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At least 73 records · Page 4

Evolution of the ROOT Tree I/O

The ROOT TTree data format encodes hundreds of petabytes of High Energy and Nuclear Physics events. Its columnar layout drives rapid analyses, as only those parts (“branches”) that are really used in a given analysis need to be read from storage. Its unique feature is the seamless C++ integration, which allows users to directly store their event classes without explicitly defining data schemas. In this contribution, we present the status and plans of the future ROOT 7 event I/O. Along with the ROOT 7 interface modernization, we aim for robust, where possible compile-time safe C++ interfaces to read and write event data. On the performance side, we show first benchmarks using ROOT’s new experimental I/O subsystem that combines the best of TTrees with recent advances in columnar data formats. A core ingredient is a strong separation of the high-level logical data layout (C++ classes) from the low-level physical data layout (storage backed nested vectors of simple types). We show how the new, optimized physical data layout speeds up serialization and deserialization and facilitates parallel, vectorized and bulk operations. This lets ROOT I/O run optimally on the upcoming ultra-fast NVRAM storage devices, as well as file-less storage systems such as object stores.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Direct I/O for RNTuple Columnar Data

RNTuple is the new columnar data format designed as the successor to ROOT’s TTree format. It allows to make use of modern hardware capabilities and is expected to be used in production by the LHC experiments during the HL-LHC. In this paper, we discuss the usage of Direct I/O to fully exploit modern SSDs, especially in the context of the recent addition of parallel RNTuple writing. We describe the alignment requirements imposed by Direct I/O and approaches to meet them for columnar data formats. Finally, we discuss performance results for both writing and reading, in synthetic benchmarks as well as real-world applications.

Hahnfeld, Jonas [CERN; Goethe U., Frankfurt (main)↗

GRUMDN: A Multi-Task Model for Predicting Human Patterns-of-Life from Stay Transition Data

Understanding human patterns-of-life (PoL) is essential towards ensuring safe and secure indoor facility environment as well as outdoor urban environment. Prediction of human movement in between places of interest is vital in understanding human PoL. Movement between spaces maybe represented and detected in one of the two forms: 1) trajectories: locations measured at regular time intervals by mobile sensors, bluetooth or GPS sensors; or 2) stay transitions: semantic PoI (points of interest) and stay duration data measurable by eventbased sensors that collect data when a check-in or check-out event is detected. Stay transition data provides a more compressed data format compared to trajectories data, especially in situations with longer stay durations, while preserving the information necessary for PoL analysis. Now as introduced briefly in the paper, our deployed end application (Digital Twin of a facility with non-player characters, besides the interactive user in virtual reality) needed a well-performing and validated AI/ML model for simulating high quality stay transitions behavior. In this study we thus primarily present our findings with developing and validating that model, which is a multi-task neural network for stay transition prediction. The neural network consists of two heads, for corresponding two tasks of stay category prediction and stay duration prediction. We evaluated gated recurrent units and multi-layer perceptrons of varying network sizes for stay category prediction; while mixture density networks, noisy generator-only networks, and generative adversarial networks of varying network sizes for stay duration prediction. We have then evaluated four multi-task models, constructed by combining these specialized models, on their ability to predict stay transition data. We tested our models on datasets from two different cases: 1) a simulation-generated dataset of indoor movement within the HFIR (high flux isotope reactor) nuclear reactor facility at Oak Ridge National Laboratory (ORNL); and 2) the GeoLife human mobility dataset of outdoor urban movement available in literature. Our results indicate that GRUMDN, which combines gated recurrent units (GRU) for stay category prediction task, and mixture density networks (MDN) for stay duration prediction task, did overall outperform other multitask models and the current state-of-the-art.

Gunaratne, Chathika [ORNL] (ORCID:0000000225088745↗

STILGAR Seismic Array Data

Two three-component dense seismic arrays were deployed above an active limestone mine in Pleasant Gap, Pennsylvania; one in the fall and one in the spring of 2023. Each campaign lasted approximately four weeks and included 80 to 100 seismic stations with stations spaced between 100 and 400 meters apart. Each campaign also included several small dense seismic arrays. Two types of seismic stations were deployed including FairfieldNodal ZLand 3C All-in-One seismometers and Geospace 3C GS-ONE geophone paired with GSX3 and GSX4 dataloggers. This dataset includes ~ 4 TB of three-component continuously recorded seismic data in the miniseed format data from both campaigns as well as a readme file for the data structure.

58 GEOSCIENCES↗

Hestia SW-IFL Onroad Fossil Fuel Carbon Dioxide (FFCO2) product: Road segment-level annual FFCO2 emissions across Arizona (2017-2022), version 1.1

The SW-IFL onroad fossil fuel carbon dioxide (FFCO2) emissions data product represents CO2 emissions from the combustion of fossil fuels by motor vehicles (e.g., passenger cars, trucks, buses, motorcycles) traveling on designated roadways. The emissions are represented geographically on each road segment within the state of Arizona spanning the 2017 to 2022 time period. This data product was developed as part of the Southwest Urban Corridor Integrated Field Laboratory (SW-IFL) project, which aims to provide new knowledge and tools that address urban environmental issues by integrating high-resolution observations, modeling, and civic engagement. The emissions data are provided in CSV (input data, ONR_FFCO2_AZ_county.csv) and GeoPackage form (output polyline objects - about 786,000 road segments, XXXX_AZ_v1.1.gpkg) designated by road class (interstates, arterials, collectors, local). The metadata file (Metadata_SW-IFL_Onroad_annualFFCO2_v1.1.docx) provides details about attributes and data formats. The GeoPackage emissions data are provided separately for local roads and nonlocal roads (interstates, arterials, collectors). The method file (Methods_SW-IFL_Onroad_annualFFCO2_v1.1.docx) describes the data processing flow and data sources. Update on 2024-04-17: Updates were made to both the input emission data file (.csv) and output segment-level emission file (.gpkg). There was an update in county-level emission input data (ONR_FFCO2_AZ_county.csv) and the entire road segments were reprocessed to reflect this update.Update on 2024-04-29: Update was made to one output segment-level emission file (Nonlocal_AZ_v1.0.gpkg). There was an error in the AADT values and the data were reprocessed to reflect this update.Update on 2024-10-22: Temporal coverage was extended to include 2022. VMT values were recalculated using new AADT data and the entire road segments were reprocessed to reflect these updates.

54 ENVIRONMENTAL SCIENCES↗

Artificial Intelligence Transforming Post-Translational Modification Research

Post-Translational Modifications (PTMs) are covalent changes to amino acids that occur after protein synthesis, including covalent modifications on side chains and peptide backbones. Many PTMs profoundly impact cellular and molecular functions and structures, and their significance extends to evolutionary studies as well. In light of these implications, we have explored how artificial intelligence (AI) can be utilized in researching PTMs. Initially, rationales for adopting AI and its advantages in understanding the functions of PTMs are discussed. Then, various deep learning architectures and programs, including recent applications of language models, for predicting PTM sites on proteins and the regulatory functions of these PTMs are compared. Finally, our high-throughput PTM-data-generation pipeline, which formats data suitably for AI training and predictions is described. We hope this review illuminates areas where future AI models on PTMs can be improved, thereby contributing to the field of PTM bioengineering.

59 BASIC BIOLOGICAL SCIENCES↗

Urban-scale Energy Modeling: Scaling Beyond Tax Assessor Data

In an attempt to attain building-specific characteristics for urban-scale building energy models, county-specific tax assessors’ data is often an initial data source. This data source can contain valuable information such as year built, area, height, HVAC type, and roof/wall descriptions.We will show examples of 2,000 fields from Hamilton County in Tennessee with examples of many fields which are not relevant to urban-scale building energy modeling, are incorrect compared to other data sources, and highlight some lessons learned working with such a data source.There are currently 3,142 counties in the United States, each with their own data format, field definitions, and data access policy. As urban-scale involves city-scale analysis potentially covering multiple counties and matures toward state- or nation-scale analysis, county-by-county approaches are not scalable. While there are efforts to unify these datasets, there is an increasing proliferation of data and algorithms that can cover wider areas and provide more accurate inputs for urban-scale models. This paper summarizes computer vision of imagery, cartographic layers, building type assessment, and model generation used to achieve scalable detection and analysis of buildings.

New, Joshua↗

Templates for developing and versioning data standards and reporting formats using GitHub

This data package contains three templates that can be used for creating README files and Issue Templates, written in the markdown language, that support community-led data reporting formats. We created these templates based on the results of a systematic review (see related references) that explored how groups developing data standard documentation use the Version Control platform GitHub, to collaborate on supporting documents. Based on our review of 32 GitHub repositories, we make recommendations for the content of README Files (e.g., provide a user license, indicate how users can contribute) and so 'README_template.md' includes headings for each section. The two issue templates we include ('issue_template_for_all_other_changes.md' and 'issue_template_for_documentation_change.md') can be used in a GitHub repository to help structure user-submitted issues, or can be modified to suit the needs of data standard developers. We used these templates when establishing ESS-DIVE's community space on GitHub (https://github.com/ess-dive-community) that includes documentation for community-led data reporting formats. We also include file-level metadata 'flmd.csv' that describes the contents of each file within this data package. Lastly, the temporal range that we indicate in our metadata is the time range during which we searched for data standards documented on GitHub.

54 ENVIRONMENTAL SCIENCES↗

Foliar isotopic and elemental biochemistry and leaf mass per area (LMA), Parque Natural Metropolitano, Panama, 2022

Foliar N and C isotope composition, bulk elemental N and C composition, and leaf mass per area (LMA) for leaves sampled from the Parque Natural Metropolitano (PNM), Panama, from January to April 2022 are presented. Measurements were made on leaves from 17 different tree, shrub and liana species, from sunlit canopy and understory locations on 8 vertical profiles. Full sample details and leaf area index (LAI) from the vertical profiles at PNM are also included in the data package. The aim of this measurement campaign was two-fold: to improve our understanding of the vertical variation in leaf-level water use efficiency, and to improve models which can predict leaf traits from leaf contact spectral measurements. Biochemistry data and sample metadata are presented in .csv files. The original isotopic data report, which includes details about standards and data accuracy, is provided in .xlsx format. Data and metadata meet the ESS-DIVE reporting format requirements for file level metadata (FLMD) and comma separated values (csv). The protocol details are provided as pdf documents. In addition to foliar biochemistry data reported here these samples were also used for measurement of leaf gas exchange, and leaf optical properties. These data can be linked using the unique sample ID and are provided in separate data packages (NGT0192 and NGT0193).

54 ENVIRONMENTAL SCIENCES↗

IK-Frag: Frag data generator for the PHITS simulation with the inverse kinematic reaction producing a focused neutron beam

IK-Frag has been developed for the creation of the nuclear cross-section data format, which is named frag data and can be used in PHITS, a Monte Carlo simulation code. IK-Frag focuses on the inverse kinematic reactions between a lithium or beryllium ion and a proton target. These reactions achieve naturally collimated neutrons and potentially reduce the necessity of radiation shielding. IK-Frag enables PHITS users to conduct simulations for the inverse kinematic reactions. The present software aims to contribute to future development of the neutron source system using the inverse kinematic reactions.

43 PARTICLE ACCELERATORS↗

Cinema:Snap: Real-time tools for analysis of dynamic diamond anvil cell experiment data

We report we developed tools and a workflow for real-time analysis of data from dynamic diamond anvil cell experiments performed at user light sources. These tools allow users to determine the phases of matter observed during the compression of materials in order to make decisions during an experiment to improve the quality of experimental results and maximize the use of scarce experimental facility time. The tools fill a gap in dynamic compression data analysis tools that are real-time, are flexible to the needs of high-pressure scientists, connect to automated processing of results, can be easily incorporated into workflows with existing tools and data formats, and support remote experimental data analysis workflows. Specific analytics developed include novel automated two-peak analysis for overlapping peaks and multiple phases, coordinated views of pressure and temperature values, full-compression contour plots, and configurable views of integrated x-ray diffraction. We present an experimental use case to show how the tools produce real-time analytics that help the scientists revise parameters for the next compression

47 OTHER INSTRUMENTATION↗

AI for Earthquake Physics

The core LANL program sponsored by Office of Science, Basic Energy Science, Chemical Sciences, Geosciences, and Biosciences (DOE-BES-CSGB) and led by PI Johnson aims to research earthquake faults to advance fault physics and earthquake hazards. All work completed is required to be made publicly available through publications and open-source codes supporting the published results. All routines are/will-be written in open source python and applied to publicly available data sets. These routines will format data from input into models, develop and test modeling frameworks for the problems addressed, and produce figures applicable to peer-reviewed manuscripts. All work is reviewed for Los Alamos Unlimited Release before submitting to a journal. This summary encompasses recently completed work and work to be complete for the duration of the program.

Johnson, Christopher↗

Urban Parameters Maricopa County 100m Grid Spacing

132 urban parameters for Maricopa County are provided in WRF-readable binary form at 100m grid spacing with index. These parameters allow regional weather modelers to account for the contribution of built structures in modeling the urban heat island. This data is also provided in CSV format. Data are generated using 2023 Model America Version 1 data (https://www.osti.gov/biblio/1774134) and will be used to represent the urban morphology in Maricopa County to the WRF model for experiments conducted for the Southwest Urban Corridor Integrated Field Laboratory (SW-IFL). Three files associated with these parameters are included in this repository: index, binary file 00001-01549.00001-01796, Maricopa_Parameters_03072024.csv . To use the binary file with the Weather Research and Forecasting (WRF) model, the binary file and the index file must be placed in their own directory in WRF_GEOG and accessed in the same way the National Urban Database and Access Portal Tool data (NUDAPT44) would be accessed. The name of the binary file must be in the format: 00001-02715.00001-01803. If, upon download, the binary filename has additional or different characters, please change them to match this format.

54 ENVIRONMENTAL SCIENCES↗

Modernization of ORIGEN Library Creation in the SCALE Computer Code

The modernization of SCALE features has been a target for recent SCALE releases. ORIGEN, the activation and depletion code in SCALE, is one such legacy code that has been targeted for modernization. A part of these modernization efforts has been to develop capabilities within ORIGEN to directly read ENDF-formatted data files. In addition, the input format for the COUPLE library creation utility was rewritten to a format more accessible to newer SCALE users. Finally, the ability of COUPLE to create ORIGEN libraries without sublibrary data has been added.KEYWORDS: ORIGEN, depletion, SCALE, API

Hart, Shane↗

Doppler Broadening and Other Temperature Effects

In this paper I attempt to document what I have learned and still remember about temperature effects, particularly Doppler broadening, on nuclear data, as it applies to ENDF formatted data. My focus is on the SIGMA1 method of Doppler broadening that I developed over 50 years ago. However, I do realize that there are currently many different methods used in computer codes, and I have tried to keep my discussion general as it applies to ALL of these methods. In particular, ALL of the MYTHS I describe below apply to all Doppler broadening methods: they all solve the parabolic diffusion equation in spherical geometry in (speed, reaction rate) versus temperature. These methods differ only in how the cross section is represented. So, at 85 years old here is what I still remember.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Counter Unmanned Aircraft System Metrics Tool

SAND2023-05387O The Counter Unmanned Aircraft System (CUAS) Metrics Tool consists of three applications: • The Data Collection Tool is designed to be used during testing and captures details that can be imported into the Figure Creator application. • The Unmanned Aircraft System (UAS) Log Converter converts different UAS logs into a standardized hierarchical data format with a timeline of geospatial data. • The Figure Creator develops relevant images for the test event. The application includes logic to ingest and correlate data from the Data Collection Tool and the UAS Log Converter to produce the chosen figures. 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.

Mayle, Ashley↗

Belowground respiration, root traits, and soil characteristics of an East Tennessee deciduous forest, 2019-2020

This dataset contains empirical physiological, morphological, and chemical data of root systems, and elemental, nutrient content for soils collected on forty individuals of eight temperate tree species, between June 2019 and July 2020 at The University of Tennessee Forest Research Center and Arboretum in Oak Ridge, Tennessee. The project used a novel methodology to empirically derive estimates of the autotrophic and heterotrophic components of soil respiration in-situ. The project consists of two measurement approaches. The first set of measurements uses a standard approach for measuring specific root respiration on excised root systems. The second used “in-situ root trays” This dataset includes 10 data files in comma separate (*.csv) ASCII format. Data include measurements of leaf and root functional traits for excised root systems and for living root systems housed within in-situ root trays, data on soil carbon and nitrogen pools, in-situ measurements of soil moisture and temperature, data on soil respiration rates for in-situ root trays (both as soil mass-based fluxes, and soil-area based fluxes), and data on the geographic coordinates and tree sizes of study trees. Forty study trees of eight temperate tree species were studied (five individuals per species). Two in-situ root trays were installed per species, each housing one entire root system comprising < 3 root orders, and still being attached to the tree via transportive root. All respiration measurements were conducted with the Li-6800 portable photosynthesis system (Li-COR, Lincoln, NE, USA). Root respiration measurements of excised root tissues were made using the Li-6800 and the Walz 3010-GWK1 gas exchange chamber (Heinz Walz GmbH, Effeltrich, Germany). Root scan images were analyzed using WinRHIZO. These images are companion files to this dataset and are contained in two compressed (*.zip) folders. Additional metadata are provided: 10 data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.

EARTH SCIENCE > BIOSPHERE > VEGETATION > LEAF CHAR↗