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DOE OSTI2026

SO(3)-invariant PCA with application to molecular data

Principal component analysis (PCA) is a fundamental technique for dimensionality reduction and denoising; however, its application to three-dimensional data with arbitrary orientations -- common in structural biology -- presents significant challenges. A naive approach requires augmenting the dataset with many rotated copies of each sample, incurring prohibitive computational costs. In this paper, we extend PCA to 3D volumetric datasets with unknown orientations by developing an efficient and principled framework for SO(3)-invariant PCA that implicitly accounts for all rotations without explicit data augmentation. By exploiting underlying algebraic structure, we demonstrate that the computation involves only the square root of the total number of covariance entries, resulting in a substantial reduction in complexity. We validate the method on real-world molecular datasets, demonstrating its effectiveness and opening up new possibilities for large-scale, high-dimensional reconstruction problems.

Fraiman, Michael [Tel Aviv Univ., Tel Aviv (Israel↗
DOE OSTI2026

Explicit Monotone Stable Super-Time-stepping Methods for Finite Time Singularities

We explore a novel way to numerically resolve the scaling behavior of finite-time singularities in solutions of nonlinear parabolic PDEs. The Runge–Kutta–Legendre (RKL) and Runge–Kutta–Gegenbauer (RKG) super-time-stepping methods were originally developed for nonlinear complex physics problems with diffusion. These are multistage single step second-order, forward-in-time methods with no implicit solves. The advantage is that the time-step size for stability scales with stage number 𝑠 as $\mathcal{O}$⁡(𝑠 2 ). Many interesting nonlinear PDEs have finite-time singularities, and the presence of diffusion often limits one to using implicit or semi-implicit time-step methods for stability constraints. Finite-time singularities are particularly challenging due to the large range of scales that one desires to resolve, often with adaptive spatial grids and adaptive time steps. Here, in this study, we show two examples of nonlinear PDEs for which the self-similar singularity structure has time and space scales that are resolvable using the RKL and RKG methods, without forcing even smaller time steps. Compared to commonly used implicit numerical methods, we achieve a significantly smaller run time while maintaining comparable accuracy. We also prove numerical monotonicity for both the RKL and RKG methods under their linear stability conditions for the constant coefficient heat equation, in the case of infinite domain and periodic boundary condition, leading to a theoretical guarantee of the superiority of the RKL and RKG methods over traditional super-time-stepping methods, such as the Runge-Kutta-Chebyshev and the orthogonal Runge-Kutta-Chebyshev methods. Code can be found at https://github.com/ZT220501/SRK-Singularity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Expedited Real Time Processing for the NETL HYPER Cyber-Physical System (Final Report)

The primary objective of the proposed project was to provide the National Energy Technology Laboratory’s Hybrid Performance (Hyper) Facility the needed numerical methods algorithm(s), software development and implementation support to enact real time cyber-physical systems (CPSs) that simulate process dynamics on the order of five milliseconds or smaller. The proposed paths forward comprised three distinct approaches to hasten transient simulations. They fell under the numerical methods categorical options of: 1) optimizing key parameters within the facility’s pre-existing real time processing scheme; 2) introducing an “informed” processing approach wherein a priori computations expedite real time attempts; and 3) implementing alternatives to the employed explicit-implicit blended finite difference (spatio-temporal) approach. Each of these three classes were proposed independently as options for improvement, yet in some cases one class of approach could have complemented another.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2021

Linear and Nonlinear Solvers for Simulating Multiphase Flow within Large-Scale Engineered Subsurface Systems

Simulation of multiphase flow in the subsurface is well-known to be computationally challenging. While there have been many studies that have explored approaches to overcoming these challenges, they often utilize relatively simple case studies. In this paper, we focus on the unique numerical challenges posed by modeling large-scale engineered subsurface systems, characterized by discrete features embedded in a heterogeneous natural subsurface setting. The man-made features such as shafts, tunnels, and barriers often cause multiple challenges in modeling the domain for multiphase porous media flow. This flow scenario can have a wide range of applications such as nuclear waste repositories, enhanced recovery of a petroleum reservoir, geothermal engineering, and carbon sequestration. An example of these severe numerical challenges is the case of performance assessment (PA) for Waste Isolation Pilot Plant (WIPP), the only operating deep geological repository in the US, which simulates extreme material properties of bedded salt rock formation and extreme contrast due to open excavation next to the formation. The models have extremes not only of permeability and porosity but also of the constitutive models needed for multiphase flow; additionally, they have process models like salt creep closure reducing porosity over time, fracturing in clay and anhydrite interbeds of the bedded salt, gas generation from the waste materials, and unintentional human borehole intrusions in some scenarios. Numerical simulations require the solution of coupled systems of nonlinear PDEs; in our work, we use the open-source simulator PFLOTRAN which is based on Finite Volume discretization. The solution of the nonlinear equations requires use of the Newton-Raphson iteration at each time step, which entails the solution of the linearized Jacobian system at each iteration. The effects of all the processes (i.e., large number of unknowns, highly nonlinear constitutive relations, large contrasts in material properties in short distances) lead to an ill-conditioned Jacobian matrix that severely challenges traditional linear solver, i.e., stabilized biconjugate gradient with block Jacobi incomplete LU preconditioner (BCGS-ILU) leading to non-convergence for traditional Newton-Raphson nonlinear solver causing unacceptably long computation time for each model. This paper presents linear solvers such as constrained pressure residual (CPR) two-stage preconditioner with alternate-block-factorization (ABF) and quasi- implicit pressure and explicit saturation (QIMPES) decouplers and flexible generalized residual solver (FGMRES). The new general-purpose nonlinear solver, Newton trust-region dogleg Cauchy (NTRDC), is also introduced to resolve extreme nonlinearities in the models. We demonstrate the effectiveness of each method relative to the default BCGS-Newton solver. The two best cases had nearly 50 times speed-up and achieved completion of a simulation in 14 hours that never completed due to non-convergence with the default solver. We also investigate the strong scalability of each method and discuss some of the deficiencies found for Block Jacobi preconditioner using parallel domain decomposition, and node packing effects of modern processor architecture.

Preconditioner, Nonlinear, Porous media, Multiphas↗
DOE OSTI2022

Entropy–Preserving and Entropy–Stable Relaxation IMEX and Multirate Time–Stepping Methods

In this work, we propose entropy-preserving and entropy-stable partitioned Runge–Kutta (RK) methods. In particular, we extend the explicit relaxation Runge–Kutta methods to IMEX–RK methods and a class of explicit second-order multirate methods for stiff problems arising from scale-separable or grid-induced stiffness in a system. The proposed approaches not only mitigate system stiffness but also fully support entropy-preserving and entropy-stability properties at a discrete level. The key idea of the relaxation approach is to adjust the step completion with a relaxation parameter so that the time-adjusted solution satisfies the entropy condition at a discrete level. The relaxation parameter is computed by solving a scalar nonlinear equation at each timestep in general; however, as for a quadratic entropy function, we theoretically derive the explicit form of the relaxation parameter and numerically confirm that the relaxation parameter works the Burgers equation. Several numerical results for ordinary differential equations and the Burgers equation are presented to demonstrate the entropy-conserving/stable behavior of these methods. We also compare the relaxation approach and the incremental direction technique for the Burgers equation with and without a limiter in the presence of shocks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

ORMATEX

The Oak Ridge Matrix Exponential (ORMATEX) software library contains methods to compute the matrix exponential and the action of the matrix exponential on a vector. Additionally, this package contains the related methods for the phi-functions which commonly appear in a wide class of exponential time integration methods. Krylov methods are provided to evaluate the matrix exponential-vector and phi-vector products for cases where the matrix is large and sparse. Utilizing these methods, ORMATEX implements performant exponential integrators for large systems of coupled ordinary differential equations (ODEs). The exponential time integration routines in ORMATEX are particularly suitable to large, stiff systems of equations. These routines may be utilized as a competitive alternative to classical implicit and explicit time integration schemes for certain classes of differential equations where the problem stiffness can be predominately explained by the linear terms.

Gurecky, William [Oak Ridge National Laboratory (O↗
DOE OSTI2021

Impact of Integration Scheme on Performance of Anisotropic Plasticity Models

Given the prevalent role of metals in a variety of industries, schemes to integrate corresponding constitutive models in finite element applications have long been studied. A number of formulations have been developed to accomplish this task; each with their own advantages and costs. Often the focus has been on ensuring the accuracy and numerical stability of these algorithms to enable robust integration. While important, emphasis on these performance metrics may often come at the cost of computational expense potentially neglecting the needs of individual problems. In the current work, the performance of two of the most common integration methods for anisotropic plasticity -- the convex cutting plane (CCP) and closest point projection (CPP) -- across a variety of metrics is assessed; including accuracy and cost. A variety of problems are considered ranging from single elements to large representative simulations including both implicit quasistatic and explicit transient dynamic type responses. The relative performance of each scheme in the different instances is presented with an eye towards guidance on when the different algorithms may be beneficial.

36 MATERIALS SCIENCE↗
DOE OSTI2017

A tightly-coupled domain-decomposition approach for highly nonlinear stochastic multiphysics systems

Multiphysics simulations often involve nonlinear components that are driven by internally generated or externally imposed random fluctuations. When used with a domain-decomposition (DD) algorithm, such components have to be coupled in a way that both accurately propagates the noise between the subdomains and lends itself to a stable and cost-effective temporal integration. We develop a conservative DD approach in which tight coupling is obtained by using a Jacobian-free Newton–Krylov (JfNK) method with a generalized minimum residual iterative linear solver. This strategy is tested on a coupled nonlinear diffusion system forced by a truncated Gaussian noise at the boundary. Enforcement of path-wise continuity of the state variable and its flux, as opposed to continuity in the mean, at interfaces between subdomains enables the DD algorithm to correctly propagate boundary fluctuations throughout the computational domain. Reliance on a single Newton iteration (explicit coupling), rather than on the fully converged JfNK (implicit) coupling, may increase the solution error by an order of magnitude. Increase in communication frequency between the DD components reduces the explicit coupling's error, but makes it less efficient than the implicit coupling at comparable error levels for all noise strengths considered. Finally, the DD algorithm with the implicit JfNK coupling resolves temporally-correlated fluctuations of the boundary noise when the correlation time of the latter exceeds some multiple of an appropriately defined characteristic diffusion time.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

CTF-R: A novel residual-based thermal hydraulic solver

The traditional scientific process has been revolutionized by the advent of computational modeling, but the nuclear industry generally uses "legacy codes," which were developed early in the evolution of computers. One example of a legacy code, the thermal hydraulic subchannel code CTF, is modernized in this work through the development of a novel residual-based version, CTF-R. Unlike its predecessor, CTF-R is not limited by the strict computational limitations of the early 1980's, and can therefore be designed such that it is inherently flexible and easy to use. A case study is examined to demonstrate how the flexibility of the code can be used to improve simulation results. In this example, the coupling between the solid and liquid fields is examined. Traditionally, this coupling is modeled explicitly, which imposes numerical stability limits on the time step size. These limits are derived and it is shown that they are removed when the coupling is made implicit. Further, the development of CTF-R will enable future improvements in next generation reactor modeling, numerical methods, and coupling to other codes. Through the further development of CTF-R and other residual-based codes, state-of-the-art simulation is possible.

42 ENGINEERING↗
DOE OSTI2016

Scalable smoothing strategies for a geometric multigrid method for the immersed boundary equations

The immersed boundary (IB) method is a widely used approach to simulating fluid-structure interaction (FSI). Although explicit versions of the IB method can suffer from severe time step size restrictions, these methods remain popular because of their simplicity and generality. In prior work (Guy et al., Adv Comput Math, 2015), some of us developed a geometric multigrid preconditioner for a stable semi-implicit IB method under Stokes flow conditions; however, this solver methodology used a Vanka-type smoother that presented limited opportunities for parallelization. This work extends this Stokes-IB solver methodology by developing smoothing techniques that are suitable for parallel implementation. Specifically, we demonstrate that an additive version of the Vanka smoother can yield an effective multigrid preconditioner for the Stokes-IB equations, and we introduce an efficient Schur complement-based smoother that is also shown to be effective for the Stokes-IB equations. We investigate the performance of these solvers for a broad range of material stiffnesses, both for Stokes flows and flows at nonzero Reynolds numbers, and for thick and thin structural models. We show here that linear solver performance degrades with increasing Reynolds number and material stiffness, especially for thin interface cases. Nonetheless, the proposed approaches promise to yield effective solution algorithms, especially at lower Reynolds numbers and at modest-to-high elastic stiffnesses.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

The NonConforming Virtual Element Method for the Stokes Equations

In this paper, we present the nonconforming virtual element method (VEM) for the numerical approximation of velocity and pressure in the steady Stokes problem. The pressure is approximated using discontinuous piecewise polynomials, while each component of the velocity is approximated using the nonconforming virtual element space. On each mesh element the local virtual space contains the space of polynomials of up to a given degree, plus suitable nonpolynomial functions. The virtual element functions are implicitly defined as the solution of local Poisson problems with polynomial Neumann boundary conditions. As typical in VEM approaches, the explicit evaluation of the non-polynomial functions is not required. This approach makes it possible to construct nonconforming (virtual) spaces for any polynomial degree regardless of the parity, for two- and three-dimensional problems, and for meshes with very general polygonal and polyhedral elements. We show that the nonconforming VEM is inf-sup stable and establish optimal a priori error estimates for the velocity and pressure approximations. Finally, numerical examples confirm the convergence analysis and the effectiveness of the method in providing high-order accurate approximations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Asymmetric kinetic equilibria: Generalization of the BAS model for rotating magnetic profile and non-zero electric field

Finding kinetic equilibria for non-collisional/collisionless tangential current layers is a key issue as well for their theoretical modeling as for our understanding of the processes that disturb them, such as tearing or Kelvin Helmholtz instabilities. The famous Harris equilibrium [E. Harris, Il Nuovo Cimento Ser. 10 23, 115–121 (1962)] assumes drifting Maxwellian distributions for ions and electrons, with constant temperatures and flow velocities; these assumptions lead to symmetric layers surrounded by vacuum. This strongly particular kind of layer is not suited for the general case: asymmetric boundaries between two media with different plasmas and different magnetic fields. The standard method for constructing more general kinetic equilibria consists in using Jeans theorem, which says that any function depending only on the Hamiltonian constants of motion is a solution to the steady Vlasov equation [P. J. Channell, Phys. Fluids (1958–1988) 19, 1541 (1976); M. Roth et al., Space Sci. Rev. 76, 251–317 (1996); and F. Mottez, Phys. Plasmas 10, 1541–1545 (2003)]. The inverse implication is however not true: when using the motion invariants as variables instead of the velocity components, the general stationary particle distributions keep on depending explicitly of the position, in addition to the implicit dependence introduced by these invariants. The standard approach therefore strongly restricts the class of solutions to the problem and probably does not select the most physically reasonable. The BAS (Belmont-Aunai-Smets) model [G. Belmont et al., Phys. Plasmas 19, 022108 (2012)] used for the first time the concept of particle accessibility to find new solutions: considering the case of a coplanar-antiparallel magnetic field configuration without electric field, asymmetric solutions could be found while the standard method can only lead to symmetric ones. These solutions were validated in a hybrid simulation [N. Aunai et al., Phys. Plasmas (1994-present) 20, 110702 (2013)], and more recently in a fully kinetic simulation as well [J. Dargent and N. Aunai, Phys. Plasmas (submitted)]. Nevertheless, in most asymmetric layers like the terrestrial magnetopause, one would indeed expect a magnetic field rotation from one direction to another without going through zero [J. Berchem and C. T. Russell, J. Geophys. Res. 87, 8139–8148 (1982)], and a non-zero normal electric field. In this paper, we propose the corresponding generalization: in the model presented, the profiles can be freely imposed for the magnetic field rotation (although restricted to a 180 rotation hitherto) and for the normal electric field. As it was done previously, the equilibrium is tested with a hybrid simulation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

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↗
DOE OSTI2016

Implicitly solving phase appearance and disappearance problems using two-fluid six-equation model

Phase appearance and disappearance issue presents serious numerical challenges in two-phase flow simulations using the two-fluid six-equation model. Numerical challenges arise from the singular equation system when one phase is absent, as well as from the discontinuity in the solution space when one phase appears or disappears. In this work, a high-resolution spatial discretization scheme on staggered grids and fully implicit methods were applied for the simulation of two-phase flow problems using the two-fluid six-equation model. A Jacobian-free Newton-Krylov (JFNK) method was used to solve the discretized nonlinear problem. An improved numerical treatment was proposed and proved to be effective to handle the numerical challenges. The treatment scheme is conceptually simple, easy to implement, and does not require explicit truncations on solutions, which is essential to conserve mass and energy. Various types of phase appearance and disappearance problems relevant to thermal-hydraulics analysis have been investigated, including a sedimentation problem, an oscillating manometer problem, a non-condensable gas injection problem, a single-phase flow with heat addition problem and a subcooled flow boiling problem. Successful simulations of these problems demonstrate the capability and robustness of the proposed numerical methods and numerical treatments. As a result, volume fraction of the absent phase can be calculated effectively as zero.

42 ENGINEERING↗
DOE OSTI2020

High Order Implicit Residual-Based Spatial Discretization Error Estimation for S N Neutron Transport

This work demonstrates our novel residual source spatial discretization error estimator (LeR/TEAD) for a DGFEM-1 discretization and assesses it along with two contemporary estimators, Ragusa and Wang's h -refinement estimator (RW) and Duo, Azmy, and Zikatanov's explicit residual-based estimator (DAZ), on a suite of Method of Manufactured Solutions (MMS) 2D problems and three realistic problem geometries. LeR/TE-AD is attractive because it directly estimates the local error in the angular flux, as opposed to a mere indicator of the error's behavior, on the same mesh and method order as the original numerical solution, thus typically being less computationally intensive than a refinement-based method. On the MMS suite, LeR/TE-AD consistently displayed a reduced performance versus its DGFEM-0 results in terms of accuracy and precision metrics, though it was not typically grossly inaccurate. This is attributed to the irregularities in the true solution across singular characteristics limiting the local accuracy of the numerical flux solution, leading to poor derivative approximations used in the residual approximations. The error transport problem then spreads the error in the residual to nearby cells, causing a greater degree of imprecision that did not afflict DAZ or RW. In testing the estimators on realistic problem geometries, however, LeR/TE-AD fared better. In practice, the true error is much larger in non-idealized geometries like in MMS, and a superlinear true solution means that RW and DAZ are not beneficially biased for DGFEM-1 error estimation. LeR/TE-AD was typically first or second in accuracy, primarily competing with RW, but the latter usually consumed 2-4 times the computational time as LeR/TE-AD, and requires a solution with four times as many unknowns. Furthermore, RW and LeR/TE-AD can be used to compute direct estimates of the error in any quantity of interest that is based on the angular ux solution, such as the fission rate density in a fuel pin, whereas DAZ requires a heuristic extension due to its norm-based nature.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Operator splitting method for simulation of dynamic flows in natural gas pipeline networks

Here, we develop an operator splitting method to simulate flows of isothermal compressible natural gas over transmission pipelines. The method solves a system of nonlinear hyperbolic partial differential equations (PDEs) of hydrodynamic type for mass flow and pressure on a metric graph, where turbulent losses of momentum are modeled by phenomenological Darcy-Weisbach friction. Mass flow balance is maintained through the boundary conditions at the network nodes, where natural gas is injected or withdrawn from the system. Gas flow through the network is controlled by compressors boosting pressure at the inlet of the adjoint pipe. Our operator splitting numerical scheme is unconditionally stable and it is second order accurate in space and time. The scheme is explicit, and it is formulated to work with general networks with loops. We test the scheme over range of regimes and network configurations, also comparing its performance with performance of two other state of the art implicit schemes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

The Challenges of Troubleshooting

Troubleshooting work presents electrical and other workers with a challenging combination of physical hazards, working conditions, and time pressure, which can lead to unwanted outcomes if not carefully managed.Summaries of several incidents in which workers were injured or at risk of injury while performing troubleshooting work are presented, identifying organizational weaknesses and error precursors that contributed to each incident.The primary challenges include:Deranged equipment. Equipment that needs troubleshooting is not in a normal operating condition. Actions that are safe when the equipment is in a normal state may not be safe in the deranged state.Work planning and control. The steps taken in troubleshooting are most often determined by the results of the immediately previous diagnostic test, making effective work planning challenging.Multiple types of hazards. Most equipment will present a troubleshooting worker with several types of hazards, including hazardous energy as defined in 29 CFR 1910.147. Portions of the troubleshooting activity may be infeasible without these hazards present.Time pressure. Restoring operation of failed equipment often involves an explicit or implicit sense of urgency.Equipment design and construction. The physical construction of the equipment in large part will determine to which hazards troubleshooters may be exposed. It will also determine which hazards may be encountered while performing the servicing needed to restore the equipment or system to operation.There are effective methods for addressing each challenge, most of which require a combination of advance preparation and management commitment.

Mertz, David E.↗
DOE OSTI2022

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↗