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Permafrost Thaw, Uneven Subsidence and Projected Drying of Ice-wedge Polygon Tundra: Modeling Archive

This dataset is a model archive of the paper Permafrost Thaw, Uneven Subsidence and Projected Drying of Ice-wedge Polygon Tundra (in prep) to support a modeling study investigating how projected increases in Arctic temperature and precipitation will jointly influence hydrologic conditions in ice-rich tundra landscapes. With this dataset, this study is to address the research question: Will Arctic tundra landscapes become wetter or drier with increasing precipitation and temperature in the future when thaw-induced ground subsidence and associated microtopographic evolution are represented? The simulations focus on ice-wedge polygon tundra, a widespread form of ice-rich permafrost terrain that is highly sensitive to thaw-driven landscape change. This dataset contains model input and output data for four study watersheds in Alaska: Anaktuvuk, Utqiagvik (formerly Barrow), Brooks Foothills, and Prudhoe Bay. Simulations were performed using the Advanced Terrestrial Simulator (ATS, v1.5), a physics-rich integrated surface–subsurface hydrologic model. For each watershed, ten modeling cases were performed representing two landscape evolution conditions (with subsidence and without subsidence) combined with five climate forcing scenarios derived from Shared Socioeconomic Pathways (SSP5, SSP5 with precipitation trend, SSP2, SSP2 with precipitation trend, and SSP2 with double precipitation trend). Particularly, for each watershed under the forcing SSP2 with precipitation trend, there are two additional simulations considering spatially heterogeneous subsidence distributions: one assumes randomly distributed scaling and the other includes elevation dependent distribution scaling. These simulations span 1980–2099 and include spin-up runs (1980–2009) followed by transient projections (2010–2099). To facilitate reproducibility of simulations, all datasets are organized by watershed. For each study watershed, the dataset contains: (1) Pre-partitioned mesh files for 32-core modeling (.par.32.XX), located in EACH_WATERSHED/mesh/basin; and also a non-partitioned mesh file (.exo) located in EACH_WATERSHED/mesh; (2) Climate forcings corresponding to the five SSP scenarios (.h5), located in EACH_WATERSHED/data; (3) Final states (.h5) from column spin-up modeling used to initialize historical watershed-scale spin-up runs from 1980 to 2009, located in EACH_WATERSHED/PreSpinupHistorical; (4) Final states (.h5) of historical watershed-scale spin-up runs from 1980 to 2009 used to initialize projection runs, located in EACH_WATERSHED/Spinup_daymetERA5; (5) ATS modeling input files (.xml), located in EACH_WATERSHED/EACH_SIMULATION_SCENARIO/inputfiles; (6) ATS modeling output files (.dat), located in in EACH_WATERSHED/EACH_SIMULATION_SCENARIO/combined_obs; (7) For the Brooks Foothills watershed, additional spatial model outputs are provided (.h5) for selected years (2033 and 2093) used to generate spatial figures in this study, located in Brooksfoothills/EACH_SIMULATION_SCENARIO/results-WITH/WITHOUT_SUBSIDENCE-year2033/2093. All data files with suffix .h5 can be accessible through Python h5py, and all data files with suffix of .dat can be imported by Python pandas. Mesh file with .exo can be visualized through Paraview or read by Python netCDF. The Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) project is a research effort to reduce uncertainty in the Department of Energy’s Energy Exascale Earth System Model (E3SM) by developing a predictive understanding of Arctic tundra ecosystems underlain by permafrost and to quantify feedbacks from the Arctic tundra to the Earth system. NGEE Arctic is supported by the Department of Energy's Office of Biological and Environmental Research. Over Phases 1–3, observations made by the NGEE Arctic team across a gradient of permafrost landscapes in Arctic Alaska improved the representation of tundra processes in the land surface component of E3SM (the E3SM Land Model, ELM). Model improvements emphasized unique aspects of permafrost environments and explored reductions in model complexity while retaining predictive power. The Arctic-informed ELM developed by NGEE Arctic has been used to make novel predictions on processes ranging from permafrost thaw to soil biogeochemical cycling to Earth system feedbacks associated with the unique characteristics of tundra plants. In Phase 4, the NGEE Arctic team is evaluating our new predictive understanding under novel conditions across the Arctic domain. In collaboration with partners at long-term pan-Arctic research sites we are examining whether an Arctic-informed ELM can faithfully simulate interactions among surface and subsurface processes at site, regional, and pan-Arctic scales. In turn, we are using variety of tools to dynamically extend and evaluate ELM inference, with an emphasis on data synthesis and pan-Arctic model evaluation, reintegration of code with an evolving E3SM, scaling across heterogeneous Arctic landscapes, and the appropriate representation of the impacts of increasingly frequent Arctic disturbances.

EARTH SCIENCE > ATMOSPHERE > PRECIPITATION↗

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 2. Evaluating Controls on Flow Persistence in an Urbanized Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in an urbanized catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, distributed temperature sensing (DTS), continuous self-potential (SP) monitoring, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Field_Application subfolder contains the ATS XML input scripts, data files, output data for the SP site. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. The flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.m can only be used with COMSOL with MATLAB) is executed using the ATS output data to simulate the potential field. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) DTS Contains collated DTS data including raw Stokes and anti-Stokes measurement (provided as .h5 file). It also includes DTS processing.ipynb, a Jupyter notebook for calibrating the DTS data using dts_calibration Python package. cooler_calibration.csv is the DTS calibration CSV used in the calibration sequence. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion. 6) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 7) SP Contains the SP data collected in field at the SP sites (provided as CSV files). 8) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). Note: Code files (.ipynb, .py, .xml) can be opened in any standard code editor, .exo file can be viewed using Paraview, .h5 files can be opened using HDFView software and h5py Python package, and .resipy file can be opened with the open-source ResIPy software.

ATS↗

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 1. Evaluating Above- and Below-ground Controls of Flow Persistence in a Forested Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in a forested catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, ground penetrating radar (GPR), continuous self-potential (SP) monitoring, electromagnetic (EM) imaging, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Contains two subfolders: Synthetic and Field_Application subfolder. Synthetic subfolder contains the ATS XML input script (can be opened using any code editor) for the four synthetic hydrological cases tested (Connected and gaining, Connected and losing, Disconnected and losing, and dry stream). It also includes other experimental cases to test the influence of precipitation and concentration gradient. For each synthetic case, the flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.mph can be opened with the commercial software COMSOL and requires a license) is executed using the ATS output data to simulate the potential field. It also includes the Synthetic_model_plot.ipynb (can be opened using any code editor) to visualize the SP result and generate manuscript figures. The data subfolder contains mesh files to run both the ATS (.exo and .stl files can be viewed using Paraview; .h5 files can be opened using HDFView software and h5py Python package) and COMSOL models. Field_Application subfolder contains two subfolders: ES_MDA_inversion and Final_Model. ES_MDA_inversion contains the Python script (.py can be opened using any code editor) and SP observation data used to run the Ensemble Smoother with Multiple Data Assimilation (ES-MDA) inversion sequence to get the optimal model parameters. The Final_model subfolder contains the ATS XML input scripts, data files, output data for the two SP sites. The same workflow steps outlined for the Synthetic subfolder apply here. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) EM Contains the CSV file of the EM data from the DUALEM-42, including spatial coordinates (x, y, z), apparent conductivity, and in-phase measurements at 2 m coil separations for horizontal coplanar (HCP) and perpendicular (PRP) geometries. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion (.resipy can be opened with the open-source ResIPy software). 6) GPR Includes GPR field datasets collected at 100 MHz and 250 MHz antenna frequencies, along with the processing/interpretation project file (GPR_process.gpz can be viewed using EKKO_Project 6, a commercial software by Sensors & Software that requires a license). 7) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 8) SP Contains the SP data collected in field at the two SP sites (one in the perennial reach and the other in the intermittent reach), provided as DAT files. 9) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). It also includes DTW.ipynb, a Jupyter notebook containing the code for the dynamic time warping (DTW) with sliding window to evaluate SP signal synchronicity.

ATS↗

IDAES-PSE 2.6.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.6.0 Release Highlights Upcoming Changes IDAES will be switching to the new Pyomo solver interface in the next release. Whilst this will hopefully be a smooth transition for most users, there are a few important changes to be aware of. The new solver interface uses a different version of the IPOPT writer (“ipopt_v2”) and thus any custom configuration options you might have set for IPOPT will not carry over and will need to be reset. By default, the new Pyomo linear presolver will be activated with ipopt_v2. Whilst are working to identify any bugs in the presolver, it is possible that some edge cases will remain. IDAES will begin deploying a new set of scaling tools and APIs over the next few releases that make use of the new solver writers. The old scaling tools and APIs will remain for backward compatibility but will begin to be deprecated. New Models, Tools and Features New Intersphinx extension automatically linking Jupyter notebook examples to project documentation New end-to-end diagnostics example demonstrated on a real problem New complementarity formulation for VLE with cubic equations of state, backward compatibility for old formulation New solver interface with presolve (ipopt_v2) in support of upcoming changes to the initialization and APIs methods, with default set to ipopt to maintain backwards compatibility; this will deprecate once all examples have been updated New forecaster and parameterized bidder methods within grid integration library Updated surrogates API and examples to support Keras 3, with backwards compatibility for older formats such as TensorFlow SavedModel (TFSM) Updated costing base dictionary to include the 2023 cost year index value Updated ProcessBlock to include information on the constructing block class Updated Flowsheet Visualizer to allow visualize() method to return value and functions Bug Fixes Fixed bug in the Modular Property Framework that would cause errors when trying to use phase-based material balances with phase equilibria. Fixed bug in Modular Properties Framework that caused errors when initializing models with non-vapor-liquid phase equilibria. Fixed typos flagged by June update to crate-ci/typos and removed DMF-related exceptions Minor corrections of units of measurement handling in power plant waste/transport costing expressions, control volume material holdup expressions, and BTX property package parameters Fixed throwing >7500 numpy deprecation warnings by replacing scalar value assignment with element extraction and item iteration calls Testing and Robustness Migrated slow tests (>10s) to integration, impacting test coverage but also yielding a nearly 30% decrease in local test runtime Pinned pint to avoid issues with older supported Python versions Pinned codecov versions to avoid tokenless upload behavior with latest version Bumped extensions to version 3.4.2 to allow pointing to non-standard install location Deprecations and Removals Python 3.8 is no longer supported. The supported Python versions are 3.9 through 3.12 The Data Management Framework (DMF) is no longer supported. Importing idaes.core.dmf will cause a deprecation warning to be displayed until the next release The SOFC Keras surrogates have been removed. The current version of the SOFC surrogate model in the examples repository is a PySMO Kriging model.

AS↗

ARM Data-Oriented Metrics and Diagnostics Package for Climate Model Evaluation

A Python-based metrics and diagnostics package is currently being developed by the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Infrastructure Team at Lawrence Livermore National Laboratory (LLNL) to facilitate the use of long-term, high-frequency measurements from the ARM Facility in evaluating the regional climate simulation of clouds, radiation, and precipitation. This metrics and diagnostics package computes climatological means of targeted climate model simulation and generates tables and plots for comparing the model simulation with ARM observational data. The Coupled Model Intercomparison Project (CMIP) model data sets are also included in the package to enable model intercomparison as demonstrated in Zhang et al. (2017). The mean of the CMIP model can serve as a reference for individual models. Basic performance metrics are computed to measure the accuracy of mean state and variability of climate models. The evaluated physical quantities include cloud fraction, temperature, relative humidity, cloud liquid water path, total column water vapor, precipitation, sensible and latent heat fluxes, and radiative fluxes, with plan to extend to more fields, such as aerosol and microphysics properties. Process-oriented diagnostics focusing on individual cloud- and precipitation-related phenomena are also being developed for the evaluation and development of specific model physical parameterizations. The version 1.0 package is designed based on data collected at ARM’s Southern Great Plains (SGP) Research Facility, with the plan to extend to other ARM sites. The metrics and diagnostics package is currently built upon standard Python libraries and additional Python packages developed by DOE (such as CDMS and CDAT). The ARM metrics and diagnostic package is available publicly with the hope that it can serve as an easy entry point for climate modelers to compare their models with ARM data. In this report, we first present the input data, which constitutes the core content of the metrics and diagnostics package in section 2, and a user's guide documenting the workflow/structure of the version 1.0 codes, and including step-by-step instruction for running the package in section 3.

54 ENVIRONMENTAL SCIENCES↗

Even Higher-Level Synthesis: An Exploration of AI Hardware Accelerators using HLS4ML

With the rise of artificial intelligence, the popularization of deep learning, and a constantly evolving industry, the demand for flexible and efficient tools has never been greater. As algorithms grow more complex, their runtime and energy consumption increase exponentially. Customized hardware accelerators, long used for specific mathematical operations, remain essential for managing modern applications' computational and power demands. Hardware accelerators can speed up complex computations by orders of magnitude, but their manual design and verification processes are often challenging and time-consuming. High-Level Synthesis (HLS) provides a solution by transforming high-level algorithm descriptions, typically written in C++ or SystemC, into synthesizable RTL suitable for hardware implementation. This approach reduces development time for RTL engineers while offering flexibility beyond what traditional handwritten RTL can provide. We extended this capability to the machine-learning domain with the open-source framework hls4ml, which allows neural networks trained in Python frameworks like Tensorflow or PyTorch to be synthesized into efficient hardware representations for the traditional FPGA and ASIC flows. This breakthrough addresses the growing need for reduced design turnaround and easy verification of ML hardware accelerators with low latency and power efficiency constraints. During this tutorial, we will demonstrate how Python complements HLS by simplifying the ML design process, bridging the gap between software and hardware development. Attendees will explore how we translate neural networks modeled in Python into fixed-point C++ models suitable for HLS workflows. We will dive into strategies like Value-Range Analysis and Quantization-Aware Training, which optimize these designs for deployment and evaluate their accuracy, power consumption, and energy efficiency. To exemplify these concepts, experts from Fermilab will share their experiences applying this technology to high-energy physics experiments, where real-time, low-latency processing is critical. Over the years, Fermilab engineers have demonstrated how deep neural networks, optimized for hardware using hls4ml, can meet the stringent requirements of trigger systems at the CERN Large Hadron Collider. These systems rely on rapid decision-making to process immense data volumes while retaining only the most relevant events for further analysis. The application of hls4ml has also been extended to innovative technologies like smart pixel arrays. These smart pixels integrate ML inference capabilities directly into sensor devices, enabling localized data processing at the pixel level. This approach drastically reduces the need to transmit raw data to external processing units, significantly decreasing power consumption and latency. By embedding neural networks within the pixel architecture, the smart pixels can identify and prioritize relevant data in real time, providing a highly efficient solution for edge computing in scenarios such as particle detectors and imaging systems. Fermilab's work highlights the potential of hardware-accelerated ML in scenarios where both speed and power efficiency are mission-critical. Through this tutorial, attendees will gain valuable insights into the challenges and solutions of deploying ML in hardware. Understanding how HLS and hls4ml streamline the development of neural network-based hardware accelerators is fundamental for the industry's future. Participants will learn how these technologies are shaping the future of AI and scientific computing.

Di Guglielmo, Giuseppe [Fermilab]↗

Intelligent Experiments through Real-Time AI: Fast Data Processing and Autonomous Detector Control for High-Energy Nuclear Experiments

The aim of this project is to develop software and hardware for fast real-time data processing and autonomous detector control and calibration for the sPHENIX and the future EIC experiments. Below summarizes Georgia Tech team efforts in the past year: 1. We developed a real-time clustering algorithm and FPGA-based pipeline architecture for processing fired pixel data from ALPIDE sensors in sPHENIX experiments. Our Columnar Clustering Co-Design introduces a hardware-aware, stream-friendly approach that segments pixel data by column pairs using a Column Pair Clustering (CPC) strategy, followed by Cluster Stitching to merge adjacent subclusters. Implemented in Vitis HLS, the pipeline comprises five stages—read-in, subclustering, stitching, analysis, and write-out—connected by tagged HLS streams with custom end-of-event signaling for robust synchronization. We designed a pipelined dataflow model optimized for throughput, low latency, and minimal buffering, enabling scalable clustering across events of arbitrary size. Our system maintains spatial precision via center-of-mass and shape key extraction and efficiently handles edge cases such as fragmented or nested clusters. Compared against DBSCAN in both software and hardware, our approach demonstrates competitive performance under FPGA constraints. 2. We also conducted a comprehensive algorithm-to-hardware co-design of connected component analysis tailored for sPHENIX experiments, focusing on real-time, low-latency processing using FPGAs and High-Level Synthesis (HLS). Starting from a Python-based particle tracking pipeline, the team translated the core logic—graph traversal via DFS and Union-Find—into an HLS-compatible C++ model, replacing dynamic memory and recursion with static arrays and pipelined control flow. The final design includes a fully streamed and dataflow-compatible Union-Find kernel optimized across five iterations, incorporating loop pipelining, array partitioning, AXI/FIFO interface tuning, and function flattening. Experimental results show up to 14.8× speedup over the CPU baseline, reducing per-graph latency to 1.58 μs and demonstrating strong resource efficiency with only ~7k LUTs and zero BRAM usage. The design maintains functional correctness against the Python reference using a Python-based C-simulation framework and Mean Squared Error metrics. This work validates the potential of HLS-driven FPGA designs for edge-level HEP data acquisition, laying a scalable foundation for future integration with real-time detector pipelines and multi-graph processing systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Improving the Performance of NEML2 with Modern Graph Compilation Backends

NEML2 vectorizes constitutive-model evaluation for large-scale multiphysics simulation, using PyTorch as its tensor backend so that a batch of material-point updates runs on CPU or GPU through a single implementation. In the two prior reports in this series it was a C++-native library, deployed through TorchScript tracing and just-in-time (JIT) compilation; it has since been rewritten from the ground up into a Python-native library deployed through Ahead-of-Time Inductor (AOTInductor), a modern PyTorch graph-compilation backend. The rewrite is driven by a persistent tension, not a language preference: NEML2 composes constitutive models at runtime from a registry of small, independently-authored pieces, and that flexibility is difficult to reconcile with the compile-time knowledge an efficient GPU kernel needs. This report documents the rewrite and the investment that accompanied it: the AOTInductor export pipeline that turns a Python-authored model into a portable, Python-free compiled artifact loadable from pure C++; the eager and compiled runtimes and the new implicit solver layer built on them; a head-to-head benchmark of legacy JIT against AOTInductor; the physics-model catalog and its worked examples; the developer tooling; and the corresponding overhaul of MOOSE’s NEML2 integration that lets MOOSE consume it. A central objective is to examine whether modern PyTorch graph-compilation backends are effective for MOOSE GPU integration. The benchmark answers directly: AOTInductor outperforms legacy JIT on every GPU scenario measured, by 1.0–4.5×. Modern graph-compilation backends are effective for MOOSE GPU integration, and AOTInductor specifically – not compilation in the abstract – is why.

Hu, Gary (Tianchen) [Argonne National Laboratory (↗

Data release for A search for extremely-high-energy neutrinos and first constraints on the ultra-high-energy cosmic-ray proton fraction with IceCube

<h1 id="summary">Summary</h1> <p>Title: Data Release for A search for extremely-high-energy neutrinos and first constraints on the ultra-high-energy cosmic-ray proton fraction with IceCube</p> <p>The IceCube observatory analyzed 12.6 years of data in search of extremely-high-energy (EHE) neutrinos above 5 PeV. The resultant limit of the search (Fig 1), and the effective area of the event selection (Fig 7), are provided in this data release.</p> <h1 id="contents">Contents</h1> <ul> <li><p>README file: this file</p> </li> <li><p><code>differential_limit_and_sensitivity.csv</code>: a comma separated value file, giving the observed experimental differential limit, and sensitivity, of the search as a function of neutrino energy. This is the content of Fig 1 in the paper. The first column is the neutrino energy in GeV. The second column is the limit in units of GeV/cm2/s/sr. The third column is the sensitivity in units of GeV/cm2/s/sr.</p> </li> <li><p><code>effective_area.csv</code>: a comma separated value file, giving the effective area of the search as a function of energy. This is the content of Fig 7 in the paper. The first column is the neutrino energy in GeV. The second column is the total effective area of the search, summed across neutrino flavors, and averaged across neutrinos and antineutrinos, in meters-squared. The third column is the effective area of the search for the average of electron neutrino and electron antineutrinos in units of meters-squared. The fourth column is the same as the third, but for muon-flavor neutrinos. The fifth column is the same as the third and fourth, but for tau-flavor neutrinos.</p> </li> <li><p><code>demo.py</code>: a short python script to demonstrate how to read the files. Run like <code>python demo.py</code>. A standard base python installation is sufficient, as the only dependencies are numpy and matplotlib.</p> </li> </ul> <h1 id="contacts">Contacts</h1> <p>For any questions about this data release, please write to analysis@icecube.wisc.edu</p>

Astronomy and Astrophysics↗

Ancient scientific basis of the "great serpent" from historical evidence

Zoological data and a growing mythology contributed to ancient Western knowledge about large serpents. Yet little modern attention has been paid to the sources, transmission, and receipt in the early Middle Ages of the ancients' information concerning "dragons" and "sea serpents." Real animals--primarily pythons and whales--lie behind the ancient stories. Other animals, conflations of different animals, simple misunderstandings, and willful exaggerations are found to account for the fanciful embellishments, but primitive myths played no significant role in this process during classical times. The expedition of Alexander the Great into India (327-325 B.C.) and the Bagradas River incident in North Africa (256 B.C.) had enormous repercussions on the development of serpent lore. Credible evidence is found for the presence of ancient populations of pythons living along the North African coast west of Egypt and along the coast of the Arabian Sea between the Indus River and the Strait of Hormuz--places where they no longer exist today. The maximum sizes of ancient pythons may have been greater than those of today's specimens.

Emblems and Insignia/history↗

A Multidisciplinary Tool for Systems Analysis of Planetary Entry, Descent, and Landing (SAPE)

SAPE is a Python-based multidisciplinary analysis tool for systems analysis of planetary entry, descent, and landing (EDL) for Venus, Earth, Mars, Jupiter, Saturn, Uranus, Neptune, and Titan. The purpose of SAPE is to provide a variable-fidelity capability for conceptual and preliminary analysis within the same framework. SAPE includes the following analysis modules: geometry, trajectory, aerodynamics, aerothermal, thermal protection system, and structural sizing. SAPE uses the Python language-a platform-independent open-source software for integration and for the user interface. The development has relied heavily on the object-oriented programming capabilities that are available in Python. Modules are provided to interface with commercial and government off-the-shelf software components (e.g., thermal protection systems and finite-element analysis). SAPE runs on Microsoft Windows and Apple Mac OS X and has been partially tested on Linux.

Samareh, Jamshid A.↗

Automated ISS Flight Utilities

During my internship at NASA Johnson Space Center, I worked in the Space Radiation Analysis Group (SRAG), where I was tasked with a number of projects focused on the automation of tasks and activities related to the operation of the International Space Station (ISS). As I worked on a number of projects, I have written short sections below to give a description for each, followed by more general remarks on the internship experience. My first project is titled "General Exposure Representation EVADOSE", also known as "GEnEVADOSE". This project involved the design and development of a C++/ ROOT framework focused on radiation exposure for extravehicular activity (EVA) planning for the ISS. The utility helps mission managers plan EVAs by displaying information on the cumulative radiation doses that crew will receive during an EVA as a function of the egress time and duration of the activity. SRAG uses a utility called EVADOSE, employing a model of the space radiation environment in low Earth orbit to predict these doses, as while outside the ISS the astronauts will have less shielding from charged particles such as electrons and protons. However, EVADOSE output is cumbersome to work with, and prior to GEnEVADOSE, querying data and producing graphs of ISS trajectories and cumulative doses versus egress time required manual work in Microsoft Excel. GEnEVADOSE automates all this work, reading in EVADOSE output file(s) along with a plaintext file input by the user providing input parameters. GEnEVADOSE will output a text file containing all the necessary dosimetry for each proposed EVA egress time, for each specified EVADOSE file. It also plots cumulative dose versus egress time and the ISS trajectory, and displays all of this information in an auto-generated presentation made in LaTeX. New features have also been added, such as best-case scenarios (egress times corresponding to the least dose), interpolated curves for trajectories, and the ability to query any time in the EVADES output. As mentioned above, GEnEVADOSE makes extensive use of ROOT version 6, the data analysis framework developed at the European Organization for Nuclear Research (CERN), and the code is written to the C++11 standard (as are the other projects). My second project is the Automated Mission Reference Exposure Utility (AMREU).Unlike GEnEVADOSE, AMREU is a combination of three frameworks written in both Python and C++, also making use of ROOT (and PyROOT). Run as a combination of daily and weekly cron jobs, these macros query the SRAG database system to determine the active ISS missions, and query minute-by-minute radiation dose information from ISS-TEPC (Tissue Equivalent Proportional Counter), one of the radiation detectors onboard the ISS. Using this information, AMREU creates a corrected data set of daily radiation doses, addressing situations where TEPC may be offline or locked up by correcting doses for days with less than 95% live time (the total amount time the instrument acquires data) by averaging the past 7 days. As not all errors may be automatically detectable, AMREU also allows for manual corrections, checking an updated plaintext file each time it runs. With the corrected data, AMREU generates cumulative dose plots for each mission, and uses a Python script to generate a flight note file (.docx format) containing these plots, as well as information sections to be filled in and modified by the space weather environment officers with information specific to the week. AMREU is set up to run without requiring any user input, and it automatically archives old flight notes and information files for missions that are no longer active. My other projects involve cleaning up a large data set from the Charged Particle Directional Spectrometer (CPDS), joining together many different data sets in order to clean up information in SRAG SQL databases, and developing other automated utilities for displaying information on active solar regions, that may be used by the space weather environment officers to monitor solar activity. I consulted my mentor Dr. Ryan Rios and Dr. Kerry Lee for project requirements and added features, and ROOT developer Edmond Offermann for advice on using the ROOT library. I also received advice and feedback from Dr. Janet Barzilla of SRAG, who tested my code. Besides these inputs, I worked independently, writing all of the code by myself. The code for all these projects is documented throughout, and I have attempted to write it in a modular format. Assuming that ROOT is updated accordingly, these codes are also Y2038-compliant (and Y10K-compliant). This allows the code to be easily referenced, modified and possibly repurposed for non-ISS missions in the future, should the necessary inputs exist. These projects have taught me a lot about coding and software design - I have become a much more skilled C++ programmer and ROOT user, and I also learned to code in Python and PyROOT (and its advantages and disadvantages compared to C++/ ROOT). Furthermore, I have learned about space radiation and radiation modeling, topics that greatly interest me as I pursue a degree in physics. Working alongside experimental physicists like Dr. Rios, I have developed a greater understanding and appreciation for experimental science, something I have always leaned towards but to which I lacked significant exposure. My work in SRAG has also given me the invaluable opportunity to witness the work environment for physicists at NASA, and what a career in academia may look like at a government laboratory such as NASA Johnson Space Center. As I continue my studies and look forward to graduate school and a future career, this experience at NASA has given me a meaningful and enjoyable opportunity to put my skills to use and see what my future career path might hold.

Offermann, Jan Tuzlic↗

Dynamic IT Security Database and Analytics for Launch Control Systems Software

During the Summer 2020 session, I worked with intern Destani S. Van Arsdalen of EGS Software. Together, we co-created a tool to aid the dynamic investigation, updated over time,of the security compliance of LCS COTS and open source software. We originally planned touse spreadsheet software for management and analysis, but through this exploratoryproject, chose to use Python and JSON after receiving feedback on our project’s current anddesired capabilities at that time.At first, the project was solely designed to help on-board new COTS software, based on aquestionnaire that could be filled out for each software package. This, combined with usingthe spreadsheet application’s web-query capabilities to fetch information from the NVD,allowed presentation and analytics cells to automatically populate as elements of themanually-filled questionnaire changed. While this system was promising, we decided tochange technologies for a few reasons. In the spreadsheet, single cells could not hold complexdata like arrays and objects. The automatic population of cells and dynamic updates made itdifficult to manage and add new features. And finally, it had limited extensibility sinceadding new software required significant understanding of how both the spreadsheet wasconstructed, and the more obscure, proprietary scripting languages packaged with it.The pivot to a standard computer science database language of JSON, aided by thescripting capabilities of Python, greatly helped to improve the project’s functionality. First,and most importantly, the script’s import and analysis of database data is easilyreproducible. Additional data analysis can be modularly added without requiringmodification of the script and is capable of routine scheduling. The revised process can besplit into three parts. First, the conversion of LCS asset and software documentation into theJSON hierarchical database format. Second, the merging of this database with the NVD,forming a new data structure, using CPEs of the CVE object as a linking element betweenthem. And third, the automatically performed analytics and analysis of the combined data,in a modular and extensible format, to produce better informed business decisions. The outputted graphs, for example, are automatically generated by the Python script inconnection with the combined database. This allows updated graphs and any analytics to be re-rendered automatically following updates to the LCS’s initial asset documentation. Afinal report can then be programmatically and easily constructed from these sources to allow fully reproducible metrics for heavily evidenced risk management decisions.

it↗

Ramdb: The NASA Raman Spectral Database (version 1.00).

Given that, in most instances, minimal sample preparation is required and due to its contactless instrument design, Raman spectroscopy is one of the most versatile vibrational spectroscopic techniques for the chemical analysis of environmental and biological specimens. The diversity of applications of Raman spectroscopy ranges anywhere from art [1] to planetary science missions [2]. The advancement in the use of Raman spectroscopy in Solar System missions, notably in post-mission sample return analysis, requires a spectral library holding the broad range of specimens that could be found in Solar System sources. For this purpose, we have initiated the development of a Raman spectral database (Ramdb) at NASA Ames Research Center. Currently, the database includes experimental and theoretical Raman spectra of PAHs [3, 4], as well as laboratory Raman spectra of amino acids, carbon allotropes, minerals, and analogs relevance to Earth Sciences [5], Exobiology [6], Planetary [7], and Astrochemistry [8] to name just a few examples. Ramdb can be found on the web at www.astrochemistry.org/ramdb, where raw and processed Raman spectra can be downloaded in CSV format. The laboratory Raman spectra are measured using a laser Raman spectrometer (JASCO NRS-5500-532QRI). The Raman instrument is equipped with three excitation lasers, with wavelengths of 405, 532, and 785 nm. A clean silicon substrate is used as the internal standard for wavenumber calibration. Powdered samples were prepared (microscopic >10 um, grounded microscopic < 10 um) on glass slides. Some raw data exhibited a background signal arising as a combination of laser-induced fluorescence from the sample. To correct this background, we developed a Python pipeline that uses open-source Python libraries. Ramdb provides both raw and processed (using Python pipeline) data, which includes tabulated Raman shift transitions and other measurement details. The theoretical Raman band positions of PAHs (pyrene monomers and tetramer clusters) were computed using density functional theory (DFT) with the help of the Gaussian 16 suite of programs [9]. In the near future, Ramdb will serve as a repository of Raman spectral data from Laboratory Astrophysics and Planetary Science experiments involving the irradiation of organic compounds under simulated space and planetary conditions. In addition, online and offline tools will be developed for utilising the database for comparison to the user’s sample.

N Punnakayathil↗

Improving Access to the GEOS Composition Forecast Model with API Development and Ingestion into Google Earth Engine

The GEOS Composition Forecast (GEOS-CF) model produces forecast and historical estimates of atmospheric composition and meteorology fields, which provide useful insight into air quality issues and events. In a year for which Canadian wildfires created adverse air quality conditions in the eastern United States, access to model fields such as PM2.5 are in high demand. The GEOS-CF team at the NASA Global Modeling and Assimilation Office (GMAO) first developed in-house solutions to improve data access via the CF API, and recently partnered with Google to ingest a collated set of model diagnostics into the Google Earth Engine (GEE) data repository. GEOS-CF model output is also being ingested into AWS storage. Creating these various open access points to GEOS-CF model diagnostics provides the public with an opportunity to easily interact with air quality information. Users are able to use a temporally consistent global grid of air quality fields in machine learning applications, mapping tools, and data informatics. Hosting GEOS-CF forecasts and the historical timeseries of these chemistry and meteorology fields in GEE allows users to create dynamic JavaScript-based air quality applications in the GEE code editor. GEOS-CF users can also access the model output via the GEE Python application programming interface (API), making it easy to perform various analyses with Python. This presentation will show two examples of accessing the GEOS-CF model through GEE. The first is an example application made in the GEE code editor which allows users to view time series plots and downscaled maps of surface level NO2. The second example exhibits using the GEE Python API to create a machine learning model to temporally gap-fill between air quality observations. These examples are an introduction to the many possible benefits of having open access to the GEOS-CF model through multiple platforms.

Callum Wayman↗

Improving Access to the GEOS Composition Forecast Model with API Development and Ingestion into Google Earth Engine

The GEOS Composition Forecast (GEOS-CF) model produces forecast and historical estimates of atmospheric composition and meteorology fields, which provide useful insight into air quality issues and events. In a year for which Canadian wildfires created adverse air quality conditions in the eastern United States, access to model fields such as PM2.5 are in high demand. The GEOS-CF team at the NASA Global Modeling and Assimilation Office (GMAO) first developed in-house solutions to improve data access via the CF API, and recently partnered with Google to ingest a collated set of model diagnostics into the Google Earth Engine (GEE) data repository. GEOS-CF model output is also being ingested into AWS storage. Creating these various open access points to GEOS-CF model diagnostics provides the public with an opportunity to easily interact with air quality information. Users are able to use a temporally consistent global grid of air quality fields in machine learning applications, mapping tools, and data informatics. Hosting GEOS-CF forecasts and the historical timeseries of these chemistry and meteorology fields in GEE allows users to create dynamic JavaScript-based air quality applications in the GEE code editor. GEOS-CF users can also access the model output via the GEE Python application programming interface (API), making it easy to perform various analyses with Python. This presentation will show two examples of accessing the GEOS-CF model through GEE. The first is an example application made in the GEE code editor which allows users to view time series plots and downscaled maps of surface level NO 2 . The second example exhibits using the GEE Python API to create a machine learning model to temporally gap-fill between air quality observations. These examples are an introduction to the many possible benefits of having open access to the GEOS-CF model through multiple platforms.

Callum Wayman↗

Xstar Atomic Database: The PyXstar Package

We present a progress report on the development of PyXstar, a Python package to manage the data (input, output, intermediate, atomic database, and model-grids) associated with the XSTAR code for treating photoionized and collisionally ionized plasmas. The PyXstar modular structure and database retrieval scheme are described, and its functionality is illustrated with Python functions and classes for performing database searches. We briefly compare PyXstar with two other Python spectrum modeling tools: PyNeb and PyAtomDB.

Claudio Mendoza↗

An Autonomous MCP Bridge to Rucio: Enhancing Data Management Accessibility for High Energy Physics

The Rucio Data Management System [1] is an important tool used by High Energy Physics experiments, including those at Fermi National Accelerator Laboratory, to store and manage exabyte-scale scientific datasets. Despite its central role in coordinating data across globally distributed storage sites, Rucio's command line interface (CLI) presents a steep learning curve, and makes it difficult for scientists to navigate through. To solve this issue, a containerized Model Context Protocol (MCP) [2] server was built that connects Large Language Models directly to Rucio, allowing AI agents to handle data tasks by using simple, natural language rather than memorized terminal commands. The core engineering focus of this project was moving the server away from slow terminal commands that require text parsing and replacing them with a native Python Client API toolset and a planned REST API framework. Moving to the Python API handles data operations directly in memory, which helps clear up formatting errors, provides the AI with clean, structured JSON data and speeds up tool execution. To prove that the system actually works, a benchmarking pipeline was also built with various questions to test the AI across four different model configurations. The questions included finding data scopes, tracking down specific datasets, and checking replication rules. Through benchmarking, early runs showed that with raw terminal text, the model would get confused and stuck, whereas switching to the Python API to feed the AI clean, structured data yielded massive improvement. By creating an intelligent and autonomous bridge to a storage network, this project shows how AI can be implemented in scientific data management, which ultimately helps scientists at Fermilab spend less time sorting through data and more time focusing on their experiments and analysis.

Akella, Kashyap [William Rainey Harper Coll.]↗