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DOE OSTI2020

UQpy: A general purpose Python package and development environment for uncertainty quantification

In this paper, we present the UQpy software toolbox, an open-source Python package for general uncertainty quantification (UQ) in mathematical and physical systems. The software serves as both a user-ready toolbox that includes many of the latest methods for UQ in computational modeling and a convenient development environment for Python programmers advancing the field of UQ. The paper presents an introduction to the software's architecture and existing capabilities, divided in the code in a set of modules centered around different UQ tasks such as sampling methods, generation of random processes and random fields, probabilistic inverse modeling, reliability analysis, surrogate modeling, and active learning. The paper also highlights the importance of the RunModel module, which is used to drive simulations in the uncertainty analyses performed in UQpy. This module conveniently allows the user to define computational models directly in Python, or to run simulations from a third-party software in serial or in parallel. To illustrate the various capabilities, two examples are tracked throughout the paper and analyzed repeatedly for various UQ tasks. The first is a Python model solving a nonlinear structural dynamics problem, used to illustrate UQpy's capabilities in sampling and forward propagation of high dimensional random vectors (stochastic processes), and probabilistic inference. The second model is a third-party Abaqus finite element model solving the thermomechanical response of a beam structure. This example is used to illustrate UQpy's capabilities in variance reduction sampling techniques, reliability analysis, surrogate modeling and active learning techniques.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Phase equilibria in iron-rich Sm–Fe–Ti and Sm–(Fe,Co)–Ti alloys at 1100–1200 °C

Iron-rich corners of ternary Sm–Fe–Ti phase diagram at 1100 °C and quasi-ternary Sm–Fe 0.8 Co 0.2 –Ti phase diagrams at 1100 and 1200 °C are constructed based on experimental investigation of equilibrated alloys with electron probe microanalysis, X-ray diffraction and thermomagnetic analysis. In addition, the upper boundaries of the temperature ranges of Sm(Fe,[Co,]Ti) 12 and Sm 3 (Fe,[Co,]Ti) 29 phases are determined with differential thermal analysis to update earlier rough estimates. The existence of a high-temperature phase of the Th 2 Ni 17 type, originally reported by Ivanova et al. [J. Alloys Compd. 224 (1995) 29], is confirmed. In the Sm–Fe 0.8 Co 0.2 –Ti system, the composition and equilibria of this hexagonal phase are established for 1200 °C; it is Sm-depleted (≈9.8 at.% Sm) compared to the 2:17 stoichiometry and it coexists with the rhombohedral 2:17 phase. The magnetic anisotropy of the cobalt-substituted Th 2 Ni 17 -type phase is planar, with the easy magnetization direction parallel to [100]. Equilibrium between a Sm-rich liquid phase and the 1:12 phase, which is important for the development of new high-performance permanent magnets, is absent up to 1000 °C, but does exist at 1100 °C (for the 1:12 phase with at least 8.7–8.9 at.% Ti) and at 1200 °C (for the 1:12 phase with as little as 7.4 at.% Ti). The development of magnets may be complicated, however, by an observed tendency of the high-temperature liquid to solidify into ferromagnetic phases including the Th 2 Ni 17 -type phase. The Curie temperatures of the α-(Fe,Ti), Sm(Fe,Ti) 12 , Sm 3 (Fe,Ti) 29 and rhombohedral Sm 2 (Fe,Ti) 17 phases are not only increased by the partial Co substitution for Fe, but their dependence on the Ti concentration is changed by this Co substitution from positive (or, for the 1:12 phase, zero) to negative values.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Molecular dynamics study of primary damage in the near-surface region in nickel

In this work, we carried out a large-scale molecular dynamics (MD) simulation to elucidate the effect of the free surface on the defect production of displacement cascades in pure nickel. These MD simulations were performed both in the bulk and near-surface regions with primary knock-on atom (PKA) energies of E PKA = 1, 5, or 10 keV and at temperatures T = 300, 425, or 525 K. Additionally, for every (T, E PKA ), near-surface cascade simulations were performed as a function of depth. In the near-surface simulations, assuming isotropic neutron fluence, the PKAs were initiated in random directions, including toward and parallel to the free surface. For both the near-surface and bulk cascades, the effect of E PKA and T on the defect production is similar. In both cases, the defect production increases with E PKA , but the temperature has minimal effect. However, the production and clustering of vacancies are higher for near-surface cascades, and they decrease with increasing depth. In contrast, the production and clustering of self-interstitial atoms are lower and increase with depth. Eventually, the production and clustering of both defect types approach bulk cascade-like behavior, and the depth at which this occurs increases with E PKA , but is independent of temperature.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Poplar: a phylogenomics pipeline

Motivation Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist. Results We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline. Availability and implementation Freely available on GitHub at https://github.com/sandialabs/poplar. Implemented using Python and supported on Linux.

Koning, Elizabeth [Sandia National Laboratories (S↗

DOE OSTI2021

Carbon and Hydrocarbon Particle Seeding in Air-Breathing Rotating Detonation Engine

Within the power generation community, the rotating detonation engine (RDE) is only growing in popularity with its increased performance, simple mechanism, and operation. Although significant testing is underway to characterize the RDE for integration with conventional gas turbines, this entire system is still at a relatively low technology readiness level. In the midst of RDE research, there is an initiative to understand solid particle seeding effects in the detonation performance. Under investigation at the University of Central Florida is a Department of Energy (DOE) 15.24 cm (6 in.) RDE, with a solid particle seeder in parallel with its H2 and air flow lines. Previous work on this system involved carbon particle detonation; however, the tested particles were taken one step further to include more sustainable, greener hydrocarbon particles. Testing of powdered sugar, peanut flour, and cornstarch, along with previous carbon black tests have shown not only successful detonability, but a noticeable effect on the detonation wave dynamics. Side-by-side with a particle burning model being developed, an operational map can be determined for the hydrocarbon particles particularly, which can be tuned with the local flow conditions to achieve peak operability while replacing fuels with sustainable alternatives that could even be grown.

Engineering↗

DOE OSTI2021

RX-PSA

This code is built on top of the ML-PSA utility and implements the ability to implement a multi-fidelity parallel simulated annealing optimization for a range of engineering problems. RX-PSA provides specializations to interact with modern nuclear reactor codes such as VERA to perform assembly and core optimization in a robust way. RX-PSA also provides LWR specific objective functions and constraints to provide a straightforward user interface that reactor designers are familiar with.

Collins, BenjaminS.↗

DOE OSTI2021

PETSc Users Manual (Revision 3.15)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

PETSc/TAO Users Manual: Revision 3.18

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

PETSc/TAO Users Manual (Rev. 3.20)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

A Case Study of LLVM-Based Analysis for Optimizing SIMD Code Generation

This paper presents a methodology for using LLVM-based tools to tune the DCA++ (dynamical cluster approximation) application that targets the new ARM A64FX processor. The goal is to describe the changes required for the new architecture and generate efficient single instruction/multiple data (SIMD) instructions that target the new Scalable Vector Extension instruction set. During manual tuning, the authors used the LLVM tools to improve code parallelization by using OpenMP SIMD, refactored the code and applied transformation that enabled SIMD optimizations, and ensured that the correct libraries were used to achieve optimal performance. By applying these code changes, code speed was increased by 1.98× and 78 GFlops were achieved on the A64FX processor. The authors aim to automatize parts of the efforts in the OpenMP Advisor tool, which is built on top of existing and newly introduced LLVM tooling.

Huber, Joseph↗

DOE OSTI2021

Parallelizing the Unpacking and Clustering of Detector Data for Reconstruction of Charged Particle Tracks on Multi-core CPUs and Many-core GPUs

We present results from parallelizing the unpacking and clustering steps of the raw data from the silicon strip modules for reconstruction of charged particle tracks. Throughput is further improved by concurrently processing multiple events using nested OpenMP parallelism on CPU or CUDA streams on GPU. The new implementation along with earlier work in developing a parallelized and vectorized implementation of the combinatoric Kalman filter algorithm has enabled efficient global reconstruction of the entire event on modern computer architectures. We demonstrate the performance of the new implementation on Intel Xeon and NVIDIA GPU architectures.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Sensor Co-design for $\textit{smartpixels}$

Pixel tracking detectors at upcoming collider experiments will see unprecedented charged-particle densities. Real-time data reduction on the detector will enable higher granularity and faster readout, possibly enabling the use of the pixel detector in the first level of the trigger for a hadron collider. This data reduction can be accomplished with a neural network (NN) in the readout chip bonded with the sensor that recognizes and rejects tracks with low transverse momentum (p$_T$) based on the geometrical shape of the charge deposition (``cluster''). To design a viable detector for deployment at an experiment, the dependence of the NN as a function of the sensor geometry, external magnetic field, and irradiation must be understood. In this paper, we present first studies of the efficiency and data reduction for planar pixel sensors exploring these parameters. A smaller sensor pitch in the bending direction improves the p$_T$ discrimination, but a larger pitch can be partially compensated with detector depth. An external magnetic field parallel to the sensor plane induces Lorentz drift of the electron-hole pairs produced by the charged particle, broadening the cluster and improving the network performance. The absence of the external field diminishes the background rejection compared to the baseline by $\mathcal{O}$(10%). Any accumulated radiation damage also changes the cluster shape, reducing the signal efficiency compared to the baseline by $\sim$ 30 - 60%, but nearly all of the performance can be recovered through retraining of the network and updating the weights. Finally, the impact of noise was investigated, and retraining the network on noise-injected datasets was found to maintain performance within 6% of the baseline network trained and evaluated on noiseless data.

Shekar, Danush [Illinois U., Chicago]↗

DOE OSTI2020

A Sparse Tensor Benchmark Suite for CPUs and GPUs

Tensor computations present significant performance chal- lenges that impact a wide spectrum of applications ranging from machine learning, healthcare analytics, social network analysis, data mining to quantum chemistry and signal processing. Efforts to improve the perfor- mance of tensor computations include exploring data layout, execution scheduling, and parallelism in common tensor kernels. This work presents a benchmark suite for arbitrary-order sparse tensor kernels using state- of-the-art tensor formats: coordinate (COO) and hierarchical coordinate (HiCOO) on CPUs and GPUs. It presents a set of reference tensor kernel implementations that are compatible with real-world tensors and power law tensors extended from synthetic graph generation techniques. We also propose Roofline performance models for these kernels to provide insights of computer platforms from sparse tensor view. This benchmark suite along with the synthetic tensor generator is publicly available.

Li, Jiajia↗

DOE OSTI2021

Improving scalability of parallel CNN training by adaptively adjusting parameter update frequency

Synchronous SGD with data parallelism, the most popular parallelization strategy for CNN training, suffers from the expensive communication cost of averaging gradients among all workers. The iterative parameter updates of SGD cause frequent communications and it becomes the performance bottleneck. In this paper, we propose a lazy parameter update algorithm that adaptively adjusts the parameter update frequency to address the expensive communication cost issue. Our algorithm accumulates the gradients if the difference of the accumulated gradients and the latest gradients is sufficiently small. Here, the less frequent parameter updates reduce the per-iteration communication cost while maintaining the model accuracy. Our experimental results demonstrate that the lazy update method remarkably improves the scalability while maintaining the model accuracy. For ResNet50 training on ImageNet, the proposed algorithm achieves a significantly higher speedup (739.6 on 2048 Cori KNL nodes) as compared to the vanilla synchronous SGD (276.6) while the model accuracy is almost not affected (<0.2% difference).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

The Tianlai Cylinder Pathfinder Array: System Functions and Basic Performance Analysis

The Tianlai Cylinder Pathfinder is a radio interferometer array designed to test techniques for 21 cm intensity mapping in the post-reionization Universe, with the ultimate aim of mapping the large scale structure of the Universe and measuring cosmological parameters such as the dark energy equation of state. Each of its three parallel cylinder reflectors are oriented in the north-south direction, and the array has a large field of view. As the Earth rotates, the northern sky is observed by drift scanning. The array is located in Hongliuxia, a radio quiet site in Xinjiang, and saw its first light in September 2016. In this first paper on the data analysis of the Tianlai cylinder array, we describe the system functions of the array, the commissioning observations during 2016- 2018, and present its basic performance characteristics. We show examples of the interferometric visibility data, then using the observational data, we derive the actual beam profile in the east-west direction, the bandpass response, and calibrate the complex gains for the array elements either with a strong astronomical point source, or with an artificial calibrator source. Based on the preliminary analysis of the data, we derive the system temperature and sensitivity of the array.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation

This Final Scientific and Technical Report summarizes work performed under the Phase IIA SBIR project “Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation” (DE-SC0020906) from August 2023 through August 2025. The objective of the Phase IIA effort was to mature and harden capabilities developed during Phase II, with the goal of enabling practical interoperability between Coreform’s isogeometric analysis (IGA) technologies and the Multiphysics Object-Oriented Simulation Environment (MOOSE), while improving robustness, performance, and scalability for complex, nuclear-relevant geometries. Over the course of Phase IIA, the project established and validated an extraction-based interoperability pathway between Coreform tools and MOOSE. A combined mesh and matrix format was defined collaboratively with MOOSE developers and integrated into the solver, enabling standard MOOSE workflows to operate on data exported from Coreform’s IGA and Flex Representation Method (FRM) pipelines. Early demonstrations validated architectural compatibility using linear solid mechanics problems, while later efforts focused on benchmark testing and external use. By the end of the project period, engineers at BWXT were able to independently set up and execute a simulation using the Coreform–MOOSE workflow and provide direct feedback that informed further refinement. In parallel, substantial effort was devoted to improving the robustness of trimmed U-spline construction for complex CAD geometries. A growing test suite of nuclear-relevant models was compiled through collaboration with multiple stakeholders and used to drive extensive bug fixing and reliability improvements. These efforts resulted in improved robustness and performance, including the addition of fallback capabilities that enhance reliability when the underlying commercial CAD kernel fails. Performance-oriented work progressed later in the project, with the development and demonstration of methods to decompose complex geometries into structured subregions and updated data representations to support more efficient solver processing. Additionally, extensive enhancements to threadsafe parallel data structures and trimming operations established a foundation for scalable processing of large assemblies. Collaboration with Sandia National Laboratories on the SGM geometric modeling kernel advanced to a functioning interface test case, positioning the workflow for future kernel integration. Overall, the Phase IIA effort successfully transitioned the project from architectural proof-of-concept to externally exercised, solver-integrated capability, while clarifying remaining technical challenges related to standardization, performance optimization, and kernel integration.

42 ENGINEERING↗

DOE OSTI2025

Altermagnetic behavior in OsO2: Parallels with RuO2

This dataset contains input and output files from DFT simulations used to reproduce the electronic and phonon band structures of bulk OsO₂ and RuO₂. The files include data from initial electronic structure and phonon calculations performed with Hubbard-U correction (i.e., Antiferromagnetic, AFM) and without Hubbard-U correction (i.e., Non-magnetic, NM). The electronic structure calculations are provided both with and without spin-orbit coupling (SOC). The computed electronic properties are compared with existing literature, while the calculated phonon density of states (PhDOS) is compared with experimental PhDOS.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Rate-induced aging effects on Parallel-Plate Avalanche Counter (PPAC) caused by heavy ion beams

The Facility for Rare Isotope Beams (FRIB) is one of the premier scientific user facilities for nuclear science with radioactive beams, capable of producing most (approximately 80%) of the isotopes expected to exist, from oxygen to uranium, at energies up to 200 MeV/u. With the increase in beam power from the present 10 kW to the planned 400 kW, FRIB experiments are about to enter a new era. An unprecedented rate capability as well as stable performance of all the planned instrumentation intended for beam diagnostics and beam tuning is required at the expected high beam intensities (> 1 MHz). A summary of aging phenomena at high heavy-ion beam rates observed in the Advanced Rare Isotope Separator (ARIS) detectors for beam diagnostics, including Parallel Plate Avalanche Counters (PPAC) and plastic scintillation for time-of-flight measurements, is discussed. Current research and development project to mitigate rate-induced aging are presented.

Aging effects↗