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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Docker Containers for MCNP ® Development

Containers are a revolutionary technology in software development and deployment that provides a lightweight, portable environment for ensuring consistency across multiple computing environments. In anticipation of the MCNP 6.3.1 release, two Docker container images have been released on DockerHub for general use. The MCNP source code is not included in the images, and users are still required to obtain it through RSICC. The images produced by Docker are compliant with the OCI (Open Container Initiative) standards, ensuring compatibility with other container engines such as Podman or Kubernetes’ CRI-O. Initially, the images are stored under the author’s personal space on DockerHub (docker.io/azukaitis), but they will be relocated to a dedicated MCNP group space once approved. In the future, they will also be available through the registry feature of the https://github.com/lanl/mcnp-containers project. The use of Docker provides a pre-configured environment for building and running MCNP, ensuring reproducibility of results across various host architectures. This significantly improves consistency when running MCNP on different systems. Notably, executables and installers from the Docker images have successfully passed the MCNP development branch testing suite on x86-64 architectures, including Windows, macOS, and Linux operating systems. Furthermore, testing has demonstrated compatibility with macOS Docker in emulation mode on the latest Apple Mac M2 Ultra hardware, ensuring robust support even on the latest platforms. In this document, we will provide a step-by-step guide to using the Docker images across multiple platforms. Additionally, we will present performance numbers for building and running the MCNP test suite.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program. BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

LISE$^{++}_{cute}$, the latest generation of the LISE ++ package, to simulate rare isotope production with fragment-separators

The LISE ++ software for fragment separator simulations has undergone a major update. The package, widely used at rare isotope beam facilities, can be used to predict intensities and purities of rare isotope beams and for planning and running of experiments using in-flight separators. It is especially useful for radioactive beam production as its results can be quickly compared to on-line data. The LISE ++ package has been ported to the Qt-framework in order to support modern compilers and computing methods. The benefits include 64-bit operation and LISE ++ availability on three different platforms: Windows, MacOS and Linux. In addition, the porting provides the ability to take advantage of future computational improvements. The updated package is named LISE$^{++}_{cute}$ to indicate a major step forward from the previous Borland-based versions. In addition to porting to the new platform, new main features and modifications have been added, mostly devoted to improving models and implementing other codes involved in rare isotope production at FRIB. Finally, a summary of modifications completed to improve the functionality of the code are discussed in this work, as well as future plans.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗
DOE OSTI2025

Thoroughly testing and integrating hundreds of Pull Requests per month: ROOT’s new Cost-efficient and Feature Rich GitHub-based CI

ROOT is an open source framework, freely available on GitHub, at the heart of data acquisition, processing and analysis of HE(N)P experiments, and beyond. It is developed collaboratively: contributions are not authored only by ROOT team members, but also by the user community at large: developers and scientists from universities, labs as well as the private sector. More than 1500 GitHub Pull Requests are merged on average per year. It is in this context that code integration acquires a primary role. The review of code contributions isn’t enough: not only they need to be thoroughly reviewed, they also need to be thoroughly tested through a powerful CI infrastructure on several different platforms to comply with the high code quality standards of the project. Since the end of 2023, ROOT moved its continuous integration system from Jenkins to GitHub Actions. In this contribution, we characterise the transition to the GitHub CI, focussing on our strategy, its implementation and the lessons learned, as well as the advantages the new system offers with respect to the previous one. Particular emphasis will be given to the evaluation of the cost-benefit ratio for Jenkins and GitHub Actions for the ROOT project. We also describe how we manage to run in less than one hour thousands of unit, integration, functional and end-to-end tests on different flavours of Windows, four versions of macOS, as well as about ten of the most used Linux distributions, taking advantage of the CERN computing infrastructure.

Piparo, Danilo [CERN]↗
DOE OSTI2021

CONSTAX2: improved taxonomic classification of environmental DNA markers

Abstract Summary CONSTAX—the CONSensus TAXonomy classifier—was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and implementation CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

AXEAP : a software package for X-ray emission data analysis using unsupervised machine learning

The Argonne X-ray Emission Analysis Package ( AXEAP ) has been developed to calibrate and process X-ray emission spectroscopy (XES) data collected with a two-dimensional (2D) position-sensitive detector. AXEAP is designed to convert a 2D XES image into an XES spectrum in real time using both calculations and unsupervised machine learning. AXEAP is capable of making this transformation at a rate similar to data collection, allowing real-time comparisons during data collection, reducing the amount of data stored from gigabyte-sized image files to kilobyte-sized text files. With a user-friendly interface, AXEAP includes data processing for non-resonant and resonant XES images from multiple edges and elements. AXEAP is written in MATLAB and can run on common operating systems, including Linux, Windows, and MacOS.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

ornladios/ADIOS2

ADIOS 2: The Adaptable Input Output (I/O) System version 2 is an open-source framework that addresses scientific data management challenges, e.g. scalable parallel I/O, as we approach the exascale era in high-performance computing (HPC). ADIOS 2 bindings are available in C++, C, Fortran, Python and can be used on supercomputers, personal computers, and cloud systems running on Linux, macOS and Windows. ADIOS 2 has out-of-the-box support for MPI and serial environments.

ECP↗
DOE OSTI2026

Scientific Core Library Stack (SCLS) v2026

SCLS (Scientific Core Library Stack) is an opinionated build and packaging system for scientific computing libraries developed at Lawrence Berkeley National Laboratory. It produces a coherent, reproducible stack of numerical libraries — including BLAS/LAPACK, MPI, sparse direct and iterative solvers, graph partitioners, and parallel I/O libraries (e.g., PETSc, SLEPc, HDF5, NetCDF, MUMPS, OpenBLAS) — that work together without manual repair by downstream scientific software. From a single recipe-and-flavor model, SCLS produces native RPM packages for RHEL-family Linux, DEB packages for Debian/Ubuntu, direct Unix-style prefix installs for HPC and locked-down environments, and native macOS builds. Multiple build "flavors" (e.g., GCC+OpenBLAS, GCC+MKL, Intel+MKL, debug) coexist in distinct prefixes on the same host. Compared to general-purpose meta-build frameworks, SCLS is deliberately curated rather than infinitely configurable. It enforces deterministic, audit-friendly behavior: explicit build dependencies, no silent feature autodetection, a clear open-source license policy, and rpath-based runtime linkage so installs integrate cleanly with standard package-manager workflows.

Messe, Christian [Lawrence Berkeley National Labor↗
DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗
DOE OSTI2021

Data from: "Snowmelt Timing Regulates Community Composition, Phenology, and Physiological Performance of Alpine Plants"

This archive contains data that were used to support conclusions drawn in “Snowmelt Timing Regulates Community Composition, Phenology, and Physiological Performance of Alpine Plants”, by Winkler et al., 2018. Data were collected throughout the 2009 growing season on Niwot Ridge, Colorado, before the site became part of the Alpine Treeline Warming Experiment (ATWE). Geospatial files are included in this archive to provide additional locational context. The files in this data package consist of five comma-separated-values (.csv) files, one keyhole markup language (.kml) file, and two ESRI shapefiles (.shp). The .csv files can be opened by Microsoft Excel, R, or any simple text-editor software, such as TextEdit (MacOS) or Notepad (Windows). The .kml files can be opened by Google Maps or Google Earth, and the .shp files are compatible with GIS softwares such as ESRI’s ArcGIS suite, and QGIS.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------We asked how plant community composition, phenology, plant water relations, and photosynthetic gas exchange of alpine-restricted and wide-ranging species differ in their responses to a ca. 40-day snowmelt gradient in the Colorado Rocky mountains (Lewisia pygmaea, Sibbaldia procumbens, and Hymenoxys grandiflora were alpine-restricted and Artemisia scopulorum, Carex rupestris, and Geum rossii were wide-ranging species). To do this, we measured percent cover and flowering initiation across 20 plots varying in snowmelt timing and measured net photosynthesis and stomatal conductance in multiple individuals of each target species in these plots in 2009.As hypothesized, species richness and foliar cover increased with earlier snowmelt, due to a greater abundance of wide-ranging species present in earlier melting plots. Flowering initiation occurred earlier with earlier snowmelt for 12 out of 19 species analyzed, while flowering duration was shortened with later snowmelt for six species (all but one were wide ranging species). We observed >50% declines in net photosynthesis from July to September as soil moisture and plant water potentials declined. Early-season stomatal conductance was higher in wide-ranging species, indicating a more competitive strategy for water acquisition when soil moisture is high. Even so, there were no associated differences in photosynthesis or transpiration, suggesting no strong differences between these groups in physiology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Blodgett 13C–labeled litter incubation 2016-2019

The dataset is from 13C-labelled (stable isotope of carbon) root-litter in-situ field incubation experiment based on the whole-soil warming experiment at the Blodgett Forest Research Station, CA, USA. The files are in both ".csv" and ".xlsx" versions, and can be opened in "maCOS numbers", and "Microsoft Excel". The files includes several sheets with all the data published in the paper: Sun, B., Zosso, C., Wiesenberg, G. L. B., Pegoraro, E., Torn, M. S., and Schmidt, M. W. I.: Warming accelerates the decomposition of root-derived hydrolysable lipids in a temperate forest and is depth- and compound class-dependent, SOIL, 11, 1077–1093, https://doi.org/10.5194/soil-11-1077-2025, 2025. This dataset includes bulk soil carbon, nitrogen, delta 13C values, the normalized concentration (to organic carbon) of hydrolysable lipids identified, the absolute concentration (normalized to bulk soil) of hydrolysable lipids, hydrolysable lipids recovery, and weighted 13C-excess of bulk soil carbon, and weighted 13C-excess of each compound class in hydrolysable lipids. These data aim to answer two research questions: 1) How will warming affect the decomposition of 13C-labelled root-litter at different depth? 2) Will the decomposition of root-derived hydrolysable lipids under warming differ among different compound classes? The experiment sites located on the foothills of the Sierra Nevada near Georgetown, CA (120°3904000W; 38°5404300 N) at 1370m above see level. The Blodgett Forest is a mixed-coniferous forest. The site has a Mediterranean climate with a mean annual air temperature of 12.5 °C and a mean annual precipitation of 1774mm.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

CCSI Toolset 3.18 Release

CCSI Toolset 3.18 Release Highlights FOQUS was updated to allow installation for users using MacOS on Apple silicon. FOQUS Cloud support was added for user plugins. The Optimality-Based Design of Experiments tutorials were updated to reflect the latest changes in the user interface flow. The plot discrete sliders were fixed for CDF and 3D plots within Uncertainty Quantification, which were not working due to a matplotlib depreciation. The installation was updated to set the default location for the PSUADE executable if found in the environment. Updates were made to allow compatibility with NumPy 1.25. Additional documentation changes were made to fix typographical errors and fix a broken link to optional software.

AS↗
DOE OSTI2024

CCSI Toolset 3.21 Release

CCSI Toolset 3.21 Release Highlights Parallelization support was added for Sequential Design of Experiments (SDOE) computations using Dask (preliminary). Input type dependent ordering capability was added to the SDOE module. With this implementation the user can specify the level of difficulty to change an input (Easy or Hard) and FOQUS will generate the appropriate ordered design depending on the input difficulty combination. Python version support was extended. FOQUS is now compatible with Python 3.8 through 3.12. Platforms used for automated testing were expanded to include macOS ARM (Apple Silicon). Updates to the FOQUS documentation to include information on how to set paths for SimSinter and TurbineLite. Turbine configuration section was added to Debugging Documentation.

AS↗
DOE OSTI2020

SimpleMass (Version 2.0.1 Report)

SimpleMass v2 is an updated GUI version of the SimpleMass Excel spreadsheet. It was developed using Python 3.7 and wxPython, a cross-platform GUI toolkit. The program was developed on Windows 10 and tested on macOS Catalina. In theory, the program should work on Linux based operating systems such as Ubuntu, but this has not been tested. Executable versions of the code were built using PyInstaller. The version described in this report is an alpha version that is still in development. It has only been tested by the developer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Vim Syntax File for MCNP Input Files

This report provides a Vim syntax file for MCNPR input files. This file has been tested with Vim 8.2.1719 on macOS 10.15.7 and incorporates many of the input cards and keywords described in [1, Chapter 3]. For convenience, the MCNP syntax file is listed in Appendix A and also provided as an electronic attachment to this PDF. Brief instructions for how to retrieve and use it are also included in Appendix A.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Initial OpenStudio Profiling Results

OpenStudio’s performance has not historically been an area of much work, but as it has successfully replaced ad hoc model generation solutions, the performance of the software is more and more central to continuing success. This report describes an initial effort to profile OpenStudio, describes the problems encountered, the solutions to those problems, and some early recommendations for further work should funding become available. The approach taken here is to use special software, referred to as profilers, to assess the code and how it executes. This approach is more appropriate for this kind of software than the checkpoint-style timing that is often done with numerical codes. Profiling was most successful on the MacOS platform, where Apple’s Instruments software was able to decipher the complexities of OpenStudio’s command line execution of a workflow. Even with the limited exploration of performance done here, the team quickly ran into limitations imposed on the code by the stateless architecture, and the team recommends an evaluation of this architecture as a good next step to improve performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

BM3DORNL

BM3DORNL is a high-performance, open-source library for removing streak and ring artifacts from computed-tomography (CT) data, developed for neutron imaging at Oak Ridge National Laboratory's Spallation Neutron Source (VENUS beamline) and applicable to X-ray CT as well. Ring artifacts — concentric rings in reconstructed slices caused by detector pixel-to-pixel response non-uniformities — appear as vertical streaks in the sinogram and degrade both image quality and quantitative analysis. BM3DORNL operates in the sinogram domain using an adaptation of the BM3D (block-matching and 3D collaborative filtering) algorithm (Dabov et al., 2007). It provides a dedicated streak-removal mode, a true multi-scale BM3D variant (after Mäkinen et al., 2021) that suppresses wide streaks single-scale methods miss, and an alternative Fourier–SVD method (~2.6× faster) combining FFT-based energy detection with rank-1 SVD. The computationally intensive core is implemented in Rust with parallel (Rayon) block matching, integral-image pre-screening, and optimized transforms, and is exposed through a simple Python API (with an optional GUI) so it integrates directly into existing tomography reconstruction pipelines. It processes both 2D sinograms and 3D sinogram stacks, is pip-installable for Linux and macOS, and is documented at https://bm3dornl.readthedocs.io.

Zhang, Chen [Oak Ridge National Laboratory (ORNL),↗