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DOE OSTI2022

MPACT Software Management Plan (V.4.3)

The MPACT code solves a discretized form of the Boltzmann transport equation on a wide variety of geometries and is distributed with a multigroup neutron cross section library. MPACT provides an advanced geometrically resolved neutral-particle transport capability to solve the flux distribution throughout the entire problem geometry, and it can model the isotopic depletion, decay, and activation of materials. The flux solution in MPACT is provided using a 2D/1D synthesis method within the framework of the 3D coarse mesh finite difference (CMFD) method for which axial and radial correction factors are obtained from 2D method of characteristics (MOC) and 1D nodal expansion method (NEM), PN, or SN. Other key characteristics of the MPACT code include the subgroup method and the embedded self-shielding method (ESSM) for resonance treatment, depletion capability based on the ORIGEN exponential matrix method, and a simplified thermal-hydraulics method for temperature/fluid feedback. The sole purpose of the simplified feedback model is to provide a mechanism for testing during code development and to provide a limited capability for educational applications. Work performed at the code level supports the VERA-QA-001, quality assurance program plan (QAPP) and VERA-QA-002, VERA Software Quality Assurance Plan.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Investigation of Portable Event-Based Monte Carlo Transport Using the NVIDIA Thrust Library

Power consumption considerations are driving future high performance computing platforms toward many-core computing architectures. Los Alamos National Laboratory's Trinity machine, available in 2016, will use both Intel Xeon Haswell processors and Intel Xeon Phi Knights Landing many integrated core (MIC) architecture coprocessors. Lawrence Livermore National Laboratory's Sierra machine, available in 2018, will use an IBM PowerPC architecture along with Nvidia graphics processing unit (GPU) architecture accelerators. These different advanced architectures make the computing landscape in upcoming years complex. Traditional approaches to Monte Carlo transport do not work efficiently on these new computing platforms. MIC architectures require vectorization to operate efficiently, and vectorization is difficult to achieve in Monte Carlo transport. GPU architectures require additional code to explicitly use the hardware, requiring significant code changes or hardware specific branches in the source code. A significant challenge for Monte Carlo transport projects is to simultaneously support within a single source code base efficient simulations for both the current generation of architectures and the different advanced computing architectures. In order to address these challenges, two important changes are typically required: a new algorithmic approach for solving Monte Carlo transport, and explicit use of hardware specific software. In this paper, we describe initial research investigations of an event-based Monte Carlo transport algorithm implemented using the Nvidia Thrust library on a GPU for a Monte Carlo test code. The event-based algorithm targets many-core architectures by increasing SIMD (single instruction multiple data) parallelism, while Thrust potentially provides portable performance by allowing one source code base to compile code targeted for both CPUs and GPUs. We described preliminary investigations of portable event-based Monte Carlo algorithms implemented using the Nvidia Thrust library in a research Monte Carlo test code. We found that an explicit CUDA implementation of an event-based Monte Carlo algorithm performed significantly more efficiently than a Thrust implementation on GPU platforms, most likely as a result of additional flexibility in access to different memory spaces on the GPU. Additionally, we showed that on GPU platforms and at large enough problem sizes the event-based implementations perform more efficiently than the serial history-based implementation running on the host CPU. While investigating this problem, we also discovered that the performance of the event-based algorithm is affected by what tallies are being used. A zonal scalar flux tally requires atomic operations that significantly impacted the performance of the code, in some cases producing slowdowns instead of speedups. We decided to remove the tally in order to focus on the effectiveness of the event-based algorithm. Future work will be required to research more effective ways of handling such tallies. Additionally, we would like to consider new ways for optimizing both the Thrust and CUDA versions, in order to see how much performance we have yet to achieve. The potential trade-off between portability and performance was demonstrated in this investigation. Thrust provides both CPU and GPU versions of the code in one code base, but it does so at a cost. We discovered approximately a factor of 2-5 performance difference between Thrust and CUDA on each GPU platform we tested. Thrust provides a tool to access the GPUs with less effort and specialization, but it does so by giving up fine grained control where extra performance can be found for this application. Future work will be required to determine whether this performance differential between Thrust and CUDA can be reduced for event-based Monte Carlo transport. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Portable Data-Parallel Surface Reconstruction on a Uniform Rectilinear Grid

With the increasing heterogeneity and on-node parallelism of high-performance computing hardware, a major challenge is to develop portable and efficient algorithms and software. In this work, we present our implementation of a portable code to perform surface reconstruction using NVIDIA's Thrust library. Surface reconstruction is a technique commonly used in volume tracking methods for simulations of multimaterial flow with interfaces. Here, we have designed a 3D mesh data structure that is easily mapped to the 1D vectors used by Thrust and at the same time is simple to use and uses familiar data structure terminology (such as cells, faces, vertices, and edges). With this new data structure in place, we have implemented a piecewise linear interface reconstruction algorithm in 3 dimensions that effectively exploits the symmetry present in a uniform rectilinear computational cell. Finally, we report performance results, which show that a single implementation of these algorithms can be compiled to multiple backends (specifically, multi-core CPUs, NVIDIA GPUs, and Intel Xeon Phi processors), making efficient use of the available parallelism on each. We also compare performance of our implementation to a legacy FORTRAN implementation in Message Passing Interface (MPI) and show performance parity on single and multi-core CPU and achieved good parallel speed-ups on GPU. In conclusion, our research demonstrates the advantage of performance portability of the underlying data-parallel programming model.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

On the performance of exponential integrators for problems in magnetohydrodynamics

Exponential integrators have been introduced as an efficient alternative to explicit and implicit methods for integrating large stiff systems of differential equations. Over the past decades these methods have been studied theoretically and their performance was evaluated using a range of test problems. While the results of these investigations showed that exponential integrators can provide significant computational savings, the research on validating this hypothesis for large scale systems and understanding what classes of problems can particularly benefit from the use of the new techniques is in its initial stages. Resistive magnetohydrodynamic (MHD) modeling is widely used in studying large scale behavior of laboratory and astrophysical plasmas. In many problems numerical solution of MHD equations is a challenging task due to the temporal stiffness of this system in the parameter regimes of interest. In this paper we evaluate the performance of exponential integrators on large MHD problems and compare them to a state-of-the-art implicit time integrator. Both the variable and constant time step exponential methods of EPIRK-type are used to simulate magnetic reconnection and the Kevin–Helmholtz instability in plasma. Performance of these methods, which are part of the EPIC software package, is compared to the variable time step variable order BDF scheme included in the CVODE (part of SUNDIALS) library. We study performance of the methods on parallel architectures and with respect to magnitudes of important parameters such as Reynolds, Lundquist, and Prandtl numbers. We find that the exponential integrators provide superior or equal performance in most circumstances and conclude that further development of exponential methods for MHD problems is warranted and can lead to significant computational advantages for large scale stiff systems of differential equations such as MHD.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges

3D polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated using scaffolded DNA origami offer complete and independent control over NP size, structure, and asymmetric functionalization on the 10–100 nm scale. However, the complex DNA sequence design needed for the synthesis of these versatile DNA-NPs has limited their widespread use to date. While the automated sequence design algorithms DAEDALUS and vHelix-BSCOR apply to DNA-NPs synthesized using either uniformly dual or hybrid single-dual duplex edges, respectively, these DNA-NPs are relatively compliant mechanically and are therefore of limited utility for some applications. Further, these algorithms are incapable of handling DNA-NP edge designs composed of more than two duplexes, which are needed to enhance DNA-NP mechanical stiffness. As an alternative, here we introduce the scaffolded DNA origami sequence design algorithm TALOS, which is a generalized procedure for the fully automated design of wireframe 3D polyhedra composed of edges of any cross section with an even number of duplexes, and apply it to DNA-NPs composed uniformly of single honeycomb edges. We also introduce a multiway vertex design that enables the fabrication of DNA-NPs with arbitrary edge lengths and vertex angles and apply it to synthesize a highly asymmetric origami object. Sequence designs are demonstrated to fold robustly into target DNA-NP shapes with high folding efficiency and structural fidelity that is verified using single particle cryo-electron microscopy and 3D reconstruction. Furthermore, in order to test its generality, we apply TALOS to design an in silico library of over 200 DNA-NPs of distinct symmetries and sizes, and for broad impact, we also provide the software as open source for the generation of custom NP designs.

3D cryo-EM reconstruction↗

DOE OSTI2022

Benchmarking second and third-generation sequencing platforms for microbial metagenomics

Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

SU-E-T-534: Level of Residual Radioactivity of Activated Parts of a Decommissioned Cyclotron

Purpose: CTI cyclotron RDS-111 was used at the Hong Kong Sanatorium and Hospital (HKSH) to produce radiopharmaceuticals and radioactive tracers for diagnostic scans between 1999 and 2007. During the operation, some machine components became radioactive by activation. For the safety of staff, decommissioning took place in 2009, two years after the cyclotron had stopped operation. This study investigates the residual radioactivity and radionuclides found in different cyclotron components in 2014 in compliance with the local regulations in Hong Kong for transfer of radioactive waste. Methods: A representative sample of each part was counted using a high-purity germanium detector (manufacturer: ORTECT) for at least four hours. GammaVision, a multichannel analyzer software, was used to identify the radionuclides found in the cyclotron components, as well as the associated activities. A standard library and a Mariscotti peak search algorithm were used to identify the present radionuclides. Only radionuclides with half-life greater than 180 days were considered. Results: Among the components, the Havar target foil has the highest specific activity ((4.6±0.6)×10{sup 2} Bq/g), with Co-60 being the most prominent ((3.8±0.5)×10{sup 2} Bq/g). The total activity of the target foil, however, is still low due to its small mass of 0.04 g. Radioisotopes Mn-54 (46±6 Bq/g), Na-22 (6.8±0.8 Bq/g), Co-57 (7.3±0.9 Bq/g), and Fe-59 (6.0±0.9 Bq/g) have also been detected in the target foil. The target window holder and the vacuum window register a specific activity of 88.3±0.6 Bq/g and 48.6±0.1 Bq/g, respectively. Other components, such as the collimator, the target tube, the valve body and the beamline, are also found with trace amounts of radionuclides. Conclusion: Even seven years after the cyclotron had stopped operation, some components still exhibited residual radioactivity from activation exceeding the IAEA clearance levels. Special consideration for radiological protection may need to be taken in the disposal of the cyclotron parts.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2017

Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

Knowledge about the role of genes under a particular growth condition is required for a holistic understanding of a bacterial cell and has implications for health, agriculture, and biotechnology. We developed the Tn-seq analysis software (TSAS) package to provide a flexible and statistically rigorous workflow for the high-throughput analysis of insertion mutant libraries, advanced the knowledge of gene essentiality in R. sphaeroides , and illustrated how Tn-seq data can be used to more accurately identify genes that play important roles in metabolism and other processes that are essential for cellular survival.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Modeling Enclosure Design in Above-Grade Walls

Building Science Corporation modeled typically well-performing wall assemblies using Wärme und Feuchte instationär (WUFI) Version 5.3 software and demonstrated that these models agree with historic experience when calibrated and modeled correctly. This technical report provides a library of WUFI modeling input data and results. Within the limits of existing experience, this information can be generalized for applications to a broad population of houses.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

Providing Experimental Infrastructure for Accelerating Advanced Reactor Demonstrations through the National Reactor Innovation Center

A suite of experimental infrastructure projects has been developed by the National Reactor Innovation Center to accelerate advanced reactor demonstrations and facilitate their development, addressing crucial gaps in data, materials characterization, and modeling. First, the Molten Salt Thermophysical Examination Capability (MSTEC) provides a specialized platform for post-irradiation characterization of molten salt reactor fuel, coolant salts, and structural materials, essential for supporting the design and operation of advanced reactors and future commercial molten salt reactor development and licensing. The Virtual Test Bed (VTB) complements these efforts by leveraging advanced modeling and simulation tools to evaluate reactor performance and safety. Serving as a library of reference models, the VTB offers a database of multiphysics reactor models, facilitating rapid safety evaluations and includes continuous software quality assurance, crucial for accelerating deployment while maintaining reliability. Additionally, the Helium Component Test Facility (HeCTF) addresses the need for high-temperature helium-cooled reactor component testing. As the first-of-its-kind facility in the United States, HeCTF emulates high-temperature gas reactor conditions, reducing time and cost associated with component validation, thereby accelerating reactor development. Finally, In-cell Thermal Creep Frames provide a unique solution for obtaining thermal creep data from irradiated materials, critical for materials qualification and licensing. Developed by the National Reactor Innovation Center, these compact frames enable the examination of previously irradiated materials, overcoming traditional limitations and enhancing the understanding of mechanical properties crucial for reactor development. Collectively, these experimental infrastructure projects form a comprehensive framework aimed at expediting advanced reactor demonstrations, fostering innovation, and ensuring the viability of next-generation nuclear energy solutions.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2017

Existing Fortran interfaces to Trilinos in preparation for exascale ForTrilinos development

This report summarizes the current state of Fortran interfaces to the Trilinos library within several key applications of the Exascale Computing Program (ECP), with the aim of informing developers about strategies to develop ForTrilinos, an exascale-ready, Fortran interface software package within Trilinos. The two software projects assessed within are the DOE Office of Science's Accelerated Climate Model for Energy (ACME) atmosphere component, CAM, and the DOE Office of Nuclear Energy's core-simulator portion of VERA, a nuclear reactor simulation code. Trilinos is an object-oriented, C++ based software project, and spans a collection of algorithms and other enabling technologies such as uncertainty quantification and mesh generation. To date, Trilinos has enabled these codes to achieve large-scale simulation results, however the simulation needs of CAM and VERA-CS will approach exascale over the next five years. A Fortran interface to Trilinos that enables efficient use of programming models and more advanced algorithms is necessary. Where appropriate, the needs of the CAM and VERA-CS software to achieve their simulation goals are called out specifically. With this report, a design document and execution plan for ForTrilinos development can proceed.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

PNNL OMICS

The PNNL Omics Library (PNNLOmics.dll) is a collection of data analysis, file I/O, and visualization routines used by several of the omics-related software developed at PNNL.

Degan, Michael↗

DOE OSTI2014

DLLExternalCode

DLLExternalCode is the a general dynamic-link library (DLL) interface for linking GoldSim (www.goldsim.com) with external codes. The overall concept is to use GoldSim as top level modeling software with interfaces to external codes for specific calculations. The DLLExternalCode DLL that performs the linking function is designed to take a list of code inputs from GoldSim, create an input file for the external application, run the external code, and return a list of outputs, read from files created by the external application, back to GoldSim. Instructions for creating the input file, running the external code, and reading the output are contained in an instructions file that is read and interpreted by the DLL.

Smith, Frank↗

DOE OSTI2022

Coupling Subsurface and Above-Surface Models for Optimizing the Design of Borefields and District Heating and Cooling Systems

Accurate dynamic energy simulation is important for the design and sizing of district heating and cooling systems with geothermal heat exchange for seasonal energy storage. Current modeling approaches in building and district energy simulation tools typically consider heat conduction through the ground between boreholes without flowing groundwater. While detailed simulation tools for subsurface heat and mass transfer exist, these fall short in simulating above-surface energy systems. To support the design and operation of such systems, the study developed a coupled model including a software package for building and district energy simulation, and software for detailed heat and mass transfer in the subsurface. For the first, it uses the open-source Modelica Buildings Library, which includes dynamic simulation models for building and district energy and control systems. For the heat and mass transfer in the soil, it uses the TOUGH simulator. The TOUGH family of codes can model heat and multi-phase, multi-component mass transport for a variety of fluid systems, as well as chemical reactions, in fractured porous media. The study validated the coupled modeling approach by comparing the simulation results with one from the g-function based ground response model. It then looked into effects when the water table and the regional groundwater flow are considered in the ground, from the perspective of heat exchange between borehole and ground, and the electrical consumption of the district heating and cooling systems. To access the simulation models, please find the links in the submission: -- For coupled approach validation: see model Buildings.Fluid.Geothermal.Borefields.Examples.BorefieldsWithTough and Buildings.Examples.DistrictReservoirNetworks.Examples.Reservoir3Variable_TOUGH from the "Modelica Building Library" resource, branch issue1495_tough_interface, commit a2667c0. -- For the study of the effect of water table: see model Buildings.Examples.DistrictReservoirNetworks.Examples.Reservoir3Variable_TOUGH from he "Modelica Building Library" resource, branch issue1495_tough_interface_moreIO, commit 760de49. -- For the study of the effect of regional groundwater flow: see Buildings.Examples.DistrictReservoirNetworks.Examples.Reservoir3Variable_TOUGH from he "Modelica Building Library" resource, branch issue1495_tough_interface_moreIO_3D, commit c2a2d2a. The coupling interface script "GrounResponse.py" can be found from the above links in the folder Buildings/Resources/Python-Sources. Also, the needed files for TOUGH simulation are in the folder Buildings/Resources/Python-Sources/ToughFiles that can be accessed through the above links. A brief description of these files is given below; detailed specifications for the first three files may be found in the TOUGH3 Users Guide (Jung et al., 2018) https://tough.lbl.gov/documentation/tough-manuals/. (1) INCON - initial conditions for each grid block (2) INFILE - main input file with material properties and control parameters (3) MESH - description of the computational grid (4) readsave - Modelica/TOUGH interface program: read the final output of TOUGH simulation after TOUGH time step and prepare for transfer to Modelica for next Modelica time step (5) readsave.inp - input parameters for program readsave (6) writeincon - Modelica/TOUGH interface program: write the output of Modelica after Modelica time step and prepare for transfer to TOUGH as initial conditions for the next TOUGH step (7) writeincon.inp - input parameters for program writeincon

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

NEML2: A High Performance Library for Constitutive Modeling

NEML2, the New Engineering Material model Library, version 2, is an offshoot of NEML, an earlier material modeling code developed at Argonne National Laboratory. NEML2 extends the key philosophy of its predecessor, i.e., material models are flexible, modular, and can be built from smaller blocks. It also provides modern features that do not exist in the framework of its predecessor such as material model vectorization, automatic differentiation, device-portable just-in-time compilation, operator fusion, lazy tensor evaluation, etc. Moreover, NEML2 can seamlessly integrate with the popular machine learning package PyTorch to take advantage of modern and fast-growing machine learning techniques. In this fiscal year, the development of core library features and capabilities are complete. The purpose of this report is not to serve as a verbatim copy of the software API reference (which is available online at https://reverendbedford.github.io/neml2/). Instead, this report documents the motivation, implementation, design choices, and usage of each core capability as well as their applications in solving practical engineering problems. This report is compiled based on the NEML2 major release 2.0.0.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Multispectral and thermal surface imagery and surface elevation mosaics - Pendleton Feb 2023

This data set contains high-resolution image products (orthomosaics) acquired from midsized uncrewed aerial systems that have been processed for value-added quality. The instrument Altum multispectral imager by Micasense, captures in six bands (blue - 475nm, green - 560nm, red - 668nm, red edge - 717nm, near-infrared - 840 and LWIR/thermal - 11000nm. The optical bands are converted to reflectance via custom code using the instantaneous band horizontal irradiance ratio to the radiance of the pixel. The code used to develop these images first uses tools from the Micasense Python library to apply dark level corrections, row gradient corrections, and radiometric corrections. Next, it uses the processing API from Agisoft Metashape software to align and mosaic the processed imagery, following the processes developed by the USGS' structure from motion workflow documentation. Captures from different altitudes are used to produce an orthomosaic at each height. A tif image containing information related to the six spectral bands, and a digital elevation model (DEM), a tif image containing information related to the elevation of the surveyed terrain. 1 https://www.arm.gov/publications/tech_reports/handbooks/doe-sc-arm-tr-281.pdf 2 https://micasense.github.io/imageprocessing/MicaSense%20Image%20Processing%20Setup.html 3 https://pubs.usgs.gov/of/2021/1039/ofr20211039.pdf

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

DCA_Tools

HPC software for ab-initio, condensed-matter physics, quantum mechanics calculations needs to be built on top of well tested libraries some of which address requirements unique to the programming domain. During the development of the DCA++ code, that we use in our research, we have developed a collection of libraries that may be of use to other computational scientists working in the same or similar domains. The libraries include: a) a pythonic input-language system, b) tensors whose shape is constructed from generalized dimension objects such at time domains. frequency domains, momentum domains, vertex domains et. al. and c) linear algebra operations that resolve to BLA/LAPACK operations when possible. This supports the implementation of Greens functions and operations on them such as are used in condensed matter physics.

Summers, Michael S↗

DOE OSTI2024

Virtual Test Bed (VTB): NRIC FY24 Program Review

NRIC: Deliver successful demonstration and deployment of advanced nuclear energy EBRII Test Bed (DOME) ZPPR Test Bed (LOTUS) Virtual Test Bed (VTB): Accelerate deployment of advanced reactors by leveraging state-of-the-art ModSim tools to evaluate performance and safety Ok, but what is it? Library of Reference Model: database of advanced multiphysics advanced reactor models that users can download, edit, and re-run Continuous Software QA: linking repository to software development to avoid legacy issues while enabling rapid code development Virtual models of the test bed: developing demonstration-relevant models (e.g., candidates for DOME/LOTUS) to accelerate safety evaluations

22 GENERAL STUDIES OF NUCLEAR REACTORS↗