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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A fast Fourier transform-based solver for elastic micropolar composites

This work presents a spectral micromechanical formulation for obtaining the full-field and homogenized response of elastic micropolar composites. The algorithm relies on a coupled set of convolution integral equations for the micropolar strains, where periodic Green’s operators associated with a linear homogeneous reference medium are convolved with functions of the Cauchy and couple stress fields that encode the material’s heterogeneity, as well as any potential material nonlinearity. Such convolution integral equations take an algebraic form in the reciprocal Fourier space that can be solved iteratively. In this vein, the fast Fourier transform (FFT) algorithm is leveraged to accelerate the numerical solution, resulting in a mesh-free formulation in which the periodic unit cell representing the heterogeneous material can be discretized by a regular grid of pixels in two dimensions (or voxels in three dimensions). For verification, the numerical solutions obtained with the micropolar FFT solver are compared with analytical solutions for a matrix with a dilute circular inclusion subjected to plane strain loading. The developed computational framework is then used to study length-scale effects and effective (micropolar) moduli of composites with various topological configurations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Discriminating Quantum States with Quantum Machine Learning

Quantum machine learning (QML) algorithms have obtained great relevance in the machine learning (ML) field due to the promise of quantum speedups when performing basic linear algebra subroutines (BLAS), a fundamental element in most ML algorithms. By making use of BLAS operations, we propose, implement and analyze a quantum k-means (qk-means) algorithm with a low time complexity of O(NKlog(D)I/C) to apply it to the fundamental problem of discriminating quantum states at readout. Discriminating quantum states allows the identification of quantum states |0⟩ and |1⟩ from low-level in-phase and quadrature signal (IQ) data, and can be done using custom ML models. In order to reduce dependency on a classical computer, we use the qk-means to perform state discrimination on the IBMQ Bogota device and managed to find assignment fidelities of up to 98.7% that were only marginally lower than that of the k-means algorithm. We also performed a cross-talk benchmark on the quantum device by applying both algorithms to perform state discrimination on a combination of quantum states and using Pearson Correlation coefficients and assignment fidelities of discrimination results to conclude on the presence of cross-talk on qubits. Evidence shows cross-talk in the (1, 2) and (2, 3) neighboring qubit couples for the analyzed device.

Quiroga, David↗
DOE OSTI2015

Fully-Implicit Orthogonal Reconstructed Discontinuous Petrov-Galerkin Method for Multiphysics Problems

This document is focussed on the development of reconstructed discontinuous Galerkin (RDG P n P m ) method, based on orthogonal basis functions. Orthogonality of basis functions is essential for enabling robust and efficient fully-implicit Newton-Krylov based time discretization. The method is designed for generic partial differential equations, including transient hyperbolic, parabolic and/or elliptic operators, which are attributed to many multiphysics problems. Our driving application of interest is additive manufacturing, which requires simulations of fluid-solid-gas systems, with compressibility effects and phase change (melting/ solidification). Thus, we demonstrate the method capabilities for solving nonlinear heat conduction equation coupled with multi-material Navier-Stokes based compressible fluid (in low Mach number limit) systems. We focus our attention to the method accuracy (in both time and space), as well as solvability of linear algebra involved in linear steps of the Newton-based solver. We demonstrate the accuracy and efficacy of the method, emphasizing the advantages from the orthogonality of basis functions, which makes better conditioning of underlying (approximate) Jacobian matrices, and rapid convergence of Krylov methods. iii

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Generalized Jacobi–Galerkin method for nonlinear fractional differential algebraic equations

In this paper, we provide an approximate approach based on the Galerkin method to solve a class of nonlinear fractional differential algebraic equations. The fractional derivative operator in the Caputo sense is utilized and the generalized Jacobi functions are employed as trial functions. The existence and uniqueness theorem as well as the asymptotic behavior of the exact solution are provided. It is shown that some derivatives of the solutions typically have singularity at origin dependence on the order of the fractional derivative. The influence of the perturbed data on the exact solutions along with the convergence analysis of the proposed scheme is also established. Some illustrative examples provided to demonstrate that this novel scheme is computationally efficient and accurate.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

QuTree: A tree tensor network package

Here we present QuTree, a C++ library for tree tensor network approaches. QuTree provides class structures for tensors, tensor trees, and related linear algebra functions that facilitate the fast development of tree tensor network approaches such as the multilayer multiconfigurational time-dependent Hartree approach or the density matrix renormalization group approach and its various extensions. We investigate the efficiency of relevant tensor and tensor network operations and show that the overhead for managing the network structure is negligible, even in cases with a million leaves and small tensors. QuTree focuses on providing simple, high-level routines while retaining easy access to the backend to facilitate novel developments. We demonstrate the capabilities of the package by computing the eigenstates of coupled harmonic oscillator Hamiltonians and performing random circuit simulations on a virtual quantum computer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A graphics processing unit accelerated sparse direct solver and preconditioner with block low rank compression

We present the GPU implementation efforts and challenges of the sparse solver package STRUMPACK. The code is made publicly available on github with a permissive BSD license. STRUMPACK implements an approximate multifrontal solver, a sparse LU factorization which makes use of compression methods to accelerate time to solution and reduce memory usage. Multiple compression schemes based on rank-structured and hierarchical matrix approximations are supported, including hierarchically semi-separable, hierarchically off-diagonal butterfly, and block low rank. Here, in this paper, we present the GPU implementation of the block low rank (BLR) compression method within a multifrontal solver. Our GPU implementation relies on highly optimized vendor libraries such as cuBLAS and cuSOLVER for NVIDIA GPUs, rocBLAS and rocSOLVER for AMD GPUs and the Intel oneAPI Math Kernel Library (oneMKL) for Intel GPUs. Additionally, we rely on external open source libraries such as SLATE (Software for Linear Algebra Targeting Exascale), MAGMA (Matrix Algebra on GPU and Multi-core Architectures), and KBLAS (KAUST BLAS). SLATE is used as a GPU-capable ScaLAPACK replacement. From MAGMA we use variable sized batched dense linear algebra operations such as GEMM, TRSM and LU with partial pivoting. KBLAS provides efficient (batched) low rank matrix compression for NVIDIA GPUs using an adaptive randomized sampling scheme. The resulting sparse solver and preconditioner runs on NVIDIA, AMD and Intel GPUs. Interfaces are available from PETSc, Trilinos and MFEM, or the solver can be used directly in user code. We report results for a range of benchmark applications, using the Perlmutter system from NERSC, Frontier from ORNL, and Aurora from ALCF. For a high frequency wave equation on a regular mesh, using 32 Perlmutter compute nodes, the factorization phase of the exact GPU solver is about 6.5× faster compared to the CPU-only solver. The BLR-enabled GPU solver is about 13.8× faster than the CPU exact solver. For a collection of SuiteSparse matrices, the STRUMPACK exact factorization on a single GPU is on average 1.9× faster than NVIDIA’s cuDSS solver.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Efficient solution of the simplified P N equations

We show new solver strategies for the multigroup SPN equations for nuclear reactor analysis. By forming the complete matrix over space, moments, and energy a robust set of solution strategies may be applied. Moreover, power iteration, shifted power iteration, Rayleigh quotient iteration, Arnoldi's method, and a generalized Davidson method, each using algebraic and physics-based multigrid preconditioners, have been compared on C5G7 MOX test problem as well as an operational PWR model. These results show that the most ecient approach is the generalized Davidson method, that is 30-40 times faster than traditional power iteration and 6-10 times faster than Arnoldi's method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A Semi-Algebraic Two Level Solver

We develop a simple semi-algebraic 2-level solver built on traditional multigrid ideas. It is designed to be easily incorporated into existing simulation software. It exhibits good convergence for many classes of challenging problems including discontinuous diffusion, convection- diffusion, and Helmholtz equations. It has built-in structure that makes it simple to generalize in several interesting directions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Matrix-Free High-Performance Saddle-Point Solvers for High-Order Problems in \(\boldsymbol{H}(\operatorname{\textbf{div}})\)

Here, this work describes the development of matrix-free GPU-accelerated solvers for high-order finite element problems in H(div). The solvers are applicable to grad-div and Darcy problems in saddle-point formulation, and have applications in radiation diffusion and porous media flow problems, among others. Using the interpolation–histopolation basis, efficient matrix-free preconditioners can be constructed for the (1, 1)-block and Schur complement of the block system. With these approximations, block-preconditioned MINRES converges in a number of iterations that is independent of the mesh size and polynomial degree. The approximate Schur complement takes the form of an M-matrix graph Laplacian and therefore can be well-preconditioned by highly scalable algebraic multigrid methods. High-performance GPU-accelerated algorithms for all components of the solution algorithm are developed, discussed, and benchmarked. Numerical results are presented on a number of challenging test cases, including the “crooked pipe” grad-div problem, the SPE10 reservoir modeling benchmark problem, and a nonlinear radiation diffusion test case.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Machine Learning meets Algebraic Combinatorics: A Suite of Benchmark Datasets to Accelerate AI for Mathematics Research

The use of benchmark datasets has become an important engine of progress in machine learning (ML) over the past 15 years. Recently there has been growing interest in utilizing machine learning to drive advances in research-level mathematics. However, off-the-shelf solutions often fail to deliver the types of insights required by mathematicians. This suggests the need for new ML methods specifically designed with mathematics in mind. The question then is: what benchmarks should the community use to evaluate these? On the one hand, toy problems such as learning the multiplicative structure of small finite groups have become popular in the mechanistic interpretability community whose perspective on explainability aligns well with the needs of mathematicians. While toy datasets are a useful benchmark for initial work, they lack the scale, complexity, and sophistication of many of the principal objects of study in modern mathematics. To address this, we introduce a new collection of benchmark datasets, Algebraic Combinatorics Benchmarks (ACBench), representing either classic or open problems in algebraic combinatorics, a subfield of mathematics that studies discrete structures arising from abstract algebra. After describing the datasets, we discuss the challenges involved in constructing “good” mathematics benchmarks, describe baseline model performance, and discuss some of the insights these datasets can provide that may be of interest even to those who are not interested in mathematics research itself.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Computation and consequences of high order amplitude- and parameter-dependent tune shifts in storage rings for high precision measurements

Nonlinear effects of the various electric field and magnetic field components of storage rings to confine the particles and bend their trajectory can cause substantial amplitude-dependent tune shifts within the beam. Furthermore, tune shifts are often sensitive to variations of system parameters, e.g. total particle momentum offsets $δp$. Such amplitude- and parameter-dependent tune shifts influence the dynamics and stability of a beam in particle storage rings. Thus, it is critical for high precision measurements to analyze and understand these influences. On this basis, we present in this paper normal form methods for the calculation of high order amplitude and system parameter dependencies of the horizontal and vertical tunes in storage rings using the differential algebra (DA) framework within COSY INFINITY. A storage ring is simulated using COSY INFINITY to generate a DA Poincaré return map describing the transverse phase space behavior after each revolution in the storage ring. The map is expanded around the parameter-dependent closed orbit of the system before transforming the resulting map into normal form coordinates to extract the high order tune dependencies on the phase space amplitude and variation in the system parameters. As a specific example, a storage ring similar to the Storage Ring of the Muon g-2 Experiment at Fermilab (E989) is investigated.

43 PARTICLE ACCELERATORS↗
DOE OSTI2013

Fixman compensating potential for general branched molecules

The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Domain decomposition and multiscale mortar mixed finite element methods for linear elasticity with weak stress symmetry

Two non-overlapping domain decomposition methods are presented for the mixed finite element formulation of linear elasticity with weakly enforced stress symmetry. The methods utilize either displacement or normal stress Lagrange multiplier to impose interface continuity of normal stress or displacement, respectively. By eliminating the interior subdomain variables, the global problem is reduced to an interface problem, which is then solved by an iterative procedure. The condition number of the resulting algebraic interface problem is analyzed for both methods. A multiscale mortar mixed finite element method for the problem of interest on non-matching multiblock grids is also studied. It uses a coarse scale mortar finite element space on the non-matching interfaces to approximate the trace of the displacement and impose weakly the continuity of normal stress. A priori error analysis is performed. It is shown that, with appropriate choice of the mortar space, optimal convergence on the fine scale is obtained for the stress, displacement, and rotation, as well as some superconvergence for the displacement. Computational results are presented in confirmation of the theory of all proposed methods.

Mathematics↗
DOE OSTI2018

Entity Resolution at Large Scale: Benchmarking and Algorithmics

We seek scalable benchmarks for entity resolution problems. Solutions to these problems range from trivial approaches such as string sorting to sophisticated methods such as statistical relational learning. The theoretical and practical complexity of these approaches varies widely, so one of the primary purposes of a benchmark will be to quantify the trade-off between solution quality and runtime. We are motivated by the ubiquitous nature of entity resolution as a fundamental problem faced by any organization that ingests large amounts of noisy text data. A benchmark is typically a rigid specification that provides an objective measure usable for ranking implementations of an algorithm. For example the Top500 and HPCG500 bench- marks rank supercomputers based on their performance of dense and sparse linear algebra problems (respectively). These two benchmarks require participants to report FLOPS counts attainable on various machines. Our purpose is slightly different. Whereas the supercomputing benchmarks mentioned above hold algorithms constant and aim to rank machines, we are primarily interested in ranking algorithms. As mentioned above, entity resolution problems can be approached in completely different ways. We believe that users of our benchmarks must decide what sort of procedure to run before comparing implementations and architectures. Eventually, we also wish to provide a mechanism for ranking machines while holding algorithmic approach constant . Our primary contributions are parallel algorithms for computing solution quality mea- sures per entity. We find in some real datasets that many entities are quite easy to resolve while others are difficult, with a heavy skew toward the former case. Therefore, measures such as global confusion matrices, F measures, etc. do not meet our benchmarking needs. We design methods for computing solution quality at the granularity of a single entity in order to know when proposed solutions do well in difficult situations (perhaps justifying extra computational), or struggling in easy situations. We report on progress toward a viable benchmark for comparing entity resolution algo- rithms. Our work is incomplete, but we have designed and prototyped several algorithms to help evalute the solution quality of competing approaches to these problems. We envision a benchmark in which the objective measure is a ratio of solution quality to runtime.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Computing the shape gradient of stellarator coil complexity with respect to the plasma boundary

Coil complexity is a critical consideration in stellarator design. The traditional two-step optimization approach, in which the plasma boundary is optimized for physics properties and the coils are subsequently optimized to be consistent with this boundary, can result in plasma shapes which cannot be produced with sufficiently simple coils. To address this challenge, we propose a method to incorporate considerations of coil complexity in the optimization of the plasma boundary. Coil complexity metrics are computed from the current potential solution obtained with the REGCOIL code (Landreman, Nucl. Fusion , vol. 57, 2017, 046003). While such metrics have previously been included in derivative-free fixed-boundary optimization (Drevlak et al. , Nucl. Fusion , vol. 59, 2018, 016010), we compute the local sensitivity of these metrics with respect to perturbations of the plasma boundary using the shape gradient (Landreman & Paul, Nucl. Fusion , vol. 58, 2018, 076023). We extend REGCOIL to compute derivatives of these metrics with respect to parameters describing the plasma boundary. In keeping with previous research on winding surface optimization (Paul et al. , Nucl. Fusion , vol. 58, 2018, 076015), the shape derivatives are computed with a discrete adjoint method. In contrast with the previous work, derivatives are computed with respect to the plasma surface parameters rather than the winding surface parameters. To further reduce the resolution required to compute the shape gradient, we present a more efficient representation of the plasma surface which uses a single Fourier series to describe the radial distance from a coordinate axis and a spectrally condensed poloidal angle. This representation is advantageous over the standard cylindrical representation used in the VMEC code (Hirshman & Whitson, Phys. Fluids , vol. 26, 1983, pp. 3553–3568), as it provides a uniquely defined poloidal angle, eliminating a null space in the optimization of the plasma surface. In comparison with previous spectral condensation methods (Hirshman & Breslau, Phys. Plasmas , vol. 5, 1998, p. 2664), the modified poloidal angle is obtained algebraically rather than through the solution of a nonlinear optimization problem. The resulting shape gradient highlights features of the plasma boundary that are consistent with simple coils and can be used to couple coil and fixed-boundary optimization.

Physics↗
DOE OSTI2021

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Eigenvectors from Eigenvalues: a survey of a basic identity in linear algebra

If $A$ is an $n \times n$ Hermitian matrix with eigenvalues $\lambda_1(A),\dots,\lambda_n(A)$ and $i,j = 1,\dots,n$, then the $j^{\mathrm{th}}$ component $v_{i,j}$ of a unit eigenvector $v_i$ associated to the eigenvalue $\lambda_i(A)$ is related to the eigenvalues $\lambda_1(M_j),\dots,\lambda_{n-1}(M_j)$ of the minor $M_j$ of $A$ formed by removing the $j^{\mathrm{th}}$ row and column by the formula $$ |v_{i,j}|^2\prod_{k=1;k\neq i}^{n}\left(\lambda_i(A)-\lambda_k(A)\right)=\prod_{k=1}^{n-1}\left(\lambda_i(A)-\lambda_k(M_j)\right)\,.$$ We refer to this identity as the \emph{eigenvector-eigenvalue identity}. Despite the simple nature of this identity and the extremely mature state of development of linear algebra, this identity was not widely known until very recently. In this survey we describe the many times that this identity, or variants thereof, have been discovered and rediscovered in the literature (with the earliest precursor we know of appearing in 1934). We also provide a number of proofs and generalizations of the identity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Generalized Bootstrap AMG and AIR-AMG for coupled PDE systems with a focus on spacetime discretizatoins

The Pennsylvania State University (“Subcontractor”) has worked on the design of new algebraic, parallel, multilevel methods that obtain the full space and time solution of systems of PDEs. In particular, the PI and his collaborators explored semi-intrusive approaches based on algebraic multigrid (AMG). The focus of the research has been on the development of these techniques for the Euler equations in 1d and 2d. The overall research focused on the development of adaptive AIR (approximate ideal restriction) AMG solvers for these problems. The PI also explored the use of smoothed aggregation and root-node energy-based AMG solvers for these problems.

97 MATHEMATICS AND COMPUTING↗