Domain Decomposition Research Articles

Iterative method for large-scale Timoshenko beam models assessed on commercial-grade paperboard

AbstractLarge-scale structural simulations based on micro-mechanical models of paper products require extensive numerical resources and time. In such models, the fibrous material is often represented by connected beams. Whereas previous micro-mechanical simulations have been restricted to smaller sample problems, large-scale micro-mechanical models are considered here. These large-scale simulations are possible on a non-specialized desktop computer with 128GB of RAM using an iterative method developed for network models and based on domain decomposition. Moreover, this method is parallelizable and is also well-suited for computational clusters. In this work, the proposed memory-efficient iterative method is numerically validated for linear systems resulting from large networks of Timoshenko beams. Tensile stiffness and out-of-plane bending stiffness are simulated and validated for various commercial-grade three-ply paperboards consisting of layers composed of two different types of paper fibers. The results of these simulations show that a linear network model produces results consistent with theory and published experimental data

MolDStruct: Modeling the dynamics and structure of matter exposed to ultrafast x-ray lasers with hybrid collisional-radiative/molecular dynamics.

We describe a method to compute photon-matter interaction and atomic dynamics with x-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically determined based on changes to their electronic occupations and the formation of a free electron cloud created from the irradiation of photons in the x-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, reducing the number of non-bonded interactions. In combination with parallelization through domain decomposition, the hybrid code handles large-scale molecular dynamics and ionization. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters, and crystals) that, when exposed to an x-ray laser pulse, turn into a plasma in the first few femtoseconds of the interaction. We present four examples demonstrating the applicability of the method. We investigate the non-thermal heating and scattering of bulk water and damage-induced dynamics of a protein crystal using an x-ray pump-probe scheme. In both cases, we compare to the experimental data. For single particle imaging, we simulate the ultrafast dynamics of a methane cluster exposed to a femtosecond x-ray laser. In the context of coherent diffractive imaging, we study the fragmentation as given by an x-ray pump-probe setup to understand the evolution of radiation damage in the time range of hundreds of femtoseconds.

High-resolution frequency domain decomposition for modal analysis of bridges using train-induced free-vibrations

Modal parameters are structural inherent characteristics that can be applied for revealing performance of railway bridges. Free vibration signals generated by a passage of train are commonly utilized to estimate the modal parameters of railway bridges due to their higher signal-to-noise ratios compared to random vibrations caused by ambient loads. However, since free vibration signals rapidly decay over time, the available free-vibration data is typically short-time. When using the fast Fourier transform-based spectral estimation method for modal identification from short-time vibration data, a phenomenon known as spectral leakage occurs, leading to miss-identification of some structural modes. In this study, the classical frequency domain decomposition (FDD) is improved for modal identification of railway bridges, in which the higher resolution auto-power spectral density (PSD) and cross-PSD functions are calculated through the autoregressive (AR) model-based method. The AR model-based method improves both the smoothness and resolution of the PSD functions compared to the fast Fourier transform technique. These AR model-based PSD functions are then employed in the FDD process to facilitate frequency and mode shape identification while avoiding spurious noise modes. The proposed eigenvalue fitting technique is subsequently utilized to estimate damping ratios. Numerical simulation data as well as vibration data from an actual bridge are analyzed to validate the proposed method, with a comparison made to the Welch’s PSD-based method. The results demonstrate that the modified FDD approach enables more effective identification of structural modes, even in the presence of closely-spaced modes.

Adaptive Space-Time Domain Decomposition for Multiphase Flow in Porous Media with Bound Constraints

Adaptive Space-Time Domain Decomposition for Multiphase Flow in Porous Media with Bound Constraints

Acceleration of computations in modelling of processes in complex objects and systems

The development of methods of parallelization of computing processes, which involve the decomposition of the computational domain, is an urgent task in the modeling of complex objects and systems. Complex objects and systems can contain a large number of elements and interactions. Decomposition allows you to break down a system into simpler subsystems, which simplifies the analysis and management of complexity. By dividing the calculation area of the part, it is possible to perform parallel calculations, which increases the efficiency of calculations and reduces simulation time. Domain decomposition makes it easy to scale the model to work with larger or more detailed systems. With the right choice of decomposition methods, the accuracy of the simulation can be improved, since different parts of the system may have different levels of detail and require appropriate methods of additional analysis. Decomposition allows the simulation to be distributed between different participants or devices, which is relevant for distributed systems or collaborative work on a project. In this work, mathematical models are built, which consist in the construction of iterative procedures for "stitching" several areas into a single whole. The models provide for different complexity of calculation domains, which makes it possible to perform different decomposition approaches, in particular, both overlapping and non-overlapping domain decomposition. The obtained mathematical models of subject domain decomposition can be applied to objects and systems that have different geometric complexity. Domain decomposition models that do not use overlap contain different iterative methods of "stitching" on a common boundary depending on the types of boundary conditions (a condition of the first kind is a Dirichlet condition, or a condition of the second year is a Neumann condition), and domain decomposition models with an overlap of two or more areas consist of the minimization problem for constructing the iterative condition of "stitching" areas. It should be noted that the obtained models will work effectively on all applied tasks that describe the dynamic behavior of objects and their systems, but the high degree of efficiency of one model may be lower than the corresponding the degree of effectiveness of another model, since each task is individual. Keywords: mathematical modelling, decomposition of the computational domain, parallelization, optimization, complex objects and systems.

Computation of Laplacian eigenvalues of two-dimensional shapes with dihedral symmetry

We numerically compute the lowest Laplacian eigenvalues of several two-dimensional shapes with dihedral symmetry at arbitrary precision arithmetic. Our approach is based on the method of particular solutions with domain decomposition. We are particularly interested in asymptotic expansions of the eigenvalues λ(n)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\lambda (n)$$\\end{document} of shapes with n edges that are of the form λ(n)∼x∑k=0∞Ck(x)nk\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\lambda (n) \\sim x\\sum _{k=0}^{\\infty } \\frac{C_k(x)}{n^k}$$\\end{document} where x is the limiting eigenvalue for n→∞\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$n\\rightarrow \\infty $$\\end{document}. Expansions of this form have previously only been known for regular polygons with Dirichlet boundary conditions and (quite surprisingly) involve Riemann zeta values and single-valued multiple zeta values, which makes them interesting to study. We provide numerical evidence for closed-form expressions of higher order Ck(x)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$C_k(x)$$\\end{document} and give more examples of shapes for which such expansions are possible (including regular polygons with Neumann boundary condition, regular star polygons, and star shapes with sinusoidal boundary).

Simulation and reconstruction for 3D elastic wave using multi-GPU and CUDA-aware MPI

3D finite-difference time-domain numerical simulation and reconstruction based on the domain decomposition technique are essential parts of high-performance computation for reverse-time migration and full-waveform inversion. However, the low GPU utilization in computing for small-sized models and the tremendous memory consumption for large-sized models may result in low computational efficiency and high memory costs. This paper proposes a contiguous memory management (CMM) method and a variable-order wavefield reconstruction (VWR) method. The CMM allocates the memory of many small-sized arrays used for MPI communications on a larger-sized contiguous memory block, which aims to reduce the number of MPI communications between subdomains and improve the communication bandwidth, thus reducing the MPI time overhead and improving the GPU utilization. Meanwhile, the VWR can flexibly set the number of layers of boundary wavefield used for source wavefield reconstruction according to the host memory capacity and accuracy requirements. Since one layer of boundary wavefield could be stored using the VWR, the memory consumption of host memory can be significantly alleviated. Numerical experiments show that GPU utilization in computing for the model with a size of 1213 can be improved from 25% to 90% using the CMM method, and the VWR method can reduce memory consumption by about 86% while maintaining good accuracy in wavefield reconstruction. In addition, the issue of how to obtain a domain decomposition scheme with optimal performance is discussed in this paper.

A global space–time Trefftz DG scheme for the time-dependent isotropic elastic wave equations

In this paper we are concerned with Trefftz discretizations of the time-dependent linear elastic wave equation in arbitrary space dimensional domains Ω⊂Rd(d∈N). We propose a Trefftz discontinuos Galerkin method, construct Trefftz basis functions and prove that the corresponding approximate solutions possess optimal-order error estimates with respect to the meshwidth. A space–time domain decomposition preconditioner is introduced for the system generated by the proposed variational formula. Besides, we propose the global Trefftz DG method combined with local DG methods to solve the nonhomogeneous model. The numerical results verify the validity of the theoretical results, and show that the resulting approximate solutions possess high accuracy, and the proposed preconditioner is effective.

A domain decomposing reduced-order method for solving the multi-domain transient heat conduction problems

In this article, a domain decomposition algorithm combined with a reduced-order model (ROM) is proposed to deal with the transient heat conduction problems in multi-domain structures. Using the domain decomposition algorithm and the finite element method (FEM), the original problem is decomposed into multiple non-overlapping subdomains, which can be solved independently under appropriate boundary conditions. However, additional inter-regional connected calculation will be brought through the simple geometry decomposition. Thus, the proper orthogonal decomposition (POD), a projection-based ROM technique, is utilized to further reduce the number of unknowns and the calculation time for each subdomain. To be more specific, the local POD bases of each subdomain are obtained by decomposing a snapshot matrix that gathered according to time by the application of the virtual boundary conditions on interfaces of the adjacent subdomains and other boundaries. Furthermore, the problems under different boundary conditions can be linked by the variable condensation technique on the interfaces, which enhances the efficiency of the numerical solver dramatically. Finally, the accuracy and efficiency of the proposed method are demonstrated by comparing the results calculated using both the proposed algorithm and the direct finite element simulation.

An Overlapping Domain Decomposition Splitting Algorithm for Stochastic Nonlinear Schrödinger Equation

An Overlapping Domain Decomposition Splitting Algorithm for Stochastic Nonlinear Schrödinger Equation

Accurate implementation of two-level asynchronous domain decomposition solvers

Recently, asynchronous coarse-grid correction has been achieved within additive Schwarz-type and primal Schur domain decomposition frameworks. Both additive and multiplicative coarse-grid corrections were discussed, however, the implemented asynchronous Schwarz-type solver with additive correction relies on the specific design of the restricted additive Schwarz (RAS) method, and also requires an overlap between the subsets of unknowns. In this paper, we first highlight a gap between the theoretical analysis from the literature and the associated RAS implementation. It turns out that communications delays would actually need to be bounded in order to fit the theory. This has to be stressed since, despite the asynchronous nature of the solver, the coarse-grid correction requires non-blocking global synchronization, which is subject to communications bottleneck. Second, we propose an implementation approach which applies to a wider class of additive Schwarz-type methods while still coping with the bounded delays requirement.

Adaptive Deep Fourier Residual method via overlapping domain decomposition

The Deep Fourier Residual (DFR) method is a specific type of variational physics-informed neural network (VPINN). It provides a robust neural network-based solution to partial differential equations (PDEs). The DFR strategy is based on minimizing the dual norm of the weak residual of a PDE, which is equivalent to minimizing the energy norm of the error. To compute the dual norm of the weak residual, the DFR method employs an orthonormal spectral basis of the test space, known for rectangles or cuboids for multiple function spaces.In this work, we extend the DFR method with ideas of traditional domain decomposition (DD). This enables two improvements: (a) to solve problems in more general polygonal domains and (b) to develop an adaptive refinement technique in the test space using a Döfler marking algorithm. In the former case, we retain the desirable equivalence between the employed loss function and the H1 error under non-restrictive assumptions, numerically demonstrating adherence to explicit bounds in the case of the L-shaped domain problem. In the latter, we show how refinement strategies lead to potentially significant improvements against a reference, classical DFR implementation with a test function space of significantly lower dimensionality, allowing us to better approximate singular solutions at a more reasonable computational cost.

A non-overlapping optimization-based domain decomposition approach to component-based model reduction of incompressible flows

We present a component-based model order reduction procedure to efficiently and accurately solve parameterized incompressible flows governed by the Navier-Stokes equations. Our approach leverages a non-overlapping optimization-based domain decomposition technique to determine the control variable that minimizes jumps across the interfaces between sub-domains. To solve the resulting constrained optimization problem, we propose both Gauss-Newton and sequential quadratic programming methods, which effectively transform the constrained problem into an unconstrained formulation. Furthermore, we integrate model order reduction techniques into the optimization framework, to speed up computations. In particular, we incorporate localized training and adaptive enrichment to reduce the burden associated with the training of the local reduced-order models. Numerical results are presented to demonstrate the validity and effectiveness of the overall methodology.

Data-Driven Enterprise Architecture for Pharmaceutical R&D

This paper addresses the research gap in the realm of data-driven transformation by leveraging the Resource-Based View (RBV) theory and the dynamic capabilities concept to the contours of a data-driven enterprise. It confronts the limitations of conventional digital and data transformation programs, which often prioritize technological enhancements over crucial organizational and cultural shifts. Proposing a more holistic perspective, the Data-Driven Enterprise Architecture Framework (DDA) is introduced, emphasizing the domain decomposition and productization of an architecture, distributed ownership, and federated governance, while ensuring the continuous harmonization of data, application, and business architecture. A case study featuring a leading pharmaceutical company illustrates the practical implementation of the DDA framework as a pillar of their Digital Transformation Strategy. By integrating scalable and distributed data architecture into the overarching Enterprise Architecture landscape, the company has initiated their data-driven transformation journey, showcased through their initial and very early results. This research not only offers valuable insights for pharmaceutical organizations navigating the complexities of data-driven transformations, but also addresses a research gap in the field.

A highly parallel algorithm for simulating the elastodynamics of a patient-specific human heart with four chambers using a heterogeneous hyperelastic model

In this paper a highly parallel method is developed for simulating the elastodynamics of a four-chamber human heart with patient-specific geometry. The heterogeneous hyperelastic model is discretized by a finite element method in space and a fully implicit adaptive method in time, and the resulting nonlinear algebraic systems are solved by a scalable domain decomposition algorithm. The deformations of the cardiac muscles are quite complex due to the realistic geometry, the heterogeneous hyperelasticity of the cardiac tissue, and the myocardial fibers with active stresses. Moreover, the deformations in different chambers and at different phases of the cardiac cycle are very different. To simulate all the muscle movements including the atrial diastole, the atrial systole, the isovolumic contraction, the ventricular ejection, the isovolumic relaxation, and the ventricular filling, the temporal-spatial mesh needs to be sufficiently fine, but not too fine so that the overall computing time is manageable, we introduce a baseline mesh in space and a two-level time stepping strategy including a uniform baseline time step size to obtain the desired time accuracy and an adaptive time stepping method within a baseline time step to guarantee the convergence of the nonlinear solver. Through numerical experiments, we investigate the performance of the proposed method with respect to the material coefficients, the fiber orientations, as well as the mesh sizes and the time step sizes. For an unstructured tetrahedral mesh with more than 200 million degree of freedoms, the method scales well for up to 16,384 processor cores for all steps of an entire cardiac cycle.

Enhancing Wireless Sensor Network in Structural Health Monitoring through TCP/IP Socket Programming-Based Mimic Broadcasting: Experimental Validation

This paper presents the implementation of a synchronous Structural Health Monitoring (SHM) framework utilizing wireless, low-cost, and off-the-shelf components. Vibration-based condition monitoring plays a crucial role in assessing the reliability of structural systems by detecting damage through changes in vibration parameters. The adoption of low-cost Micro-Electro-Mechanical Systems (MEMS) sensors in Wireless Sensor Networks (WSNs) has gained traction, emphasizing the need for precise time synchronization to schedule wake-up times of multiple sensor nodes for data collection. To address this challenge, our proposed method introduces a TCP/IP socket programming-based mimic broadcasting mechanism and a scalable sensing network controlled by a central gateway, leveraging the Raspberry Pi Python platform. The system operates using Internet of Things (IoT) concepts and adopts a star topology, where a packet is transmitted from the gateway to initiate measurements simultaneously on multiple sensor nodes. The sensor node comprises a MEMS accelerometer, a real time clock DS3231 module and Raspberry Pi Zero 2W (RPi0-2W), while the gateway employs a Raspberry Pi 4 (RPi4). To ensure accurate time synchronization, all Pi0-2W nodes were configured as Network Time Protocol (NTP) clients, synchronizing with an RPi4 server using chrony, the reliable implementation of the NTP. Through experimental evaluations, the system demonstrates its effectiveness and reliability in achieving initial time synchronization. This study addresses the challenge of achieving precise time alignment between sensor nodes through the utilization of the Dynamic Time Wrapping (DTW) method for Frequency Domain Decomposition (FDD) applications. The contribution of this research significantly enhances the field by improving the accuracy and reliability of time-aligned measurements, with a specific focus on utilizing low-cost sensors. By developing a practical and cost-effective SHM framework, this work advances the accessibility and scalability of structural health monitoring solutions, facilitating more widespread adoption and implementation in various engineering applications

GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems.

Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models.

MaCaw: Domain-Decomposed Monte Carlo Neutral Particle Transport on Unstructured Mesh in MOOSE

MaCaw is a Multiphysics Object-Oriented Simulation Environment (MOOSE)–based application that enables domain-decomposed neutral particle transport calculations in MOOSE. It leverages MOOSE’s ray-tracing module for unstructured mesh particle tracking and OpenMC for collision physics. Additionally, the OpenMC implementation of several calculation steps (e.g. initialization and normalization) needed in a Monte Carlo particle transport eigenvalue calculation were adapted for domain decomposition. This paper reports on MaCaw’s implementation and several limitations, a single verification case, and early single-node scaling studies. This paper also serves as an announcement of the public release of MaCaw on the Idaho National Laboratory GitHub at https://github.com/idaholab/macaw.

Robust methods for multiscale coarse approximations of diffusion models in perforated domains

For the Poisson equation posed in a domain containing a large number of polygonal perforations, we propose a low-dimensional coarse approximation space based on a coarse polygonal partitioning of the domain. Similarly to other multiscale numerical methods, this coarse space is spanned by locally discrete harmonic basis functions. Along the subdomain boundaries, the basis functions are piecewise polynomial. The main contribution of this article is an error estimate regarding the H1-projection over the coarse space; this error estimate depends only on the regularity of the solution over the edges of the coarse partitioning. For a specific edge refinement procedure, the error analysis establishes superconvergence of the method even if the true solution has a low general regularity. Additionally, this contribution numerically explores the combination of the coarse space with domain decomposition (DD) methods. This combination leads to an efficient two-level iterative linear solver which reaches the fine-scale finite element error in few iterations. It also bodes well as a preconditioner for Krylov methods and provides scalability with respect to the number of subdomains.

Fully automated operational modal identification based on scale-space peak picking algorithm and power spectral density estimation

Modal analysis is a fundamental and essential research direction in the field of structural engineering. The ultimate goal is to determine the modal parameters of the structures. However, the existing modal analysis algorithms often require a large number of parameter adjustments and manual intervention during operation, which cannot be fully automated. In order to realize the automatic identification of modal parameters, the automatic operational modal identification method (AOMI) is proposed based on the interpolated power spectral density estimation (IPSE). To achieve more precise spectrum analysis in the low-frequency band, IPSE is employed to perform Fourier transform on the original frequency domain segment with optimized frequency resolution. This enhances the sharpness of the obtained spectrum in the low-frequency range, making peak frequencies more discernible. Subsequently, the scale-space peak picking algorithm is used to automatically obtain the peak of the power spectral density (PSD), thus enabling the automatic identification of the natural frequency. Finally, the frequency domain decomposition method (FDD) is used to identify modal parameters based on the natural frequencies. The effectiveness of AOMI is verified through the modal identification of the old steel truss bridge and the three layer framework. Under the environmental excitation, the frequencies identified by the IPSE method is close to that of FDD, Bayesian fast fourier transform (FFT) and covariance driven stochastic subspace identification (SSI-COV). Furthermore, the PSD obtained through IPSE has sharper peak than that of FDD and the Welch’s method. The damping ratio identification accuracy and modal assurance criterion (MAC) are satisfactory in AOMI, which can improve the automatic performance.