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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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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Evaluation of OpenAI Codex for HPC Parallel Programming Models Kernel Generation

We evaluate AI-assisted generative capabilities on fundamental numerical kernels in high-performance computing (HPC), including AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG. We test the generated kernel codes for a variety of language-supported programming models, including (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). We use the GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code as of April 2023 to generate a vast amount of implementations given simple + + prompt variants. To quantify and compare the results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. Results suggest that the OpenAI Codex outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general purpose Python can benefit from adding code keywords, while Julia prompts perform acceptably well for its mature programming models (e.g., Threads and CUDA.jl). We expect for these benchmarks to provide a point of reference for each programming model's community. Overall, understanding the convergence of large language models, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

Godoy, William↗
DOE OSTI2022

Optimal checkpointing for adjoint multistage time-stepping schemes

Here, we consider checkpointing strategies that minimize the number of recomputations needed when performing discrete adjoint computations using multistage time-stepping schemes that require computing several substeps within one complete time step. Specifically, we propose two algorithms that can generate optimal checkpoint-ing schedules under weak assumptions. The first is an extension of the seminal Revolve algorithm adapted to multistage schemes. The second algorithm, named CAMS, is developed based on dynamic programming, and it requires the least number of recomputations when compared with other algorithms. The CAMS algorithm is made publicly available in a library with bindings to C and Python. Numerical results show that the proposed algorithms can deliver up to two times the speedup compared with that of classical Revolve. Moreover, we discuss the utilization of the CAMS library in mature scientific computing libraries and demonstrate the ease of using it in an adjoint workflow. The proposed algorithms have been adopted by the PETSc TSAdjoint library. Their performance has been demonstrated with a large-scale PDE-constrained optimization problem on a leadership-class supercomputer. This work is a significant extension of the authors' conference paper.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

MontePy: a Python library for reading, editing, and writing MCNP input files.

The Monte Carlo N-Particle (MCNP) radiation transport code is a highly capable and accurate code with a long legacy. MCNP uses the Monte Carlo simulation process to simulate the path of particles (e.g., neutrons, photons, charged particles, etc.), and their interaction with materials. It is widely used in nuclear engineering, high-energy physics, and other fields. Its origins in the mid-twentieth century predate many modern software conventions. MCNP users provide an input file to MCNP, which it then uses to create an internal representation of the simulation problem. These input files originally had to be stored as punchcard decks, and the user manual still uses the terminology of cards and decks, despite moving beyond punchcards. MCNP predates nearly all modern human readable markup or data serialization languages, such as the extensible Markup Language (XML), the Standard Generalized Markup Language (SGML), YAML (YAML Ain’t Markup Language), and Javascript Object Notation (JSON). Due to this, MCNP uses an entirely custom defined syntax language for its input, making off-the-shelf libraries for XML, YAML, and JSON impossible to use for scripting various operations on MCNP input files (Kulesza et al., 2022).

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Validation of MCNP Critical Benchmark Models of PU-MET-FAST-016

A new centralized repository of high-quality MCNP models of critical benchmark experiments is currently under development at Los Alamos National Laboratory (LANL). The repository is the combined effort of the Nuclear Criticality Safety, Nuclear Data, and Monte Carlo code development/application organizations at LANL. The initial set of benchmark models in the repository are derived from the Whisper Suite provided with MCNP6.2 and are evaluated against the benchmark experiments described in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook. The goal is to build a single LANL benchmark collection that is up to date with the latest ICSBEP revision, has a formal review and revision process, is contained in an open-source repository, and utilizes new Python tools for improved input and output file review. This paper describes the validation of the models associated with PU-MET-FAST-016, “Flooded 3X3X3 Arrays of 3-kg Plutonium (Pu) Metal Cylinders – Phase I”. In this critical experiment, twenty-seven 3-kg Pu metal cylinders with a height of 46.33 ± 0.15 mm and diameter of 65.25 ± 0.05 mm were arranged in a cubic array. The Pu cylinders were sealed in aluminum cans, and three cans were placed in each of nine perforated aluminum sleeves, as shown in Fig. 1. The nine sleeves were supported by an aluminum frame that allowed for control of the lateral spacing of the cylinders, both in the X and Y directions. The benchmark experiment measured thirteen configurations. Of these configurations, six were modeled using MCNP.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Common Electric Power Transmission System Model JSON Schema Specification

The Common Electric Power Transmission System Model (CTM) is an intuitive, extensible, language-agnostic, and error-resistant specification of electric power network components parameter names and units, and relation between components, intended for use by the research community developing new computational methods for power systems operations and simulation. Power system datasets following the CTM specification can be read as dictionaries and manipulated in that form in most programming languages (e.g., Python, Julia, C++). This standard data structure in CTM makes it easy to work in multiple power systems domains (e.g., economic operation, reliability assessment, electricity markets, stability assessment, etc.) without requiring conversions between use-case-specific file formats with information loss in the process. This repository specifies CTM as a JSON Schema, provides documentation, derivate (code-generated) implementations of CTM, and example data and usage of the schema for important use cases.

Aravena Solis, Ignacio↗
DOE OSTI2024

BioXTAS RAW 2 : new developments for a free open-source program for small-angle scattering data reduction and analysis

BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI ; updated automated Guinier fitting and D max finding algorithms; automated series ( e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares ( REGALS ); creation of electron-density reconstructions using electron density via solution scattering ( DENSS ); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Autodifferentiable Spectrum Model for High-dispersion Characterization of Exoplanets and Brown Dwarfs

We present an autodifferentiable spectral modeling of exoplanets and brown dwarfs. This model enables a fully Bayesian inference of the high-dispersion data to fit the ab initio line-by-line spectral computation to the observed spectrum by combining it with the Hamiltonian Monte Carlo in recent probabilistic programming languages. An open-source code, ExoJAX, developed in this study, was written in Python using the GPU/TPU compatible package for automatic differentiation and accelerated linear algebra, JAX. We validated the model by comparing it with existing opacity calculators and a radiative transfer code and found reasonable agreements for the output. As a demonstration, we analyzed the high-dispersion spectrum of a nearby brown dwarf, Luhman 16 A, and found that a model including water, carbon monoxide, and H 2 /He collision-induced absorption was well fitted to the observed spectrum (R = 10 5 and 2.28-2.30 μm). As a result, we found that T0 = 1295$^{-32}_{+35}$ K at 1 bar and C/O = 0.62 ± 0.03, which is slightly higher than the solar value. This work demonstrates the potential of a full Bayesian analysis of brown dwarfs and exoplanets as observed by high-dispersion spectrographs and also directly imaged exoplanets as observed by high-dispersion coronagraphy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Virtual Engineering Software Framework for Integrated Biomass Conversion Modeling

This presentation covers the design and implementation of a software tool to systematically connect computational models of unit operations to simulate an integrated process of low-temperature conversion of biomass to fuel. This virtual engineering (VE) software was designed with the overarching goal of connecting unit models written in various programming languages and requiring different computational resources within a single, flexible framework. The models and features currently considered for the VE library include mechanistic models for pretreatment, enzymatic hydrolysis, and aerobic bioreaction; high-fidelity computational fluid dynamics (CFD) simulations for enzymatic hydrolysis and aerobic bioreaction; and the capability to perform techno-economic analyses (TEA) using Aspen Plus, a commercial software package. The CFD models require access to high-performance computing (HPC) resources, so in addition to handling multiple programming languages and interfaces, the VE software must also be capable of interacting with an HPC scheduler to submit, run, and post-process jobs. Using the Python programming language, a new VE software package has been developed that contains functionality to manage the input-output communication between various unit models, schedule simulations to run on NREL's HPC and analyze those results, and interface with existing TEA software workflows. A Jupyter-notebook GUI was also created to solicit user input and provide documentation. In cases where multiple models for a particular unit-operation exist, selection between models is accomplished through a simple checkbox, with the appropriate inputs and outputs being parsed and converted seamlessly in the background. Each operation makes use of a different programming language, but the flow of information from pretreatment to enzymatic hydrolysis to bioreaction is managed with an intuitive, centralized file-communication strategy. In this talk, the programming approach and implementation details of the notebook are presented for multiple possibilities of the conversion process, including a demonstration of the ability to manage HPC resources. Additionally, an example of a sensitivity study of treatment parameters governing the overall conversion outcome is shown which highlights the ease of defining new problems using the VE Notebook workflow and leads into a discussion of ongoing work to enable outer-loop optimization studies.

biofuel↗
DOE OSTI2021

Hoobas: A highly object-oriented builder for molecular dynamics

Polydispersity and random sequences are ubiquitous features of polymers, and molecular dynamics simulations can help elucidate the impact of disorder in polymer systems. However, currently available packages for building polymer topologies do not enable the user to include randomness in a straightforward fashion. Here, we introduce Hoobas, a molecular builder package that easily handles polydispersity using a prototype-builder design pattern. This enables fast and easy building of systems comprised of thousands of distinct objects. It is written in the Python programming language, which ensures compatibility with a wide range of molecular dynamics packages and tools, as well as easy integration into most workflows.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Implementing a Laser Stabilization System for Trapping Ca+ Ions: an Internship Reflection

At Lawrence Livermore National Laboratory, I contributed to a project developing 3D printed micro ion traps for quantum computing. I designed, implemented, and assessed a laser stabilization system that locked lasers to the frequencies required for calibrating our High Finesse WS8-10 wavelength meter and for laser cooling and trapping of Ca+ ions. I also programmed a Python interface for hardware communication, data collection, and statistical analysis. Additionally, I optimized and aligned laser beam paths, and I implemented a closed digital feedback loop using Proportional, Integral, and Derivative (PID) control parameters. I analyzed both the long-term and short-term behavior of our locked lasers and adjusted PID parameters to enhance performance. Furthermore, I used COMSOL to simulate the capacitance of a linear Paul trap design and predict our trap’s performance. The procedures I developed for the interface, analysis, and simulations will continue to support the ion trapping experiment after my appointment. I strengthened my skills in data analysis, Python coding, and optical alignment for laser systems. My confidence as a researcher grew, particularly in communicating my research. This experience taught me the importance of careful planning and consideration in research and solidified my desire to continue exploring novel quantum technology as an undergraduate

42 ENGINEERING↗
DOE OSTI2021

Performance of Julia for High Energy Physics Analyses

We argue that the Julia programming language is a compelling alternative to currently more common implementations in Python and C++ for common data analysis workflows in high energy physics. We compare the speed of implementations of different workflows in Julia with those in Python and C++. Furthermore, our studies show that the Julia implementations are competitive for tasks that are dominated by computational load rather than data access. For work that is dominated by data access, we demonstrate an application with concurrent file reading and parallel data processing.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

P SI4 1.4: Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4 's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. We announce a rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
DOE OSTI2024

xesn: Echo state networks powered by Xarray and Dask

Xesn is a Python package that allows scientists to easily design Echo State Networks (ESNs) for forecasting problems. ESNs are a Recurrent Neural Network architecture introduced by Jaeger (2001) that are part of a class of techniques termed Reservoir Computing. One defining characteristic of these techniques is that all internal weights are determined by a handful of global, scalar parameters, thereby avoiding problems during backpropagation and reducing training time significantly. Because this architecture is conceptually simple, many scientists implement ESNs from scratch, leading to questions about computational performance. Xesn offers a straightforward, standard implementation of ESNs that operates efficiently on CPU and GPU hardware. The package leverages optimization tools to automate the parameter selection process, so that scientists can reduce the time finding a good architecture and focus on using ESNs for their domain application. Importantly, the package flexibly handles forecasting tasks for out-of-core, multi-dimensional datasets, eliminating the need to write parallel programming code. Xesn was initially developed to handle the problem of forecasting weather dynamics, and so it integrates naturally with Python packages that have become familiar to weather and climate scientists such as Xarray (Hoyer & Hamman, 2017). However, the software is ultimately general enough to be utilized in other domains where ESNs have been useful, such as in signal processing (Jaeger & Haas, 2004).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

PyDislocDyn: Code Manual

PyDislocDyn [1] is a suite of python programs designed to perform various calculations for basic research in dislocation dynamics in metals with various crystal symmetries in the continuum limit.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

An end-to-end workflow for executing a classically bootstrapped variational quantum algorithm on an academic quantum computer

Academic quantum computing platforms often face unique challenges in executing quantum workloads due to fragmented software environments and limited engineering support. Unlike commercial ecosystems, academic devices typically evolve without full-stack integration in mind, making it difficult to run complex applications—such as variational quantum algorithms (VQA)—reliably and efficiently. Issues such as incompatible software layers and lack of automated job management significantly increase the overhead of theory-experiment collaboration. To address these challenges, we develop a modular, end-to-end workflow that decouples application-layer code from low-level hardware control, automates circuit submission and result collection, and supports fine-grained circuit-level job scheduling and recovery. The architecture employs a dual-end application programming interface (API) design, enabling robust operation across unstable or resource-constrained hardware backends. For practical use, the framework is lightweight and user-friendly, allowing rapid prototyping of full-stack workflows using basic Python tools. We validate this workflow on a high-fidelity trapped-ion quantum computer by demonstrating a variational quantum eigensolver (VQE) experiment with a classically bootstrapped ansatz initialization technique. The system successfully executed over 60,000 circuits across multiple molecular test cases with minimal human intervention, highlighting the framework’s effectiveness in enabling reproducible, resilient quantum experimentation in academic settings.

Clifford↗
DOE OSTI2020

Enabling Catalog Simulations of Transient and Variable Sources Based on LSST Cadence Strategies

The American Astronomical Society. All rights reserved.. The Large Synoptic Survey Telescope (LSST) project will conduct a 10 year multi-band survey starting in 2022. Observing strategies for this survey are being actively investigated, and the science capabilities can be best forecasted on the basis of simulated strategies from the LSST Operations Simulator (OpSim). This paper describes the way in which OpSim simulates a stochastic realization of the sequence of LSST pointings over the survey duration, and is based on a model of the observatory (including telescope) and historical data of observational conditions. OpSim outputs contain a record of each simulated pointing of the survey along with a complete characterization of the pointing in terms of observing conditions, and some useful quantities derived from the characteristics of the pointing. Thus, each record can be efficiently used to derive the properties of observations of all astrophysical sources found in that pointing. However, in order to obtain the time series of observations (light curves) of a set of sources, it is often more convenient to compute all observations of an astrophysical source, and iterate over sources. In this document, we describe the open source python package OpSimSummary, which allows for a convenient reordering. The objectives of this package are to provide users with an Application Programming Interface for accessing all such observations and summarizing this information in the form of intermediate data products usable by third party software such as SNANA, thereby also bridging the gap between official LSST products and preexisting simulation codes.

79 ASTRONOMY AND ASTROPHYSICS↗