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DOE OSTI2023

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

Background: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2012

An Assessment of CFD/CSD Prediction State-of-the-Art by Using the HART II International Workshop Data

Over the past decade, there have been significant advancements in the accuracy of rotor aeroelastic simulations with the application of computational fluid dynamics methods coupled with computational structural dynamics codes (CFD/CSD). The HART II International Workshop database, which includes descent operating conditions with strong blade-vortex interactions (BVI), provides a unique opportunity to assess the ability of CFD/CSD to capture these physics. In addition to a baseline case with BVI, two additional cases with 3/rev higher harmonic blade root pitch control (HHC) are available for comparison. The collaboration during the workshop permits assessment of structured, unstructured, and hybrid overset CFD/CSD methods from across the globe on the dynamics, aerodynamics, and wake structure. Evaluation of the plethora of CFD/CSD methods indicate that the most important numerical variables associated with most accurately capturing BVI are a two-equation or detached eddy simulation (DES)-based turbulence model and a sufficiently small time step. An appropriate trade-off between grid fidelity and spatial accuracy schemes also appears to be pertinent for capturing BVI on the advancing rotor disk. Overall, the CFD/CSD methods generally fall within the same accuracy; cost-effective hybrid Navier-Stokes/Lagrangian wake methods provide accuracies within 50% the full CFD/CSD methods for most parameters of interest, except for those highly influenced by torsion. The importance of modeling the fuselage is observed, and other computational requirements are discussed.

Smith, Marilyn J.↗

DOE OSTI2024

LLNL FESP Theory Highlights: August 2024

The 2024 ABOUND SciDAC and BOUT++ combined workshop was held August 5-9 th 2024 at the University of California Livermore Collaboration Center (UCLC) in Livermore. Bringing together leading scientists and researchers from across the globe, this pivotal event focused on advancing plasma physics and boundary plasma dynamics within the context of fusion energy research. Key discussions throughout the meeting highlighted significant advancements in the BOUT++ framework, including enhanced simulations of small Edge Localized Modes (ELMs) and the initiation of integrating the integration of the 5D GEM gyrokinetic turbulence core code with the 2D SOLPS-ITER boundary transport code. These developments are crucial for managing heat loads in fusion reactors and supporting the longevity of plasma-facing components. The event also featured a session on Inter-SciDAC Collaborations, where principal investigators from multiple U.S. FES SciDAC tokamak projects explored opportunities for cross-collaboration. Additionally, the meeting showcased cutting-edge advancements in GPU acceleration and AI/ML technologies, poised to drive the next generation of fusion research. In his closing remarks, Dr. Xueqiao Xu emphasized the importance of the collaborative efforts and discussions that took place, noting their potential to shape future breakthroughs in fusion energy. The event underscored the global nature of the BOUT++ collaboration, with contributions from over 57 institutions worldwide. The 2024 BOUT++ and ABOUND Joint Hybrid Meeting continues to drive forward the research and innovations needed to achieve fusion energy, setting the stage for future collaboration and discovery.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

IEEE 1547-2018 Based Interoperable PV Inverter with Advanced Grid-Support Functions

Grid integration of photovoltaic (PV) inverters has been increasing in the past decade. As a result of the uncertainties introduced with high penetrations of PV, better monitoring and control of the PV inverters becomes crucial for improving overall system stability. This paper focuses on the communications capability of the inverter controller and on enabling interoperability. Multiple standards are available to enable interoperability in PV inverters. In this paper, an interoperable controller, enabled by Distributed Network Protocol 3 (DNP3) communications protocols, is developed for a grid-connected, three-phase PV inverter. The DNP3 server for the PV inverter is programmed on the real-time layer of the field-programmable gate array (FPGA)-based inverter controller. Set points for advanced inverter control functions, such as volt/VAr curves, ride-through curves, are sent from a DNP3 client, a simulated distribution management system application, to the PV inverter through DNP3. This communications capability of the inverter controller is validated using a controller-hardware-in-the-loop experimental setup. The code developed to achieve the interoperability is available in the public domain through open-source software licensing. This interoperability will enable smoother grid integration of smart PV inverters with advanced grid-support functions as well as allow better monitoring and control of PV inverters for grid stability.

14 SOLAR ENERGY↗

DOE OSTI2025

The SAS4A/SASSYS-1 Version 5.8 Safety Analysis Code System

SAS4A/SASSYS-1 is a software simulation tool used to perform deterministic analysis of anticipated events as well as design basis and beyond design basis accidents for advanced nuclear reactors. Detailed, mechanistic models of steady-state and transient thermal, hydraulic, kinetic, and mechanical phenomena are employed to describe the response of the reactor core, the reactor primary and secondary coolant loops, the reactor control and protection systems, and the balance-of-plant to accidents caused by changes in coolant flow, loss of heat rejection, or reactivity insertion. The consequences of single and double-fault accidents can be modeled, including fuel and coolant heating, fuel and cladding mechanical behavior, core reactivity feedbacks, coolant loop performance including natural circulation, and decay heat removal. Analyses are typically terminated upon demonstration of reactor and plant shutdown to permanently coolable conditions, or upon violation of design basis margins. The objective of the analysis is to quantify accident consequences as measured by the transient behavior of system performance parameters, such as fuel and cladding temperatures, reactivity, and cladding strain. Originally developed for analysis of sodium cooled reactors with oxide fuel clad by stainless steel, the models were subsequently extended and specialized to metallic fuel clad with advanced alloys and to several other coolant options, including lead, LBE, and water.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS1987

Advances in 3-D Inelastic Analysis Methods for hot section components

3-D Inelastic Analysis Methods are described. These methods consist of a series of new computer codes embodying a progression of mathematical models (mechanics of materials, specialty finite element, boundary element) for streamlined analysis of: (1) combustor liners, (2) turbine blades, and (3) turbine vanes. These models address the effects of high temperatures and thermal/mechanical loadings on the local (stress/strain) and global (dynamics, buckling) structural behavior of the three selected components. Three computer codes, referred to as MOMM (Mechanics of Materials Model), MHOST (MARC-Hot Section Technology), and BEST (Boundary Element Stress Technology), have been developed and are briefly described in this paper.

Chamis, Christos C.↗

DOE OSTI2021

Accelerate Nuclear Research and Development by Reducing Time and Cost Spend in the Pre-conceptual Design Phase of Advanced Reactor Experiments

The design process of every new concept, such as advanced nuclear reactors or associated experiments, starts with the pre-conceptual design phase. In this phase, the viability of a wide range of design options needs to be assessed quickly, to understand the operating envelope and its feasibility. A variety of physics models (thermal-hydraulics, neutronics, mechanical design, etc.) has to be considered at this very first design stage and optimum component sizes and materials (e.g. heat exchangers, piping, turbomachinery, coolant type, etc.) have to be chosen for a given set of boundary conditions (e.g. heat source, heat sink, flow rate, etc.). Detailed solutions such as provided by high fidelity methods like computational fluid dynamics (CFD), Monte Carlo methods, etc. and even lower fidelity tools such as system or subchannel codes, etc. are usually not used during the pre-conceptual design due to the relatively long time needed to create input models, the computational time to obtain a solution and the lack of flexibility to quickly investigate different combinations of components, individual component sizes and material properties. High fidelity tools are usually only employed in the conceptual design and later phases once a base concept has been identified during the pre-conceptual design stage. The current practice during the pre-conceptual design stage is that analysts collect the needed equations, material properties, closure laws, etc. and create ad-hoc solutions form scratch for every new problem. There clearly is a lack of a flexible scoping tool that can be used during pre-conceptional design before higher fidelity tools (as described above) come into play. To reduce user errors in ad-hoc solutions and increase fidelity and efficiency, this project aims to investigate and develop a user-friendly scoping tool to address the thermal-hydraulic designing needs during preconceptual experiment design, i.e. Thermal-hydraulic Research Universal Scoping Tool (TRUST). The success of TRUST will provide the nuclear engineers with an easy-to-use and affordable calculator for early reactor system design and optimization.

42 ENGINEERING↗

NASA NTRS1987

Numerical simulation of transonic propeller flow using a 3-dimensional small disturbance code employing novel helical coordinates

The numerical simulation of three-dimensional transonic flow about propeller blades is discussed. The equations for the unsteady potential flow about propellers is given for an arbitrary coordinate system. From this the small disturbance form of the equation is derived for a new helical coordinate system. The new coordinate system is suited to propeller flow and allows cascade boundary conditions to be applied straightforward. A numerical scheme is employed which solves the steady flow as an asymptotic limit of unsteady flow. Solutions are presented for subsonic and transonic flow about a 5 percent thick bicircular arc blade of an eight bladed cascade. Both high and low advance ratio cases are given which include a lifting case as well as nonlifting cases. The nonlifting cases are compared to solutions from a Euler code.

Snyder, Aaron↗

NASA NTRS1987

Numerical simulation of transonic propeller flow using a three-dimensional small disturbance code employing novel helical coordinates

Snyder, Aaron↗

DOE OSTI2024

A study on the impact of using a subchannel resolution for modeling of large break loss of coolant accidents

The nuclear industry is investigating the feasibility of transitioning from 18- to 24-month fuel cycles because of the positive impact it would have on the operational costs for the current fleet of light-water reactors. A challenge to making this change is the increased risk of fuel fragmentation, relocation, and dispersal (FFRD) due to the known potential for ceramic fuel to pulverize into fine particles at the higher discharge burnups. Previous work has been performed by the Nuclear Energy Advanced Modeling and Simulation program to assess FFRD risk in high-burnup cores using the BISON fuel performance code and a coarse mesh thermal hydraulics (T/H) solution for a loss-of-coolant accident (LOCA) using the TRACE system T/H code. Because of the importance of the T/H solution for FFRD assessment, this study seeks to investigate the impact of using higher-fidelity subchannel techniques for modeling of the LOCA transient. CTF was used to model a subregion of a high-burnup core that was depleted by the Virtual Environment for Reactor Applications (VERA) multiphysics core simulator. Both coarse-mesh and pin-resolved models were created in CTF, and a consistent coarse-mesh TRACE model was also developed to allow for benchmarking the code results. Further, a large-break loss-of-coolant accident (LBLOCA) reflood transient was simulated using these three models, and results were compared. Results showed some consistent differences between the CTF and TRACE coarse models, including a higher peak cladding temperature (PCT) prediction in CTF and later quenching in CTF; however, the transient clad temperature behavior was similar, and these differences are likely due to post-critical heat flux heat transfer modeling differences and minimum film boiling temperature model differences. The pin-resolved results indicate that the PCT in the lumped model is often under-predicted by as much as 70 °C and that PCT occurs at a different location than the high-power pin in the assembly. The lumped model predicts a difference of 10 °C or less between the average and hot pins in the assembly, whereas the pin-resolved model predicts a range of over 100 °C. These results indicate that higher-fidelity T/H results may have an impact on predicted core behavior during LOCA, which may be important to consider when assessing FFRD risk.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2026

Fast solvers for tokamak fluid models with PETSc

Multigrid (MG) is widely recognized as a highly effective solver for the model problem, the Laplacian, but textbook MG fails on most problems of interest. MG methods have been applied to complex, real-world applications with careful consideration of the physical model and discretization. In this work we develop the first step in applying MG methods to science and engineering relevant magnetohydrodynamics (MHD) tokamak models in the M3D-C1 (https://m3dc1.pppl.gov) fusion energy science code. The semi-implicit time integrator in M3D-C1 is composed of many linear solves. The implicit advance of the momentum equation is the most challenging and is the focus of this work. The current production solver in M3D-C1 is a block Jacobi (BJ) preconditioner within a Krylov solver, where blocks group degrees of freedom on planes of constant toroidal coordinate. BJ convergence degrades as the number of planes increases due to the spectral properties of the matrix preconditioned with BJ. The partially magnetic field-aligned, regular toroidal grid structure in M3D-C1 is amenable to semi-coarsening geometric MG in the toroidal direction. This paper develops such a solver and demonstrates competitive performance on a runaway electron model of a SPARC (https://cfs.energy/technology/sparc) disruption, and superior robustness on a stellarator model on which the BJ solver fails to converge.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Design and physics basis for the upcoming DIII-D SAS-VW campaign to quantify tungsten leakage and transport in a new slot divertor geometry

A set of experiments are planned to exploit the high SOL collisionality enabled by a tightly baffled slot divertor geometry to suppress tungsten leakage in DIII-D. A toroidal row of graphite tiles from the Small Angle Slot (SAS) divertor is being coated with 10–15 μ m of tungsten. New spectroscopic viewing chords with in-vacuo optics will measure the W gross erosion source from the divertor surface with high spatial and temporal resolution. In parallel, the bottom of the SAS divertor is changed from a flat to a ‘V’ shape. New SOLPS-ITER/DIVIMP simulations conducted with drifts using the planned ‘V’ shape predict a substantial reduction in W sourcing and SOL accumulation in either B × ∇B direction relative to either the old SAS divertor shape or the open, lower divertor. Dedicated studies are planned to carefully characterize the level of W sourcing, leakage, and scrape-off-layer (SOL) accumulation in DIII-D over a wide range of plasma scenarios. Various actuators will be assessed for their efficacy in further reducing high-Z impurity sources and leakage from the slot divertor geometry. Finally, this coupled code-experiment validation effort will be used to stress-test physics models and build confidence in extrapolations to advanced, high-Z divertor geometries for next-step devices.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

169 Tm ( n , γ ) cross section and statistical decay properties from measurements at the DANCE facility

Background: Radiative neutron capture on thulium, which is a monoisotopic element, plays a role in different applications such as nuclear astrophysics or nuclear burning environments. Considerable discrepancies—reaching 20%—exist between evaluations in the unresolved-resonance region. Furthermore, experimental data on statistical 𝛾 decay in odd-odd rare-earth nuclei is scarce. There are still open questions about the systematics of the so-called scissors mode in the 𝑀⁢1 photon strength function, especially in odd-odd nuclei. Purpose: This work is focused on two main topics—deriving experimental 169 Tm ⁢(𝑛,𝛾) cross section and studying statistical 𝛾 decay of 170 Tm, in particular properties of the scissors mode. Methods: The capture experiments to obtain experimental cross section were performed at the Los Alamos Neutron Science Center using the time-of-flight technique and employing the Detector for Advanced Neutron Capture Experiments. Measured coincident 𝛾-ray spectra were also compared with statistical simulations using the dicebox code to test different models of level density and photon strength functions. Results: The capture cross section was determined from 1.8 eV to 0.97 MeV, the broadest neutron-energy range ever measured for this isotope. Several new resonances have been observed. The statistical 𝛾 decay of 170 Tm cannot be reproduced without a scissors mode resonance centered at ≈ 3.3MeV. Conclusions: The measured cross section in the unresolved-resonance region is generally lower than the latest evaluations. The derived 169 Tm 𝑠-process abundance is expected to increase by a factor of 1.26, while the changes of the abundances of elements heavier than 169 Tm are in the order of 0.2%. The scissors mode properties in 170 Tm are similar to those deduced in previous analyses of neighboring nuclei 168 Er and 166 Ho .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Solving the electronic structure problem for over 100000 atoms in real space

Using a real-space high-order finite-difference approach, we investigate the electronic structure of large spherical silicon nanoclusters. Within Kohn-Sham density functional theory and using pseudopotentials, we report the self-consistent field convergence of a system with over 100000 atoms: a Si 107,641 ⁢H 9,084 nanocluster with a diameter of 16 nm. Our approach uses Chebyshev-filtered subspace iteration to speed up the convergence of the eigenspace, and blockwise Hilbert space-filling curves to speed up sparse matrix-vector multiplications, all of which are implemented in the parsec code. For the largest system, we utilized 2048 nodes (114 688 cores) on the Frontera machine in the Texas Advanced Computing Center. Our quantitative analysis of the electronic structure shows how it gradually approaches its bulk counterpart as a function of nanocluster size. The band gap is enlarged due to quantum confinement in nanoclusters, but decreases as the system size increases, as expected. In conclusion, our work serves as a proof of concept for the capacity of the real-space approach in efficiently parallelizing very large calculations using high-performance computer platforms, which can straightforwardly be replicated in other systems with more than 10 5 atoms.

0-dimensional systems↗

DOE OSTI2020

Summer Proceedings 2019

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers and heterogeneous computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program includes the organization of a weekly seminar series and the publication of this summer proceedings.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Celeritas R&D Report: Accelerating Geant4

Celeritas is a new Monte Carlo (MC) detector simulation code designed for computationally intensive applications on high-performance heterogeneous architectures. In the past two years Celeritas has advanced from prototyping a Graphics Processing Unit (GPU)-based single physics model in infinite medium to implementing a full set of electromagnetic (EM) physics processes in complex geometries. The current release of Celeritas, version 0.4, has incorporated full device-based navigation, an event loop in the presence of magnetic fields, and detector hit scoring. New functionality incorporates a scheduler to offload electromagnetic physics to the GPU within a Geant4-driven simulation, enabling straightforward integration of Celeritas into the high energy physics (HEP) experimental frameworks CMSSW and ATLAS FullSimLight. On the Perlmutter supercomputer, Celeritas performs EM physics between 3× and 18× faster using the machine’s Nvidia GPUs compared to using only CPUs, corresponding to an electrical power efficiency up to a factor of 5. When running a multithreaded Geant4 ATLAS test beam application with full hadronic physics, using Celeritas to accelerate the EM physics results in an overall simulation speedup of 1.7–2.2× on GPU and 1.2× on CPU. In a CMS test application using tt¯ events and the prototype Run 4 configuration, compared to Geant4 CPU, Celeritas with a Nvidia A100 improves overall throughput up to a factor of 2.7× but cannot be efficiently shared with more than 8 cores.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Evaluation of Mechanistic and Empirical Models against Existing FFRD and LOCA Experimental Databases

The desire of the nuclear industry to improve the economics of existing nuclear power plants has necessitated research into the potential of a phenomenon known as fuel fragmentation, relocation, and dispersal (FFRD). This phenomenon is possible during a loss-of-coolant accident (LOCA) at relatively high burnup. The Nuclear Energy Advanced Modeling and Simulation program has been developing simulation capabilities for FFRD and LOCA in the BISON fuel performance code for multiple years. This year, the effort has been focused on evaluating new lower length scale informed pulverization thresholds as well as updating and adding new empirical models for various phenomena. Models added or updated this year include a preliminary transient fission gas release model, new high-temperature Zircaloy creep models, a Zircaloy rupture opening area model, and a temperature-dependent emissivity during radiation from the fuel rod to the surrounding atmosphere. The models are verified through implementation tests to demonstrate code correctness after addition to BISON. The models are then assessed against a subset of the existing BISON validation suite for LOCA and FFRD cases. Two new cases, Studsvik Rods 192 and 193, have been added. The results indicate that the inclusion of a bubble pressure evolution model in the bubbles in the high-burnup structure has the largest impact compared to the 3D fracture criterion on reducing the calculated amount of pulverized fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Enabling Parallel Performance and Portability of Solid Mechanics Simulations Across CPU and GPU Architectures

Efficiently simulating solid mechanics is vital across various engineering applications. As constitutive models grow more complex and simulations scale up in size, harnessing the capabilities of modern computer architectures has become essential for achieving timely results. This paper presents advancements in running parallel simulations of solid mechanics on multi-core CPUs and GPUs using a single-code implementation. This portability is made possible by the C++ matrix and array (MATAR) library, which interfaces with the C++ Kokkos library, enabling the selection of fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. MATAR simplifies the transition from Fortran to C++ and Kokkos, making it easier to modernize legacy solid mechanics codes. We applied this approach to modernize a suite of constitutive models and to demonstrate substantial performance improvements across different computer architectures. This paper includes comparative performance studies using multi-core CPUs along with AMD and NVIDIA GPUs. Results are presented using a hypoelastic–plastic model, a crystal plasticity model, and the viscoplastic self-consistent generalized material model (VPSC-GMM). The results underscore the potential of using the MATAR library and modern computer architectures to accelerate solid mechanics simulations.

Morgan, Nathaniel (ORCID:0000000276118449)↗