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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 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

An adaptive scalable fully implicit algorithm based on stabilized finite element for reduced visco-resistive MHD

The magnetohydrodynamics (MHD) equations are continuum models used in the study of a wide range of plasma physics systems, including the evolution of complex plasma dynamics in tokamak disruptions. However, efficient numerical solution methods for MHD are extremely challenging due to disparate time and length scales, strong hyperbolic phenomena, and nonlinearity. Additionally, therefore the development of scalable, implicit MHD algorithms and high-resolution adaptive mesh refinement strategies is of considerable importance. In this work, we develop a high-order stabilized finite-element algorithm for the reduced visco-resistive MHD equations based on the MFEM finite element library (mfem.org). The scheme is fully implicit, solved with the Jacobian-free Newton-Krylov (JFNK) method with a physics-based preconditioning strategy. Our preconditioning strategy is a generalization of the physics-based preconditioning methods in Chacón et al. (2002) to adaptive, stabilized finite elements. Algebraic multigrid methods are used to invert sub-block operators to achieve scalability. A parallel adaptive mesh refinement scheme with dynamic load-balancing is implemented to efficiently resolve the multi-scale spatial features of the system. Our implementation uses the MFEM framework, which provides arbitrary-order polynomials and flexible adaptive conforming and non-conforming meshes capabilities. Results demonstrate the accuracy, efficiency, and scalability of the implicit scheme in the presence of large scale disparity. The potential of the AMR approach is demonstrated on an island coalescence problem in the high Lundquist-number regime (≥ 10 7 ) with the successful resolution of plasmoid instabilities and thin current sheets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Multi-material swept face remapping on polyhedral meshes

Remapping is a conservative interpolation of a discretized intensive quantity between two meshes. In this article, we propose a novel multi-material flux remapping method that avoids the geometric computation of mesh-mesh intersections needed for an accurate intersection based remap. The flux remap is applicable to scalar quantities such as material density describing the multi-material flow between meshes with the same connectivity but small mesh displacements. Herein, the method is described for two- and three-dimensional polygonal/polyhedral meshes as it is implemented in Portage. Another open source library, Tangram, is used to calculate material interfaces in cells containing more than one material. Performance and accuracy of the flux remap are discussed with respect to Arbitrary Lagrangian-Eulerian simulations and compared to an accurate intersection based remap. In particular, cyclic remapping shows that the accuracy of the flux remap is limited to first order on material boundaries while maintaining second order accuracy in pure material regions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Uncertainty quantification in scientific machine learning: Methods, metrics, and comparisons

Neural networks (NNs) are currently changing the computational paradigm on how to combine data with mathematical laws in physics and engineering in a profound way, tackling challenging inverse and ill-posed problems not solvable with traditional methods. However, quantifying errors and uncertainties in NN-based inference is more complicated than in traditional methods. This is because in addition to aleatoric uncertainty associated with noisy data, there is also uncertainty due to limited data, but also due to NN hyperparameters, overparametrization, optimization and sampling errors as well as model misspecification. Although there are some recent works on uncertainty quantification (UQ) in NNs, there is no systematic investigation of suitable methods towards quantifying the total uncertainty effectively and efficiently even for function approximation, and there is even less work on solving partial differential equations and learning operator mappings between infinite-dimensional function spaces using NNs. In this work, we present a comprehensive framework that includes uncertainty modeling, new and existing solution methods, as well as evaluation metrics and post-hoc improvement approaches. Further, to demonstrate the applicability and reliability of our framework, we present an extensive comparative study in which various methods are tested on prototype problems, including problems with mixed input-output data, and stochastic problems in high dimensions. In the Appendix, we include a comprehensive description of all the UQ methods employed. Further, to help facilitate the deployment of UQ in Scientific Machine Learning research and practice, we present and develop in [1] an open-source Python library (github.com/Crunch-UQ4MI/neuraluq), termed NeuralUQ, that is accompanied by an educational tutorial and additional computational experiments.

11 physics-informed neural networks↗
DOE OSTI2024

Sparse-grid discontinuous Galerkin methods for the Vlasov–Poisson–Lenard–Bernstein model

Sparse-grid methods have recently gained interest in reducing the computational cost of solving high-dimensional kinetic equations. In this paper, we construct adaptive and hybrid sparse-grid methods for the Vlasov–Poisson–Lenard–Bernstein (VPLB) model. This model has applications to plasma physics and is simulated in two reduced geometries: a 0x3v space homogeneous geometry and a 1x3v slab geometry. Here we use the discontinuous Galerkin (DG) method as a base discretization due to its high-order accuracy and ability to preserve important structural properties of partial differential equations. We utilize a multiwavelet basis expansion to determine the sparse-grid basis and the adaptive mesh criteria. We analyze the proposed sparse-grid methods on a suite of three test problems by computing the savings afforded by sparse-grids in comparison to standard solutions of the DG method. The results are obtained using the adaptive sparse-grid discretization library ASGarD.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Democratizing uncertainty quantification

Uncertainty Quantification (UQ) is vital to safety-critical model-based analyses, but the widespread adoption of sophisticated UQ methods is limited by technical complexity. In this paper, we introduce UM-Bridge (the UQ and Modeling Bridge), a high-level abstraction and software protocol that facilitates universal interoperability of UQ software with simulation codes. It breaks down the technical complexity of advanced UQ applications and enables separation of concerns between experts. UM-Bridge democratizes UQ by allowing effective interdisciplinary collaboration, accelerating the development of advanced UQ methods, and making it easy to perform UQ analyses from prototype to High Performance Computing (HPC) scale. In addition, we present a library of ready-to-run UQ benchmark problems, all easily accessible through UM-Bridge. These benchmarks support UQ methodology research, enabling reproducible performance comparisons. We demonstrate UM-Bridge with several scientific applications, harnessing HPC resources even using UQ codes not designed with HPC support.

Benchmarks↗
DOE OSTI2026

Structure preservation using discrete gradients in the Vlasov-Poisson-Landau system

We present a novel structure-preserving framework for solving the Vlasov-Poisson-Landau system of equations using a particle in cell (PIC) discretization combined with discrete gradient time integrators. The Vlasov-Poisson-Landau system is an accurate model for studying hot plasma dynamics at a kinetic scale where small-angle Coulomb collisions dominate. Our scheme guarantees conservation of mass, momentum and energy as well as preservation of the monotonicity of entropy production in both the time-continuous and discrete systems. We employ the conservative integrator for both the Hamiltonian Vlasov-Poisson equations and the dissipative Landau equation using the PETSc library (www.mcs.anl.gov/petsc) to showcase structure-preserving properties.

Discrete gradients↗
DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Diffusion in undoped and Cr-doped amorphous UO 2

UO 2 fuel pellets are often doped with chromium oxide to obtain favourable properties such as higher density, improved thermal stability, large grain sizes, improved pellet-clad interaction margins, and increased fission gas retention during transients. Chromium has a low solubility limit in UO 2 , with past experimental work reporting solubility limits ranging between 0.004 to 0.06 wt.% Cr. Due to its low solubility, segregation of Cr ions to the grain boundary may occur. Further, the complexity of these boundaries may be high as observed in other ceramics resulting in disordered or amorphous regions along the boundary, affecting a range of material and operational properties of the fuel pellet. To assess these disordered regions, in this work we study amorphous undoped and Cr doped UO 2 systems (containing 10–50 at.% Cr 3+ ) that have been modelled using classical molecular dynamics methods incorporating Cr 3+ into the well-used CRG potential library. Diffusion coefficients, pre-exponential factors, and activation energies for diffusion were computed for oxygen ions, assessing the impact of structure and extrinsic species on migration. Oxygen diffusion was observed to be much faster in the undoped amorphous system compared to its crystalline counterpart. Oxygen diffusion in doped systems decreased with increasing Cr concentration, highlighting the importance of additives to retain fission products and other migratory species.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

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

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

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Optimizing the hypre solver for manycore and GPU architectures

The solution of large-scale combustion problems with codes such as Uintah on modern computer architectures requires the use of multithreading and GPUs to achieve performance. Uintah uses a low-Mach number approximation that requires iteratively solving a large system of linear equations. The Hypre iterative solver has solved such systems in a scalable way for Uintah, but the use of OpenMP with Hypre leads to at least slowdown due to OpenMP overheads. The proposed solution uses the MPI Endpoints within Hypre, where each team of threads acts as a different MPI rank. This approach minimizes OpenMP synchronization overhead and performs as fast or (up to 1.44) faster than Hypre's MPI-only version, and allows the rest of Uintah to be optimized using OpenMP. The profiling of the GPU version of Hypre shows the bottleneck to be the launch overhead of thousands of micro-kernels. The GPU performance was improved by fusing these micro-kernels and was further optimized by using Cuda-aware MPI, resulting in an overall speedup of 1.16—1.44 compared to the baseline GPU implementation. The above optimization strategies were published in the International Conference on Computational Science 2020 [1]. This work extends the previously published research by carrying out the second phase of communication-centered optimizations in Hypre to improve its scalability on large-scale supercomputers. Additionally, this includes an efficient non-blocking inter-thread communication scheme, communication-reducing patch assignment, and expression of logical communication parallelism to a new version of the MPICH library that utilizes the underlying network parallelism [2]. The above optimizations avoid communication bottlenecks previously observed during strong scaling and improve performance by up to 2 on 256 nodes of Intel Knight's Landing processor.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

PythonFOAM: In-situ data analyses with OpenFOAM and Python

Here, we outline the development of a general-purpose Python-based data analysis tool for OpenFOAM. Our implementation relies on the construction of OpenFOAM applications that have bindings to data analysis libraries in Python. Double precision data in OpenFOAM is cast to a NumPy array using the NumPy C-API and Python modules may then be used for arbitrary data analysis and manipulation on flow-field information. We highlight how the proposed wrapper may be used for an in-situ online singular value decomposition (SVD) implemented in Python and accessed from the OpenFOAM solver PimpleFOAM. Here, 'in-situ' refers to a programming paradigm that allows for a concurrent computation of the data analysis on the same computational resources utilized for the partial differential equation solver. In addition, to demonstrate parallel deployments, we deploy a distributed SVD, which collects snapshot data across the ranks of a distributed simulation to compute the global left singular vectors. Crucially, both OpenFOAM and Python share the same message passing interface (MPI) communicator for this deployment which allows Python objects and functions to exchange NumPy arrays across ranks. Subsequently, we provide scaling assessments of this distributed SVD on multiple nodes of Intel Broadwell and KNL architectures for canonical test cases such as the large eddy simulations of a backward facing step and a channel flow at friction Reynolds number of 395. Finally, we demonstrate the deployment of a deep neural network for compressing the flow-field information using an autoencoder to demonstrate an ability to use state-of-the-art machine learning tools in the Python ecosystem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Parallel algorithms for finding connected components using linear algebra

Finding connected components is one of the most widely used operations on a graph. Optimal serial algorithms for the problem have been known for half a century, and many competing parallel algorithms have been proposed over the last several decades under various different models of parallel computation. This paper presents a class of parallel connected-component algorithms designed using linear-algebraic primitives. These algorithms are based on a PRAM algorithm by Shiloach and Vishkin and can be designed using standard GraphBLAS operations. Here, we demonstrate two algorithms of this class, one named LACC for Linear Algebraic Connected Components, and the other named FastSV which can be regarded as LACC’s simplification. With the support of the highly-scalable Combinatorial BLAS library, LACC and FastSV outperform the previous state-of-the-art algorithm by a factor of up to 12x for small to medium scale graphs. For large graphs with more than 50B edges, LACC and FastSV scale to 4K nodes (262K cores) of a Cray XC40 supercomputer and outperform previous algorithms by a significant margin. This remarkable performance is accomplished by (1) exploiting sparsity that was not present in the original PRAM algorithm formulation, (2) using high-performance primitives of Combinatorial BLAS, and (3) identifying hot spots and optimizing them away by exploiting algorithmic insights.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Fast GPU 3D diffeomorphic image registration

3D image registration is one of the most fundamental and computationally expensive operations in medical image analysis. Here, we present a mixed-precision, Gauss–Newton–Krylov solver for diffeomorphic registration of two images. Our work extends the publicly available CLAIRE library to GPU architectures. Despite the importance of image registration, only a few implementations of large deformation diffeomorphic registration packages support GPUs. Our contributions are new algorithms to significantly reduce the run time of the two main computational kernels in CLAIRE: calculation of derivatives and scattered-data interpolation. Additionally, we deploy (i) highly-optimized, mixed-precision GPU-kernels for the evaluation of scattered-data interpolation, (ii) replace Fast-Fourier-Transform (FFT)-based first-order derivatives with optimized 8th-order finite differences, and (iii) compare with state-of-the-art CPU and GPU implementations. As a highlight, we demonstrate that we can register clinical images in less than 6 s on a single NVIDIA Tesla V100. This amounts to over 20 speed-up over the current version of CLAIRE and over 30 speed-up over existing GPU implementations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

MATAR: A performance portability and productivity implementation of data-oriented design with Kokkos

There is a need for simple, fast, and memory-efficient multidimensional data structures for dense and sparse storage that arise with numerical methods and in software applications. The data structures must perform equally well across multiple computer architectures, including CPUs and GPUs. For this purpose, we developed MATAR, a C++ software library that allows for simple creation and use of intricate data structures that is also portable across disparate architectures using Kokkos. Here, the performance aspect is achieved by forcing contiguous memory layout (or as close to contiguous as possible) for multidimensional and multi-size dense or sparse MATrix and ARray (hence, MATAR) types. Our results show that MATAR has the capability to improve memory utilization, performance, and programmer productivity in scientific computing. This is achieved by fitting more work into the available memory, minimizing memory loads required, and by loading memory in the most efficient order. This document describes the purpose of the work, the implementation of each of the data types, and the resulting performance both in some simple baseline test cases and in an application code.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

PUMIPic: A mesh-based approach to unstructured mesh Particle-In-Cell on GPUs

Unstructured mesh particle-in-cell, PIC, simulations executing on the current and next generation of massively parallel systems require new methods for both the mesh and particles to achieve performance and scalability on GPUs. The traditional approach to implementing PIC simulations defines data structures and algorithms in terms of particles with a full copy of the unstructured mesh on every process. To effectively scale the unstructured mesh and particles, mesh-based PIC uses the unstructured mesh as the predominant data structure with the particles stored in terms of the mesh entities. Here, this paper details the PUMIPic library, a framework for developing efficient and performance-portable mesh-based PIC simulations on GPU systems. A pseudo physics simulation based on a five-dimensional gyro-kinetic code for modeling plasma physics is used to examine the performance of PUMIPic. Scaling studies of the unstructured mesh partition and number of particles are performed up to 4096 nodes of the Summit system at Oak Ridge National Laboratory. The studies show that mesh-based PIC can utilize a partitioned mesh and maintain scaling up to system limitations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Towards elastic in situ analysis for high-performance computing simulations

In situ analysis and visualization have grown increasingly popular for enabling direct access to data from high-performance computing (HPC) simulations. As a simulation progresses and interesting physical phenomena emerge, however, the data produced may become increasingly complex, and users may need to dynamically change the type and scale of in situ analysis tasks being carried out and consequently adapt the amount of resources allocated to such tasks. To date, none of the production in situ analysis frameworks offer such an elasticity feature, and for good reason: the assumption that the number of processes could vary during run time would force developers to rethink software and algorithms at every level of the in situ analysis stack. In this paper we present Colza, a data staging service with elastic in situ visualization capabilities. We demonstrate the use of Colza with the Deep Water Impact and the AMR-Wind simulations, coupling them with the ParaView Catalyst and Ascent in situ libraries, and show that Colza enables dynamic rescaling of these widely-used frameworks with no interruption to the simulation or staging service. Here, we highlight the challenges of enabling such elasticity, which requires overcoming these frameworks' reliance on MPI, using distinct engineering approaches, namely dependency injection and dependency overload. To the best of our knowledge, this work is the first to enable elastic in situ visualization capabilities for HPC applications on top of existing production analysis tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Measuring residual stress in Ti-6Al-4V with HR-EBSD, using reference patterns from annealed material

In this study, elastic strain and residual stress values in an engineering material were determined by high-resolution EBSD (HR-EBSD) using reference patterns from annealed, recrystallized material. Specifically, rolled Ti-6Al-4V sheet was analyzed using HR EBSD in both an as-annealed and a strained state, the latter established via a static two-point bend fixture. The commercial software CrossCourt4 (CC4) was used to evaluate the relative intragranular strain tensor components of the alpha grains mapped by HR-EBSD. The intragranular reference patterns identified in each grain by the software were then replaced with similarly-oriented patterns from scans of the as-annealed, recrystallized material. The CC4 analysis was then repeated to provide calibrated strain and residual stress values. Elastic strains on the order of 10–3 were detected, with corresponding residual stress values on the order of 1 GPa. Subsequent analyses using high energy synchrotron x-ray diffraction showed good correlation with the elastic strains measured by HR-EBSD using the annealed reference patterns. Additionally, the maximum macroscopic stress analytically predicted for two-point bending was in agreement with the residual stress observed. Good repeatability of the methodology and insight into the state of individual grains were also observed. The findings provide encouraging evidence that accurate intragranular and long-range residual stress measurements of engineering significance can be made with HR-EBSD using a physical reference pattern library.

36 MATERIALS SCIENCE↗
DOE OSTI2020

High-throughput synthesis and corrosion behavior of sputter-deposited nanocrystalline Al x (CoCrFeNi) 100-x combinatorial high-entropy alloys

High-entropy alloys (HEAs) are inherently complex and potentially span a vast composition space, making their research and discovery challenging. In the present study, high-throughput synthesis of an Al x (CoCrFeNi) 100-x combinatorial material library covering x = 4.5–40 atomic percent Al is achieved, using magnetron cosputtering. The effects of Al on the microstructure and corrosion behavior are investigated. With the increased amount of Al, crystal-structures of thin films transform from face-centered cubic (FCC) to body-centered cubic (BCC). Both the FCC and BCC thin films demonstrate a uniform elemental distribution. Corrosion characteristics of combinatorial samples immersed in the 3.5 wt% (wt%) NaCl solution are evaluated via electrochemical tests. Complementary X-ray photoelectron spectroscopy analysis reveals the compositional variation of passivated films formed on the sample surface after immersion. The results show that the Al x (CoCrFeNi) 100-x HEA thin films possess outstanding corrosion-resistant properties, but the resistance diminishes with the increasing Al content. The decreased corrosion resistance is revealed to be directly related to the constituents of passivated films.

36 MATERIALS SCIENCE↗