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At least 37 records · Page 2

Implicit fast sweeping method for hyperbolic systems of conservation laws

Implicit time-accurate methods are often used to integrate stiff problems where explicit schemes impose severe time step restrictions. This paper presents an efficient numerical framework based on the Fast Sweeping Method (FSM) for solving linear and nonlinear hyperbolic systems of conservation laws. The solution at each discrete location is computed by sweeping the numerical domain in several predetermined directions that follow the causality of the characteristic families. The use of a fractional step strategy eliminates the need for a solution selection criterion while one-sided stencils limit the number of sweeps to at most 2 d for d space dimensions. This work focuses on the first-order implicit upwind method since it constitutes the building block for high-order conservative schemes. For problems where the degree of stiffness evolves over time, implicit-explicit hybridization can be accomplished with the same algorithm by simply switching the stencil at each time level. As opposed to traditional implicit solvers, the sweeping method does not require a local time linearization of the fluxes thereby preserving the nonlinear stability properties of the original implicit scheme. It also avoids the large computational and memory requirements associated with solving large block-diagonal systems of equations. Here, a series of one- and two-dimensional test cases are presented for the inviscid Burgers' equation and the reactive Euler equations. The results indicate that the implicit FSM can allow a major reduction in the number of time steps even in the presence of discontinuous solution profiles.

74 ATOMIC AND MOLECULAR PHYSICS↗

Physics constrained learning for data-driven inverse modeling from sparse observations

Deep neural networks (DNN) have been used to model nonlinear relations between physical quantities. Those DNNs are embedded in physical systems described by partial differential equations (PDE) and trained by minimizing a loss function that measures the discrepancy between predictions and observations in some chosen norm. This loss function often includes the PDE constraints as a penalty term when only sparse observations are available. As a result, the PDE is only satisfied approximately by the solution. However, the penalty term typically slows down the convergence of the optimizer for stiff problems. We present a new approach that trains the embedded DNNs while numerically satisfying the PDE constraints. We develop an algorithm that enables differentiating both explicit and implicit numerical solvers in reverse-mode automatic differentiation. This allows the gradients of the DNNs and the PDE solvers to be computed in a unified framework. We demonstrate that our approach enjoys faster convergence and better stability in relatively stiff problems compared to the penalty method. Furthermore, our approach allows for the potential to solve and accelerate a wide range of data-driven inverse modeling, where the physical constraints are described by PDEs and need to be satisfied accurately.

97 MATHEMATICS AND COMPUTING↗

Metrics for the Complexity of Material Models

Quantitative measures are proposed for characterizing the complexity of material models used in computational mechanics. The algorithms for evaluating these metrics operate on the mathematical equations in the model rather than a code implementation and are different from software complexity measures. The metrics do not rely on a physical understanding of the model, using instead only a formal statement of the equations. A new algorithm detects the dependencies, whether explicit or implicit, between all the variables. The resulting pattern of dependencies is expressed in a set of pathways, each of which represents a chain of dependence between the variables. These pathways provide the raw data used in the metrics, which correlate with the expected ease of understanding, coding, and applying the model. Usage of the ComplexityMetrics code is described, with examples.

97 MATHEMATICS AND COMPUTING↗

Semi-implicit method to solve compressible multiphase fluid flows without acoustic time step restrictions

A new 3D multiphase numerical capability is presented here for simulating multiphase flow regimes at all Mach numbers (M). The new method is a semi-implicit extension of the finite volume discrete equation method (DEM) of Chinnaya et al. (2004), which originally used explicit time-stepping. The capability is also developed to work with another extension of the DEM to moving grids for arbitrary Lagrangian-Eularian (ALE) methods detailed in Dunn (2011). Rather than solving all phase equations simultaneously, the DEM reduces the equations to a system of single-phase Riemann solves, where each phase has its own velocity and thermodynamic state. Exchanges between the phases are modeled through source terms accounting for the phase interactions. Furthermore, since the original multiphase scheme uses an explicit time-advancement scheme, it has time step restrictions dictated by the speed of sound, which limits the model's ability to simulate weakly compressible flows which typically need to be integrated for longer time periods. Here, we extend the current multiphase formulation by implementing a pressure-correcting step to enable implicit calculations and remove acoustic time step limitations. The new semi-implicit algorithm allows use of relatively large time steps compared to an explicit method. Validation and benefits of the new implicit time-step method are illustrated using several examples including weakly compressible flows and strong shock waves. The scheme presented here is general and may be used for a variety of applications which require capabilities for handling multiphase flow at a wide range of Mach numbers. However, the goal of this research is to simulate all stages of high energy explosions, including the shock formation (high Mach numbers) and evolution of the buoyant cloud (low Mach numbers).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Implicit-Explicit Multirate Infinitesimal GARK Methods

This work focuses on the development of a new class of high-order accurate methods for multirate time integration of systems of ordinary differential equations. Unlike other recent work in this area, the proposed methods support mixed implicit-explicit (IMEX) treatment of the slow time scale. In addition to allowing this slow time scale flexibility, the proposed methods utilize a so-called infinitesimal formulation for the fast time scale through definition of a sequence of modified “fast" initial-value problems that may be solved using any viable algorithm. We name the proposed class as implicit-explicit multirate infinitesimal generalized-structure additive Runge--Kutta (IMEX-MRI-GARK) methods. In addition to defining these methods, we prove that they may be viewed as specific instances of GARK methods and derive a set of order conditions on the IMEX-MRI-GARK coefficients to guarantee both third and fourth order accuracy for the overall multirate method. Additionally, we provide three specific IMEX-MRI-GARK methods, two of order three and one of order four. We conclude with numerical simulations on two multirate test problems, demonstrating the methods' predicted convergence rates and comparing their efficiency against both legacy IMEX multirate schemes and recent third and fourth order implicit MRI-GARK methods.

97 MATHEMATICS AND COMPUTING↗

Semi-implicit time integration of atmospheric flows with characteristic-based flux partitioning

Here, this paper presents a characteristic-based flux partitioning for the semi-implicit time integration of atmospheric flows. Nonhydrostatic models require the solution of the compressible Euler equations. The acoustic time scale is significantly faster than the advective scale, yet it is typically not relevant to atmospheric and weather phenomena. The acoustic and advective components of the hyperbolic flux are separated in the characteristic space. High-order, conservative additive Runge-Kutta methods are applied to the partitioned equations so that the acoustic component is integrated in time implicitly with an unconditionally stable method, while the advective component is integrated explicitly. The time step of the overall algorithm is thus determined by the advective scale. Benchmark flow problems are used to demonstrate the accuracy, stability, and convergence of the proposed algorithm. The computational cost of the partitioned semi-implicit approach is compared with that of explicit time integration.

54 ENVIRONMENTAL SCIENCES↗

A scalable matrix-free spectral element approach for unsteady PDE constrained optimization using PETSc/TAO

In this work, we provide a new approach for the efficient matrix-free application of the transpose of the Jacobian for the spectral element method for the adjoint-based solution of partial differential equation (PDE) constrained optimization. This results in optimizations of nonlinear PDEs using explicit integrators where the integration of the adjoint problem is not more expensive than the forward simulation. Solving PDE constrained optimization problems entails combining expertise from multiple areas, including simulation, computation of derivatives, and optimization. The Portable, Extensible Toolkit for Scientific computation (PETSc) together with its companion package, the Toolkit for Advanced Optimization (TAO), is an integrated numerical software library that contains an algorithmic/software stack for solving linear systems, nonlinear systems, ordinary differential equations, differential algebraic equations, and large-scale optimization problems and, as such, is an ideal tool for performing PDE-constrained optimization. This paper describes an efficient approach in which the software stack provided by PETSc/TAO can be used for large-scale nonlinear time-dependent problems. Time integration can involve a range of high-order methods, both implicit and explicit. The PDE-constrained optimization algorithm used is gradient-based and seamlessly integrated with the simulation of the physical problem.

97 MATHEMATICS AND COMPUTING↗

Implicit–explicit multirate infinitesimal stage-restart methods

Implicit–Explicit (IMEX) methods are flexible numerical time integration methods which solve an initial-value problem (IVP) that is split into stiff and nonstiff processes with the goal of lower computational costs than a purely implicit or explicit approach. A complementary form of flexible IVP solvers are multirate infinitesimal methods for problems split into fast- and slow-changing dynamics, that solve a multirate IVP by evolving a sequence of “fast” IVPs using any suitably accurate algorithm. This article introduces a new class of high-order implicit–explicit multirate methods that are designed for multirate IVPs in which the slow-changing dynamics are further split in an IMEX fashion. This new class, which we call implicit–explicit multirate infinitesimal stage-restart (IMEX-MRI-SR), both improves upon the previous implicit–explicit multirate infinitesimal generalized-structure additive Runge Kutta (IMEX-MRI-GARK) methods by allowing for far easier creation of new embedded methods, and extends multirate exponential Runge Kutta (MERK) methods by allowing the fast-changing dynamics to be nonlinear and the methods to be implicit. We leverage GARK theory to derive conditions for orders of accuracy up to four, and we provide second- and third-order accurate example methods, which are the first known embedded MRI methods with IMEX structure. We then perform numerical simulations demonstrating convergence rates and computational performance in both fixed-step and adaptive-step settings.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

thornado+FLASH-X: A Hybrid Discontinuous Galerkin–Implicit-explicit and Finite-volume Framework for Neutrino-radiation Hydrodynamics in Core-collapse Supernovae

We present neutrino-transport algorithms implemented in the toolkit for high-order neutrino-radiation hydrodynamics (thornado) and their coupling to self-gravitating hydrodynamics within the adaptive mesh refinement–based multiphysics simulation framework FLASH-X. thornado, developed primarily for simulations of core-collapse supernovae (CCSNe), employs a spectral, six-species two-moment formulation with algebraic closure and special-relativistic observer corrections accurate to $\mathcal{O}(v/c)$, and uses discontinuous Galerkin (DG) methods for phase-space discretization combined with implicit-explicit time stepping. A key development is a nonlinear neutrino–matter coupling algorithm based on nested fixed-point iteration with Anderson acceleration, enabling fully implicit treatment of collisional processes, including energy-coupling interactions such as neutrino–electron scattering and pair production. Coupling to finite-volume (FV) hydrodynamics is achieved through a hybrid DG-FV representation of the fluid variables and operator-split evolution within FLASH-X. The implementation is verified using basic transport tests with idealized opacities and relaxation and deleptonization problems with tabulated microphysics. Spherically symmetric CCSN simulations demonstrate accuracy and robustness of the coupled scheme, including close agreement with the CCSN simulation code Chimera. An axisymmetric CCSN simulation further demonstrates the viability of DG-based neutrino transport for multidimensional supernova modeling within FLASH-X. thornado’s neutrino-transport solver is GPU-enabled using OpenMP offloading or OpenACC, and all CCSN applications included in this work use the GPU implementation. Together, these results establish a foundation for future enhancements in physics fidelity, numerical algorithms, and computational performance, for increasingly realistic large-scale CCSN simulations.

Endeve, Eirik [Oak Ridge National Laboratory (ORNL↗

Fully implicit Particle-in-cell algorithms for multiscale plasma simulation

The outline of the paper is as follows: Particle-in-cell (PIC) methods for fully ionized collisionless plasmas, explicit vs. implicit PIC, 1D ES implicit PIC (charge and energy conservation, moment-based acceleration), and generalization to Multi-D EM PIC: Vlasov-Darwin model (review and motivation for Darwin model, conservation properties (energy, charge, and canonical momenta), and numerical benchmarks). The author demonstrates a fully implicit, fully nonlinear, multidimensional PIC formulation that features exact local charge conservation (via a novel particle mover strategy), exact global energy conservation (no particle self-heating or self-cooling), adaptive particle orbit integrator to control errors in momentum conservation, and canonical momenta (EM-PIC only, reduced dimensionality). The approach is free of numerical instabilities: ω pe Δt >> 1, and Δx >> λ D . It requires many fewer dofs (vs. explicit PIC) for comparable accuracy in challenging problems. Significant CPU gains (vs explicit PIC) have been demonstrated. The method has much potential for efficiency gains vs. explicit in long-time-scale applications. Moment-based acceleration is effective in minimizing N FE , leading to an optimal algorithm.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Efficient hybrid explicit-implicit learning for multiscale problems

Splitting method is a powerful method to handle application problems by splitting physics, scales, domain, and so on. Many splitting algorithms have been designed for efficient temporal discretization. Here, in this paper, our goal is to use temporal splitting concepts in designing machine learning algorithms and, at the same time, help splitting algorithms by incorporating data and speeding them up. We propose a machine learning assisted splitting scheme which improves the efficiency of the scheme meanwhile preserves the accuracy. We consider a recently introduced multiscale splitting algorithms, where the multiscale problem is solved on a coarse grid. To approximate the dynamics, only a few degrees of freedom are solved implicitly, while others explicitly. This splitting concept allows identifying degrees of freedom that need implicit treatment. In this paper, we use this splitting concept in machine learning and propose several strategies. First, the implicit part of the solution can be learned as it is more difficult to solve, while the explicit part can be computed. This provides a speed-up and data incorporation for splitting approaches. Secondly, one can design a hybrid neural network architecture because handling explicit parts requires much fewer communications among neurons and can be done efficiently. Thirdly, one can solve the coarse grid component via PDEs or other approximation methods and construct simpler neural networks for the explicit part of the solutions. We discuss these options and implement one of them by interpreting it as a machine translation task. This interpretation of the splitting scheme successfully enables us using the Transformer since it can perform model reduction for multiple time series and learn the connection between them. We also find that the splitting scheme is a great platform to predict the coarse solution with insufficient information of the target model: the target problem is partially given and we need to solve it through a known problem which approximates the target. Our machine learning model can incorporate and encode the given information from two different problems and then solve the target problems. We conduct four numerical examples and the results show that our method is stable and accurate.

97 MATHEMATICS AND COMPUTING↗

An integrated model-driven method for in-treatment upper airway motion tracking using cine MRI in head and neck radiation therapy

Purpose: For the first time, MRI-guided radiation therapy systems can acquire cine images to dynamically monitor in-treatment internal organ motion. However, the complex head and neck (H&N) structures and low-contrast/resolution of on-board cine MRI images make automatic motion tracking a very challenging task. In this study, the authors proposed an integrated model-driven method to automatically track the in-treatment motion of the H&N upper airway, a complex and highly deformable region wherein internal motion often occurs in an either voluntary or involuntary manner, from cine MRI images for the analysis of H&N motion patterns. Methods: Considering the complex H&N structures and ensuring automatic and robust upper airway motion tracking, the authors firstly built a set of linked statistical shapes (including face, face-jaw, and face-jaw-palate) using principal component analysis from clinically approved contours delineated on a set of training data. The linked statistical shapes integrate explicit landmarks and implicit shape representation. Then, a hierarchical model-fitting algorithm was developed to align the linked shapes on the first image frame of a to-be-tracked cine sequence and to localize the upper airway region. Finally, a multifeature level set contour propagation scheme was performed to identify the upper airway shape change, frame-by-frame, on the entire image sequence. The multifeature fitting energy, including the information of intensity variations, edge saliency, curve geometry, and temporal shape continuity, was minimized to capture the details of moving airway boundaries. Sagittal cine MR image sequences acquired from three H&N cancer patients were utilized to demonstrate the performance of the proposed motion tracking method. Results: The tracking accuracy was validated by comparing the results to the average of two manual delineations in 50 randomly selected cine image frames from each patient. The resulting average dice similarity coefficient (93.28% ± 1.46%) and margin error (0.49 ± 0.12 mm) showed good agreement between the automatic and manual results. The comparison with three other deformable model-based segmentation methods illustrated the superior shape tracking performance of the proposed method. Large interpatient variations of swallowing frequency, swallowing duration, and upper airway cross-sectional area were observed from the testing cine image sequences. Conclusions: The proposed motion tracking method can provide accurate upper airway motion tracking results, and enable automatic and quantitative identification and analysis of in-treatment H&N upper airway motion. By integrating explicit and implicit linked-shape representations within a hierarchical model-fitting process, the proposed tracking method can process complex H&N structures and low-contrast/resolution cine MRI images. Future research will focus on the improvement of method reliability, patient motion pattern analysis for providing more information on patient-specific prediction of structure displacements, and motion effects on dosimetry for better H&N motion management in radiation therapy.

60 APPLIED LIFE SCIENCES↗

A Global, Multi-Resolution Approach to Regional Ocean Modeling

In this collaborative research project between Pennsylvania State University, Colorado State University and Florida State University, we mainly focused on developing multi-resolution algorithms which are suitable to regional ocean modeling. We developed hybrid implicit and explicit adaptive multirate time integration method to solve systems of time-dependent equations that present two ignorantly different scales. We studied the e ects of spatial simplicial meshes on the stability and the conditioning of fully discrete approximations. We also studies adaptive nite element method (AFEM) based upon the Centroidal Voronoi Tessellation (CVT) and superconvergent gradient recovery. Some of these techniques are now being used by geoscientists(such as those at LANL).

58 GEOSCIENCES↗

Clustering-Based Predictive Analytics to Improve Scientific Data Discovery

Given the sheer volume of scientific data archived within the data-intensive projects at the US Department of Energy's Oak Ridge National Laboratory, finding precisely what data we are looking for may not be a trivial task; conversely, we may also miss a more prominent data product. To address such issues, we propose improving the data discovery system and using data analytics methods to comprehend what specific users might be interested in based on their physiological state, search patterns, and past data usage history. This work's primary goal is to prune the complexity, increase the visibility of popular data products, and direct users toward the data that best meet their needs. The proposed algorithm constructs a user profile based on the user's explicit or implicit interactions with the system, such as items they are currently looking at on-site and the key metadata mappings related to the data set. The pattern is then used to build a training data set, which will help find relevant data to recommend to the user.

Devarakonda, Ranjeet↗

In situ monitoring of the stopped muon flux at Mu2e

The specific object of Mu2e search is the neutrino-less coherent $\mu^-\rightarrow e^-$ conversion in the field of an aluminum nucleus and the signal is a monoenergetic electron of energy $ \approx 104.97$ MeV. This process is forbidden in the Standard Model but allowed in many of its extensions: with minimal changes to include neutrino masses and oscillation, the Branching Ratio of this process, or the similarly interesting $\mu\rightarrow e \gamma$ decay, is expected to be of the order of $\mathcal{O}(10^{-54})$. Values like these are below any currently achievable experimental sensitivity, and the observation of a signal would be unambiguous evidence of New Physics. The upper limit on the muon conversion was set by SINDRUM II at $7\times10^{-13}$ (90\% C.L.) and the goal of the Mu2e collaboration is an improvement of 4 order of magnitudes.\\ The Mu2e experiment can be conceptually divided into three stages: interaction of the primary proton pulse with the tungsten target a nd production of $\pi$ and $\mu$; collection and transport of the produced particles down to the aluminum stopping target; interaction with the stopping target and measurement of the output particles. The measurement of the stopped muon flux is of cardinal importance for the normalization of the Mu2e results. The baseline design includes two detectors developed to measure this flux, counting $\gamma$ emitted by the muonic atoms: HPGe and LaBr$_3$(Ce). The studies performed by the Mu2e Collaboration show that these two systems can be reliably used to determine the overall normalization.\\ The number of stopped muons is proportional to the number of protons on target, which itself depends on the extraction system for the proton beam. The Mu2e beam delivery system will use a resonant extraction to create the proton pulses and this method is characterized by intensity fluctuations on the time scale of milliseconds. These fluctuations, aside from the proportional fluctuation of t he number of muons, have a non-trivial impact on the overall! performance of the apparatus. For example, higher intensity proton bunches translate into higher veto rates by the Cosmic Rays Veto system, which is triggered by secondary particles generated by the proton interaction. Another example is the effect of the instantaneous luminosity on the reconstruction efficiency: higher intensity translates into higher detector occupancy, which in turn reduces the reconstruction efficiency.\\ The two cited detectors encounter limitations when trying to monitor the flux at the millisecond timescales: HPGe is by construction a slow detector while the rate of emission of the $\gamma (1809\textrm{ keV})$ the LaBr$_3$(Ce) will measure is too low. As of today, no system allows to monitor these fluctuations and the goal of this Thesis is to try filling this gap. The method we developed to monitor the fluctuations of the stopped muon flux, and by extension, the fluctuation in the proton pulses intensity is based on counting the number of muons capt ured in the stopping target by counting the number of protons produced in the process of the nuclear muon capture. This is one of the possible processes a stopped muon can undergo and it can lead to the ejection of charged particles.\\ The reconstruction algorithms were developed by the Mu2e collaboration with the explicit (and sometimes implicit) aim to reconstruct tracks of electrons in an energy range of a conversion electron. The protons we are interested in behave quite differently from these electrons and the cardinal task of this study has been to tailor the reconstruction routines to these particles. This has been done by analyzing simulated events consisting of a single proton to optimize the procedure and understand the features of these tracks. A major difference with respect to the electrons is the non-relativistic nature of $100\div300$ MeV$/c$ protons: accounting for the low velocity is both a challenge and a unique signature of the tracks.\\ The use of a pulse d beam and the need to allow produced $\pi$ to decay and $\m! u$ to int! eract in the stopping target forces the definition of a Mu2e \textit{event}: an event is comprised by everything which happens in a $1.7\ \mu$s window between the incidence two consecutive proton pulses. This means that the reconstruction will be performed in an environment crowded by many different particles. The next step of this study has been to estimate the performance of the method in a fully-fledged Mu2e simulated event and to study what kind of selections would improve it.\\ Our results are satisfactory since the number of reconstructed protons is significant (few per event), and show that a monitor on the timescale of milliseconds is indeed possible.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗

Verification of an energy-conserving semi-implicit electrostatic particle-in-cell scheme for modeling high-density plasma at scale

A verification study of a semi-implicit energy-conserving electrostatic particle-in-cell algorithm is presented. The algorithm relaxes the time-step and mesh-size constraints that require resolution of the plasma period and Debye length associated with traditional explicit momentum-conserving particle-in-cell algorithms. Physical implications and applicability of using the semi-implicit scheme for modeling high-density plasmas are discussed. Where possible, numerical results are compared against analytical solutions. The simulation results indicate that the algorithm is stable at time steps larger than twice the inverse plasma frequency and cell sizes larger than the Debye length. It is found that the algorithm gives adequate results, provided that the distribution function and the spatiotemporal scales dictating the physics of the problem are resolved. As such, the algorithm may provide a robust method for kinetic modeling of high-density plasmas at scale.

Cyclotron resonance↗