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At least 217 records · Page 12

Comparison of steady-state analytical wake models implemented in wind farm analysis software

A common set of mathematical wind turbine wake models are implemented in a few, well-adopted computational tools for wind farm wake modelling. Although the referenced mathematical formulations are common, implementation details may lead to differences in results. This study presents a systematic comparison of the implementation of mathematical wake models in open source, Python-based wind turbine wake modelling software, and a set of the models are directly compared. Despite aligning only the mathematical model parameters and retaining the default computational model parameters, good agreement is found across most of the model implementations, and additional agreement is expected upon further parameters alignment.

17 WIND ENERGY↗

Terrestrial laser scanning data (Levels 0 and 1) for Pasoh, Malaysia, Sep 2024

This data package contains data from terrestrial laser scanning (TLS) at the Pasoh Forest Reserve, Malaysia. The Pasoh Forest Reserve is a facility of the Forest Research Institute Malaysia, and contains evergreen lowland dipterocarp forest. The Next-Generation Ecosystem Experiments Tropics (NGEE-Tropics) study areas at Pasoh were established to study how different species respond to climatic variation and soil water availability. Two study areas were chosen representing different topography and species. The TLS data archived here were collected to provide detailed, three-dimensional information about forest structure. Specifically, data were collected to allow tree-level characterization of woody structure and leaf area for 12 focal trees with FloraPulse and sap flux sensors, facilitating estimation of woody biomass and leaf area to allow upscaling of water content and transpiration data to the tree-level. Scan positions were not selected to provide consistent data for non-focal trees with the study areas. This data package contains the following data: - High-level files document further details of the campaign and data package: 1_CampaignSummary.csv provides details about the campaign and study site, 2_ScanAreasDetail.csv provides details about each separate scan area (groups of scans post-processed into a single point cloud), 3_TerrestrialLidarSensor.csv provides further technical details about the Riegl VZ-400i TLS sensor, TLS_CSV_dd.csv is a CSV Data Dictionary providing information about the fields in CSV files following the ESS-DIVE CSV File Formatting Guidelines Reporting Format, TLS_flmd.csv is a File Level Metadata file providing information about each file in the data package following the ESS-DIVE File Level Metadata Reporting Format, and README.txt is a text file describing the overall project and file structure. - Level 0 data are the raw data (.PROJ folders) as recorded by the Riegl VZ-400i TLS instrument before scan co-registration and post-processing with the Riegl's proprietary RiSCAN PRO software, which requires a license. - Level 1 data contain post-processed, co-registered data from each scan area. The "PointClouds" folder for each scan area contains a .las file with 1 cm resolution point cloud data exported from RiSCAN PRO. These are the main files likely to be of interest to most users and can be further processed with any software capable of manipulating .las files (e.g. Python, R CloudCompare). The "Project Information" folder contains log files from post-processing in RiSCAN PRO that may be of interest to users who want to see detailed records of post-processing, including all PDF reports generated by RiSCAN PRO. The "ScanPositions" folder contains information about the final position of all TLS scans, after post-processing, in multiple formats. The file ScanPositions_*.csv provides final geo-referenced scan positions, and the file SOP_backup_*.csv can be used in RiSCAN PRO to restore the co-registered scan positions if users wish to re-process raw data (Level 0 .PROJ folders) with RiSCAN PRO software (e.g., subsample to a different resolution, exclude a certain scan position, or apply different filters on reflectance or deviation values) without redoing time-consuming co-registration steps.

54 ENVIRONMENTAL SCIENCES↗

Terrestrial laser scanning data (Levels 0 and 1) from Urban Biogeochemistry Pilot Project sites, Knoxville, Tennessee, Jul 2024 - Jul 2025

This data package contains data from terrestrial laser scanning (TLS) at five urban park sites in Knoxville, Tennessee, USA. All parks include open-grown and/or closed-canopy trees and mixed nearby land use. These study sites were established as part of the Urban Biogeochemistry Pilot Project, which has an overall goal of better understanding how hydrobiogeochemical cycling is altered within the human environment. These five sites represent a gradient of urbanization, and were instrumented to understand hydrological and biogeochemical cycling (e.g., soil moisture, soil physical properties and biogeochemistry, tree transpiration, species type). The TLS data archived here were collected to provide detailed, three-dimensional information about forest structure. Specifically, data were collected to allow tree- and stand-level characterization of woody structure and leaf area. TLS scans were placed to capture the area around trees with sap flow sensors, and as much of a 50 m radius area around the meteorological station as possible given site property limits. Derived products will allow upscaling of water content and transpiration data. This data package contains the following data: - High-level files document further details of the campaign and data package: 1_CampaignSummary.csv provides details about the campaign and study site, 2_ScanAreasDetail.csv provides details about each separate scan area (groups of scans post-processed into a single point cloud), 3_TerrestrialLidarSensor.csv provides further technical details about the Riegl VZ-400i TLS sensor, TLS_CSV_dd.csv is a CSV Data Dictionary providing information about the fields in CSV files following the ESS-DIVE CSV File Formatting Guidelines Reporting Format, TLS_flmd.csv is a File Level Metadata file providing information about each file in the data package following the ESS-DIVE File Level Metadata Reporting Format, and README.txt is a text file describing the overall project and file structure. - Level 0 data are the raw data (.PROJ folders) as recorded by the Riegl VZ-400i TLS instrument before scan co-registration and post-processing with the Riegl's proprietary RiSCAN PRO software, which requires a license. - Level 1 data contain post-processed, co-registered data from each scan area. The "PointClouds" folder for each scan area contains a .las file with 1 cm resolution point cloud data exported from RiSCAN PRO. These are the main files likely to be of interest to most users and can be further processed with any software capable of manipulating .las files (e.g. Python, R CloudCompare). The "Project Information" folder contains log files from post-processing in RiSCAN PRO that may be of interest to users who want to see detailed records of post-processing, including all PDF reports generated by RiSCAN PRO. The "ScanPositions" folder contains information about the final position of all TLS scans, after post-processing, in multiple formats. The file ScanPositions_*.csv provides final geo-referenced scan positions, and the file SOP_backup_*.csv can be used in RiSCAN PRO to restore the co-registered scan positions if users wish to re-process raw data (Level 0 .PROJ folders) with RiSCAN PRO software (e.g., subsample to a different resolution, exclude a certain scan position, or apply different filters on reflectance or deviation values) without redoing time-consuming co-registration steps.

54 ENVIRONMENTAL SCIENCES↗

TRINIDI (Time-of-Flight Resonance Imaging with Neutrons for Isotopic Density Inference)

This software is an open-source Python library that provides tools for processing hyperspectral neutron time-of-flight radiography data. This type of data allows material decomposed reconstructions to be generated with the use of material characteristic spectral responses and the algorithms provided in this code library. The software library will contain tools for pre-processing the neutron measurement data, estimating measurement system parameters, reconstructing material decomposed radiographs, and computing material decomposed computed tomography (CT). Furthermore, it will have capability to generate and process simulated neutron time-of-flight data with the goal of benchmarking and demonstrating the tools that are provided. The software will include thorough documentation and application examples.

Balke, Thilo↗

Hydrologic Model Data for the East Fork Poplar Creek Watershed Simulated with the Advanced Terrestrial Simulator (ATS): Streamflow and Network Expansion–Contraction Dynamics

This dataset supports hydrologic modeling and stream network expansion–contraction analysis for the East Fork Poplar Creek (EFPC) Watershed in Tennessee. It includes a Jupyter notebook for model setup, model configuration files, simulation outputs, and derived products used to evaluate model performance and investigate stream dynamics under varying hydrologic conditions. The dataset was generated using the Watershed Workflow Python package and the Advanced Terrestrial Simulator (ATS), enabling integrated surface–subsurface hydrologic simulations using a stream-aligned mesh. Outputs include high-resolution time series of streamflow, active network length, water table depth, and related hydrologic variables. Also included are spatially explicit stream persistency indices and classifications of reaches as perennial or non-perennial. These data facilitate reproducibility and support further research on stream intermittency and variability in network extent.The model data archive is organized in following directories:1) model_setup_inputsContains the Watershed Workflow Jupyter notebooks (accessed through any open source code editor), selected input datasets, and resulting ATS input files, including XML files (access through any open source code editor), computational mesh (.exo files can be viewed using Paraview), and meteorological forcing files (.h5 files can be accessed through h5py python package and HDFView open source software). 2) model_outputsIncludes ATS simulation outputs relevant to this study. Time series of spatially integrated or averaged variables (e.g., streamflow, water table depth) are provided as CSV files. Select spatial fields (e.g., ponded depth and water table depth) are saved as pickled Python objects to reduce file size, and can be accessed through pickle package in Python. Key geometry objects from Watershed Workflow—such as the surface mesh and river tree—are also included to support analysis of streamflow persistency and expansion–contraction dynamics. These files can also be accessed through Watershed Workflow Python package.3) model_evaluationProvides observed streamflow time series and field survey-based flow regime classifications used to evaluate model performance. Jupyter notebooks for processing ATS outputs and comparing model predictions with observations to build confidence in the model prior to scientific analysis are also included.4) Q_L_relationshipsContains workflows for generating time series of discharge, active network length, and related hydrologic variables used in the stream network expansion–contraction analysis. Includes routines for delineating baseflow-dominated periods. For each catchment, notebooks and processed data (as pickled DataFrames accessed through Pandas Python package) are provided. 5) figure_scriptsProvides the Jupyter notebooks used to generate the figures presented in the paper.

54 ENVIRONMENTAL SCIENCES↗

Integrating ytopt and libEnsemble to autotune OpenMC

Ytopt is a Python machine-learning-based autotuning software package developed within the ECP PROTEAS-TUNE project. The ytopt software adopts an asynchronous search framework that consists of sampling a small number of input parameter configurations and progressively fitting a surrogate model over the input-output space until exhausting the user-defined maximum number of evaluations or the wall-clock time. libEnsemble is a Python toolkit for coordinating workflows of asynchronous and dynamic ensembles of calculations across massively parallel resources developed within the ECP PETSc/TAO project. libEnsemble helps users take advantage of massively parallel resources to solve design, decision, and inference problems and expands the class of problems that can benefit from increased parallelism. In this paper we present our methodology and framework to integrate ytopt and libEnsemble to take advantage of massively parallel resources to accelerate the autotuning process. Specifically, we focus on using the proposed framework to autotune the ECP ExaSMR application OpenMC, an open source Monte Carlo particle transport code. OpenMC has seven tunable parameters some of which have large ranges such as the number of particles in-flight, which is in the range of 100,000 to 8 million, with its default setting of 1 million. Setting the proper combination of these parameter values to achieve the best performance is extremely time-consuming. Therefore, we apply the proposed framework to autotune the MPI/OpenMP offload version of OpenMC based on a user-defined metric such as the figure of merit (FoM) (particles/s) or energy efficiency energy-delay product (EDP) on Crusher at Oak Ridge Leadership Computing Facility. In conclusion, the experimental results show that we achieve the improvement up to 29.49% in FoM and up to 30.44% in EDP.

Autotuning↗

PyDDA: A Pythonic Direct Data Assimilation Framework for Wind Retrievals

This software assimilates data from an arbitrary number of weather radars together with other spatial wind fields (eg numerical weather forecasting model data) in order to retrieve high resolution three dimensional wind fields. PyDDA uses NumPy and SciPy’s optimization techniques combined with the Python Atmospheric Radiation Measurement (ARM) Radar Toolkit (Py-ART) in order to create wind fields using the 3D variational technique (3DVAR). PyDDA is hosted and distributed on GitHub at https://github.com/openradar/PyDDA. PyDDA has the potential to be used by the atmospheric science community to develop high resolution wind retrievals from radar networks. These retrievals can be used for the evaluation of numerical weather forecasting models and plume modelling. This paper shows how wind fields from 2 NEXt generation RADar (NEXRAD) WSR-88D radars and the High Resolution Rapid Refresh can be assimilated together using PyDDA to create a high resolution wind field inside Hurricane Florence.

54 ENVIRONMENTAL SCIENCES↗

CMLM (Co-Optimized Machine-Learned Manifolds) [SWR-23-41]

Co-optimized Machine-Learned Manifolds (CMLM) is a data-driven approach for developing reduced-order manifold models for high-dimensional chemically reacting systems. It involves a specially designed neural network, the training of which simultaneously optimizes linear combinations of species that define the manifold, nonlinear mapping to outputs of interest such as reaction rates, and (optionally) subfilter closure for large eddy simulation. This software package provides an implementation of the CMLM approach in Python using the PyTorch machine learning library. A few example cases are included, showing how the tool can be applied to different types of data from 0D and 1D reacting simulations performed using Cantera. The neural networks can be saved in a format that is readable by the Pele suite of combustion solvers for use in reacting computational fluid dynamics simulations. This software repository contains several python scripts to perform various tasks associated with the Co-optimized Machine Learned Manifolds (CMLM) model, which is described in Perry, Henry de Frahan, and Yellapantula, CNF, 2022 (https://doi.org/10.1016/j.combustflame.2022.112286). This includes not only the code that defines the CMLM model, but also scripts to generate suitable training data, scripts to pre-process the data, scripts to train the CMLM model, and scripts to plot the output, as well as various other helper files. The scripts depend on several commonly used python libraries for data analysis and chemical reaction computations. The trained models that result from this tool are designed to work with the an interface being implemented in the Pele suite of reacting flow solvers (https://github.com/AMReX-Combustion).

Perry, Bruce↗

Sensitivity Analysis of MFiX-PIC Parameters Using Nodeworks, PSUADE, and DAKOTA

The study presented in this report was aimed to demonstrate UQ analysis performed not only with Nodeworks, but also two other well-established UQ software tools from the U.S. DOE’s National Laboratories (PSUADE from Lawrence Livermore National Laboratory and DAKOTA from Sandia National Laboratory). It is important to emphasize that the motivation of this study was not to determine the best UQ software, but to verify if the global sensitivity analyses from the end-to-end workflow in Nodeworks are consistent with the results of other two UQ software. The components of Nodeworks from Python’s ecosystem have been tested as standalone libraries. However, an assessment study for the complete workflow targeting a specific UQ analysis has not been performed for Nodeworks. Hence, this study is expected to serve as an equivalent of solution verification for Nodeworks using other established UQ tools as reference solution. For this purpose, three distinct flow configurations (i.e., settling bed, bubbling fluidized, and circulating fluidized bed) have been used as representative multiphase flow problems of interest. The results of the systematic simulation campaigns performed in an earlier study using the particle-in-cell (PIC) approach in the Multiphase Flow with Interphase eXchanges (MFIX) suite of solvers (i.e., MFiX-PIC) was utilized. The same set of tabulated results was provided as input to the different UQ software for global sensitivity analysis. Results for the three cases indicate that based on the Sobol’ Sensitivity Indices method the order of importance ranking determined by Nodeworks for the Sobol’ Total Sensitivity Indices is consistent with PSUADE and DAKOTA in each case for the five model parameters considered. The input files for Nodeworks for the three cases are also shared through NETL’s Gitlab repository for the reader interested in reproducibility and further analysis (See Section 1.2).

97 MATHEMATICS AND COMPUTING↗

Cardinal: Seismic and Geoacoustic Array Processing

Data collected via seismic and infrasound array deployments are leveraged in the geosciences to detect and characterize a myriad of natural and anthropogenic sources. These deployments consist of numerous sensors placed in a predetermined configuration to amplify signal strength and improve the efficacy of array processing techniques used to measure signal directionality and waveform coherence. High‐fidelity feature extraction is often predicated on interstation distance as well as the frequency content and wavelength of an incident signal. Numerous array processing softwares analyze data in sequential frequency bands to obtain a more detailed characterization of a signal. However, current algorithms are limited in their ability to determine optimal array configuration for each band. We introduce an open‐source Python code, called Cardinal, to process seismic and infrasound array data in discretized time–frequency space with the option of applying an adaptive array design to determine optimal subarray configuration for each frequency band. To reduce computational time, the array processing step can be run in parallel using multithreading. Furthermore, the software has the capability to aggregate array processing results from different time–frequency pixels to produce separate sets of detections, or families, with added utility via the application of an adaptive semblance threshold, which aids in isolating signals‐of‐interest from coherent background noise. Upon appropriate configuration, Cardinal exhibits the potential to combine distinct seismic and infrasound phases into separate families.

Adaptive Array↗

AtomAI framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy

Over the past several decades, electron and scanning probe microscopes have become critical components of condensed matter physics, materials science and chemistry research. At the same time, the infrastructure for establishing a connection between microscopy observations and materials behaviour over a broader parameter space is lacking. In this work, we introduce AtomAI, an open-source software package bridging instrument-specific Python libraries, deep learning and simulation tools into a single ecosystem. AtomAI allows direct applications of deep neural networks for atomic and mesoscopic image segmentation converting image and spectroscopy data into class-based local descriptors for downstream tasks such as statistical and graph analysis. For atomically resolved imaging data, the output is types and positions of atomic species, with an option for subsequent refinement. AtomAI further allows the implementation of a broad range of image and spectrum analysis functions, including invariant variational autoencoders for disentangling structural factors of variation and im2spec type of encoder–decoder models for mapping structure–property relationships. Finally, our framework allows seamless connection to the first principles modelling with a Python interface on the inferred atomic positions.

36 MATERIALS SCIENCE↗

Serpent and MCNP Calculations of the Energy Deposition in the Transformational Challenge Reactor

This paper focuses on the calculation of the energy deposition in the Transformational Challenge Reactor by two major Monte Carlo codes: Serpent and MCNP. The first software computation relies on Kinetic Energy Released per unit Mass (KERMA) factors while the second one relies on Q-values. The results from these two independent computation methodologies are in very good agreement; however, Serpent runs much faster than MCNP (for the same computational model) and allows for a detailed energy deposition distribution from a 1-mm-side square mesh with a relative statistical error between 0.5% and 1%. This detailed energy deposition is suitable for multiphysics analyses aimed at design optimizations. In order to calculate the energy deposition, Serpent needs enhanced ACE files (distributed by the software developers). Unlike other Monte Carlo software that uses inputs based on Python or Java languages, the Serpent input syntax is very similar to that of MCNP; a Python script can convert a MCNP input to a Serpent input in seconds. For simulations not requiring the calculation of the energy deposition, Serpent can also read nuclear data from MCNP ACE files, which eventually improves the comparison of the results of the two codes.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Quantum simulations of SO(5) many-fermion systems using qudits

The structure and dynamics of many-body systems are the result of a delicate interplay between underlying interactions. Fermionic pairing, for example, plays a central role in various physical systems, ranging from condensed matter to nuclear systems, where it can lead to collective phenomena such as superconductivity and superfluidity. In atomic nuclei, the interplay between pairing and particle-hole interactions leads to a high degree of complexity and intricate entanglement structures. Despite this apparent complexity, symmetries emerge and manifest themselves in observable regular patterns. These symmetries and their breakings have long been used to determine relevant degrees of freedom and simplify classical descriptions of many-body systems. Here, this work explores the potential utility of quantum computers with arrays of qudits in simulating interacting fermionic systems, when the qudits can naturally map the relevant degrees of freedom determined by an underlying symmetry group. The Agassi model of fermions interacting via particle-hole and pairing interactions is based on an underlying so(5) algebra. Such systems can intuitively be partitioned into pairs of modes with five basis states, which thus naturally map to arrays of d = 5 qudits (qu5its). Classical noiseless simulations of the time evolution of systems with up to twelve qu5its are performed, by implementing quantum circuits that are developed herein, using PYTHON codes invoking Google's CIRQ software. The resource requirements of the qu5it circuits are analyzed and compared with two different mappings to qubit systems: a physics-aware Jordan-Wigner mapping requiring four qubits per mode pair and a state-to-state mapping requiring three qubits per mode pair. While the dimensionality of Hilbert spaces in mappings to qu5it systems are less than those for the corresponding qubit systems, the number of entangling operations, depending on the available hardware, can either be greater or smaller than for the physics-aware Jordan-Wigner mapping. The state-to-state mapping, while having a smaller Hilbert space than Jordan-Wigner mappings, appears to be the least efficient in gate counts. Further, a previously unknown sign problem has been identified from Trotterization errors in time evolving high-energy excitations. There appear to be advantages in employing quantum computers with arrays of qudits to perform simulations of many-body dynamics that exploit the role of underlying symmetries, specifically in lowering the required quantum resources and in reducing anticipated errors that take the simulation out of the physical space. If the necessary entangling gates are not directly supported by the hardware, physics-aware mappings to qubits may, however, be advantageous for other aspects.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SHARP-Net: Platform for Self-Healing and Attack Resilient PMU Networks

Synchrophasor technology plays a pivotal role in developing the next generation of wide-area monitoring, protection, and control in the smart grid environment. As technology and communications infrastructures evolve, however, so do the attack surfaces in the synchrophasor network that can be exploited by advanced persistent threat (APT) actors to affect power system stability and reliability. In this paper, we propose a novel platform for developing a self-healing and attack-resilient PMU network (SHARP-Net) by instituting a state-of-the-art intrusion detection system (IDS) with an intrusion mitigation system (IMS) and an alert management system (AMS). In particular, the proposed platform detects anomalies during cyberattacks on phasor data concentrators (PDCs) based on the rules defined in the IDS, then the generated alerts are published to the IMS through the AMS. The proposed IMS proceeds to take automated corrective responses to mitigate cyberattacks by reconfiguring the synchrophasor network to isolate the compromised PDCs, and it orchestrates new PDCs to prevent the future propagation of attacks. Further, the IMS restores the system's observability by reconnecting the new PDCs to make the grid attack-resilient. In this work, the SHARP-Net platform is developed by using Python-based libraries, minimega's software-defined network, and virtual machine orchestration. We implement and validate the proposed SHARP-Net architecture by testing a PMU network in the smart grid environment. SHARP-Net showed promising performance in detecting cyberattacks and mitigating them through the network reconfiguration.

computer architecture↗

qsp4pde v1.0

The software program is a collection of Python implementations of quantum circuits for solving linear partial differential equations using quantum signal processing. The circuits are implemented using the qiskit SDK.

Kim, Hyeongjin [Lawrence Berkeley National Laborat↗

Enabling AI in synthetic biology through Construction File specification

The Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases 'Experiment' objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. The CF specification not only standardizes and modularizes molecular biology operations but also promotes collaboration, automation, and reuse, significantly reducing potential errors. The potential integration of CF with artificial intelligence, particularly GPT-4, suggests innovative automation strategies for synthetic biology. While challenges such as token limits, data storage, and biosecurity remain, proposed solutions promise a way forward in harnessing AI for experiment design. This shift from human-driven design to AI-assisted workflows, steered by high-level objectives, charts a potential future path in synthetic biology, envisioning an environment where complexities are managed more effectively.

59 BASIC BIOLOGICAL SCIENCES↗

Data used in: "Salinity exposure affects lower-canopy specific leaf area of upland trees in a coastal deciduous forest"

We conducted an observational study of SLA in a mid-Atlantic (USA) coastal deciduous forest, taking advantage of a natural gradient in salinity along a tidal creek. Measured SLA of the 239 trees and seven species sampled ranged from Carya glabra (N = 6 trees, mean SLA = 277.9 ± 36.3 cm2 g-1) to Fagus grandifolia (N = 60, 321.9 ± 62.9 cm2 g-1). This work is in press at Forest Ecology and Management.This dataset has two files, "sla_data.csv" (the data) and "sla_metadata.txt" (the metadata). Both are plain-text files and can be read by most software such as text editors, R, Python, Excel, etc. The data file is comma-separated values with 11 columns and 239 rows of data. The metadata file has 11 rows, one for each data column, and giving a plain-text description for each column and any associated units.

54 ENVIRONMENTAL SCIENCES↗