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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 OSTI2024

Status of SAS4A/SASSYS-1 Software Development and Application (FY2024)

SAS4A/SASSYS-1 is a simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal-cooled nuclear reactors. With its origin as SAS1A in the late 1960s, the SAS series of codes has been under continuous use and development for over fifty years. It has been identified as a critical element of safety analysis capabilities for the U.S. Department of Energy and is utilized within industry to perform the transient safety analyses required to support the licensing of Liquid Metal-cooled Fast Reactors (LMFRs). This report summarizes the code development and update activities carried out during FY2024. In FY2024, programmatic activities focused on key improvements to software useability, such as enhanced user interfaces for reactivity feedback modeling, improvements in stability/useability of the Code Manual, and improvements to the acceptance testing infrastructure, including automation of acceptance testing and generation of the Acceptance Testing Report. To support end user applications, an open training was held, a semi-public forum was maintained, and a practical benchmarking and validation matrix was developed which allowed limitations of existing testing capabilities to be assessed. The existing fuel models were also enhanced with improved modeling capabilities and testing for the oxide and annular fuel models.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

The MOSAiC Distributed Network: Observing the coupled Arctic system with multidisciplinary, coordinated platforms

Central Arctic properties and processes are important to the regional and global coupled climate system. The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) Distributed Network (DN) of autonomous ice-tethered systems aimed to bridge gaps in our understanding of temporal and spatial scales, in particular with respect to the resolution of Earth system models. By characterizing variability around local measurements made at a Central Observatory, the DN covers both the coupled system interactions involving the ocean-ice-atmosphere interfaces as well as three-dimensional processes in the ocean, sea ice, and atmosphere. The more than 200 autonomous instruments (“buoys”) were of varying complexity and set up at different sites mostly within 50 km of the Central Observatory. During an exemplary midwinter month, the DN observations captured the spatial variability of atmospheric processes on sub-monthly time scales, but less so for monthly means. They show significant variability in snow depth and ice thickness, and provide a temporally and spatially resolved characterization of ice motion and deformation, showing coherency at the DN scale but less at smaller spatial scales. Ocean data show the background gradient across the DN as well as spatially dependent time variability due to local mixed layer sub-mesoscale and mesoscale processes, influenced by a variable ice cover. The second case (May–June 2020) illustrates the utility of the DN during the absence of manually obtained data by providing continuity of physical and biological observations during this key transitional period. We show examples of synergies between the extensive MOSAiC remote sensing observations and numerical modeling, such as estimating the skill of ice drift forecasts and evaluating coupled system modeling. The MOSAiC DN has been proven to enable analysis of local to mesoscale processes in the coupled atmosphere-ice-ocean system and has the potential to improve model parameterizations of important, unresolved processes in the future.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Status Update for the Canister Deposition Field Demonstration

This report updates the high-level test plan for evaluating surface deposition on three commercial 32PTH2 spent nuclear fuel (SNF) canisters inside NUTECH Horizontal Modular Storage (NUHOMS) Advanced Horizontal Storage Modules (AHSMs) from Orano (formerly Transnuclear Inc.) and provides a description of the surface characterization activities that have been conducted to date. The details contained in this report represent the best designs and approaches explored for testing as of this publication. Given the rapidly developing nature of this test program, some of these plans may change to accommodate new objectives or requirements. The goal of the testing is to collect highly defensible and detailed dust deposition measurements from the surface of dry storage canisters in a marine coastal environment to guide chloride-induced stress corrosion crack (CISCC) research. To facilitate surface sampling, the otherwise highly prototypic dry storage systems will not contain SNF but rather will be electrically heated to mimic the decay heat and thermal hydraulic environment. Test and heater design is supported by detailed computational fluid dynamics modeling. Instrumentation throughout the canister, storage module, and environment will provide extensive information about thermal-hydraulic behavior. Manual sampling over a comprehensive portion of the canister surface at regular time intervals will offer a high-fidelity quantification of the conditions experienced in a harsh yet realistic environment. Functional testing of the finalized heater assemblies and test apparatus is set to begin in December 2022. The proposed delivery of the canisters to the host test site is June/July 2023, which is well ahead of when the AHSM installations would be completed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Automated Defect Identification for Tri-structural Isotropic Fuels (AUDIT)

During the manufacture of tri-structural isotropic (TRISO)-coated nuclear fuel particles, the potential exists for the formation of internal fissure defects in the uranium oxycarbide (UCO) kernels. These fissures result in a defective fuel particle that can fracture during subsequent fuel processing. Therefore, it is necessary to detect the presence of fissured kernels in a batch to determine if the batch meets specification prior to blending with other batches and upgrading processes. Previous attempts at identifying fissures involved manual inspection of micrographs of UCO fuel kernel cross-sections. This process is tedious, time-consuming and may introduce counting errors making it a good candidate for automation. This work presents a method for the automated detection of fissures in UCO kernels. Image segmentation is used for the extraction of relevant features in the micrographs which then serve as the input to a convolutional neural network used to automatically distinguish between fissured and non-fissured kernels.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Design and testing of ultrasound probe adapters for a robotic imaging platform

Medical imaging-based triage is a critical tool for emergency medicine in both civilian and military settings. Ultrasound imaging can be used to rapidly identify free fluid in abdominal and thoracic cavities which could necessitate immediate surgical intervention. However, proper ultrasound image capture requires a skilled ultrasonography technician who is likely unavailable at the point of injury where resources are limited. Instead, robotics and computer vision technology can simplify image acquisition. As a first step towards this larger goal, here, we focus on the development of prototypes for ultrasound probe securement using a robotics platform. The ability of four probe adapter technologies to precisely capture images at anatomical locations, repeatedly, and with different ultrasound transducer types were evaluated across more than five scoring criteria. Testing demonstrated two of the adapters outperformed the traditional robot gripper and manual image capture, with a compact, rotating design compatible with wireless imaging technology being most suitable for use at the point of injury. Next steps will integrate the robotic platform with computer vision and deep learning image interpretation models to automate image capture and diagnosis. This will lower the skill threshold needed for medical imaging-based triage, enabling this procedure to be available at or near the point of injury.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Automated tabletop exfoliation and identification of monolayer graphene flakes

Over the past two decades, graphene has been intensively studied because of its remarkable mechanical, optical, and electronic properties. Initial studies were enabled by manual “Scotch Tape” exfoliation; nearly two decades later, this method is still widely used to obtain chemically pristine flakes of graphene and other 2D van der Waals materials. Unfortunately, the yield of large, pristine flakes with uniform thickness is inconsistent. Thus, significant time and effort are required to exfoliate and locate flakes suitable for fabricating multilayer van der Waals heterostructures. Here, we describe a relatively affordable tabletop device (the “eXfoliator”) that can reproducibly control key parameters and largely automate the exfoliation process. In a typical exfoliation run, the eXfoliator produces 3 or more large (≥ 400 μm 2 ) high-quality graphene monolayer flakes, allowing new users to produce such flakes at a rate comparable to manual exfoliation by an experienced user. Furthermore, we use an automated mapping system and a computer vision algorithm to locate candidate flakes. Our results provide a starting point for future research efforts to identify more precisely which parameters matter for the success of exfoliation and to optimize them.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Building a Simplistic Automatic Extruder: Instrument Development Opportunities for the Laboratory

This work presents an automatic extruder as a research experience for undergraduate students. The system offers a user-friendly approach to preparing vesicles, such as liposomes or polymersomes, with a defined size and polydispersity properties crucial for research in biology and macromolecules. It comprises two syringe pumps connected by a membrane filter. The setup is controlled by software. Compared to manual extrusion, this automated system provides advantages, such as precisely controlled variables. The project describes a tool to enhance undergraduate learning in science and engineering laboratories. Building an automatic extruder serves as a simplified model of a complex industrial process. It offers a clear advantage: automating a well-understood manual extrusion process. To make this project accessible, it is broken down into three manageable tasks: software development, hardware assembly, and testing procedures. This breakdown describes the software created, the hardware components used, and the testing procedures conducted for this project. All project data, including software code, testing data, and procedures, are freely available online. This allows undergraduate students to not only begin their own projects but also contribute to this educational instrument’s ongoing development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Guide for Joint Participation in a DOE Complex Wide SAVY-4000 Surveillance Program

This document describes LANL Storage Program best practices when working with other User Sites to implement DOE M441.1-1 Manual requirements through the use of the SAVY nuclear material packaging system. It is a Manual directive for Field Element Managers to review and approve the SAVY-4000 container series design (with supporting technical basis) as a packaging system for use at their respective sites. This review and approval incorporates an evaluation of the User Site methodology for SAVY surveillance and the process for documenting its nuclear materials storage program. This document aims to assist the Field Element Mangers and User Sites in the processes necessary to credit LANL SAVY surveillance for key elements of the User Site surveillance plan.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

L-PBF High-Throughput Data Pipeline Approach for Multi-modal Integration

Abstract Metal-based additive manufacturing requires active monitoring solutions for assessing part quality. Multiple sensors and data streams, however, generate large heterogeneous data sets that are impractical for manual assessment and characterization. In this work, an automated pipeline is developed that enables feature extraction from high-speed camera video and multi-modal data analysis. The framework removes the need for manual assessment through the utilization of deep learning techniques and training models in a weakly supervised paradigm. We demonstrate this pipeline’s capability over 700,000 high-speed camera frames. The pipeline successfully extracts melt pool and spatter geometries and links them to corresponding pyrometry, radiography, and processparameter information. 715 individual prints are examined to reveal melt pool areas that exceeds 0.07 mm 2 and pyrometry signal over a threshold (375 pyrometry units) were more likely to have defects. These automated processes enable massive throughput of characterization techniques.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Comparison of automated chemical-guided segmentation and human annotation of soil organic matter in X-ray microcomputed tomography imaging in contrasted soil types

Soil organic matter (OM) formation and persistence is strongly influenced by the spatial distribution of organic substrates and microscale soil heterogeneity by dictating OM accessibility to microorganisms. However, traditional size and/or density fractionation techniques disrupt aggregate architecture, eliminating spatial information needed to fully understand intra-aggregate OM distribution. To quantify three-dimensional OM spatial distribution and automate segmentation in X-ray microcomputed tomography (µCT) imaging without human annotation bias, we developed an iodine gas vapor (I2) based staining workflow that eliminates labor-intensive manual annotation while maintaining segmentation accuracy, using aggregates from four taxonomically diverse soils (Xerofluvent, Haploxeroll Sphagnofibrist, Palehumult) with an 8-fold range of soil organic carbon. Human annotation of 10 µCT slices by the experienced and inexperienced annotators resulted in variations up to 3% in the Dice similarity coefficient (DSC), reflecting a degree of inherent subjectivity of manual labeling. Such inconsistencies are expected to compound as the number of manually annotated slices increases. Dual-energy µCT imaging at 33.1 keV (below the iodine (I) K-edge) and 33.2 keV (above the I K-edge) was used to resolve aggregate microstructure following I2 staining. The automated image subtraction pipeline identified OM regions by the I Kedge induced brightness increases, achieving DSC values of 0.58–0.83 relative to an experienced annotator. Sensitivity analyses revealed that the reconstruction alpha value—optimized via the open-source tool TomocuPy—and the 3D registration slice count were the primary determinants of accuracy, providing a novel benchmark for dual-energy soil imaging. The pipeline without GPU acceleration achieved 9.6 to 43.2 times faster than manual annotation. Using GPU-accelerated image post-processing and affine transformation matrices, the pipeline successfully segmented OM elements for large-scale datasets (3232×3232 pixel, 2048 slices) within ~5200 s from raw file acquisition to segmented output. The high-throughput approach enables the quantification of OM spatial distribution across diverse and heterogeneous soil.

Soil microbial biomass↗

DOE OSTI2026

Heat load measurements for the PIP-II pHB650 cryomodule

Phase-3 testing of the pHB650 cryomodule at the PIP-II Injector Test Facility was conducted to evaluate the effectiveness of heat load mitigations performed after earlier phases of testing and to continue pinpointing any sources of unexpectedly high heat loads.. The programme measured HTTS, LTTS, and 2 K isothermal/non-isothermal loads under "standard", "linac", and "simulated dynamic" operating modes, recording data both inside the cryomodule and across the bayonet can circuits. Thermal-acoustic oscillations were eliminated by replacing the original G10 cooldown-valve stem with a stainless-steel stem fitted with wipers. A newly developed Python script automated acquisition of ACNET data, performed real-time heat-load calculations, and generated plots and tables that were posted to the electronic logbook within minutes, vastly reducing manual effort and accelerating feedback between SRF and cryogenics teams. Analysis showed that JT heat-exchanger effectiveness and temperature stratification in the two-phase and relief piping strongly influence the observed loads and helped isolate sources of excess heat. The campaign demonstrates that rigorous pre-test planning, real-time diagnostics, and automated reporting can improve both accuracy and efficiency, providing a template for future PIP-II cryomodule tests and for implementing targeted heat-load mitigations.

Porwisiak, D. [Fermilab; Wroclaw Tech. U.] (ORCID:↗

DOE OSTI2024

Investigation of Anion-Exchange Method for Purification of Fission-Produced 99 Mo

The LEU-Modified Cintichem (LMC) process is a small-scale (50- to 100-mL) method for purifying fission-produced 99 Mo. Traditionally, the process utilizes custom-made glassware and requires significant manual operations with hot cell manipulators. As an alternative to the LMC process, there is great interest in developing a 99 Mo purification method that could be automated to minimize remote handling while achieving the same purity specifications for the 99 Mo product. This report explores an ion-exchange approach to purifying fission-produced 99 Mo and discusses the decontamination factors for various fission products that are present after initial recovery of Mo on a titania column from a sulfate-based and uranium-containing solution.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2024

PETSc/TAO Users Manual Revision 3.22

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 (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

CAKE: Consistent Automatic Kinetic Equilibrium reconstruction

Magnetohydrodynamic equilibrium reconstructions with kinetic constraints are an essential input of many tokamak stability and transport analysis work- flows. The reconstructions themselves also contain useful information about pressure and current density distributions within the plasma which can be used to drive other calculations. While standardized magnetic-only, and partially kinetic equilibrium reconstruction is widely available and used, re- constructions for well diagnosed machines such as DIII-D, that incorporates a large and heterogeneous set of internal diagnostic measurements yet robustly reaching high numerical accuracy have been a time intensive, manual process. The Consistent Automatic Kinetic Equilibrium reconstruction tool (CAKE) has been developed and implemented at DIII-D for producing low error, kinetically constrained reconstructions without human intervention, and to identify strategies for doing so that would be broadly applicable. Here, the techniques employed to allow CAKE to handle data of limited quality and availability, as well as the full automation of the workflow may assist future efforts to form kinetic constraint profiles in real time plasma control applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Ontologizing health systems data at scale: making translational discovery a reality

Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68–99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2022

In vivo hypermutation and continuous evolution

Directed evolution has revolutionized biomolecular engineering by applying cycles of mutation, amplification and selection to genes of interest (GOIs). However, classical directed evolution methods that rely on manually staged evolutionary cycles constrain the scale and depth of the evolutionary search that is possible. Here we describe genetic systems that achieve cycles of rapid mutation, amplification and selection fully inside living cells, enabling the continuous evolution of GOIs as cells grow. These systems advance the scale, evolutionary search depth, ease and overall power of directed evolution and access important new areas of protein evolution and engineering.

59 BASIC BIOLOGICAL SCIENCES↗