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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Comparison of unfolding methods using RooFitUnfold

In this study we describe RooFitUnfold, an extension of the RooFit statistical software package to treat unfolding problems, and which includes most of the unfolding methods that commonly used in particle physics. The package provides a common interface to these algorithms as well as common uniform methods to evaluate their performance in terms of bias, variance and coverage. In this paper we exploit this common interface of RooFitUnfold to compare the performance of unfolding with the Richardson–Lucy, Iterative Dynamically Stabilized, Tikhonov, Gaussian Process, bin-by-bin and inversion methods on several example problems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

FlexDRL v1.0

FlexDRL is a framework that can be used as a benchmarking tool to evaluate different Deep Reinforcement Learning algorithms in a building energy management setting. OpenAI Gym was used as wrapper to the co-simulation environment (EnergyPlus for envelope and HVAC and Modelica for battery and PV) to interface with DRL algorithms, which are developed in PyTorch. In order to facilitate the usage of FlexDRL, all the required dependencies have been packaged into a Docker container.

Touzani, Samir↗
DOE OSTI2022

Discovery of two-dimensional binary nanoparticle superlattices using global Monte Carlo optimization

Binary nanoparticle (NP) superlattices exhibit distinct collective plasmonic, magnetic, optical, and electronic properties. Here, we computationally demonstrate how fluid-fluid interfaces could be used to self-assemble binary systems of NPs into 2D superlattices when the NP species exhibit different miscibility with the fluids forming the interface. We develop a basin-hopping Monte Carlo (BHMC) algorithm tailored for interface-trapped structures to rapidly determine the ground-state configuration of NPs, allowing us to explore the repertoire of binary NP architectures formed at the interface. By varying the NP size ratio, interparticle interaction strength, and difference in NP miscibility with the two fluids, we demonstrate the assembly of an array of exquisite 2D periodic architectures, including AB-, AB 2 -, and AB 3 -type monolayer superlattices as well as AB-, AB 2 -, A 3 B 5 -, and A 4 B 6 -type bilayer superlattices. Our results suggest that the interfacial assembly approach could be a versatile platform for fabricating 2D colloidal superlattices with tunable structure and properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A Generalized Transformer-Based Pulse Detection Algorithm

Pulse-like signals are ubiquitous in the field of single molecule analysis, e.g., electrical or optical pulses caused by analyte translocations in nanopores. The primary challenge in processing pulse-like signals is to capture the pulses in noisy backgrounds, but current methods are subjectively based on a user-defined threshold for pulse recognition. Here, we propose a generalized machine-learning based method, named pulse detection transformer (PETR), for pulse detection. PETR determines the start and end time points of individual pulses, thereby singling out pulse segments in a time-sequential trace. It is objective without needing to specify any threshold. It provides a generalized interface for downstream algorithms for specific application scenarios. PETR is validated using both simulated and experimental nanopore translocation data. It returns a competitive performance in detecting pulses through assessing them with several standard metrics. Finally, the generalization nature of the PETR output is demonstrated using two representative algorithms for feature extraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Benchmark Solutions for Radiation Transport in Stochastic Media with Inhomogeneous Material Statistics

Accurately solving implicit Monte Carlo (IMC) thermal photon transport problems with mixed material cells is important in realistic applications. The production IMC package at LLNL treats mixed material cells arising from ALE remap and hydrodynamics using the same approximate model. The new Imp IMC thermal photon transport package currently under development has both a material interface reconstruction (MIR) algorithm and a Levermore-Pomraning (LP) stochastic medium algorithm for treating mixed material cells. Existing stochastic medium algorithms for treating mixed material cells in IMC lack a complete theoretical basis. The IMC LP algorithm implementation has been demonstrated to reproduce published deterministic LP solutions for the particular case of spatially homogeneous material statistics. Realistic simulations will include spatially inhomogeneous material statistics (material mean chord lengths). In a previous investigation, the LP-model for transport in binary stochastic media in rod geometry was generalized to accommodate spatially varying material chord lengths, i.e., the mixing statistics were allowed to be nonhomogeneous. Analytical solutions were obtained and used to produce a verifi cation suite for the Imp IMC Levermore-Pomraning implementation for different spatial variations of the chord lengths. However, the accuracy of the LP model when the mixing statistics are nonhomogeneous has not been assessed and leaves open the question of whether local accuracy is improved or further degraded when chord lengths are not uniform. This shortcoming is rectifi ed here by developing benchmark analytic solutions for transport in binary Markovian stochastic mixtures in rod geometry with nonhomogeneous mixing statistics, using spatially varying chord lengths considered in the previous investigation based on the LP model. Methods for sampling a nonhomogeneous Poisson process (NHPP) are first described and used to construct individual realizations of the binary mixtures in rod geometry. Analytic solutions are then obtained for the forward and backward directed fluxes on a given realization, now viewed as a deterministic medium with alternating layers of the two materials with known interface locations. Finally, material averaged scalar fluxes are obtained using these sampling schemes with spatially linear and quadratic chord lengths and used to assess the accuracy of the previously obtained LP-model results.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Auto-BLAST (AutoBLAST) [SWR-20-93]

Battery life modeling often involves a lot of manual parameter fitting and is not easy for users to adopt the model and use it. To reduce the difficulties for users to adopt battery lifetime models, an automatic battery lifetime modeling analysis and simulation tool suite, Auto-BLAST, has been developed. Auto-BLAST includes a lithium-loss-base life model, a battery electric model, and an algorithm which automatically fits all key parameters in the electric and life models using user provided data. The models and algorithm are packaged into two user-friendly GUIs, Auto-LifeMod, for easy battery life prognostic model fitting and Auto-LifeSim, for easy battery lifetime simulation. The lithium-loss-based life model adopts a similar model framework that models degradations using aging rate models, using battery cycling data to predict battery degradation and expected lifetime. The electric model is an equivalent circuit model which simulates battery voltage responses based on current/power demand profiles. The auto-fitting algorithm uses the user-input data to generate custom battery life model(s). Two GUIs, wrapping around the life model and the auto-fitting algorithm, provide friendly interfaces for users to generate a life model and use it for case study. One GUI requires summary data from accelerated battery life degradation tests as an input and produces battery life models predicting (a) capacity degradation, and (b) resistance growth of the battery. The GUI displays the electrical model response and the input experimental data against the life model predictions with fitted model parameters and fitting error. The GUI also generates an output file to save the fitted model parameters. The second GUI uses the life model from the first GUI and a user-defined battery cycling profile to predict battery lifetime degradation and expected lifetime. Predicted capacity and resistance vs. time are plotted in the GUI and saved to output file. There is a user guide for both GUIs

Mishra, Partha↗
DOE OSTI2024

minervachem

Minervachem is a tool for cheminformatics and machine learning in chemistry. It includes both algorithms from existing literature and algorithms which we have developed. Its features center around two main themes: molecular representations and algorithms, both for molecular machine learning. It provides a scikit-learn transformer interface for molecular featurization and an estimator interface for machine learning algorithms. It also provides visualization tools for explaining machine learning predictions. We aim to continue developing this software to improve its performance and usability and expand its capabilities within the realm of molecular machine learning, cheminformatics, and visualization.

Lubbers, Nicholas↗
DOE OSTI2020

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Flexible and Modular Simultaneous Modeling of Flow and Reactive Transport in Rivers and Hyporheic Zones

Investigations of coupled multiphysics processes in rivers and hyporheic zones have extensively used numerical models. Most existing models use a sequential, one-way coupling between the surface and subsurface domains. Such one-way coupling potentially introduces error. To overcome this, a fully coupled model, hyporheicFoam, was developed using the open-source computational platform OpenFOAM. It captures the coupled flow and multicomponent reactive transport processes within both surface and subsurface domains and across their interface. The coupling between two domains is implemented by mapping conservative flux boundary conditions at the interface through an iterative algorithm. Reactive transport is enabled by specifying a reaction network. To start, we have implemented reaction kinetics following the double Monod-type model with inhibition. The model capability is illustrated through modeling of both conservative and reactive hyporheic flow and transport through dune bedforms. With the novel coupled model, it is now possible to quantify reactions wherein the reactants and products are constantly exchanging between domains and have feedbacks. hyporheicFoam can simulate large, three-dimensional cases owing to the computational flexibility and power offered by the code structure and parallel design of OpenFOAM.

58 GEOSCIENCES↗
DOE OSTI2025

Optimizing Grain Boundary Structures with LAMMPS Using Evolutionary Algorithms

Grain boundary structure optimization is an important part of materials modeling. Current methods for grain boundary structure optimization involve inefficient, time-consuming processes that do not fully explore the interface parameter space. Evolutionary algorithms have recently been demonstrated to be effective at determining both stable and metastable grain boundary interface structures. In this work, we demonstrate the use of GBOpt, a grain boundary structure optimization software designed to use the Large-scale Atomic/Molecular Massively Parallel Simulation (LAMMPS) software to efficiently determine grain boundary structures. We demonstrate that a only a few manipulations, namely atom insertion, atom removal, and relative grain displacement, are sufficient to explore much of the grain boundary structure parameter space. The efficacy of this approach is demonstrated on an FCC Ni system, and a BCC Fe system. The computational cost is compared against the gamma-surface sampling approach to demonstrate performance improvement.

Evolutionary algorithms↗
DOE OSTI2021

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Livermore tomography tools: Accurate, fast, and flexible software for tomographic science

Livermore Tomography Tools (LTT) is a customizable scientific software package that enables a broad range of research and development efforts into computed tomography (CT). Here, it was developed to process x-ray and neutron CT data accurately and rapidly from raw detector counts to reconstructed volumes with the flexibility to handle many special cases. LTT fulfills long-term CT software goals to provide quantitatively accurate results reported in physical units (e.g., mm -1 or cm -1 ) while exploiting all available computational advantages to maximize speed. Written in C/C++ with support for multiple CPUs and GPUs, LTT runs on many computing platforms (Linux/Unix, Windows, and Mac; laptops to supercomputers). As a result, LTT can:process data acquired from various custom-built and commercially available CT scanners, model and simulate x-ray and neutron interactions to encourage algorithm prototyping, and allow for rapid insertion of the latest algorithms.We describe LTT’s software architecture, user interfaces, and its 88 algorithms (as of this writing) for pre-processing, reconstruction, post-processing, and simulation that support many scanner geometries (parallel-, fan-, cone-beam, and custom). Several applications are presented that illustrate LTT’s accuracy, speed, and flexibility relative to other solutions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

An implicit barotropic mode solver for MPAS-ocean using a modern Fortran solver interface

Here, we demonstrate use of a modern Fortran solver interface to manage solver algorithms for an implicit barotropic mode solver in the Model for Predictions Across Scales-Ocean (MPAS-O). ForTrilinos, a Fortran interface to Trilinos that contains a large collection of solver capabilities written in C++, has been implemented in MPAS-O to provide access to a suite of linear solver options. By virtue of the simplified wrapper and interface generator (SWIG) automation tool that generates modern Fortran interfaces to C++ code, we were able to implement the Fortran solver interface in MPAS-O using a familiar Fortran coding style while minimizing performance degradation. The ForTrilinos solver interface is written within MPAS-O’s time stepping modules as a subroutine in conjunction with MPAS-O code. Applied to an idealized ocean and a high-resolution realistic ocean test case, parallel performance of ForTrilinos solvers is examined. It is found that parallel scalability of the ForTrilinos solvers is highly dependent on the number of global synchronization points per solver iteration in each iterative solver algorithm. ForTrilinos solvers perform best compared to the Fortran hand-crafted (FHC) solver when the amount of work per processor is large enough. However, parallel scalability is better with the FHC solver and so when the work per core is modest FHC outperforms ForTrilinos. The intercomparison between the ForTrilinos and FHC solvers reveals that this performance hit in the ForTrilinos solver mostly comes from the global synchronization process, while suggesting that the matrix-vector multiplication process in the FHC solver needs to be optimized for better performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

RxnRover/CyRxnOpt

CyRxnOpt aims to provide a single software interface to various optimization algorithms, mainly designed for chemical process optimization applications. CyRxnOpt generalizes the optimization process into four high-level “phases”: Installation, Configuration, Training, and Prediction. This allows developers to program to a general interface for each phase of the optimization, simplifying the development of user-friendly tools to lower the barrier of entry into chemical process optimization, especially for automated laboratory workflows which can greatly benefit from access to various optimization techniques. It is also designed so researchers can easily add new or existing algorithms into existing workflows in a user-friendly manner.

Kulathunga, Dulitha Prasanna [Iowa State Universit↗
DOE OSTI2020

An Eulerian multimaterial framework for simulating high-explosive aquarium tests

Aquarium tests of cylindrical high-explosive charges provide optical data of the detonation front velocity and shape, propagation of the shock wave in the surrounding water, and expansion rates of the detonation products behind the front. Data from aquarium experiments is often used for calibration of reactive burn models based on phenomenological equations of state (EOS) and reaction rate laws. This paper presents a multimaterial numerical modeling framework to solve the 2D axisymmetric reactive Euler equations for high-explosive aquarium tests, in particular for ammonium nitrate - fuel oil (ANFO) explosives. An extension of the Ghost Fluid Method (GFM) is used to handle the dynamic material interfaces for the ANFO explosion products, the charge-confining material (polymethyl methacrylate PMMA), and the surrounding water. This study analyzes the sensitivity of calculations (both computational efficiency and numerical accuracy) to different algorithms for the material interface models including the original GFM versus Riemann solver-based strategies. A novel method for defining the left and right states in the interfacial Riemann problem eliminates the need for sorting or nodal interpolation during the projection along the material interface. Numerical tests indicate that populating the interface node values using the Riemann solution mitigate the overheating error observed in steady-state calculations. Solution convergence and computational efficiency are explored as a function of the spatial and temporal order of the schemes. Results from the computational model with analytical equations of state and fitted reaction rate parameters show very good quantitative agreement with experimentally observed detonation front velocity, reaction products expansion, and shock wave propagation in the surrounding water for a cylindrical ANFO charge encased in PMMA. Finally, the proposed modeling framework, in conjunction with experimental tests, provides a reliable tool to assess equations of state and reaction rate expressions for reactive burn models of confined high explosives.

42 ENGINEERING↗
DOE OSTI2025

Sharp front tracking with geometric interface reconstruction

Here, this paper presents a novel sharp front-tracking method designed to address limitations in classical front-tracking approaches, specifically their reliance on smooth interpolation kernels and extended stencils for coupling the front and fluid mesh. In contrast, the proposed method employs exclusively sharp, localized interpolation and spreading kernels, restricting the coupling to the interfacial fluid cells–those containing the interface/front. This localized coupling is achieved by integrating a divergence-preserving velocity interpolation method with a piecewise parabolic interface calculation (PPIC) and a polyhedron intersection algorithm to compute the indicator function and local interface curvature. Surface tension is computed using the Continuum Surface Force (CSF) method, maintaining consistency with the sharp representation. Additionally, we propose an efficient local roughness smoothing implementation to account for surface mesh undulations, which is easily applicable to any triangulated surface mesh. Building on our previous work, the primary innovation of this study lies in the localization of the coupling for both the indicator function and surface tension calculations. By reducing the interface thickness on the fluid mesh to a single cell, as opposed to the 4–5 cell spans typical in classical methods, the proposed sharp front-tracking method achieves a highly localized and accurate representation of the interface. This sharper representation mitigates parasitic currents and improves force balancing, making it particularly suitable for scenarios where the interface plays a critical role, such as microfluidics, fluid-fluid interactions, and fluid-structure interactions. The proposed method is comprehensively validated and tested on canonical interfacial flow problems, including stationary and translating Laplace equilibria, oscillating droplets, and rising bubbles. The presented results demonstrate that the sharp front-tracking method significantly outperforms the classical approach in terms of accuracy, stability, and computational efficiency. Notably, parasitic currents are reduced by approximately two orders of magnitude and stable results are obtained for parameter ranges where classical front tracking fails to converge.

42 ENGINEERING↗
DOE OSTI2021

Multichannel Analysis of Surface Waves Accelerated (MASWAccelerated): Software for efficient surface wave inversion using MPI and GPUs

Multichannel Analysis of Surface Waves (MASW) is a technique frequently used in geotechnical engineering and engineering geophysics to infer 1D layered models of seismic shear wave velocities in the top tens to hundreds of meters of the subsurface. We aim to accelerate MASW calculations by capitalizing on modern computer hardware available in the workstations of most engineers: multiple cores and graphics processing units (GPUs). We propose new parallel and GPU accelerated algorithms for computing 1D MASW inversion, and provide software implementations in C using Message Passing Interface (MPI) and CUDA. These algorithms take advantage of sparsity that arises in the problem, and the work balance between processes considers typical data trends. We compare our methods to an existing open source Matlab MASW tool. Our serial C implementation achieves a 2x speedup over the Matlab software, and we continue to see improvements by parallelizing the problem with MPI. Here we see nearly perfect strong and weak scaling for uniform data, and improve strong scaling for realistic data by repartitioning the problem to process mapping. By utilizing GPUs available on most modern workstations, we observe an additional 1.3x speedup over the serial C implementation on the first use of the method. We typically repeatedly evaluate theoretical dispersion curves as part of an optimization procedure, and on the GPU the kernel can be cached for faster reuse on later runs. We observe a 3.2x speedup on the cached GPU runs compared to the serial C runs. This work is the first open-source parallel or GPU-accelerated software tool for MASW imaging, and should enable geotechnical engineers to fully utilize all computer hardware at their disposal.

58 GEOSCIENCES↗