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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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NASA NTRS2012

General MACOS Interface for Modeling and Analysis for Controlled Optical Systems

The General MACOS Interface (GMI) for Modeling and Analysis for Controlled Optical Systems (MACOS) enables the use of MATLAB as a front-end for JPL s critical optical modeling package, MACOS. MACOS is JPL s in-house optical modeling software, which has proven to be a superb tool for advanced systems engineering of optical systems. GMI, coupled with MACOS, allows for seamless interfacing with modeling tools from other disciplines to make possible integration of dynamics, structures, and thermal models with the addition of control systems for deformable optics and other actuated optics. This software package is designed as a tool for analysts to quickly and easily use MACOS without needing to be an expert at programming MACOS. The strength of MACOS is its ability to interface with various modeling/development platforms, allowing evaluation of system performance with thermal, mechanical, and optical modeling parameter variations. GMI provides an improved means for accessing selected key MACOS functionalities. The main objective of GMI is to marry the vast mathematical and graphical capabilities of MATLAB with the powerful optical analysis engine of MACOS, thereby providing a useful tool to anyone who can program in MATLAB. GMI also improves modeling efficiency by eliminating the need to write an interface function for each task/project, reducing error sources, speeding up user/modeling tasks, and making MACOS well suited for fast prototyping.

Sigrist, Norbert↗

NASA NTRS2008

MACOS Version 3.31

Version 3.31 of Modeling and Analysis for Controlled Optical Systems (MACOS) has been released. MACOS is an easy-to-use computer program for modeling and analyzing the behaviors of a variety of optical systems, including systems that have large, segmented apertures and are aligned with the technology of wavefront sensing and control. Two previous versions were described in "Improved Software for Modeling Controlled Optical Systems" (NPO-19841) NASA Tech Briefs, Vol. 21, No. 12 (December 1997), page 42 and "Optics Program Modified for Multithreaded Parallel Computing" (NPO-40572) NASA Tech Briefs, Vol. 30, No. 1 (January 2006) page 13a. The present version incorporates the following enhancements over prior versions: a) A powerful system-optimization facility includes algorithms for linear, nonlinear, unconstrained, and constrained optimization of optical systems under a variety of settings. b) There is now enhanced capability to perturb optical components individually and on subsystem levels, and to optimize system performance by adjusting selected individual components as well as subsystems. c) Capabilities for modeling a variety of new optical aperture types have been added. d) Effects of multilayer thin-film coats on optical surfaces can now be taken into account when tracing polarized rays. e) Major software-engineering work was performed to make MACOS more reliable, flexible, and manageable for purposes of maintenance and further development.

Redding, David↗

NASA NTRS2006

Integrated, Kerberized Login on MacOS X

Context for this information. MacOS X login process and available hooks. Authorization Services configuration. Authorization Services plug-in s. Kerberos plug-in s. Other bugs and recommendations. Authorization Services Called by loginwindow, screen saver and fast user switching. It calls Directory Services, Login Hook, and Login Items (System Preferences).

MacOSX↗

NASA NTRS2006

Optics Program Modified for Multithreaded Parallel Computing

A powerful high-performance computer program for simulating and analyzing adaptive and controlled optical systems has been developed by modifying the serial version of the Modeling and Analysis for Controlled Optical Systems (MACOS) program to impart capabilities for multithreaded parallel processing on computing systems ranging from supercomputers down to Symmetric Multiprocessing (SMP) personal computers. The modifications included the incorporation of OpenMP, a portable and widely supported application interface software, that can be used to explicitly add multithreaded parallelism to an application program under a shared-memory programming model. OpenMP was applied to parallelize ray-tracing calculations, one of the major computing components in MACOS. Multithreading is also used in the diffraction propagation of light in MACOS based on pthreads [POSIX Thread, (where "POSIX" signifies a portable operating system for UNIX)]. In tests of the parallelized version of MACOS, the speedup in ray-tracing calculations was found to be linear, or proportional to the number of processors, while the speedup in diffraction calculations ranged from 50 to 60 percent, depending on the type and number of processors. The parallelized version of MACOS is portable, and, to the user, its interface is basically the same as that of the original serial version of MACOS.

Lou, John↗

NASA NTRS2012

RxGen General Optical Model Prescription Generator

RxGen is a prescription generator for JPL's in-house optical modeling software package called MACOS (Modeling and Analysis for Controlled Optical Systems), which is an expert optical analysis software package focusing on modeling optics on dynamic structures, deformable optics, and controlled optics. The objectives of RxGen are to simplify and automate MACOS prescription generations, reducing errors associated with creating such optical prescriptions, and improving user efficiency without requiring MACOS proficiency. RxGen uses MATLAB (a high-level language and interactive environment developed by MathWorks) as the development and deployment platform, but RxGen can easily be ported to another optical modeling/analysis platform. Running RxGen within the modeling environment has the huge benefit that variations in optical models can be made an integral part of the modeling state. For instance, optical prescription parameters determined as external functional dependencies, optical variations by controlling the in-/exclusion of optical components like sub-systems, and/or controlling the state of all components. Combining the mentioned capabilities and flexibilities with RxGen's optical abstraction layer completely eliminates the hindering aspects for requiring proficiency in writing/editing MACOS prescriptions, allowing users to focus on the modeling aspects of optical systems, i.e., increasing productivity and efficiency. RxGen provides significant enhancements to MACOS and delivers a framework for fast prototyping as well as for developing very complex controlled optical systems.

Sigrist, Norbert↗

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↗

NASA NTRS2011

General Tool for Evaluating High-Contrast Coronagraphic Telescope Performance Error Budgets

The Coronagraph Performance Error Budget (CPEB) tool automates many of the key steps required to evaluate the scattered starlight contrast in the dark hole of a space-based coronagraph. The tool uses a Code V prescription of the optical train, and uses MATLAB programs to call ray-trace code that generates linear beam-walk and aberration sensitivity matrices for motions of the optical elements and line-of-sight pointing, with and without controlled fine-steering mirrors (FSMs). The sensitivity matrices are imported by macros into Excel 2007, where the error budget is evaluated. The user specifies the particular optics of interest, and chooses the quality of each optic from a predefined set of PSDs. The spreadsheet creates a nominal set of thermal and jitter motions, and combines that with the sensitivity matrices to generate an error budget for the system. CPEB also contains a combination of form and ActiveX controls with Visual Basic for Applications code to allow for user interaction in which the user can perform trade studies such as changing engineering requirements, and identifying and isolating stringent requirements. It contains summary tables and graphics that can be instantly used for reporting results in view graphs. The entire process to obtain a coronagraphic telescope performance error budget has been automated into three stages: conversion of optical prescription from Zemax or Code V to MACOS (in-house optical modeling and analysis tool), a linear models process, and an error budget tool process. The first process was improved by developing a MATLAB package based on the Class Constructor Method with a number of user-defined functions that allow the user to modify the MACOS optical prescription. The second process was modified by creating a MATLAB package that contains user-defined functions that automate the process. The user interfaces with the process by utilizing an initialization file where the user defines the parameters of the linear model computations. Other than this, the process is fully automated. The third process was developed based on the Terrestrial Planet Finder coronagraph Error Budget Tool, but was fully automated by using VBA code, form, and ActiveX controls.

Marchen, Luis F.↗

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 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 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 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),↗