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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

PsDNS

PsDNS is a Python package which makes it easy to solve partial differential equation using a pseudo-spectral method. The code uses Python classes and Numpy-like arrays to provide a simple interface with which users can construct equations, integrators, and diagnostics. It also includes implementation for common problems, in particular, the incompressible Navier-Stokes equation in a periodic domain, which is commonly used as a benchmark problem for turbulence research. PsDNS uses MPI to allow massively parallel computation for large problems.

Israel, Daniel↗
DOE OSTI2022

pyJSPEC - A Python Module for IBS and Electron Cooling Simulation

The intrabeam scattering is an important collective effect that can deteriorate the property of a high-intensity beam and electron cooling is a method to mitigate the IBS effect. JSPEC (JLab Simulation Package on Electron Cooling) is an open-source C++ program developed at Jefferson Lab, which simulates the evolution of the ion beam under the IBS and/or the electron cooling effect. The Python wrapper of the C++ code, pyJSPEC, for Python 3.x environment has been recently developed and released. It allows the users to run JSPEC simulations in a Python environment. It also makes it possible for JSPEC to collaborate with other accelerator and beam modeling programs as well as plentiful python tools in data visualization, optimization, machine learning, etc. In this paper, we will introduce the features of pyJSPEC and demonstrate how to use it with sample codes and numerical results.

Zhang, H.↗
NASA NTRSDate not supplied

Graphical User Interface (GUI) Implementation for Agent-Based Microbial Radiobiology Model

Sending human life past the Low Earth Orbit (LEO) to explore the Moon and Mars will be challenging. The Earth’s magnetic field naturally protects life from deep-space particle radiation such as Galactic Cosmic Rays (GCR) and Solar Particle Events (SPE); these will pose health risks to humans in deep space. Research has been done to investigate these effects, like BioSentinel, the first biological CubeSat to fly beyond the LEO, designed to culture yeast in a microfluidic device and record optical measurements of growth and metabolism. However, experiments can only report cell damage as bulk growth curves, while deep-space radiation causes damage that is heterogeneous among individual cells. AMMPER is an open-source, agent-based, computational model coded in Python to simulate the effects of deep-space radiation on individual yeast cells (Saccharomyces cerevisiae) to facilitate interpretation of biological radiation experiments. Version 1.0 of the code ran in a command line interface (CLI), limiting use to those familiar with modularization, object-oriented programming, and computational models. Here we present a graphical user interface (GUI) for AMMPER to increase its accessibility. GUI development included converting input points and UI files, designing an application and logo, and expanding program packages. Additionally, we added optical assistance that corresponded with simulation parameters, which included simulation type, cell type, ROS model, and radiation dosage, as well as customizable display and file exportation features. Following a pilot testing period, its structure was updated further to enhance abilities, adding increased runs, video visualization, data plotting, and an educational/tutorial component. Future work will include creating a bit installer and runtime environment for AMMPER. Ultimately, the creation of the GUI has two main goals: to facilitate the integration of computational models into the work of researchers in microbial radiobiology, and to act as an interactive and visual resource for space biology education.

yeast↗
DOE OSTI2023

UQpy v4.1: Uncertainty quantification with Python

This paper presents the latest improvements introduced in Version 4 of the UQpy, Uncertainty Quantification with Python, library. In the latest version, the code was restructured to conform with the latest Python coding conventions, refactored to simplify previous tightly coupled features, and improve its extensibility and modularity. To improve the robustness of UQpy, software engineering best practices were adopted. A new software development workflow significantly improved collaboration between team members, and continuous integration and automated testing ensured the robustness and reliability of software performance. Continuous deployment of UQpy allowed its automated packaging and distribution in system agnostic format via multiple channels, while a Docker image enables the use of the toolbox regardless of operating system limitations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Limits on wCDM from the EFTofLSS with the PyBird code

We apply the Effective Field Theory of Large-Scale Structure to analyze the wCDM cosmological model. By using the full shape of the power spectrum and the BAO post-reconstruction measurements from BOSS, the Supernovae from Pantheon, and a prior from BBN, we set the competitive CMB-independent limit $w=-1.046_{-0.052}^{+0.055}$ at 68% C.L. After adding the Planck CMB data, we find $w=-1.023_{-0.030}^{+0.033}$ at 68% C.L. Our results are obtained using PyBird, a new, fast Python-based code which we make publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Curifactory: A research experiment manager

Curifactory is a command line tool and framework for organizing Python experiment code, configuration parameters, and results. It is an opinionated and lightweight approach to workflow management infrastructure and is primarily intended to support researchers conducting experiments on one machine. This software was developed to support the reproducibility of results for several data science projects in the Nuclear Nonproliferation Division at Oak Ridge National Laboratory. Curifactory is intended to be a general framework and is not specific to machine learning or data science. It can aid in any field in which experiments are primarily computation-based studies and can be implemented in Python (e.g., high-energy physics, astronomy, computational chemistry). Here, the design emphasizes the automated caching of intermediate data analysis artifacts to speed up development involving computationally intensive tasks. It also allows for data provenance and experiment reproduction. Individual experiment runs are tracked through logs and their output reports, and entire copies of a run with all cached data and metadata can be exported for others to run using Curifactory on another machine. Curifactory experiments can either be integrated into a project from the beginning or can be written on top of an existing codebase without needing significant modification. A few important views of the Curifactory library can be seen in Figure 1.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

INGRID: An interactive grid generator for 2D edge plasma modeling

A fusion boundary-plasma domain is defined by axisymmetric magnetic surfaces where the geometry is often complicated by the presence of one or more X-points; and modeling boundary plasmas usually relies on computational grids that account for the magnetic field geometry. The new grid generator INGRID (Interactive Grid Generator) presented in this work is a Python-based code for calculating grids for fusion boundary plasma modeling, for a variety of configurations with one or two X-points in the domain. INGRID first performs partitioning over the domain consisting of a small number of patches conforming to the magnetic field and wall geometry; then it generates a subgrid on each of the patches and joins them into a global grid. This domain partitioning strategy makes possible a uniform treatment of various configurations with one or two X-points in the domain. This includes single-null, double-null, and other configurations with two X-points in the domain. The INGRID design allows generating grids either interactively, via a parameter-file driven GUI, or using a non-interactive script-controlled workflow. Results of testing demonstrate that INGRID is a flexible, robust, and user-friendly grid-generation tool for fusion boundary-plasma modeling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Machine learning guided optimal composition selection of niobium alloys for high temperature applications

Nickel- and cobalt-based superalloys are commonly used as turbine materials for high-temperature applications. However, their maximum operating temperature is limited to about 1100 °C. Therefore, to improve turbine efficiency, current research is focused on designing materials that can withstand higher temperatures. Niobium-based alloys can be considered as promising candidates because of their exceptional properties at elevated temperatures. The conventional approach to alloy design relies on phase diagrams and structure–property data of limited alloys and extrapolates this information into unexplored compositional space. In this work, we harness machine learning and provide an efficient design strategy for finding promising niobium-based alloy compositions with high yield and ultimate tensile strength. Unlike standard composition-based features, we use domain knowledge-based custom features and achieve higher prediction accuracy. We apply Bayesian optimization to screen out novel Nb-based quaternary and quinary alloy compositions and find these compositions have superior predicted strength over a range of temperatures. We develop a detailed design flow and include Python programming code, which could be helpful for accelerating alloy design in a limited alloy data regime.

Mohanty, Trupti (ORCID:0000000342701430)↗
DOE OSTI2025

Demonstration of TOFFEE: A Response Uncertainty Quantification Tool

A key characteristic in neutron transport is nuclear data. Cross-section uncertainty is not used in MCNP6.3 to propagate response uncertainty without external analysis. Here, the TOol For Fast Error Estimation (TOFFEE) is a Python-based code developed to automate the propagation of cross-section uncertainty for MCNP evaluations. TOFFEE implements the sandwich rule to calculate the uncertainty from cross sections with sensitivity coefficients from MCNP6.3 and ENDF/B covariance data. In this paper, TOFFEE has been tested with benchmark experiments, and it has been compared to the uncertainty quantification capabilities of Sampler and TSUNAMI, within SCALE, to verify the application’s capabilities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

${\tt Warm}$SPy: a numerical study of cosmological perturbations in warm inflation

We present ${\tt Warm}$SPy, a numerical code in Python designed to solve for the perturbations' equations in warm inflation models and compute the corresponding scalar power spectrum at CMB horizon crossing. In models of warm inflation, a radiation bath of temperature T during inflation induces a dissipation (friction) rate of strength Q ∝ T c /Φ m in the equation of motion for the inflaton field Φ. While for a temperature-independent dissipation rate (c = 0) an analytic expression for the scalar power spectrum exists, in the case of a non-zero value for c the set of equations can only be solved numerically. For c > 0 (c < 0), the coupling between the perturbations in the inflaton field and radiation induces a growing (decaying) mode in the scalar perturbations, generally parameterized by a multiplicative function G(Q) which we refer to as the scalar dissipation function. Using ${\tt Warm}$SPy, we provide an analytic fit for G(Q) for the cases of c = {3,1,-1}, corresponding to three cases that have been realized in physical models. Compared to previous literature results, our fits are more robust and valid over a broader range of dissipation strengths Q ϵ [10 -7 ,10 4 ]. Additionally, for the first time, we numerically assess the stability of the scalar dissipation function against various model parameters, inflationary histories as well as the effects of metric perturbations. As a whole, the results do not depend appreciably on most of the parameters in the analysis, except for the dissipation index c, providing evidence for the universal behaviour of the scalar dissipation function G(Q).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural complexity of snapshots of two-dimensional Fermi-Hubbard systems

The development of quantum gas microscopy for two-dimensional optical lattices has provided an unparalleled tool to study the Fermi-Hubbard model (FHM) with ultracold atoms. Spin-resolved projective measurements, or snapshots, have played a significant role in quantifying correlation functions, theory verification, and thus the uncovering of underlying physical phenomena such as antiferromagnetism at commensurate filling on bipartite lattices and other charge and spin correlations, as well as dynamical properties at various densities. Here we employ a recent concept, the multiscale structural complexity, and show that when computed for the snapshots (of single spin species, local moments, or total density) it can provide a theory-free property, immediately accessible to experiments. Specifically, after benchmarking results for Ising and $XY$ models, we study the structural complexity of snapshots of the repulsive FHM in the two-dimensional square lattice as a function of doping and temperature. We generate projective measurements using determinant quantum Monte Carlo and compare their complexities against those from the experiment. We demonstrate that these complexities are linked to relevant physical observables such as the entropy and double occupancy. Their behaviors capture the development of correlations and relevant length scales in the system. Furthermore, we provide an open-source code in python which can be implemented into data analysis routines in experimental settings for the square lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Characterization and Optimization of the Fitting of Quantum Correlation Functions

This case study presents a characterization and optimization of an application code for extracting parton distribution functions from high energy electron-proton scattering data. Profiling this application code reveals that the phase-space density computation accounts for 93% of the overall execution time for a single iteration on a single core. When executing multiple iterations in parallel on a multicore system, the application spends 78% of its overall execution time idling due to load imbalance. We address these issues by first transforming the application code from Python to C++ and then tackling the application load imbalance via a hybrid scheduling strategy that combines dynamic and static scheduling. These techniques result in a 62% reduction in CPU idle time and a 2.46x speedup in overall execution time per node. In addition, the typically enabled power-management mechanisms in supercomputers (e.g., AMD Turbo Core, Intel Turbo Boost, and RAPL) can significantly impact intra-node scalability when more than 50% of the CPU cores are used. This finding underscores the importance of understanding system interactions with power management, as they can adversely impact application performance, and highlights the necessity of intra-node scaling tests to identify performance degradation that inter-node scaling tests might otherwise overlook.

Chuang, Pi-Yueh [Virginia Tech,Dept. of Computer S↗
DOE OSTI2021

Sudoku Online Testing Framework v.0.2

The Sudoku Online Testing Framework provides a configurable basis for testing user interactions to solve visualization-related problems with sudoku puzzles and games. It consists of a server, a client, and test code. The python server implements sudoku puzzle logic and board selection functions. The JavaScript client implements a graphical user interface (GUI) front-end to display the puzzles and facilitate interactions with users. Within the GUI, logical rules may be selected. Cells may be selected to “pivot” on to make a board for each possible value in the cell. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-6409 O

Leger, Michelle↗
DOE OSTI2023

LLNL Automized Surface Titration Model

The LLNL Automized Surface Titration Model (L-ASTM) is a community data-driven surface complexation modeling workflow for simulating potentiometric titration of mineral surfaces. The model accepts raw experimental potentiometric titration data formatted in a findable, accessible, interoperable, and reusable (FAIR) structure. The workflow was coded in Python and coupled to PHREEQC for surface complexation modeling and PEST for data fitting and parameter estimation.

Solchan, Han↗
DOE OSTI2024

Metric DBSCAN

SAND2025-11725O Metric DBSCAN is an implementation of the popular DBSCAN clustering algorithm that works in general metric spaces. DBSCAN is a clustering algorithm, a fundamental building block in machine learning. It takes a set of objects and, given some notion of distance, identifies coherent groups of objects. With Metric DBSCAN, users can provide an arbitrary function to compute distance. Nearly all existing implementations of DBSCAN restrict distance to one of a few formulations. Metric DBScan accomplishes this cleanly and efficiently. The Python source code is on Github. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Dalbey, Keith↗
DOE OSTI2020

Alaskan carbon-climate feedbacks will be weaker than inferred from short-term manipulations: Alaskan Benchmark Data and Model runs

This submission aimed to assess differences in short-term step warming manipulations and long-term chronic response to climate change in Alaskan ecosystems. Briefly, climate warming is occurring fastest at high latitudes. Based on short-term field experiments, this warming is projected to stimulate soil organic matter decomposition, and promote a positive feedback to climate change. We show here that the tightly coupled, nonlinear nature of high-latitude ecosystems implies that short-term (< 10 year) warming experiments produce emergent ecosystem carbon stock temperature sensitivities inconsistent with emergent multi-decadal responses. We first demonstrate that a well-tested mechanistic ecosystem model accurately represents observed carbon cycle and active layer depth responses to short-term summer warming in four diverse Alaskan sites. We then show that short-term warming manipulations do not capture the non-linear, long-term dynamics of vegetation, and thereby soil organic matter, that occur in response to thermal, hydrological, and nutrient transformations belowground. Our results demonstrate significant spatial heterogeneity in multi-decadal Arctic carbon cycle trajectories and argue for more mechanistic models to improve predictive capabilities.The model used in the current study is available publicly (https://github.com/jinyun1tang/ECOSYS), and the current submission contains the python/ matlab codes for analyzing output from the model (includng a readme file to explain the codes). The benchmark data, also enclosed, was collected from a range of published and publicly available sources (extracted using GRABIT: https://www.mathworks.com/matlabcentral/fileexchange/7173-grabit). These sources describe warming induced changes in tundra/ boreal ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

IDAES-PSE 2.1.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost, most environmentally sustainable solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.1.0 Release Highlights New IDAES Examples Repository Starting with this release, the IDAES examples are developed in the new IDAES/examples repository. Along with many content and usability improvements, the most significant changes are: To install the examples, after installing IDAES, run pip install idaes-examples The idaes get-examples command, previously used for this, has been removed The HTML version is now available at https://idaes-examples.readthedocs.io The previous URL, https://idaes.github.io/examples-pse, will not be updated and may be removed at some point in the future For more details, refer to the resources available at IDAES/examples. Removal of Non-Functional Apps A review of the code in the idaes/apps and idaes/models_extra folders was undertaken, and a number of tools were identified as being outdated or non-functional and no longer supported by their development teams. Due to this, the following tools have been removed: idaes/apps/alamopy_depr (note that the new ALAMOpy interface remains avaialble in idaes/core/surrogates) idaes/apps/helmet idaes/apps/ripe idaes/apps/roundingRegression idaes/models_extra/carbon_capture Pyomo 6.6 This version of IDAES is the first requiring Pyomo 6.6. This version of Pyomo contains multiple internal improvements and refactorings. While for the majority of cases this should have positive or no impact on solvability of IDAES models, we are aware of a small number of models that have been affected as a result of these changes. For more information, refer to the Pyomo 6.6.1 release notes. Other highlights Model Initialization A prototype API for a new approach to initializing IDAES models is now available which makes available some new techniques for initializing models. This is documented in the Initializing Models Reference Guide Modular Properties Framework Support for some transport properties Helmholtz Equation of State properties Better error checking for case where unit models are set to include phase equilibrium but the property package is set to support only a single phase Multi-Stream Contactor model: a new base model for systems involving contacting of two or more streams with mass transfer. This model is intended to be used as the foundation for models such as membrane separators, solvent extraction and other similar processes. This is documented in the Multi-Stream Contactor Reference Guide idaes/models_extra/power_generation report() methods for unit models using Helmholtz equation of state General Code Maintenance Streamlining of dependencies and creation of new optional dependency groupings to support non-core tools General linting of codebase to ensure compliance with most pylint checks Spell checking of all code and doc strings Removal of backward compatibility code for Python 2

IDAES↗