FASTER TENSOR KERNELS VIA RUST-FROM-PYTHON IMPLEMENTATION
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Harding, Kimberly Ann [Sandia National Laboratorie↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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pvplr-python: Python package implementation of PVplr for Performance Loss Rate (PLR) analysis
Due to software fragmentation, PV system modeling teams can be limited to language specific packages, preventing cross-sectional analysis of different modeling techniques and workflows. To this end, PVplr, a popular PV performance modeling R software package, has been ported to the Python programming language. To verify and test the robustness of the port, NSRDB data has been used to simulated PV installations at native resolution (~2 million Sites), with a variety of degradation rates, degradation patterns, and modules. Performance Ratios were calculated using the ported functions from pvplr-python and compared against Rdtools YoY values. Due to the complicated nature of degradation, a new metric has been proposed to quantify the performance loss of a system. The cumulative production loss, is the total amount of energy lost due to the degrading performance of the system. Cumulative production loss alleviates the problems with fitting linear functions to non-linear degradation. Cumulative Production loss was shown to better estimate the total lost revenue for non-linear degradation patterns. $XbX + UTC$ was found to most accurately predict the total lost revenue in simulated systems.
Kumar, Suraj↗
pyEGAF: Modernization of the EGAF database
One of the most comprehensive resources for thermal neutron-capture data is the Evaluated Gamma-ray Activation File (EGAF), containing data from prompt gamma activation analysis measurements carried out at the Budapest Research Reactor for 245 isotopes. Although these valuable datasets have been freely available for many years, the outdated and cryptic adopted format makes it difficult to utilize the data and it is not generally suitable for modern computational technologies. Furthermore, to help overcome these challenges, we have converted the datasets into an open standard JSON format. Additionally, we have developed a Python implementation of an open-source software package, pyEGAF, designed to interact with the JSON data structures for general purpose access, manipulation, and rapid assessment of the capture-gamma data in EGAF.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Efficient Scalable Contact Network Generation from Population Data
Modeling the contacts among a population is critical to understanding the dynamics of a disease outbreak. Contact networks, where nodes are individuals and edges are contacts among them, are used to represent these complex individual-level interactions. In this work, we are given the daily activity schedules of an urban population that represent the activity location and time of individuals in a population during a single twenty four hour period over multiple days. Using collocation to determine contact between individuals, our goal is to extract hourly contact networks from large-scale activity data. We improve upon the existing adjacency matrix-based method by implementing our custom sparse matrix multiplication algorithm. Starting with a Python implementation, we achieve a 1600x speed up in the computation with a fast custom designed sparse matrix multiplier algorithm implemented in the C++ language. This work is central to future parallel designs of the problem.
97 MATHEMATICS AND COMPUTING↗
PALS Python v0.1.0
This is a Python implementation for the Particle Accelerator Lattice Standard (PALS). To define the PALS schema, Pydantic is used to map to Python objects, perform automatic validation, and serialize/deserialize data classes to/from many modern file formats. Various modern file formats (e.g., YAML, JSON, TOML, XML, etc.) are supported, which makes the implementation of the schema-following files in any modern programming language easy (e.g., Python, Julia, C++, LUA, Javascript, etc.). Here, we do Python.
Huebl, Axel [Lawrence Berkeley National Laboratory↗
Black Box Equations of State: Creating Semi-analytic Solutions to the Noh Problem and Verifying Equation of State Interfaces
The objective of this report is threefold. First, it details a method for deriving a semi-analytic solution to the Noh Problem when using a “black-box” equation of state. Such capability allows us to perform verification on complicated, more realistic equations of state. Examples include Steinberg equations of state for materials and tabulated equations of state. The second objective is to apply the methodology to verify the singularity-eos equation of state library. We do so by solving the Rankine-Hugoinot jump conditions for the Noh Problem, ensuring singularity derives the correct solution and comparing the error to an exact implementation of the equation of state. The third objective is to perform verification of the xRAGE Eulerian hydrodynamics code when interfaced with singularity. We provide the theory, analysis, documentation for a python implementation of the proposed solver, and verification results.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
PySAGES: flexible, advanced sampling methods accelerated with GPUs
Abstract Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes. In this sense, software that can be seamlessly adapted to a broad range of complex systems is essential. Building on past efforts to provide open-source community-supported software for advanced sampling, we introduce PySAGES, a Python implementation of the Software Suite for Advanced General Ensemble Simulations (SSAGES) that provides full GPU support for massively parallel applications of enhanced sampling methods such as adaptive biasing forces, harmonic bias, or forward flux sampling in the context of molecular dynamics simulations. By providing an intuitive interface that facilitates the management of a system’s configuration, the inclusion of new collective variables, and the implementation of sophisticated free energy-based sampling methods, the PySAGES library serves as a general platform for the development and implementation of emerging simulation techniques. The capabilities, core features, and computational performance of this tool are demonstrated with clear and concise examples pertaining to different classes of molecular systems. We anticipate that PySAGES will provide the scientific community with a robust and easily accessible platform to accelerate simulations, improve sampling, and enable facile estimation of free energies for a wide range of materials and processes.
Chemistry↗
Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits
Abstract The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein–protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.
Genetics & Heredity↗
nautilus : boosting Bayesian importance nested sampling with deep learning
ABSTRACT We introduce a novel approach to boost the efficiency of the importance nested sampling (INS) technique for Bayesian posterior and evidence estimation using deep learning. Unlike rejection-based sampling methods such as vanilla nested sampling (NS) or Markov chain Monte Carlo (MCMC) algorithms, importance sampling techniques can use all likelihood evaluations for posterior and evidence estimation. However, for efficient importance sampling, one needs proposal distributions that closely mimic the posterior distributions. We show how to combine INS with deep learning via neural network regression to accomplish this task. We also introduce nautilus, a reference open-source python implementation of this technique for Bayesian posterior and evidence estimation. We compare nautilus against popular NS and MCMC packages, including emcee, dynesty, ultranest, and pocomc, on a variety of challenging synthetic problems and real-world applications in exoplanet detection, galaxy SED fitting and cosmology. In all applications, the sampling efficiency of nautilus is substantially higher than that of all other samplers, often by more than an order of magnitude. Simultaneously, nautilus delivers highly accurate results and needs fewer likelihood evaluations than all other samplers tested. We also show that nautilus has good scaling with the dimensionality of the likelihood and is easily parallelizable to many CPUs.
97 MATHEMATICS AND COMPUTING↗
Virtual Trajectories for I–24 MOTION: Data and Tools
This paper introduces a toolbox for generating virtual trajectories, which we call VT-tools v1.0, to address challenges in analyzing large but imperfect trajectory datasets. VT-tools v1.0 is able to generate virtual trajectories from large raw datasets that are typically challenging to process due to their size. We also provide a set of these virtual trajectories resulting from I–24 MOTION INCEPTION v1.0 data and demonstrate the practical utility of these trajectories in as-sessing speed variability and travel times across different lanes within the INCEPTION dataset. The virtual trajectory toolbox opens future research on traffic waves and their impact on energy. The VT-tools v1.0 Python implementation and sample data are publicly available at https://i24motion.org.
42 ENGINEERING↗
TICC Clustering Library v.1.0
SAND2024-01234O TICC is a clustering algorithm that labels a sequence of data points according to numerical properties. This library is a Python implementation of the algorithm described in "Toeplitz Inverse Covariance-Based Clustering of Multivariate Time Series Data" (Hallac et al. 2017). It includes documentation, performance improvements, examples, and test coverage. This library allows users to automatically segment a series of multivariate data points according to their covariance—that is, the way the values at each data point are changing in relation to one another. This is useful for identifying periods in which a system is behaving. For example, if a sensor is measuring a car's velocity, steering wheel angle, braking and acceleration, TICC can determine when the car was stopped, beginning/exiting a turn, slowing or accelerating at an intersection, or driving on straight or curved roads. TICC can be applied to measure multiple quantities at known times. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525
Dalbey, Keith↗
HPB_strengthmodel
Python-implementation of the Hunter-Preston strength model, but with generalized drag coefficient B. For details, see D. N. Blaschke, A. Hunter, and D. L. Preston, Int. J. Plast. 131 (2020) 102750. This code was used to generate most of the figures in this paper.
Blaschke, Daniel N.↗
qsp4pde v1.0
The software program is a collection of Python implementations of quantum circuits for solving linear partial differential equations using quantum signal processing. The circuits are implemented using the qiskit SDK.
Kim, Hyeongjin [Lawrence Berkeley National Laborat↗
pyFLANK, a graph neural network based null distribution inference model for F ST outlier detection
Detecting genomic regions under selection is essential for understanding how populations adapt to different environments, yet it remains challenging due to the confounding effects of demographic history and linkage disequilibrium (LD). Fixation index (F ST ) is a widely used statistic to identify genomic regions under adaptation. However, identifying genes under selection by defining F ST outliers often remains challenging, owing to confounding effects of underlying demographic history. Traditional methods assume independence among loci and rely on simple demographic models, while newer models perform much better but are computationally expensive and not easily scalable. Here, we present pyFLANK, an open-source and automated Python implementation which detects F ST outliers using a null distribution inferred from quasi-independent loci. Our tool integrates three approaches to identify loci obeying a null distribution: graph neural network (GNN) inference, linkage disequilibrium (LD)-based inference, and user-defined input. Because pyFLANK uses GNN-based inference of quasi-independent loci, it yields a more accurate null model with less need for user parameter input. In simulation experiments, pyFLANK achieved lower false positive rates than current methods while maintaining comparable detection power, indicating that its refined null model better distinguishes true adaptive loci from background variation. The GNN-based model, in particular, detected additional loci associated with phenotypic variance that were not identified by existing methods. Assessments of simulation and real data from different species demonstrate that pyFLANK achieves lower false positive rates compared with other commonly used F ST outlier detectors, while maintaining comparable detection power and excellent computational performance, providing a robust and user-friendly tool for identifying loci under divergent selection. It extends existing F ST outlier frameworks by incorporating explicit LD-aware strategies for null model calibration. The method is intended as a practical and scalable complement to existing genome scan approaches.
FST↗
Peregrine Software Development: Report on the Code Conversion From Python to C++
This work package seeks to convert the Peregrine software tool from its original Python implementation to a production version based on the C++ language. Peregrine is a powerful research platform with a multitude of advanced data analytics and data visualization functionalities. Developed by scientists to explore multimodal and multidimensional data related to the production of components using powder bed additive manufacturing processes, the tool implements state-of-the-art algorithms to assist machine users in making build or part quality determinations. Given that Peregrine is data-intensive, the goal of this conversion is to enhance the tool’s flexibility and interactivity and reduce the number of code dependencies to facilitate its deployment as part of the ongoing technology transfer campaign. This brief document provides an overview of Peregrine’s functionalities and capabilities, along with a detailed description of the core functionalities that have been implemented to date in the new C++ version. This document serves as a development update at the end of the first year of the ongoing conversion and will be regularly updated as progress continues.
97 MATHEMATICS AND COMPUTING↗
The Impact of Void-finding Algorithms on Galaxy Classification
We explore how the definition of a void influences the conclusions drawn about the impact of the void environment on galactic properties using two void-finding algorithms in the Void Analysis Software Toolkit: Voronoi Voids (V 2 ), a Python implementation of ZOnes Bordering On Voidness (ZOBOV); and VoidFinder, an algorithm that grows and merges spherical void regions. Using the Sloan Digital Sky Survey Data Release 7, we find that galaxies found in VoidFinder voids tend to be bluer and fainter and to have higher (specific) star formation rates than galaxies in denser regions. Conversely, galaxies found in V 2 voids show less significant differences when compared to galaxies in denser regions, less consistent with the large-scale environmental effects on galaxy properties expected from both simulations and previous observations. These results align with previous simulation results that show V 2 -identified voids “leak” into the dense walls between voids because their boundaries extend up to the density maxima in the walls. As a result, when using ZOBOV-based void-finders, galaxies likely to be part of wall regions are instead classified as void galaxies, a misclassification that can be critical to our understanding of galaxy evolution.
cosmic web↗
Well-balanced Hydrodynamics for the Piecewise Parabolic Method with Characteristic Tracing
Well-balanced reconstruction techniques have been developed for stellar hydrodynamics to address the challenges of maintaining hydrostatic equilibrium during evolution. I show how to adapt a simple well-balanced method to the piecewise parabolic method for hydrodynamics. A python implementation of the method is provided.
hydrodynamics↗
The Transactive Energy Network Template Metamodel
While transactive energy, which is defined as an allocation of electricity based on dynamically discovered values or prices, has been extensively studied, its uptake and use has been slow. This report describes a tool, the transactive network template, which should hasten the creation and uptake of transactive energy networks. Some basic principles of transactive energy are familiar from existing wholesale electricity markets. Locational prices are calculated today for zones within bulk electric transmission systems. Locational prices differ while accounting for the locational costs of electricity generation and the losses and constraints incurred when electricity is transmitted from generators and distributed to consumers. A transactive energy network might include these transmission zones. However, current research strives to apply transactive energy also in electricity distribution circuits, buildings, and even for individual generating and consuming devices. At the same time, researchers explore how to apply transactive energy in real time during increasingly shorter time intervals. Automated computational agents become necessary as transactive energy becomes applied to smaller circuit zones and at faster dynamic timescales. A transactive energy network is an example of a multi-agent system. Each zone in the network is represented by its transactive agent, which makes decisions for and acts on behalf of a business entity that is responsible for and manages one of the circuit regions. A transactive energy network is also an example of a decentralized, distributed control system. Control decisions and responsibilities are distributed among the network’s transactive agents. The transactive agents are independent; that is, there typically is no centralized authority or oversight function. Instead, transactive agents exchange transactive signals and thereby negotiate the prices and quantities of electricity that they will exchange. Initially, the circuit regions and responsibilities of transactive agents appear to be very dissimilar. Each circuit region may comprise transmission, distribution, or building-level circuits. Each has a unique position and electrical connectivity within the transactive energy network. Each possesses unique assets that either generate or consume electricity, and these (e.g., renewable energy generator, diesel generator, aggregate utility load, building load, space conditioning, refrigerator, etc.) may further differ in their price flexibility and in their strategies for responding to dynamic electricity prices. Given such diversity, an implementer’s first inclination might be to start from scratch to define all these devices and to engineer their seemingly unique interactions. Given that each implementer’s perspective may be narrow within a transactive energy network, it is unlikely that uniquely engineered systems would interact well. This is where the transactive network template is applicable. The transactive network template is a metamodel that has been developed to guide implementers as they configure their own transactive agent within a network of such agents. The object-oriented design of the transactive network template provides basic code object types that may be used and extended by implementers to represent each of the assets in their circuit region. These objects further facilitate the transactive agent’s necessary computations, which are divided among responsibilities to schedule power usage, balance electric supply and demand, and coordinate the exchange of electricity with the other transactive agents. This report addresses the conceptual transactive network template design. Implementers are directed to more formal design documents and reference implementations. A Python™-based1 reference implementation of the transactive network template has been coded, and three implementations have been configured to represent a national laboratory and two university campuses. Version 2 of the transactive node template generalizes the market class and its methods to facilitate multiple, and more diverse market coordination mechanisms than were facilitated by and demonstrated using Version 1. Version 3 includes new Appendix B, which addresses the designs of methods that would make dynamic prices track approved electricity rates. In the future, the author wishes to make the transactive network template more generally applicable to networks that require more accurate power flow. Development of the transactive network template is jointly funded by the U.S. Department of Energy (DOE) Energy Efficiency and Renewable Energy and the DOE Office of Electricity. In late 2015, one of the first projects to be funded by the DOE Grid Laboratory Modernization Laboratory Consortium was the Clean Energy and Transactive Campus project, led by Pacific Northwest National Laboratory. DOE funds were matched by an investment by the Washington Department of Commerce through its Clean Energy Fund. The transactive network template was developed to guide the implementation of transactive energy networks within this project’s scope.
24 POWER TRANSMISSION AND DISTRIBUTION↗