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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Geometric electrostatic particle-in-cell algorithm on unstructured meshes

We present a geometric particle-in-cell (PIC) algorithm on unstructured meshes for studying electrostatic perturbations with frequency lower than electron gyrofrequency in magnetized plasmas. In this method, ions are treated as fully kinetic particles and electrons are described by the adiabatic response. The PIC method is derived from a discrete variational principle on unstructured meshes. To preserve the geometric structure of the system, the discrete variational principle requires that the electric field is interpolated using Whitney 1-forms, the charge is deposited using Whitney 0-forms and the electric field is computed by discrete exterior calculus. The algorithm has been applied to study the ion Bernstein wave (IBW) in two-dimensional magnetized plasmas. The simulated dispersion relations of the IBW in a rectangular region agree well with theoretical results. In a two-dimensional circular region with fixed boundary condition, the spectrum and eigenmode structures of the IBW are obtained from simulations. We compare the energy conservation property of the geometric PIC algorithm derived from the discrete variational principle with that of previous PIC methods on unstructured meshes. The comparison shows that the new PIC algorithm significantly improves the energy conservation property.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

An Accelerated Clip Algorithm for Unstructured Meshes: A Batch-Driven Approach

The clip technique is a popular method for visualizing complex structures and phenomena within 3D unstructured meshes. Meshes can be clipped by specifying a scalar isovalue to produce an output unstructured mesh with its external surface as the isovalue. Similar to isocontouring, the clipping process relies on scalar data associated with the mesh points, including scalar data generated by implicit functions such as planes, boxes, and spheres, which facilitates the visualization of results interior to the grid. In this paper, we introduce a novel batch-driven parallel algorithm based on a sequential clip algorithm designed for high-quality results in partial volume extraction. Our algorithm comprises five passes, each progressively processing data to generate the resulting clipped unstructured mesh. The novelty lies in the use of fixed-size batches of points and cells, which enable rapid workload trimming and parallel processing, leading to a significantly improved memory footprint and run-time performance compared to the original version. On a 32-core CPU, the proposed batch-driven parallel algorithm demonstrates a run-time speed-up of up to 32.6x and a memory footprint reduction of up to 4.37x compared to the existing sequential algorithm. The software is currently available under an open-source license in the VTK visualization system.

Tsalikis, Spiros↗
DOE OSTI2021

Asynchronous distributed-memory task-parallel algorithm for compressible flows on unstructured 3D Eulerian grids

Here, we discuss the implementation of a finite element method, used to numerically solve the Euler equations of compressible flows, using an asynchronous runtime system (RTS). The algorithm is implemented for distributed-memory machines, using stationary unstructured 3D meshes, combining data-, and task-parallelism on top of the Charm++ RTS. Charm++’s execution model is asynchronous by default, allowing arbitrary overlap of computation and communication. Task-parallelism allows scheduling parts of an algorithm independently of, or dependent on, each other. Built-in automatic load balancing enables continuous redistribution of computational load by migration of work units based on real-time CPU load measurement. The RTS also features automatic checkpointing, fault tolerance, resilience against hardware failure, and supports power-, and energy-aware computation. We demonstrate scalability up to 25 x 10 9 cells at $\mathscr{O}$10 4 compute cores and the benefits of automatic load balancing for irregular workloads. The full source code with documentation is available at https://quinoacomputing.org.

42 ENGINEERING↗
DOE OSTI2019

A Scalable Hybrid Scheme for Ray-Casting of Unstructured Volume Data

We present an algorithm for parallel volume rendering that is a hybrid between classical object order and image order techniques. The algorithm operates on unstructured grids (and structured ones), and thus can deal with block boundaries interleaving in complex ways. It also deals effectively with cases that are prone to load imbalance, i.e., cases where cell sizes differ dramatically, either because of the nature of the input data, or because of the effects of the camera transformation. The algorithm divides work over resources such that each phase of its processing is bounded in the amount of computation it can perform. We demonstrate its efficacy through a series of studies, varying over camera position, data set size, transfer function, image size, and processor count. At its biggest, our experiments scaled up to 8,192 processors and operated on data sets with more than one billion cells. In total, we find that our hybrid algorithm performs well in all cases. This is because our algorithm naturally adapts its computation based on workload, and can operate like either an object order technique or an image order technique in scenarios where those techniques are efficient.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A Study on Particle Trajectory Error in Finite-Element Particle-in-Cell Algorithms

Particle-in-cell (PIC) algorithms are widely used for the simulation of kinetic plasmas. PIC algorithms account for the interaction between charged particles in a plasma and the electromagnetic field in ambient space, including self-field interactions. The objective of this article is to study the error in charged particle trajectories present in finite-element (FE)-based PIC algorithms on unstructured meshes. We study how the trajectory error behaves according to the FE mesh resolution and the matrix solver employed in the FE algorithm. The study is performed by considering a trajectory established by a parabolic electric potential and an axial magnetic force acting on the charged particle. Under a proper choice combination of electric and magnetic field parameters, the 2-D particle trajectories comprise closed orbits. Numerical errors cause small perturbations on the trajectories, with cumulative effects. As a result, the resulting orbital trajectories exhibit distortions including spurious apsidal precession. These distortions provide a clear imprint of the numerical error. Here, we also study the numerical error in a quantitative fashion by computing the distance norm between the trajectories obtained by the exact fields and numerical fields.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

NucMesh: nuclear reactor geometry creation and mesh generation module in NEMoSys

NucMesh is a parameterized geometry and mesh generator for nuclear reactors developed within the Nuclear Energy Modeling System NEMoSys at Illinois Rocstar. NEMoSys is a platform developed for mesh generation, adaptive refinement, and solution verification. NucMesh is implemented to be generalized and extensible with a robust computer aided design engine and multiple mesh generation algorithms for unstructured triangular, quad-dominant, and structured quadrilateral meshing. In this paper, we present the geometric and meshing features of NucMesh. Geometrically objects are constructed bottom-to-top and overlaps are addressed automatically. A sophisticated object tracking algorithm prevents data from being lost for segmented objects. We discuss the primitive objects of circle and polygons that constitute the module and show how they are used with example inputs. Arrays of primitives and arrays of arrays are utilized to build large assemblies of objects. The concept of saved objects is discussed to demonstrate how repetitive objects can be reused easily and augmented in place. Three dimensional meshes can be obtained through mesh extrusion where all materials and side sets are extended to three dimensions. We show that side sets can be defined nearly anywhere within the geometry and can then be applied to the mesh. Finally, example reactor meshes are demonstrated for the Idaho National Laboratory Advanced Test Reactor and Los Alamos National Lab Empire reactor, both of which use control drums that NucMesh handles easily. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

XGC-6D

XGC-6D is a geometric full-f Particle-In-Cell code on unstructured meshes including XGC-like unstructured mesh, tetrahedral mesh, etc. The code is particularly suitable to study boundary plasma with steep gradient and frequency higher than ion gyro-frequency. References: Wang Z, Qin H, Sturdevant B, Chang CS. Geometric electrostatic particle-in-cell algorithm on unstructured meshes. Journal of Plasma Physics. 2021;87(4):905870406.

Wang, Zhenyu [Princeton Plasma Physics Laboratory ↗
DOE OSTI2023

XGC-6D

XGC-6D is a geometric full-f Particle-In-Cell code on unstructured meshes including XGC-like unstructured mesh, tetrahedral mesh, etc. The code is particularly suitable to study boundary plasma with steep gradient and frequency higher than ion gyro-frequency. References: Wang Z, Qin H, Sturdevant B, Chang CS. Geometric electrostatic particle-in-cell algorithm on unstructured meshes. Journal of Plasma Physics. 2021;87(4):905870406.

Wang, Zhenyu [Princeton Plasma Physics Laboratory ↗
DOE OSTI2021

Clinical Natural Language Processing for Radiation Oncology: A Review and Practical Primer

Natural language processing (NLP), which aims to convert human language into expressions that can be analyzed by computers, is one of the most rapidly developing and widely used technologies in the field of artificial intelligence. Natural language processing algorithms convert unstructured free text data into structured data that can be extracted and analyzed at scale. In medicine, this unlocking of the rich, expressive data within clinical free text in electronic medical records will help untap the full potential of big data for research and clinical purposes. Recent major NLP algorithmic advances have significantly improved the performance of these algorithms, leading to a surge in academic and industry interest in developing tools to automate information extraction and phenotyping from clinical texts. Thus, these technologies are poised to transform medical research and alter clinical practices in the future. Radiation oncology stands to benefit from NLP algorithms if they are appropriately developed and deployed, as they may enable advances such as automated inclusion of radiation therapy details into cancer registries, discovery of novel insights about cancer care, and improved patient data curation and presentation at the point of care. However, challenges remain before the full value of NLP is realized, such as the plethora of jargon specific to radiation oncology, nonstandard nomenclature, a lack of publicly available labeled data for model development, and interoperability limitations between radiation oncology data silos. Successful development and implementation of high quality and high value NLP models for radiation oncology will require close collaboration between computer scientists and the radiation oncology community. Here, we present a primer on artificial intelligence algorithms in general and NLP algorithms in particular; provide guidance on how to assess the performance of such algorithms; review prior research on NLP algorithms for oncology; and describe future avenues for NLP in radiation oncology research and clinics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

A Structured Quasi-Newton Algorithm for Optimizing with Incomplete Hessian Information

We present a structured quasi-Newton algorithm for unconstrained optimization problems that have unavailable second-order derivatives or Hessian terms. We provide a formal derivation of the well-known Broyden--Fletcher--Goldfarb--Shanno (BFGS) secant update formula that approximates only the missing Hessian terms, and we propose a linesearch quasi-Newton algorithm based on a modification of Wolfe conditions that converges to first-order optimality conditions. We also analyze the local convergence properties of the structured BFGS algorithm and show that it achieves superlinear convergence under the standard assumptions used by quasi-Newton methods using secant updates. In conclusion, we provide a thorough study of the practical performance of the algorithm on the CUTEr suite of test problems and show that our structured BFGS-based quasi-Newton algorithm outperforms the unstructured counterpart(s).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

HPC formulations of optimization algorithms for tensor completion

Tensor completion is a powerful tool used to estimate or recover missing values in multi-way data. It has seen great success in domains such as product recommendation and healthcare. Tensor completion is most often accomplished via low-rank sparse tensor factorization, a computationally expensive non-convex optimization problem which has only recently been studied in the context of parallel computing. In this work, we study three optimization algorithms that have been successfully applied to tensor completion: alternating least squares (ALS), stochastic gradient descent (SGD), and coordinate descent (CCD++). We explore opportunities for parallelism on shared- and distributed-memory systems and address challenges such as memory- and operation-efficiency, load balance, cache locality, and communication. Among our advancements are a communication-efficient CCD++ algorithm, an ALS algorithm rich in level-3 BLAS routines, and an SGD algorithm which combines stratification with asynchronous communication. Furthermore, we show that introducing randomization during ALS and CCD++ can accelerate convergence. We evaluate our parallel formulations on a variety of real datasets on a modern supercomputer and demonstrate speedups through 16384 cores. Further, these improvements reduce time-to-solution from hours to seconds on real-world datasets. We show that after our optimizations, ALS is advantageous on parallel systems of small-to-moderate scale, while both ALS and CCD++ provide the lowest time-to-solution on large-scale distributed systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

An unstructured body-of-revolution electromagnetic particle-in-cell algorithm with radial perfectly matched layers and dual polarizations

A novel electromagnetic particle-in-cell algorithm has been developed for fully kinetic plasma simulations on unstructured (irregular) meshes in complex body-of-revolution geometries. The algorithm, implemented in the BORPIC++ code, utilizes a set of field scalings and a coordinate mapping, reducing the Maxwell field problem in a cylindrical system to a Cartesian finite element Maxwell solver in the meridian plane. The latter obviates the cylindrical coordinate singularity in the symmetry axis. The choice of an unstructured finite element discretization enhances the geometrical flexibility of the BORPIC++ solver compared to the more traditional finite difference solvers. Symmetries in Maxwell’s equations are explored to decompose the problem into two dual polarization states with isomorphic representations that enable code reuse. The particle-in-cell scatter and gather steps preserve charge conservation at the discrete level. Our previous algorithm (BORPIC+) discretized the E and B field components of TE Φ and TM Φ polarizations on the finite element (primal) mesh. Here, we employ a new field-update scheme. Using the same finite element (primal) mesh, this scheme advances two sets of field components independently: (1) E and B of TE Φ polarized fields, (E z , E ρ , B Φ ) and (2) D and H of TM Φ polarized fields, (D Φ , H z , H ρ ). Since these field updates are not explicitly coupled, the new field solver obviates the coordinate singularity, which otherwise arises at the cylindrical symmetric axis, ρ = 0 when defining the discrete Hodge matrices (generalized finite element mass matrices). Here, a cylindrical perfectly matched layer is implemented as a boundary condition in the radial direction to simulate open space problems, with periodic boundary conditions in the axial direction. We investigate effects of charged particles moving next to the cylindrical perfectly matched layer. We model azimuthal currents arising from rotational motion of charged rings, which produce TMΦ polarized fields. Several numerical examples are provided to illustrate the first application of the algorithm.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Hardware Implementation of Grover's Search Algorithm

Grover's algorithm searches through an unstructured database, offering a quadratic speedup over classical search algorithms. We implement it, as well as two deterministic variants, on IBM (Kingston) and IQM (Garnet) hardware. Additionally, we test dynamical decoupling as an error mitigation technique. We compare our results to a classical, brute force approach to evaluate current hardware capabilities.

Pressman, Daniel [Fermilab]↗
DOE OSTI2021

Higher-order particle representation for particle-in-cell simulations

In this paper we present an alternative approach to the representation of simulation particles for unstructured electrostatic and electromagnetic PIC simulations. In our modified PIC algorithm we represent particles as having a smooth shape function limited by some specified finite radius, r 0 . A unique feature of our approach is the representation of this shape by surrounding simulation particles with a set of virtual particles with delta shape, with fixed offsets and weights derived from Gaussian quadrature rules and the value of r 0 . As the virtual particles are purely computational, they provide the additional benefit of increasing the arithmetic intensity of traditionally memory bound particle kernels. The modified algorithm is implemented within Sandia National Laboratories' unstructured EMPIRE-PIC code, for electrostatic and electromagnetic simulations, using periodic boundary conditions. We show results for a representative set of benchmark problems, including electron orbit, a transverse electromagnetic wave propagating through a plasma, numerical heating, and a plasma slab expansion. In this work, good error reduction across all of the chosen problems is achieved as the particles are made progressively smoother, with the optimal particle radius appearing to be problem-dependent.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Pairing Directional Solar Inputs From Ray Tracing to Solar Receiver/Reactor Heat Transfer Models on Unstructured Meshes: Development and Case Studies

A novel method for pairing surface irradiation and volumetric absorption from Monte Carlo ray tracing to computational heat transfer models is presented. The method is well-suited to directionally and spatially complex concentrated radiative inputs (e.g., solar receivers and reactors). The method employs a generalized algorithm for directly mapping absorbed rays from a Monte Carlo ray tracing model to boundary or volumetric source terms in the computational mesh. The algorithm is compatible with unstructured, two and three-dimensional meshes with varying element shapes. Four case studies were performed on a directly irradiated, windowed solar thermochemical reactor model to validate the method. The method was shown to conserve energy and preserve spatial variation when mapping rays from a Monte Carlo ray tracing model to a computational heat transfer model in ansys fluent.

14 SOLAR ENERGY↗
DOE OSTI2018

An Introduction of Numerical Methods for Unconstrained Nonlinear Equations

Many applications in computational physics are nonlinear problems. These nonlinear problems include quantitative object reconstruction problems, inverse transport problems, nuclear weapon design problems, and particle tracking on unstructured meshes. The numerical algorithms used to solve nonlinear equations should be robust, reliable, and efficient. Numerical methods for unconstrained nonlinear equations are introduced in the slides.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Scalable algorithms for domain decomposition of Monte Carlo neutral particle transport simulations on unstructured mesh

Monte Carlo simulations are the gold standard in particle transport simulations, for shielding and nuclear reactor simulations Full core simulations can require terabytes of memory for tracking pin-resolved (up to 50k pins), nuclide (200 tracked), axial (20-200 zones) reaction rates Domain decomposition, splitting the calculation and the memory storage, among several nodes is challenging as it involves communication of particles across domain boundaries We created a new MOOSE application, MaCaw, to study this problem Algorithms developed for ray tracing in MOOSE were adapted for simulating neutral particle transport Physics and tally routines in OpenMC, dynamically linked, are called from the application

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Multilevel well modeling in aggregation-based nonlinear multigrid for multiphase flow in porous media

A full approximation scheme (FAS) nonlinear multigrid solver for two-phase flow and transport problems driven by wells with multiple perforations is developed here. It is an extension to our previous work on FAS solvers for diffusion and transport problems. The solver is applicable to discrete problems defined on unstructured grids as the coarsening algorithm is aggregation-based and algebraic. To construct coarse basis that can better capture the radial flow near wells, coarse grids in which perforated well cells are not near the coarse-element interface are desired. This is achieved by an aggregation algorithm proposed in this paper that makes use of the location of well cells in the cell-connectivity graph. Numerical examples in which the FAS solver is compared against Newton's method on benchmark problems are given. In particular, for a refined version of the SAIGUP model, the FAS solver is at least 35% faster than Newton's method for time steps with a CFL number greater than 10.

58 GEOSCIENCES↗