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DOE OSTI2021

Upgrade of hardware controls for the STAR experiment at RHIC

The STAR experiment has been delivering significant physics results for more than 20 years. Stable operation of the experiment was achieved by using a robust controls system based on the Experimental Physics and Industrial Control System (EPICS). Now an object-oriented approach with Python libraries, adapted for EPICS software, is going to replace the procedural-based EPICS C libraries previously used at STAR. Advantages of the new approach include stability of operation, code reduction and straightforward project documentation. The first two sections of this paper introduce the STAR experiment, give an overview of the EPICS architecture, and present the use of Python for controls software. Therefore, specific examples, as well as upgrades of user interfaces, are outlined in the following sections.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Enhancing Monte Carlo Workflows for Nuclear Reactor Analysis with Metamodel-Driven Modeling

Monte Carlo codes are essential components of many reactor physics simulation workflows as high-fidelity continuous-energy neutron transport solvers. Among Monte Carlo radiation transport codes, MCNP is particularly notable due to its diverse simulation capabilities, large user base, and long validation history. Despite being a powerful simulation tool, MCNP provides limited capabilities to allow automated execution, model transformation, or support for user-defined logic and abstractions that limit its compatibility with modern workflows. Here, to better integrate MCNP into a modern scientific workflow, we have developed an intuitive yet full-featured MCNP Application Program Interface (API) in Python, named MCNPy, which provides a specialized set of classes for MCNP input development. Moreover, to guarantee that our reading, writing, and modeling capabilities remain self-consistent (and to render the huge scope of the MCNP API manageable), we have adopted a strategy of model-driven software development in which a generalized model of the MCNP input format has been created. From this generalized model, or “metamodel,” problem-specific implementations such as an engine for input validation or a codebase for programmatic operations may be automatically generated. Since MCNPy primarily acts as a Python front-end to the underlying Java API that directly interfaces with the metamodel, it is intrinsically linked to the metamodel and thus remains maintainable. With MCNPy, users can programmatically read, write, and modify any syntactically valid MCNP input file regardless of its origin. These capabilities allow users to automate complicated tasks like design optimization and model translation for nuclear systems. As examples, this work demonstrates the use of MCNPy to find the critical radius of a plutonium sphere and to translate a 9000+ line MCNP input file into a corresponding OpenMC model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Portable, heterogeneous ensemble workflows at scale using libEnsemble

libEnsemble is a Python-based toolkit for running dynamic ensembles, developed as part of the DOE Exascale Computing Project. The toolkit utilizes a unique generator–simulator–allocator paradigm, where generators produce input for simulators, simulators evaluate those inputs, and allocators decide whether and when a simulator or generator should be called. The generator steers the ensemble based on simulation results. Generators may, for example, apply methods for numerical optimization, machine learning, or statistical calibration. libEnsemble communicates between a manager and workers. Flexibility is provided through multiple manager–worker communication substrates each of which has different benefits. These include Python’s multiprocessing, mpi4py, and TCP. Multisite ensembles are supported using Balsam or Globus Compute. We overview the unique characteristics of libEnsemble as well as current and potential interoperability with other packages in the workflow ecosystem. We highlight libEnsemble’s dynamic resource features: libEnsemble can detect system resources, such as available nodes, cores, and GPUs, and assign these in a portable way. These features allow users to specify the number of processors and GPUs required for each simulation; and resources will be automatically assigned on a wide range of systems, including Frontier, Aurora, and Perlmutter. Such ensembles can include multiple simulation types, some using GPUs and others using only CPUs, sharing nodes for maximum efficiency. We also describe the benefits of libEnsemble’s generator–simulator coupling, which easily exposes to the user the ability to cancel, and portably kill, running simulations based on models that are updated with intermediate simulation output. We demonstrate libEnsemble’s capabilities, scalability, and scientific impact via a Gaussian process surrogate training problem for the longitudinal density profile at the exit of a plasma accelerator stage. In conclusion, the study uses gpCAM for the surrogate model and employs either Wake-T or WarpX simulations, highlighting efficient use of resources that can easily extend to exascale.

Dynamic ensembles↗

DOE OSTI2024

Community Geothermal: Soil Conductivity, Borehole Design, Energy Models, and Load Data for a Residential System Development - Hinesburg, VT

This dataset contains materials from the Coalition for Community-Supported Affordable Geothermal Energy Systems (C2SAGES) project, which evaluated the techno-economic feasibility of a community geothermal system for a residential development in Hinesburg, VT. The dataset includes detailed soil conductivity test reports, energy models, borehole design reports, hourly energy loads for heating, cooling, and hot water, and design layouts. EnergyPlus was used to model building energy loads, and Modelica software was applied for geothermal loop sizing based on these loads and soil conductivity results. Python scripts for network design further refined the models. Key files include PDF reports on borehole design (with projections for 1-year, 15-year, and 30-year systems), soil conductivity test results, EnergyPlus modeling outputs, and 2D/3D design drawings in PDF, DWG, and DXF formats. Python notebooks for network design and OnePipe model files are also provided, with Modelica required for viewing certain files. Outputs and modeling data are in various formats including CSV, JPG, HTML, and IDF, with units and data clearly labeled to support understanding of system design and performance for the proposed geothermal solution.

15 GEOTHERMAL ENERGY↗

DOE OSTI2023

Geothermal Play Fairway Analysis for Low-Temperature Resources in the Denver Basin

This dataset is part of an effort to highlight the advantages of incorporating low-temperature (< 150 C) geothermal resource evaluation into the implementation of combined heat and power (CHP), and geothermal direct use (GDU) technologies (e.g., space heating and/or cooling). For this Denver Basin example, resource favorability maps were created to identify potentially favorable areas for further geothermal exploration and are provided here. Favorability was based on three types of data: (1) geologic, (2) economic, and (3) risk. This raw data is also provided below. Geologic data include bottom-hole temperatures (BHT) from oil and gas wells, water co-production volumes from oil and gas wells, well groundwater levels, hot spring locations, temperatures, and chemistries, faults, and earthquakes. Economic feasibility data include population, thermal energy demand, infrastructure, and roads. Risk data (which includes data on excluded areas) include flood plains, protected lands (e.g. wildlife conservation areas, national parks). The included report describes this project in detail, covering workflows, relevant datasets, Python code, and both common and composite maps used to create low-temperature geothermal resource favorability maps for the Denver Basin, which extends across Colorado, Nebraska, and Wyoming. The figures in this report include: maps of the original datasets; maps of transformed data and derived parameters (such as the geothermal gradient or thermal conductivity); results of uncertainty analyses; results of data completeness (using the GeoRePORT tool); examples of the data combination and processing (using the geoPFA Python library, which is introduced in the attached report); favorability maps for each criteria; and a final combined favorability map. This project is designed to facilitate future deployment of CHP and GDU by providing data, tools, and a workflow applicable to low-temperature geothermal resources in sedimentary basins.

15 GEOTHERMAL ENERGY↗

DOE OSTI2021

Numerical Model of IProTech PIP WEC Device

iProTech PIP wave energy converter (WEC) is a slack moored, single hull device with no moving parts in the water, joints or bearings. This submission includes data of the simulation, reports, and code for the iProTech PIP (WEC) project. The organization of the data included in the provided archive is detailed below and in the data description of the archive. The data teamer-iprotech-nrel folder includes and explains matlab and python code developed to hydrodynamically model the PIP WEC device in WEC-Sim. The subfolders cover the following steps: 1) report: explanatory information on device geometry 2) pip_mesher: python code to generate mesh panels from device profile data 3) wec-sim_models: matlab code to run WEC-Sim The data uploaded is a snapshot as of 11/02/2121 of code residing in a Github repository administered by David Ogden of NREL.

16 TIDAL AND WAVE POWER↗

DOE OSTI2024

TEAMER: Numerical Modeling and Optimization of the iProTech Pitching Inertial Pump (PIP) Wave Energy Converter (WEC)

This project focused on developing an automated workflow to evaluate and optimize the iProTech Pitching Inertial Pump (PIP) wave energy converter (WEC) using open-source Python packages and the MATLAB/Simulink tool, WEC-Sim. The process involved parameterizing key design variables, running time-domain simulations, and performing sensitivity analyses to determine their impact on power output. The workflow, designed for the PIP device, is generalized and can be extended to optimize other WECs that can be simulated in WEC-Sim. This work establishes a foundation for future time-domain-based WEC design optimizations. Included in this submission are all figures from the final report and the model inputs required to generate them. This includes Python scripts with inputs that produce the meshes, boundary element method (BEM) models, hydrodynamic coefficients, and the WEC-Sim models used for time-domain analyses. Although data for every single run is not included to save space, all of it can be reproduced using the provided models. Detailed instructions for setting up the environment and running the codes are also included.

16 TIDAL AND WAVE POWER↗

DOE OSTI2024

HERO WEC 2024 Hydraulic Configuration Deployment Data

The following submission includes raw and processed data from the in water deployment of NREL's Hydraulic and Electric Reverse Osmosis Wave Energy Converter (HERO WEC), in the form of parquet files, TDMS files, CSV files, bag files and MATLAB workspaces. This dataset was collected in March 2024 at the Jennette's pier test site in North Carolina. This submission includes the following: - Data description document (HERO WEC FY24 Hydraulic Deployment Data Descriptions.doc) - This document includes detailed descriptions of the type of data and how it was processed and/or calculated. - Processed MATLAB workspace - The processed data is provided in the form of a single MATLAB workspace containing data from the full deployment. This workspace contains data from all sensors down sampled to 10 Hz along with all array Value Added Products (VAPs). - MATLAB visualization scripts - The MATLAB workspaces can be visualized using the file "HERO_WEC_2024_Hydraulic_Config_Data_Viewer.m/mlx". The user simply needs to download the processed MATLAB workspaces, specify the desired start and end times and run this file. Both the .m and .mlx file format has been provided depending on the user's preference. - Summary Data - The fully processed data was used to create a summary data set with averages and important calculations performed on 30-minute intervals to align with the intervals of wave resource data reported from nearby CDIP ocean observing buoys located 20km East of Jennette's pier and 40km Northeast of Jennette's pier. The wave resource data provided in this data set is to be used for reference only due the difference in water depth and proximity to shore between the Jennette's pier test site and the locations of the ocean observing buoys. This data is provided in the Summary Data zip folder, which includes this data set in the form of a MATLAB workspace, parquet file, and excel spreadsheet. - Processed Parquet File - The processed data is provided in the form of a single parquet file containing data from all HERO WEC sensors collected during the full deployment. Data in these files has been down sampled to 10 Hz and all array VAPs are included. - Interim Filtered Data - Raw data from each sensor group partitioned into 30-minute parquet files. These files are outputs from an intermediate stage of data processing and contain the raw data with no Quality Control (QC) or calculations performed in a format that is easier to use than the raw data. - Raw Data - Raw, unprocessed data from this deployment can be found in the Raw Data zip folder. This data is provided in the form of TDMS, CSV, and bag files in the original format output by the MODAQ system. - Python Data Processing Script - This links to an NREL public github repository containing the python script used to go from raw data to fully processed parquet files. Additional documentation on how to use this script is included in the github repository. This data set has been developed by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. Funding provided by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Water Power Technologies Office.

16 TIDAL AND WAVE POWER↗

DOE OSTI2024

Data and Scripts associated with “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling.”

This data package is associated with the publication “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling” submitted to Geoscientific Model Development (Muller et al., 2024). In this manuscript, organic matter chemistry and thermodynamics are directly connected to reactive transport simulators through the newly developed Lambda-PFLOTRAN (Parallel Reactive Flow and Transport model) workflow tool that succinctly incorporates organic matter chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate aerobic respiration of the organic matter and the resulting biogeochemistry. Lambda-PFLOTRAN is a python-based workflow, executed through a Jupyter Notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow, and transport code PFLOTRAN. This data package contains Jupyter Notebook based workflows for two test cases for running biogeochemical simulations of organic matter oxidation identified by FTICR-MS. It contains four primary folders (workflow, data, src, and analysis), a file-level metadata file (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_flmd.csv) that lists all the files contained in this data package with a short description of each, and a data dictionary (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_dd.csv) file that describes the tabular column headers. The ‘workflow’ folder contains the Jupyter Notebook based workflows for running the lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘data’ folder contains the FTICR-MS data, initial conditions, and incubation data for test cases 1 and 2 in folders titled ‘WHONDRS’ and ‘Colloids’, respectively. The data folder also has a ‘Database’ folder containing a reaction network for bulk organic matter (assumed to be CH2O) and a general database for PFLOTRAN (hanford_rxn_network). The CH2O reaction network defines bulk organic matter oxidation. Biogeochemical simulations are completed for both the lambda binned organic matter and bulk organic matter reaction networks. The ‘hanford_rxn_network’ database includes information required for PFLTORAN simulations including ion size, molar mass, and charge of the aqueous species, gases, and minerals phases. The ‘src’ folder contains python source codes for performing lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘analysis’ folder contains outputs from the test cases 1 and 2 including lambda analysis, PFLOTRAN runs and the calibration results.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Annual Technology Baseline: ATB-calc Open Source Tools [Slides]

The Annual Technology Baseline (ATB) team will introduce the new open-source Python tools for processing and interacting with electricity ATB data and provide helpful user demonstrations, including how to: extract data from the ATB workbook and calculate levelized cost of electricity (LCOE) in Python; programmatically interact with and modify ATB data; and use the tools to modify the tax credit assumptions of the ATB to account for bonus credits from the Inflation Reduction Act of 2022.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2026

plexosdb: A Modular Library for Programmatic PLEXOS Model Construction

plexosdb is a lightweight Python library for constructing PLEXOS models using a SQLite-backed data structure. It provides a clear, modular interface that maps relational data directly to model components. By leveraging SQLite and idiomatic Python, it enables fast iteration and reproducible workflows. The result is a performant, composable foundation for scalable PLEXOS model development.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS2002

Using scripting languages in optical interferometry

We discuss client-side CORBA scripts implemented in Tcl, Perl, and Python. These are all technologies that are either currently being used on testbeds at JPL or being evaluated for future use. Finally, a Python example demonstrating implementation of a simple CORBA server is presented.

CORBA↗

NASA NTRSDate not supplied

Science Workflows using Kamodo

Kamodo is a powerful python software package based on data functionalization. Once a given data set is functionalized, a large variety of capabilities are easily accessible in Kamodo, including unit conversions, custom analysis via function composition, interactive publication quality visualizations, and LaTeX encoding. The entirety of capabilities available in Kamodo are easily applied to both simulated and observed data across the multiple domains of Heliophysics and even in other disciplines. This work includes a variety of science workflows using Kamodo in combination with other resources, including with other python software packages, that expand the utility of Kamodo even further. These workflows include model-data comparisons, ensemble modeling examples, satellite mission planning examples, and other applications, all of which are freely available on CCMC’s Kamodo Github page for the community to adapt to their own uses (https://github.com/nasa/Kamodo). We invite the community to use these workflows and to contribute their own to share.

software↗

NASA NTRSDate not supplied

Science Workflows using Kamodo

python↗

NASA NTRS2025

PACE Water Resources: Demonstrating the Use of NASA's PACE Hyperspectral Ocean Color Instrument Data for Enhanced Coastal Management

This project developed tools to support the future use of Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) hyperspectral imagery in water resource monitoring and research by NASA DEVELOP teams and members of the PACE applications community. We sought to address a need for support in processing and visualizing hyperspectral PACE Ocean Color Instrument (OCI) data among researchers and decision-makers working in coastal water quality management and harmful algal bloom (HAB) monitoring. To supplement the day of simulated PACE imagery available, we used Aqua MODIS earth observations with Level 3 processing from March 2022 to build a Python graphical user interface (GUI) for visualizing ocean biogeochemical parameters relevant to the early detection and monitoring of HABs. We used simulated PACE OCI Level 2 data derived from the Python Top of Atmosphere Simulation Tool (PyTOAST) to build Jupyter Notebooks for band subset and selection. The Level 3 PACE Viewer components support users with quick visualizations as well as the creation of geoTIFFs and time-series. The Level 2 Jupyter Notebooks address users’ concerns over the volume and complexity of hyperspectral imagery. The PACE Viewer is useful for visual inspection and netCDF data processing but should not be used for geospatial analysis. Once PACE launches, this tool will alleviate the technical burdens of working with hyperspectral data and support the early detection and monitoring of HABs using PACE satellite imagery.

Python Top of Atmosphere Simulation Tool↗

NASA NTRS2023

The SunPy Project: An Interoperable Ecosystem for Solar Data Analysis

The SunPy Project is a community of scientists and software developers creating an ecosystem of Python packages for solar physics. The project includes the sunpy core package as well as a set of affiliated packages. The sunpy core package provides general purpose tools to access data from different providers, read image and time series data, and transform between commonly used coordinate systems. Affiliated packages perform more specialized tasks that do not fall within the more general scope of the sunpy core package. In this article, we give a high-level overview of the SunPy Project, how it is broader than the sunpy core package, and how the project curates and fosters the affiliated package system. We demonstrate how components of the SunPy ecosystem, including sunpy and several affiliated packages, work together to enable multi-instrument data analysis workflows. We also describe members of the SunPy Project and how the project interacts with the wider solar physics and scientific Python communities. Finally, we discuss the future direction and priorities of the SunPy Project.

Solar physics↗

DOE OSTI2022

Implementation of real‐time TDDFT for periodic systems in the open‐source PySCF software package

Abstract We present a new implementation of real‐time time‐dependent density functional theory (RT‐TDDFT) for calculating excited‐state dynamics of periodic systems in the open‐source Python‐based PySCF software package. Our implementation uses Gaussian basis functions in a velocity gauge formalism and can be applied to periodic surfaces, condensed‐phase, and molecular systems. As representative benchmark applications, we present optical absorption calculations of various molecular and bulk systems and a real‐time simulation of field‐induced dynamics of a (ZnO) 4 molecular cluster on a periodic graphene sheet. We present representative calculations on optical response of solids to infinitesimal external fields as well as real‐time charge‐transfer dynamics induced by strong pulsed laser fields. Due to the widespread use of the Python language, our RT‐TDDFT implementation can be easily modified and provides a new capability in the PySCF code for real‐time excited‐state calculations of chemical and material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗