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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 145 records · Page 8

SPADES (Scalable Parallel Discrete Events Simulation) [SWR-24-99]

SPADES (Solver for PArallel Discrete Event Simulation) is an open-source parallel discrete event simulation (PDES) package built on the AMReX library. Targeted at solving discrete event systems in parallel, this software package aims to be performance portable and scalable on heterogeneous computing architectures, e.g., graphic processing units (GPU). SPADES implements optimistic synchronization with rollback through an implementation of the Time Warp algorithm. An alternative conservative synchronization approach is also implemented using the Lower Bound on Incoming Time Stamp. In our implementation, logical processes are represented as cells in a grid and event messages are represented as particles. SPADES supports various parallel decomposition strategies, including the use of the Message Passing Interface (MPI) and OpenMP threading. All major GPU architectures (e.g., Intel, AMD, NVIDIA) are supported through the use of performance portability functionalities implemented in AMReX. The SPADES software is released in NREL Software Record SWR-24-99 “SPADES (Scalable Parallel Discrete Events Simulation)”.

Henry de Frahan, Marc [National Renewable Energy L↗

DeePKS-kit: A package for developing machine learning-based chemically accurate energy and density functional models

We introduce DeePKS-kit, an open-source software package for developing machine learning based energy and density functional models. DeePKS-kit is interfaced with PyTorch, an open-source machine learning library, and PySCF, an ab initio computational chemistry program that provides simple and customized tools for developing quantum chemistry codes. It supports the DeePHF and DeePKS methods. In addition to explaining the details in the methodology and the software, we also provide an example of developing a chemically accurate model for water clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MolSym : A Python package for handling symmetry in molecular quantum chemistry

A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program’s environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. Furthermore, this package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗

InverseBench: Inverse design benchmark suite that contains inverse problems from science and engineering (InverseBench) v0.0.1

A software package that contains three inverse design blackbox problems to investigate the efficiency and accuracy of inverse design machine learning models. The software contains highly accurate forward machine learning models that can be used to assess the inverse predictions. The package also contains separate test data for each problem. The inverse design problems that are in the package are: airfoil inverse design, scalar boundary reconstruction and photonic surfaces inverse design.

Grbcic, Luka [Lawrence Berkeley National Laborator↗

Architecture for Quantum Time-dependent Circuits (ArQTIC) v1.0

ArQTiC is a domain-specific full-stack software package built for the dynamic simulations of materials on quantum computers. Its main contributions include providing a software library for high-level programming of such simulations on quantum computers, and providing post-processing capabilities that allow users to more efficiently analyze results from the quantum computer. Paired with the power to optimize and execute quantum circuits, ArQTiC opens the field of dynamic materials simulations on quantum computers to a broader community of scientists from a wider range of domain sciences, paving the way for accelerated progress towards physical quantum supremacy.

Bassman, Lindsay↗

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↗

Mappymatch FKA: YAMM (Yet Another Map-Matcher) [SWR 22-38]

A surprisingly non-trivial technical challenge is to associate points in space (e.g., GPS data) with specific segments of a road network or map. The software package ( allows users to match GPS point data to a road network (commonly known as "map matching"). The software is designed such that a user could match a set of GPS points to a variety of different road network representations using a variety of map matching algorithms. There are currently several "built-in" road networks and map matching algorithms but the software has been designed to enable new ones to be added with minimal overhead.

Reinicke, Nicholas↗

hybridlane (fka CV-DV Quantum Circuit API)

This software package will abstract building a CV-DV quantum circuit for simulation and running on hardware. Existing simulation software each has their own API. This software intends to define a common API to be executed on several simulation and physical hardware backends.

Stavenger, Tim [Pacific Northwest National Laborat↗

SAS4A/SASSYS-1 VERIFICATION AND VALIDATION TEST SUITE

SAS4A/SASSYS-1 is a safety analysis software package already under copyright by Argonne National Laboratory. There is interest from third-party users of the software to gain access to our internal verification and validation test suite. Therefore we are seeking to establish copyright over the test suite, which includes input files and reference results for hundreds of test cases that demonstrate functionality of the software. Making the test suite available to licensed users allows them to utilize the broad range of tests for commercial grade dedication activities needed to qualify the SAS4A/SASSYS-1 software under their own Software Quality Assurance program for use in a regulatory environment (e.g. with the Nuclear Regulatory Commission).

FANNING, THOMAS↗

SmoQyDQMC.jl: A flexible implementation of determinant quantum Monte Carlo for Hubbard and electron-phonon interactions

We introduce the SmoQyDQMC.jl package, a Julia implementation of the determinant quantum Monte Carlo algorithm. SmoQyDQMC.jl supports generalized tight-binding Hamiltonians with on-site Hubbard and generalized electron-phonon ( e e -ph) interactions, including non-linear e e -ph coupling and anharmonic lattice potentials. Our implementation uses hybrid Monte Carlo methods with exact forces for sampling the phonon fields, enabling efficient simulation of low-energy phonon branches, including acoustic phonons. The SmoQyDQMC.jl package also uses a flexible scripting interface, allowing users to adapt it to different workflows and interface with other software packages in the Julia ecosystem. The code for this package can be downloaded from our GitHub repository at https://github.com/SmoQySuite/SmoQyDQMC.jl or installed using the Julia package manager. The online documentation, including examples, can be obtained from our document page at https://smoqysuite.github.io/SmoQyDQMC.jl/stable/.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Codebase release r0.3 for SmoQyDQMC.jl

We introduce the SmoQyDQMC.jl package, a Julia implementation of the determinant quantum Monte Carlo algorithm. SmoQyDQMC.jl supports generalized tight-binding Hamiltonians with on-site Hubbard and generalized electron-phonon ( e e -ph) interactions, including non-linear e e -ph coupling and anharmonic lattice potentials. Our implementation uses hybrid Monte Carlo methods with exact forces for sampling the phonon fields, enabling efficient simulation of low-energy phonon branches, including acoustic phonons. The SmoQyDQMC.jl package also uses a flexible scripting interface, allowing users to adapt it to different workflows and interface with other software packages in the Julia ecosystem. The code for this package can be downloaded from our GitHub repository at https://github.com/SmoQySuite/SmoQyDQMC.jl or installed using the Julia package manager. The online documentation, including examples, can be obtained from our document page at https://smoqysuite.github.io/SmoQyDQMC.jl/stable/.

Cohen-Stead, Benjamin (ORCID:0000000279156280)↗

ORNL Package Testing Program Software Quality Assurance Plan

The Oak Ridge National Laboratory (ORNL) Package Testing Program (PTP) uses commercial off-the-shelf (COTS) software in performing data collection of thermal test results for package designs that contain radioactive materials. Specifically, this software is used to collect temperature data from the furnace, packages, and ambient air to prepare and execute the thermal test specified in 10 CFR 71.73, “Thermal Test.” This software quality assurance (SQA) plan sets forth the guidelines, standards, and procedures that shall be used to provide SQA for PTP software applications. This is a living document that will be maintained for the lifecycle of the PTP program. The SQA plan follows the requirements set forth in ORNL Standards Based Management System (SBMS): Information Technology; Subject Area: Software Quality Assurance. When applicable to the requirements as described in ORNL SBMS, Software Quality Assurance, the software shall be listed in the ORNL Software Registration System (SRS). Exemptions to this SBMS are COTS and firmware that are not modified; spreadsheet applications and personal productivity tools that do not have a utility or safety application, research applications, legacy software, system software, vendor-supplied software used to interface with the vendor’s services, software used within the organization to facilitate processing or management of information, and software developed for applications not specific to the US Department of Energy (DOE).

97 MATHEMATICS AND COMPUTING↗

RadSim: Math, Utility & RTK

This package includes three parts, (1) gov.llnl.math, (2)gov.llnl.utility and (3)gov.llnl.rtk, which are utilized in the development of Radiation Detector Simulator (RadSim) project. RadSim is being developed to provide the capability to: (1) simulate radiation source emissions, (2) interpolate results from radiation transport tools into a common format to prepare incident flux, and (3) model radiation detector response to rapidly produce synthetic radiation measurement templates. RadSim is targeted for open-source release, which will enable researchers and industry partners to model gamma-ray detectors response to simulated flux from the transport tool of their choice. The techniques and implementation will be entirely transparent, which will allow for improvements and boutique modifications by future researchers beyond the lifespan of this specific project. The first tool of the package, gov.llnl.math, includes classes and functions to define and perform basic math operations. Some of the example features available in the package include defining statistical distributions and performing algebra and matrix operations, all of which are already accessible on publicly available software packages such as MATLAB and ROOT. The second package gov.llnl.utility includes tools commonly used to enable optimization and readability of various data structures such as Java lists and external xml files. Lastly, the gov.llnl.rtk package includes classes and functions to implement methods commonly used in radiation physics, such as data structures to represent and characterize photon spectra and tools to apply well-defined and published methods to calibrate a given spectra.

Cheung, Hoi Sing↗

PathTrace and MPVEASI: A Path Analysis Comparative Validation Study

Developed in 2018, PathTrace is a software package built with the intention of making path analysis simple and intuitive. PathTrace is a top-down pathway analysis software where a user is able to explore vulnerable pathways into a facility. The intention of utilizing a software tool like PathTrace is to characterize an existing physical protection system (PPS) and to upgrade the system to achieve a high level of response interruption, or probability of interruption (P I ) of the adversary. There are four steps for conducting path analysis using PathTrace. The first step is to identify an image to use to build the model and scale the model within PathTrace using a section of known distance (wall or fence perimeter, for example). The scaling process will produce a grid of cells through which the user is able to build a model. The second step is to fill out the grid of cells with four categories of materials: Barriers, Detection Areas, Jumps, and Targets. These materials apply associated delay and detection values to the cells in which they are applied. The third step is to represent the adversary and response forces. The adversaries are represented by their capabilities in interacting with the materials identified in step two, and the response is represented by how quickly they will be able to respond to an adversary attack. Finally, the user is able to take all of the information from the previous three steps and perform a Most Vulnerable Path (MVP) analysis. In this stage, the user is able to visualize vulnerable adversary pathways and reason about how to upgrade these pathways to provide a high level of P I .

97 MATHEMATICS AND COMPUTING↗

Stabilizing a strongly nonlinear structure through shaker dynamics in fixed frequency voltage control tests

Bifurcations are commonly encountered during force controlled swept and stepped sine testing of nonlinear structures, which generally leads to the so-called jump-down or jump-up phenomena between stable solutions. There are various experimental closed-loop control algorithms, such as control-based continuation and phase-locked loop, to stabilize dynamical systems through these bifurcations, but they generally rely on specialized control algorithms that are not readily available with many commercial data acquisition software packages. A recent method was developed to experimentally apply sequential continuation using the shaker voltage that can be readily deployed using commercially available software. By utilizing the stabilizing effects of electrodynamic shakers and the force dropout phenomena in fixed frequency voltage control sine tests, this approach has been demonstrated to stabilize the unstable branch of a nonlinear system with three branches, allowing for three multivalued solutions to be identified within a specific frequency bandwidth near resonance. Recent testing on a strongly nonlinear system with vibro-impact nonlinearity has revealed jumping behavior when performing sequential continuation along the voltage parameter, like the jump phenomena seen during more traditional force controlled swept and stepped sine testing. Here, this paper investigates the stabilizing effects of an electrodynamic shaker on strongly nonlinear structures in fixed frequency voltage control tests using both numerical and experimental methods. The harmonic balance method is applied to the coupled shaker-structure system with an electromechanical model to simulate the fixed voltage control tests and predict the stabilization for different parameters of the model. The simulated results are leveraged to inform the design of a set of experiments to demonstrate the stabilization characteristics on a fixture-pylon assembly with a vibro-impact nonlinearity. Through numerical simulation and experimental testing on two different strongly nonlinear systems, the various parameters that influence the stability of the coupled shaker-structure are revealed to better understand the performance of fixed frequency voltage control tests.

42 ENGINEERING↗

2025 ASMS Investigation of the Collision-Induced Dissociation Mechanism of Protonated TODGA with IRIS

Title (20 words): Investigation of the Collision-Induced Dissociation Mechanism of Protonated TODGA with IRIS Introduction (120 words): One of the challenges facing wide-spread adoption of nuclear power is the development of efficient separation processes for used nuclear fuel. The molecules in separation processes are subjected to an extreme environment due to the high radiation fields from the used fuel and highly acidic media used for fuel dissolution, which results in significant molecular degradation, leading to reduced process efficiency. These degradation products must be identified and studied so mitigation strategies can be developed to maintain process efficiency. However, complex systems can have many degradation products, complicating identification. Untargeted analysis tools could be used to understand radiation chemistry in complex systems. However, this would necessitate improved understanding of the gas-phase fragmentation mechanisms of fuel cycle molecules like tetraoctyldiglycolamide (TODGA). Methods (120 words): The gas-phase fragmentation of protonated TODGA was investigated using collision-induced dissociation (CID), resonance ejection, and infrared ion spectroscopy (IRIS). CID and resonance ejection experiments were conducted using a Bruker Daltonics (Bremen, Gemany) SolariX XR fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. IRIS spectra of protonated TODGA and its two CID fragmentation products were measured using a modified Bruker amaZon Speed ETD 3D quadrupole ion trap mass spectrometer coupled to the Free Electron Lasers for Infrared eXperiments (FELIX) free electron laser. Measured spectra were compared with density functional theory (DFT) calculations using the Gaussian 16, Revision C.02 software package with the ?B97X-D functional and def2-TZVPP basis sets. Candidate structures were generated using the CREST 3.0 conformational sampling software tool. Preliminary Data (300 words): Collision-induced dissociation of protonated TODGA ([C36H73N2O3]+, m/z=581.562) results two fragment ions, one at m/z=340.285 assigned as [C20H38NO3]+ and the other at m/z=312.290, assigned as [C19H38NO2]+. Based on the assigned formula and the structure of protonated TODGA, the fragment at m/z=340.285 is likely formed from elimination of neutral dioctylamine. Comparison of the IRIS spectrum of m/z=340.285 with DFT predictions suggests it contains a ring structure, and is assigned as N-octyl-N-(6-oxo-1,4-dioxan-2-ylidene)octan-1-aminium. Based on this structure and the structure of protonated TODGA, we hypothesize this fragment formed from elimination of neutral dioctylamine followed by a ring closure mechanism. Comparison of the IRIS spectrum of the fragment at m/z=312.290 with DFT predictions also indicated the presence of a ring structure, assigned as N-(1,3-dioxolan-4-ylidene)-N-octyloctan-1-aminium. This product could be formed from elimination of carbon monoxide from the ring of m/z=340.285 as a sequential fragmentation or formed directly from protonated TODGA via elimination of neutral N,N-dioctylformamide followed by a ring closure. Resonance ejection experiments where m/z=340 was continuously ejected from the IRC cell showed no decrease in intensity of m/z=312.290 across several collision energies, suggesting that the later, direct formation mechanism, dominates. The location of the ionizing proton in protonated TODGA is important for modeling the fragmentation mechanisms. DFT calculations suggested that the position of bands involving the coupled vibrations of the amide C—N and C=O bonds in TODGA are the most sensitive to proton location. Evaluation of the IRIS spectrum of protonated TODGA suggests that the ionizing proton is located between the two amid oxygens. This protonation location was calculated to lie approximately 30 kJ/mol lower in energy than the next lowest energy location, with the proton located solely on one of the amide oxygens. Novel aspect (20 words): Infrared ion spectroscopy combined with resonance ejection experiments and density functional theory to probe the collision-induced dissociation mechanism of tetraoctyldiglycolamide.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗