 0 (ThI) = 3.537(8) eV, D 0 (UCl) = 4.989(3) eV, D 0 (UBr) = 4.313(3) eV, and D 0 (UI) = 3.449(8) eV. Here, the estimated error limit is given in parentheses in units of the last reported digit. Spinor-based coupled cluster calculations have also been carried out on the halides of this work, including also ThF and UF. Here, the final D 0 values after including contributions due to basis set incompleteness, outer-core-correlation, picture-change, and QED effects are within 0.04 eV of the present experimental values in each case.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Topological structure of complex predictions

Abstract Current complex prediction models are the result of fitting deep neural networks, graph convolutional networks or transducers to a set of training data. A key challenge with these models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into a simplified topological view of the prediction landscape. The result is a map of the predictions that enables inspection of the model results with more specificity than dimensionality-reduction methods such as tSNE and UMAP. The methods scale up to large datasets across different domains. We present a case study of a transformer-based model previously designed to predict expression levels of a piece of DNA in thousands of genomic tracks. When the model is used to study mutations in the BRCA1 gene, our topological analysis shows that it is sensitive to the location of a mutation and the exon structure of BRCA1 in ways that cannot be found with tools based on dimensionality reduction. Moreover, the topological framework offers multiple ways to inspect results, including an error estimate that is more accurate than model uncertainty. Further studies show how these ideas produce useful results in graph-based learning and image classification.

Computer Science↗