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At least 235 records · Page 13

Identifying stochastic dynamics via finite expression methods

Modeling stochastic differential equations (SDEs) is crucial for understanding complex dynamical systems in various scientific fields. Recent methods often employ neural network-based models, which typically represent SDEs through a combination of deterministic and stochastic terms. However, these models usually lack interpretability and have difficulty in generalizing beyond their training domain. Here, this paper introduces the Finite Expression Method (FEX), a symbolic learning approach designed to derive interpretable mathematical representations of the deterministic component of SDEs. For the stochastic component, we integrate FEX with advanced generative modeling techniques to provide a comprehensive representation of SDEs. The numerical experiments on linear, nonlinear, and multidimensional SDEs demonstrate that FEX generalizes well beyond the training domain and delivers more accurate long-term predictions compared to neural network-based methods. The symbolic expressions identified by FEX not only improve prediction accuracy but also offer valuable scientific insights into the underlying dynamics of the systems.

Complex dynamical systems↗

Evolution of coupled weakly driven waves in a dissipative plasma

The nonlinear collisional dynamics of coupled driven plasma waves in the presence of background dissipation is studied analytically within kinetic theory. Sufficiently near marginal stability, phase space correlations are poorly preserved and time delays become unimportant. The system is then shown to be governed by two first-order coupled autonomous differential equations of cubic order for the wave amplitudes and two complementary first-order equations for the evolution of their phases. That system of equations can be decoupled and further simplified to a single second-order differential equation of Liénard's type for each amplitude. Numerical solutions for this equation are obtained in the general case, while analytic solutions are obtained for special cases in terms of parameters related to the spacing of the resonances of the two waves in frequency space, e.g., wave lengths and oscillation frequencies. These parameters are further analyzed to find classes of quasi-steady saturation and pulsating scenarios. To classify equilibrium points, local stability analysis is applied, and bifurcation conditions are determined. When the two waves saturate at similar amplitude levels, their combined signal is shown to invariably exhibit amplitude beating and phase jumps of nearly π. In conclusion, the obtained analytical results can be used to benchmark simulations and to interpret eigenmode amplitude measurements in fusion experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Active operator learning with predictive uncertainty quantification for partial differential equations

With the increased prevalence of neural operators being used to provide rapid solutions to partial differential equations (PDEs), understanding the accuracy of model predictions and the associated error levels is necessary for deploying reliable surrogate models in scientific applications. Existing uncertainty quantification (UQ) frameworks employ ensembles or Bayesian methods, which can incur substantial computational costs during both training and inference. Here, we propose a lightweight predictive UQ method tailored for Deep operator networks (DeepONets) that also generalizes to other operator networks. Numerical experiments on linear and nonlinear PDEs demonstrate that the framework’s uncertainty estimates are unbiased and provide accurate out-of-distribution uncertainty predictions with a sufficiently large training dataset. Our framework provides fast inference and uncertainty estimates that can efficiently drive outer-loop analyses that would be prohibitively expensive with conventional solvers. We demonstrate how predictive uncertainties can be used in the context of Bayesian optimization and active learning problems to yield improvements in accuracy and data-efficiency for outer-loop optimization procedures. In the active learning setup, we extend the framework to Fourier Neural Operators (FNO) and describe a generalized method for other operator networks. To enable real-time deployment, we introduce an inference strategy based on precomputed trunk outputs and a sparse placement matrix, reducing evaluation time by more than a factor of five. Our method provides a practical route to uncertainty-aware operator learning in time-sensitive settings.

97 MATHEMATICS AND COMPUTING↗

LOKI

LOKI is a simulation code that models weakly-coupled plasma evolution using Eulerian kinetic models in four phase space dimensions. The code is useful to understand basic plasma nonlinear plasma physics phenomena - in particular, wave-particle and wave-wave resonances that occur in laser plasma interactions. LOKI can simulate fundamental physical process in low-density plasmas on a scale of hundreds of light wavelengths. It does so by solving the relativistic Vlasov and Valsov-Fokker-Planck differential transport equations describing the collision less and low-collisionality evolution of charged particles in electromagnetic fields in two configuration space and two velocity space dimensions. Two principle electromagnetic models are provided: electrostatic (Poisson's Equation) and electromagnetic (Maxwell's equations).

DIMITS, ANDRIS↗

PETSc/TAO Users Manual V.3.21

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and optimizers that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started ). The library is organized hierarchically, enabling users to employ the abstraction level most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users.

97 MATHEMATICS AND COMPUTING↗

PETSc/TAO Users Manual (Rev. 3.19)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and opti mization that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than packages such as MATLAB or a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or lldb, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. There are several packages, built on PETSc, that may satisfy your needs without requiring directly using PETSc. We recommend reviewing these packages functionality before starting to code directly with PETSc. PETSc can be used to provide a “MPI parallel linear solver” in an otherwise sequential, or OpenMP parallel code. This approach cannot provide extremely large improvements in the application time by utilizing large numbers of MPI processes but can still improve the performance. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect true scalability to large numbers of MPI processes. See PCMPI for details on how to utilize the PETSc MPI linear solver server. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc has been supported for twenty-five years; see mailing list information on our website for information on contacting support.

97 MATHEMATICS AND COMPUTING↗

Pyomo.DOE: An open-source package for model-based design of experiments in Python

Predictive mathematical models are a cornerstone of science and engineering. Yet selecting, calibrating, and validating said science-based models often remains an art in practice. Model-based design of experiments (MBDoE) provides a systematic framework to maximize information gain from experiments while minimizing time and resource costs. But MBDoE remains limited to niche application areas, in part because practitioners must integrate expertise in statistics, computational optimization, and modeling. To help reduce this barrier, we introduce Pyomo.DOE, an open-source package for MBDoE. Pyomo.DOE uses a nonlinear sensitivity analysis code k_aug to quickly approximate the Fisher information matrix and leverages a new stochastic programming abstraction. We demonstrate Pyomo.DOE with the first application of MBDoE to fixed-bed breakthrough experiments, which highlights the power of Pyomo.DOE to quantify the value of experimental modifications a priori for large-scale partial differential-algebraic equation (PDAE) models. Here we also provide a mathematical primer on MBDoE targeted at general chemical engineers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards sharp error analysis of extended Lagrangian molecular dynamics

The extended Lagrangian molecular dynamics (XLMD) method provides a useful framework for reducing the computational cost of a class of molecular dynamics simulations with constrained latent variables. The XLMD method relaxes the constraints by introducing a fictitious mass ε for the latent variables and solving a set of singularly perturbed ordinary differential equations. While favorable numerical performance of XLMD has been demonstrated in several different contexts in the past decade, mathematical analysis of the method remains scarce. Here, we propose the first error analysis of the XLMD method in the context of a classical polarizable force field model. While the dynamics with respect to the atomic degrees of freedom are general and nonlinear, the key mathematical simplification of the polarizable force field model is that the constraints on the latent variables are given by a linear system of equations. We prove that when the initial value of the latent variables is compatible in a sense that we define, XLMD converges as the fictitious mass ε is made small with $\mathscr{O}$(ε) error for the atomic degrees of freedom and with $\mathscr{O}$($\sqrt{ε}$) error for the latent variables, when the dimension of the latent variable d' is 1. Furthermore, when the initial value of the latent variables is improved to be optimally compatible in a certain sense, we prove that the convergence rate can be improved to $\mathscr{O}$(ε) for the latent variables as well. Numerical results verify that both estimates are sharp not only for d'=1, but also for arbitrary d'. In the setting of general d', we do obtain convergence, but with the non-sharp rate of $\mathscr{O}$($\sqrt{ε}$) for both the atomic and latent variables.

74 ATOMIC AND MOLECULAR PHYSICS↗

Quantum-inspired method for solving the Vlasov-Poisson equations

Kinetic simulations of collisionless (or weakly collisional) plasmas using the Vlasov equation are often infeasible due to high-resolution requirements and the exponential scaling of computational cost with respect to dimension. Recently, it has been proposed that matrix product state (MPS) methods, a quantum-inspired but classical algorithm, can be used to solve partial differential equations with exponential speed-up, provided that the solution can be compressed and efficiently represented as a MPS within some tolerable error threshold. Here, in this work, we explore the practicality of MPS methods for solving the Vlasov-Poisson equations for systems with one coordinate in space and one coordinate in velocity, and find that important features of linear and nonlinear dynamics, such as damping or growth rates and saturation amplitudes, can be captured while compressing the solution significantly. Furthermore, by comparing the performance of different mappings of the distribution functions onto the MPS, we develop an intuition of the MPS representation and its behavior in the context of solving the Vlasov-Poisson equations, which will be useful for extending these methods to higher-dimensional problems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ARKODE: A Flexible IVP Solver Infrastructure for One-step Methods

We describe the ARKODE library of one-step time integration methods for ordinary differential equation (ODE) initial-value problems (IVPs). In addition to providing standard explicit and diagonally implicit Runge–Kutta methods, ARKODE supports one-step methods designed to treat additive splittings of the IVP, including implicit-explicit (ImEx) additive Runge–Kutta methods and multirate infinitesimal (MRI) methods. We present the role of ARKODE within the SUNDIALS suite of time integration and nonlinear solver libraries, the core ARKODE infrastructure for utilities common to large classes of one-step methods, as well as its use of “time stepper” modules enabling easy incorporation of novel algorithms into the library. Numerical results show example problems of increasing complexity, highlighting the algorithmic flexibility afforded through this infrastructure, and include a larger multiphysics application leveraging multiple algorithmic features from ARKODE and SUNDIALS.

97 MATHEMATICS AND COMPUTING↗

Consistent coupling algorithms for coupled core-edge simulations of plasma turbulence

Two schemes for coupling gyrokinetic simulations of microturbulence in tokamaks are proposed. The first scheme is based on an additive Schwarz domain decomposition. In this work, we show that, because the goal of turbulence is long-time averages of the dynamics rather than temporal accuracy, the iteration to self-consistency across domains, which is typically required by Schwarz schemes, can be avoided, thereby accelerating the computation. Second, we propose a coupling scheme that relies entirely on the addition of source terms, leaving the boundary conditions arbitrary. The practical motivations for such a scheme are discussed, and forms of the source terms that ensure consistency and stability are derived. The schemes are tested on a nonlinear, one-dimensional model problem, and the first scheme is further tested on the Hasegawa–Wakatani model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Scalable Algorithms for Inverse Problems With High-Dimensional Parameter Spaces

Inverse problems, which involve inferring unknown parameters from observed data, present significant computational challenges, especially in large-scale settings with high-dimensional unknown parameters and nonlinear relationships between the unknowns and observations. Bayesian inference provides an approach for addressing these problems, often relying on sequential sampling methods like Markov chain Monte Carlo (MCMC) to approximate the posterior distribution of the parameters. However, MCMC methods become computationally demanding as the dimensionality of the problem increases, particularly in large-scale systems where likelihood evaluations rely on solving partial differential equations (PDEs) on large spatial domains with finely resolved meshes. To overcome these limitations, recent advancements have focused on designing scalable computa tional techniques – for both PDE simulations and sampling strategies – to make Bayesian methods feasible for high-dimensional problems.

97 MATHEMATICS AND COMPUTING↗

Jacobian-free Newton–Krylov method for the simulation of non-thermal plasma discharges with high-order time integration and physics-based preconditioning

A preconditioning framework for the numerical simulation of non-thermal streamer discharges is developed using the Jacobian-free Newton-Krylov (JFNK) method. A reduced plasma fluid model is considered, consisting of electrons, one positive ion, one negative ion, and the electrostatic potential. Here, the plasma kinetics model includes ionization, electron-ion recombination, electron attachment, electron detachment, and ion-ion recombination. The governing equations are made dimensionless, discretized in space with finite differences, and integrated in time with a fully implicit method based on high-order backward differentiation formulas. The preconditioning framework is based on a linearized form of the governing equations and physics-based operator splitting. The efficiency of the preconditioning strategy is assessed through two test cases: streamer propagation between parallel plates and an axisymmetric pin-to-pin discharge. The fully implicit approach overcomes traditional restrictions in the time step size due to processes such as electron drift, electron diffusion, and dielectric relaxation. Excellent performance is observed through relevant statistics of the JFNK solver, although the number of linear iterations increases for the pin-to-pin discharge when nonlinear numerical boundary conditions are imposed at the electrodes. Performance studies show scalability with O(100-1000) processors for O(10M) unknowns with ample room for optimization.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A conservative phase-space moving-grid strategy for a 1D-2V Vlasov–Fokker–Planck Solver

In this work, we develop a conservative configuration- and velocity-space (i.e., phase-space) moving-grid strategy for the Vlasov–Fokker–Planck (VFP) equation in a planar geometry. The velocity-space grid is normalized and shifted in terms of the thermal speed and the bulk-fluid velocity, respectively. The configuration-space grid is moved according to a mesh-motion-partial-differential equation (MMPDE), which equidistributes a monitor function that is inversely proportional to the gradient-length scales of the macroscopic plasma quantities. The resulting inertial terms in the transformed VFP equations are discretized to ensure the discrete conservation of mass, momentum, and energy. To satisfy the discrete conservation theorems in the presence of phase-space mesh motion, we employ the method of discrete nonlinear constraints – explored in previous studies – but the underlying symmetries are determined in a much more efficient manner than before. The conservative grid-adaptivity strategy provides an efficient scheme that resolves important physical structures in the phase-space while controlling the computational complexity at all times. We demonstrate the favorable features of the proposed algorithm through a set of test cases of increasing complexity. The problems test independent components of the algorithms, as well as the integrated capability on settings relevant to inertial confinement fusion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

PETSc Users Manual (Rev. 3.13)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear solvers, nonlinear solvers, and time integrators that may be used in application codes written in Fortran, C, C++, and Python. PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than \rolling them" yourself.

97 MATHEMATICS AND COMPUTING↗

A High-Order Eulerian–Lagrangian Runge–Kutta Finite Volume (EL–RK–FV) Method for Scalar Nonlinear Conservation Laws

Abstract We present a class of high-order Eulerian–Lagrangian Runge–Kutta finite volume methods that can numerically solve Burgers’ equation with shock formations, which could be extended to general scalar conservation laws. Eulerian–Lagrangian (EL) and semi-Lagrangian (SL) methods have recently seen increased development and have become a staple for allowing large time-stepping sizes. Yet, maintaining relatively large time-stepping sizes post shock formation remains quite challenging. Our proposed scheme integrates the partial differential equation on a space-time region partitioned by linear approximations to the characteristics determined by the Rankine–Hugoniot jump condition. We trace the characteristics forward in time and present a merging procedure for the mesh cells to handle intersecting characteristics due to shocks. Following this partitioning, we write the equation in a time-differential form and evolve with Runge–Kutta methods in a method-of-lines fashion. High-resolution methods such as ENO and WENO-AO schemes are used for spatial reconstruction. Extension to higher dimensions is done via dimensional splitting. Numerical experiments demonstrate our scheme’s high-order accuracy and ability to sharply capture post-shock solutions with large time-stepping sizes.

Chen, Jiajie↗

Physics vs structure: A systematic benchmark of learning strategies for multi-zone building thermal dynamics

Recent advances in physics-informed and data-driven machine learning promise improved thermal models for advanced building control, yet there is limited quantitative evidence on when added physics structure and architectural complexity are beneficial. Here, this work presents a systematic benchmark of five representative system identification methods for modeling multi-zone building thermal dynamics: linear state-space models, multi-layer perceptrons, neural state-space models, neural ordinary differential equations, and physically-consistent neural networks. The methods are evaluated across multiple data regimes and zone coupling strategies. Using a high-fidelity multi-zone commercial building emulator, we examine short-term and long-term prediction accuracy, computational efficiency, and ease of development. Our results reveal critical trade-offs between prediction performance, model complexity, and physical consistency. We demonstrate that decoupled, nonlinear black-box models consistently outperform coupled physics-constrained architectures in both predictive accuracy and out-of-distribution robustness in majority of the test cases for the building type considered in the study. Our findings quantify the cost of complexity in building thermal modeling and provide concrete, actionable, scenario-based guidelines for selecting model classes for control-oriented applications.

Building thermal modeling↗

An Eulerian Vlasov-Fokker–Planck algorithm for spherical implosion simulations of inertial confinement fusion capsules

Here, we present a numerical algorithm that enables a phase-space adaptive Eulerian Vlasov–Fokker–Planck (VFP) simulation of inertial confinement fusion (ICF) capsule implosions. The approach relies on extending a recent mass, momentum, and energy conserving phase-space moving-mesh adaptivity strategy to spherical geometry. In configuration space, we employ a mesh motion partial differential equation (MMPDE) strategy while, in velocity space, the mesh is expanded/contracted and shifted with the plasma’s evolving temperature and drift velocity. The mesh motion is dealt with by transforming the underlying VFP equations into a computational (logical) coordinate, with the resulting inertial terms carefully discretized to ensure conservation. To deal with the spatial and temporally varying dynamics in a spherically imploding system, we have developed a novel nonlinear stabilization strategy for MMPDE in the configuration space. The strategy relies on a nonlinear optimization procedure that optimizes between mesh quality and the volumetric rate change of the mesh to ensure both accuracy and stability of the solution. Implosions of ICF capsules are driven by several boundary conditions: (1) an elastic moving wall boundary; (2) a time-dependent Maxwellian Dirichlet boundary; and (3) a pressure-driven Lagrangian boundary. Of these, the pressure-driven Lagrangian boundary driver is new to our knowledge. The implementation of our strategy is verified through a set of test problems, including the Guderley and Van-Dyke implosion problems — the first-ever reported using a Vlasov–Fokker–Planck model.

1D2V↗