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DOE OSTI2023

Domain Aware Deep-learning Algorithms Integrated with Scientific-computing Technologies (DADAIST)

This technical report summarized the contribution of the DADAIST project funded by the Data Model Convergence Initiative via the Laboratory Directed Research and Development (LDRD) investments at Pacific Northwest National Laboratory (PNNL). Specifically, we report the development of the NeuroMANCER (Neural Modules with Adaptive Nonlinear Constraints and Efficient Regularizations), a new open-source Scientific Machine Learning library for formulating and solving parametric constrained optimization problems, physics-informed system identification, and parametric optimal control problems. NeuroMANCER is using differentiable programming to combine modern data-driven models and optimization modeling language into a coherent algorithmic and software framework. NeuroMANCER is a Pytorch-based framework and adopts much of its philosophy focused on research and development, rapid prototyping, and streamlined deployment. Strong emphasis is given to extensibility, interoperability with the PyTorch ecosystem, and quick adaptability to custom domain problems. Neuromancer repository contains a comprehensive library of differentiable modules, including custom activation functions, matrix factorizations, deep learning architectures, neural differential equations, differential equation solvers, implicit layers such as iterative solvers, high-level API for symbolic expressions, API for modeling and control of dynamical systems, and extensive set of tutorial code examples in the form of python scripts and jupyter notebooks.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

EDRIXS: An open source toolkit for simulating spectra of resonant inelastic x-ray scattering

Resonant inelastic x-ray scattering (RIXS) has become a very powerful experimental technique to probe a broad range of intrinsic elementary excitations, for example, from low energy phonons and (bi-)magnons to high energy d-d, charge-transfer and plasmon excitations in strongly correlated electronic systems. Due to the complexity of the RIXS cross-section and strong core-hole effects, theoretical simulation of the experimental RIXS spectra is still a difficult task which hampers the understanding of RIXS spectra and the development of the RIXS technique. In this work, we present an open source toolkit (dubbed EDRIXS) to facilitate the simulations of RIXS spectra of strongly correlated materials based on exact diagonalization (ED) of certain model Hamiltonians. The model Hamiltonian can be from a single atom, small cluster or Anderson impurity model, with model parameters from density functional theory plus Wannier90 or dynamical mean-field theory calculations. The spectra of x-ray absorption spectroscopy (XAS) and RIXS are then calculated using Krylov subspace techniques. This toolkit contains highly efficient ED, XAS and RIXS solvers written in modern Fortran 90 language and a convenient Python library used to prepare inputs and set up calculations. We first give a short introduction to RIXS spectroscopy, and then we discuss the implementation details of this toolkit. Lastly, we show three examples to demonstrate its usage.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Benchmark Tracking System for Performance Monitoring

Benchmarking is essential for high-performance software development, particularly for monitoring performance across code iterations. This project focused on enhancing the benchmarking process for Lamellar, an asynchronous runtime for High-Performance Computing (HPC) systems developed at Pacific Northwest National Laboratory. Prior to this work, benchmark results were difficult to track and compare across code versions, presenting significant challenges in identifying performance regressions and long-term trends. The primary objective was to establish a systematic, reproducible approach for measuring performance and detecting regressions following code commits. Our methodology involved three key components: standardizing benchmark outputs, implementing data versioning, and developing analysis tools. We standardized the benchmark output format to JSON Line records containing specific fields (execution time, hardware specifications, and environmental variables). To address data management challenges, we evaluated several options and eventually chose a git repository dedicated to benchmark data. We developed a suite of Python tools that processed benchmark results, enriched them with metadata, and facilitated search in the repository. The resulting system enables more efficient filtering and comparison of performance metrics across commit histories, hardware configurations, and benchmark variants through a unified query interface. Our implementation reduces computational overhead by first checking for existing results through configuration matching before initiating new benchmark runs, thereby conserving resources. The system has been validated by Lamellar developers. It organizes results by benchmark type and build configurations for efficient retrieval. Future developments include a planned Large Language Model interface for predicting benchmark performance, incorporating the criterion package for statistical analysis, which will enable automated detection of statistically significant performance changes, and integration with continuous integration pipelines. Despite these enhancements being reserved for future work, this project has successfully provided the Lamellar development team with a framework for maintaining consistent performance standards and identifying optimization opportunities across workloads and hardware environments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Lowest-dimensional portals to SU( N ) exotics

New matter fields charged under the strong nuclear force would have dramatic phenomenological implications. In this work, we systematically explore how these new states, which we postulate belong to some representation of SU(3) of quantum chromo-dynamics, could interact with standard model fields: We analyze all lowest-dimensional “portal” operators for any SU(3) representation, and motivated by grand unification, we extend our results to SU( N ) for N > 3. We provide a publicly available python code, “tessellation,” that automatically constructs said lowest-dimensional portal operators for any new exotic matter field charged under SU( N ) for any N .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Choppy Lite

The existing methodologies for gathering and computing zonal statistics from the combination of a raster image and a shapefile either require advanced programming knowledge in at least one language or the use of proprietary software such as ArcGIS. The software “Choppy Lite” offers several solutions for acquiring zonal statistics that can be used without proprietary software or programming knowledge. This software provides a Docker-based ecosystem, allowing users of any experience level to simply run a single line command in a terminal prompt independent of the operating system. Intermediate to advanced users can import the class provided by the software package into their own Python scripts.

Grant, JoshuaN.↗

DOE OSTI2022

High Performance Computing Innovation Center Open Source Developer Tools

The High Performance Computing Innovation Center (HPCIC) aims to ease the transition for developers to use open source software provided by the lab. HPCIC Developer Tools is a collection of software, containers, cloud configurations, and associated documentation that make it easy to deploy tutorials or small apps to demonstrate lab-developed software. For example, building a tutorial container that includes lab software and interactive interfaces; a command line or web-based tool that accepts user preferences for the tutorial; supporting tools and software development kits (SDKs) for developer interactions or productivity in different languages embraced by the larger developer community such as Go, Rust, and Python; and automation in version control to support continued update of software and associated resources. These tools are best developed in an open source environment such as GitHub, not only to champion the lab's open source software, but for purposes of branding and demonstrating the lab's leadership in open source. Such an effort that brings in more developers to use and contribute to lab software can further improve the quality of the software, and developer experience at the lab.

Beckingsale, DavidA↗

DOE OSTI2021

Rattlesnake User's Manual

Rattlesnake is a combined-environments, multiple input/multiple output control system for dynamic excitation of structures under test. It provides capabilities to control multiple responses on the part using multiple exciters using various control strategies. Rattlesnake is written in the Python programming language to facilitate multiple input/multiple output vibration research by allowing users to prescribe custom control laws to the controller. Rattlesnake can target multiple hardware devices, or even perform synthetic control to simulate a test virtually. Rattlesnake has been used to execute control problems with up to 200 response channels and 12 drives. This document describes the functionality, architecture, and usage of the Rattlesnake controller to perform combined environments testing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

MontePy: a Python library for reading, editing, and writing MCNP input files.

The Monte Carlo N-Particle (MCNP) radiation transport code is a highly capable and accurate code with a long legacy. MCNP uses the Monte Carlo simulation process to simulate the path of particles (e.g., neutrons, photons, charged particles, etc.), and their interaction with materials. It is widely used in nuclear engineering, high-energy physics, and other fields. Its origins in the mid-twentieth century predate many modern software conventions. MCNP users provide an input file to MCNP, which it then uses to create an internal representation of the simulation problem. These input files originally had to be stored as punchcard decks, and the user manual still uses the terminology of cards and decks, despite moving beyond punchcards. MCNP predates nearly all modern human readable markup or data serialization languages, such as the extensible Markup Language (XML), the Standard Generalized Markup Language (SGML), YAML (YAML Ain’t Markup Language), and Javascript Object Notation (JSON). Due to this, MCNP uses an entirely custom defined syntax language for its input, making off-the-shelf libraries for XML, YAML, and JSON impossible to use for scripting various operations on MCNP input files (Kulesza et al., 2022).

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Rattlesnake User's Manual (V.3)

Rattlesnake is a combined-environments, multiple input/multiple output control system for dynamic excitation of structures under test. It provides capabilities to control multiple responses on the part using multiple exciters using various control strategies. Rattlesnake is written in the Python programming language to facilitate multiple input/multiple output vibration research by allowing users to prescribe custom control laws to the controller. Rattlesnake can target multiple hardware devices, or even perform synthetic control to simulate a test virtually. Rattlesnake has been used to execute control problems with up to 200 response channels and 24 shaker drives. This document describes the functionality, architecture, and usage of the Rattlesnake controller to perform combined environments testing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Automatic Differentiation for Adjoint Stencil Loops

Stencil loops are a common motif in computations including convolutional neural networks, structured-mesh solvers for partial differential equations, and image processing. Stencil loops are easy to parallelise, and their fast execution is aided by compilers, libraries, and domain-specific languages. Reverse-mode automatic differentiation, also known as algorithmic differentiation, autodiff, adjoint differentiation, or back-propagation, is sometimes used to obtain gradients of programs that contain stencil loops. Unfortunately, conventional automatic differentiation results in a memory access pattern that is not stencil-like and not easily parallelisable. In this paper we present a novel combination of automatic differentiation and loop transformations that preserves the structure and memory access pattern of stencil loops, while computing fully consistent derivatives. The generated loops can be parallelised and optimised for performance in the same way and using the same tools as the original computation. We have implemented this new technique in the Python tool PerforAD, which we release with this paper along with test cases derived from seismic imaging and computational fluid dynamics applications.

Automatic Differentiation↗

DOE OSTI2020

CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms

Background: Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiotics. The explosive growth of genome sequencing brings a new set of challenges and issues for researchers, such as a systematic investigation of CYPs across all kingdoms in terms of identification, classification, and pan-CYPome analyses. Such investigation requires an automated tool that can handle an enormous amount of sequencing data in a timely manner. Results: CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data. The performance of CYPminer was evaluated with three datasets from fungal and bacterial genome sequences. Conclusions: CYPminer completes CYP analyses for large-scale genomes from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs. CYPminer also can be extended and adapted easily for broader usage.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Data From: "Warming and snow loss increase reliance on old groundwater in a Colorado River headwater"

This repository contains the data and code associated with the paper titled "Warming and snow loss increase reliance on old groundwater in a Colorado River headwater," published in Nature Geoscience, 2026. This study seeks to answer how various ages of groundwater interact with mountainous streamflow in mountainous headwaters such as the East River. It includes various model-data processing scripts, primarily for ParFlow-CLM analysis of simulated water years 2015-2021, and two numerical warming experiments (+2.5 and +4.0 degrees C), including run scripts, forcing scripts, and post-processing, as well as comparison to observation datasets, detailed below. This data requires the use of R (.r, .rmd), Python (.py), Jupyter Notebook or Jupyter Lab (.ipynb), ParFLOW-CLM, EcoSLIM. Further information on the use of all file formats mentioned below (e.g. .tff. .nc) are provided within the associated scripts and directory where the files are located. Contents & Usage ASO/: Contains the bash and python scripts used to convert airborne snow observatory (ASO) data (ASO, 2023) in various data formats (georeferenced tiff file, NetCDF, UTM, and to latitude/longitude) then regrided to the ParFlow equivalent grid. Output data are in regrid_regll_data.zip and subsequently visualized and analyzed in plot_and_compare.py for Supplementary Figures A14 and A15. The wksht_ASO_comparison.xlsx spreadsheet is used to calculate the data for Supplementary Figure A16. EcoSLIM/: Contains the scripts and input files to run the EcoSLIM particle tracking simulations (/run_scripts) and the post-processing python script (/plot_scripts/eco_agedist_plots.ipynb). Jasechko et al./: Contains the jupyter notebook (Extract_Elevation.ipynb) to determine the outlet elevations of the 260 watersheds used in Jasechko et al. (2016), and the corresponding table, Table_S1_Watersheds_alt.csv. Used to create Supplementary Information Figure A2. PLM_Wells/: Contains the QA/QC-ed groundwater level time series of the PLM-1 and PLM-6 Monitoring Wells from Faybishenko et al. (2023), reformatted to water years used for Supplementary Figures A19 and and A20. ParFlow/: Contains the input files and run scripts to run ParFlow-CLM (/run_scripts), the python and tool command language (Tcl) scripts to create and distribute the ParFlow forcing simulation files (/forcing), and various scripts and intermediary files to analyze the model outputs (/post_process). SQUIRE/: Contains the processing scripts and intermediary files for the Surface QUantitatIve pRecipitation Estimation (SQUIRE) data (Grover, 2023) used to generate Supplementary Figure A18. USGS_Streamflow/: Contains the raw and gap-filled United States Geological Survey streamflow data (U.S. Geological Survey, 2026) used at the Almont station (site number 09112500). Gap-filling is performed in the R script with data from the Taylor station (site number 09110000). (/USGS_09112500_EAST_RIVER_AT_ALMONT_GAP_FILLED/code_almont_streamflow_gap_fill.Rmd). discharge/: Contains the gap-filled discharge data at the Watershed Function SFA East River pumphouse site (Newcomer et al., 2022) used to generate Supplementary Figure A13 and to compute hourly Nash-Sutcliffe model efficiency coefficients (NSE) in Table A4. snotel_and_flux_tower/: Contains the snow telemetry data (U.S. Department of Agriculture, 2024) from the Butte (site ID 380) and Schofield (site ID 737) stations, reformatted by water year, accessed with the snotelr R package. Used to create Supplementary Figure A17. Also contains the flux tower observational data (FluxTower_Pumphouse_ESS-DIVE.ET_only.h.txt) from Ryken et al. (2022) and sap flux transpiration data (MaxB_Transpiration_5Sites.daily_sums.h.txt) from Ryken (2021), used to create Supplementary Figures A22 and A23, respectively. Raw EcoSLIM model outputs are in excess of 24TB, and are stored on National Energy Research Scientific Computing Center (NERSC) and publicly available via the external link provided in the paper.

atmospheric warming↗

DOE OSTI2022

Demonstrating solarpilot ’s Python Application Programmable Interface Through Heliostat Optimal Aimpoint Strategy Use Case

solarpilot is a software package that generates solar field layouts and characterizes the optical performance of concentrating solar power (CSP) tower systems. solarpilot was developed by the National Renewable Energy Laboratory (NREL) as a stand-alone desktop application but has also been incorporated into NREL’s System Advisor Model (SAM) in a simplified format. Prior means for user interaction with solarpilot have included the application’s graphical interface, the SAM routines with limited configurability, and through a built-in scripting language called “LK.” This article presents a new, full-featured, python-based application programmable interface (API) for solarpilot, which we hereafter refer to as CoPylot. CoPylot enables python users to perform detailed CSP tower analysis utilizing either the Hermite expansion technique (analytical) or the SolTrace ray-tracing engine. CoPylot’s enables CSP researchers to perform analysis that was previously not possible through solarpilot’s existing interfaces. This article discusses the capabilities of CoPylot and presents a use case wherein we populate a model that obtains optimal solar field aiming strategies.

14 SOLAR ENERGY↗

DOE OSTI2023

Optimization to Generate Equations of State for Hydrogen Production

On a high level, the larger project in question, HydroGEN, aims to develop software used for finding equations of state (EOS) to optimize catalyst configuration for H 2 production through water splitting. In particular, this summer project focused on solving the nonlinear equations used in fitting the equations. This problem involved using Python to solve a linear system with nonlinear constraints. In order for this to be achieved, Pyomo was used to build a model and the solver Ipopt, interior point optimizer, was used. Pyomo is a Python-based language developed at Sandia; it is an optimization modeling language. Rather than solving the entire problem at once, a toy problem was created, simplifying the problem down to the most important focus. This problem had a known solution, comparable to the calculated solution to assess accuracy and as progress was made towards finding solutions, complexity was gradually added to the problem. After building and solving the toy problem, it was found that it gave reasonably accurate solutions, better compared to the two existing solvers previously used with this project in terms of functionality. The solver is now ready for implementation into the project’s main software.

08 HYDROGEN↗

DOE OSTI2020

Language Independent Static Analysis (LISA)

Software is becoming increasingly important in nearly every aspect of global society and therefore in nearly every aspect of national security as well. While there have been major advancements in recent years in formally proving properties of program source code during development, such approaches are still in the minority among development teams, and the vast majority of code in this software explosion is produced without such properties. In these cases, the source code must be analyzed in order to establish whether the properties of interest hold. Because of the volume of software being produced, automated approaches to software analysis are necessary to meet the need. However, this software boom is not occurring in just one language. There are a wide range of languages of interest in national security spaces, including well-known languages such as C, C++, Python, Java, Javascript, and many more. But recent years have produced a wide range of new languages, including Nim, (2008), Go (2009), Rust (2010), Dart (2011), Kotlin (2011), Elixir (2011), Red (2011), Julia (2012), Typescript (2012), Swift (2014), Hack (2014), Crystal (2014), Ballerina (2017) and more. Historically, automated software analyses are implemented as tools that intermingle both the analysis question at hand with target language dependencies throughout their code, making re-use of components for different analysis questions or different target languages impractical. This project seeks to explore how mission-relevant, static software analyses can be designed and constructed in a language-independent fashion, dramatically increasing the reusability of software analysis investments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

System Advisor Model (SAM) General Description (Version 2017.9.5)

This document describes the capabilities of the System Advisor Model (SAM) developed and distributed by the U.S. Department of Energy's National Renewable Energy Laboratory. The document is for potential users and others wanting to learn about the model's capabilities. SAM is a techno-economic computer model that calculates performance and financial metrics of renewable energy projects. Project developers, policy makers, equipment manufacturers, and researchers use graphs and tables of SAM results in the process of evaluating financial, technology, and incentive options for renewable energy projects. SAM simulates the performance of photovoltaic, concentrating solar power, solar water heating, wind, geothermal, biomass, and conventional power systems. The financial models are for projects that either buy and sell electricity at retail rates (residential and commercial) or sell electricity at a price determined in a power purchase agreement (PPA). SAM's simulation tools facilitate parametric and sensitivity analyses, Monte Carlo simulation and weather variability (P50/P90) studies. SAM can also read input variables from Microsoft Excel worksheets. For software developers, the SAM software development kit (SDK) makes it possible to use SAM simulation modules in their applications written in C/C plus plus, C sharp, Java, Python, MATLAB, and other languages. NREL provides both SAM and the SDK as free downloads at https://sam.nrel.gov. SAM is an open source project, so its source code is available to the public. Researchers can study the code to understand the model algorithms, and software programmers can contribute their own models and enhancements to the project. Technical support and more information about the software are available on the website.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

Advanced Energy System Design (AESD): Technical Manual for the Records API

The Records API (application program interface) for Advanced Energy System Design (AESD) enables software that serves multidimensional record-oriented data to interoperate with software than uses such data. In the context of the Records API, multidimensional data records are simply tuples of real numbers, integers, and character strings, where each data value is tagged by a variable name, according to a pre-defined schema, and each record is assigned a unique integer identifier. Conceptually, these records are isomorphic to rows in a relational database, JSON objects, or key-value maps. Records servers might supply static datasets, sensor measurements that periodically update as new telemetry become available, or the results of simulations as the simulations generate new output. Records client software might display or analyze the data, but in the case of simulations the client request the creation of new ensembles for specified input parameters. It is also possible to chain records clients and servers together so that a client consuming data from a server might transform that data and serve it to further clients. This minimalist API avoids imposing burdensome metadata, structural, or implementation requirements on developers by relying on open-source technologies that is readily available for common programming languages. In particular, the API has been designed to place the smallest possible burden on services that provide data. This document defines the message format for the Records API, a transport mechanism for communicating the data, and semantics for interpreting it. The message format is specified as Google Protocol Buffers and the transport mechanism uses WebSockets. We discuss three major use cases for serving and consuming records data: (i) static data, (ii) dynamically augmented data, (iii) on-demand simulations, (iv) with filters, and (v) with bookmarks. Separate implementations of the API exist in C++, Haskell, JavaScript, Python, and R.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

MCNP AND CFD MODELING OF A SODIUM FAST REACTOR SUB-ASSEMBLY CHANNEL TO CAPTURE LOCALIZED TEMPERATURE PEAKING

Typical evaluation tools for sodium-cooled fast reactors (SFR) use simplified neutronic/thermal models to efficiently compute the power and temperature distributions within the core. However, their modeling capability can be limited in extreme cases such as when sharp inter-assembly power gradients occur, or for non-standard SFR assembly geometries. Higher fidelity tools that rely on Monte Carlo methods for neutron transport, and Computational Fluid Dynamics (CFD) for thermal analysis, are better suited in these instances. The higher accuracy comes at the cost of higher computational expense. MCNP and STAR CCM+ were selected for this analysis. While MCNP is capable of generating pin-level power distributions for a whole-core SFR model, it is prohibitively expensive to then conduct CFD analysis for every single assembly. A semi-empirical model was therefore developed to rapidly estimate pin temperature distributions throughout the whole core. It relies on a geometric correction factor for turbulent flow-mixing. The correction factor is obtained from a CFD simulation of a single fuel assembly with a uniform power distribution and an adiabatic boundary condition. Without using CFD, each sub-channel outlet temperature is calculated separately using 1-D heat-balance and Nusselt number correlations and the MCNP calculated pin-powers. The rudimentary 1-D model is then corrected for the flow-mixing effect based on the CFD data. The temperature calculation is performed by a code written in the Python language called CFD Monte-Carlo Developed Reconstruction of Sub-channel at a Quasi-Representative Level (CMDR-SQRL). CMDR-SQRL was shown to adequately predict CFD evaluated temperature distribution for a wide range of SFR configurations, including an extreme case with fuel assemblies nearby containing moderating material. The agreement demonstrates how geometric and power-driven effects can be decoupled within an SFR assembly. CMDR-SQRL is intended to be mainly used for scoping studies to provide core-wide evaluations efficiently.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗