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Arkin, Adam P. (ORCID:0000000249992931)↗
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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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Real-time 3D analysis during electron tomography using tomviz
The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.
36 MATERIALS SCIENCE↗
A database of battery materials auto-generated using ChemDataExtractor
A database of battery materials is presented which comprises a total of 292,313 data records, with 214,617 unique chemical-property data relations between 17,354 unique chemicals and up to five material properties: capacity, voltage, conductivity, Coulombic efficiency and energy. 117,403 data are multivariate on a property where it is the dependent variable in part of a data series. The database was auto-generated by mining text from 229,061 academic papers using the chemistry-aware natural language processing toolkit, ChemDataExtractor version 1.5, which was modified for the specific domain of batteries. The collected data can be used as a representative overview of battery material information that is contained within text of scientific papers. Public availability of these data will also enable battery materials design and prediction via data-science methods. To the best of our knowledge, this is the first auto-generated database of battery materials extracted from a relatively large number of scientific papers. We also provide a Graphical User Interface (GUI) to aid the use of this database.
25 ENERGY STORAGE↗
GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging
Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.
36 MATERIALS SCIENCE↗
TEMImageNet training library and AtomSegNet deep-learning models for high-precision atom segmentation, localization, denoising, and deblurring of atomic-resolution images
Abstract Atom segmentation and localization, noise reduction and deblurring of atomic-resolution scanning transmission electron microscopy (STEM) images with high precision and robustness is a challenging task. Although several conventional algorithms, such has thresholding, edge detection and clustering, can achieve reasonable performance in some predefined sceneries, they tend to fail when interferences from the background are strong and unpredictable. Particularly, for atomic-resolution STEM images, so far there is no well-established algorithm that is robust enough to segment or detect all atomic columns when there is large thickness variation in a recorded image. Herein, we report the development of a training library and a deep learning method that can perform robust and precise atom segmentation, localization, denoising, and super-resolution processing of experimental images. Despite using simulated images as training datasets, the deep-learning model can self-adapt to experimental STEM images and shows outstanding performance in atom detection and localization in challenging contrast conditions and the precision consistently outperforms the state-of-the-art two-dimensional Gaussian fit method. Taking a step further, we have deployed our deep-learning models to a desktop app with a graphical user interface and the app is free and open-source. We have also built a TEM ImageNet project website for easy browsing and downloading of the training data.
25 ENERGY STORAGE↗
An open experimental database for exploring inorganic materials
The use of advanced machine learning algorithms in experimental materials science is limited by the lack of sufficiently large and diverse datasets amenable to data mining. If publicly open, such data resources would also enable materials research by scientists without access to expensive experimental equipment. Here, we report on our progress towards a publicly open High Throughput Experimental Materials (HTEM) Database (htem.nrel.gov). This database currently contains 140,000 sample entries, characterized by structural (100,000), synthetic (80,000), chemical (70,000), and optoelectronic (50,000) properties of inorganic thin film materials, grouped in >4,000 sample entries across >100 materials systems; more than a half of these data are publicly available. This article shows how the HTEM database may enable scientists to explore materials by browsing web-based user interface and an application programming interface. This paper also describes a HTE approach to generating materials data, and discusses the laboratory information management system (LIMS), that underpin HTEM database. Finally, this manuscript illustrates how advanced machine learning algorithms can be adopted to materials science problems using this open data resource.
36 MATERIALS SCIENCE↗
Qresp, a tool for curating, discovering and exploring reproducible scientific papers
We propose a strategy and present a simple tool to facilitate scientific data reproducibility by making available, in a distributed manner, all data and procedures presented in scientific papers, together with metadata to render them searchable and discoverable. In particular, we describe a graphical user interface (GUI), Qresp, to curate papers (i.e. generate metadata) and to explore curated papers and automatically access the data presented in scientific publications.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
An approach to and web-based tool for infectious disease outbreak intervention analysis
Infectious diseases are a leading cause of death globally. Decisions surrounding how to control an infectious disease outbreak currently rely on a subjective process involving surveillance and expert opinion. However, there are many situations where neither may be available. Modeling can fill gaps in the decision making process by using available data to provide quantitative estimates of outbreak trajectories. Effective reduction of the spread of infectious diseases can be achieved through collaboration between the modeling community and public health policy community. However, such collaboration is rare, resulting in a lack of models that meet the needs of the public health community. Here we show a Susceptible-Infectious-Recovered (SIR) model modified to include control measures that allows parameter ranges, rather than parameter point estimates, and includes a web user interface for broad adoption. We apply the model to three diseases, measles, norovirus and influenza, to show the feasibility of its use and describe a research agenda to further promote interactions between decision makers and the modeling community.
60 APPLIED LIFE SCIENCES↗
An Error Analysis Toolkit for Binned Counting Experiments
We introduce the MINERvA Analysis Toolkit (MAT), a utility for centralizing the handling of systematic uncertainties in HEP analyses. The fundamental utilities of the toolkit are the MnvHnD, a powerful histogram container class, and the systematic Universe classes, which provide a modular implementation of the many universe error analysis approach. These products can be used stand-alone or as part of a complete error analysis prescription. They support the propagation of systematic uncertainty through all stages of analysis, and provide flexibility for an arbitrary level of user customization. This extensible solution to error analysis enables the standardization of systematic uncertainty definitions across an experiment and a transparent user interface to lower the barrier to entry for new analyzers.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
On the existence of the optimal order for wavefunction extrapolation in Born-Oppenheimer molecular dynamics
Wavefunction extrapolation greatly reduces the number of self-consistent field (SCF) iterations and thus the overall computational cost of Born-Oppenheimer molecular dynamics (BOMD) that is based on the Kohn–Sham density functional theory. Going against the intuition that the higher order of extrapolation possesses a better accuracy, we demonstrate, from both theoretical and numerical perspectives, that the extrapolation accuracy firstly increases and then decreases with respect to the order, and an optimal extrapolation order in terms of minimal number of SCF iterations always exists. We also prove that the optimal order tends to be larger when using larger MD time steps or more strict SCF convergence criteria. By example BOMD simulations of a solid copper system, we show that the optimal extrapolation order covers a broad range when varying the MD time step or the SCF convergence criterion. Therefore, we suggest the necessity for BOMD simulation packages to open the user interface and to provide more choices on the extrapolation order. Another factor that may influence the extrapolation accuracy is the alignment scheme that eliminates the discontinuity in the wavefunctions with respect to the atomic or cell variables. We prove the equivalence between the two existing schemes, thus the implementation of either of them does not lead to essential difference in the extrapolation accuracy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Adaptive smart simulator for characterization and MPPT construction of PV array
Partial shading conditions are among the most important problems in large photovoltaic array. Many works of literature are interested in modeling, control and optimization of photovoltaic conversion of solar energy under partial shading conditions, The aim of this study is to build a software simulator similar to hard simulator and to produce a shading pattern of the proposed photovoltaic array in order to use the delivered information to obtain an optimal configuration of the PV array and construct MPPT algorithm. Graphical user interfaces (Matlab GUI) are built using a developed script, this tool is easy to use, simple, and has a rapid of responsiveness, the simulator supports large array simulations that can be interfaced with MPPT and power electronic converters.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
An HDF5-Based Framework for the Distribution and Analysis of Ultrasonic Concrete Data
There are many commercial ultrasonic tomography devices (UTDs) available for use in nondestructive evaluation (NDE) of reinforced concrete structures. These devices emit, measure, and store ultrasonic signals typically in the 25 kHz to 5 MHz frequency range. UTDs are characterized by a composition of multiple transducers, also known as a transducer array or phased array. Often, UTDs data are in a proprietary format. Consequently, NDE research data is limited to those who have prior non-disclosure agreements or the appropriate licenses. Thus, there is a need for a proper universal data framework to exist such that proprietary file datasets for different concrete specimens can be converted, organized, and stored with relative metadata for individual or collaborative NDE research. Building upon the Hierarchical Data Format (HDF5) model, we have developed a UTD data management framework and Graphic User Interface (GUI) to promote the algorithmic reconstruction of ultrasonic data in a controlled environment for easily reproducible and publishable results.
concrete NDE↗
A parametric SPICE model for the simulation of spark gap switches
The use of SPICE-based software for the simulation of pulsed power systems—even large complex systems—has become commonplace in the pulsed power community. This is in contrast to earlier work in the field that relied on specially developed simulation codes such as Sandia’s Screamer or the Navy Research Lab’s Bertha, which natively incorporated models for common pulsed power components such as spark gap switches. Unlike these programs, SPICE programs provide a simple and familiar user interface and wide availability. However, SPICE programs do not include realistic models for key pulsed power circuit devices—including the spark gap switch. While simple switch models do exist in SPICE programs, these can only crudely approximate the behavior of a spark gap. This effort focuses on developing an SPICE circuit model for a gas-filled spark gap switch that is physically realistic while being simple enough to permit simulations to run in reasonable times on typical personal computers. Detailed information is provided for implementation in two common versions of SPICE: LTspice and Orcad PSPICE. Adaptation to other SPICE programs is possible with minimal modification. The model is intended as a design tool that uses physical parameters as inputs to connect it directly to the development of useable pulsed power systems. Data collected from the operation of a high-pressure pulsed-charged switch and a complete 12-stage Marx generator have been used to demonstrate the implementation and accuracy of the model over a wide range of parameters.
Pouncey, J. Cameron (ORCID:0000000153500816)↗
A field programmable gate array-based timing and control system for the dynamic compression sector
A field programmable gate array (FPGA)-based timing and trigger control system has been developed for the Dynamic Compression Sector (DCS) user facility located at the Advanced Photon Source (APS) at Argonne National Laboratory. The DCS is a first-of-its-kind capability dedicated to dynamic compression science. All components of the DCS laser shock station—x-ray choppers, single-shot shutter, internal laser triggers, and shot diagnostics—must be synchronized with respect to the arrival of x rays in the hutch. An FPGA synchronized to the APS storage ring radio frequency clock (352 MHz) generates trigger signals for each stage of the laser and x-ray shutter system with low jitter. The developed FPGA-based control system was the first system used to control the laser and the shutter system since its commissioning, and it has been developing since then to improve the timing jitter. The system is composed of a Zynq FPGA, a debug card, line drivers, and a power supply. The delay and offsets of the trigger signals can be adjusted by using a user-friendly graphical user interface with high precision. Here, the details of the system architecture, timing requirements, firmware, and software implementation along with the performance evaluation are presented in this paper. The system offers low timing jitter (15.5 ps rms) with respect to the APS 352 MHz clock, suitable for the 100 ps (FWHM) x-ray bunch duration at the APS.
47 OTHER INSTRUMENTATION↗
Characterization of a new ultra-high pressure shock tube facility for combustion and propulsion studies
A new shock tube facility has been designed, constructed, and characterized at the University of Central Florida. This facility is capable of withstanding pressures of up to 1000 atm, allowing for combustion diagnostics of extreme conditions, such as in rocket combustion chambers or in novel power conversion cycles. For studies with toxic gas impurities, the high initial pressures required the development of a gas delivery system to ensure the longevity of the facility and the safety of the personnel. Data acquisition and experimental propagation were implemented with remote access to ensure safety, paired with a LabVIEW- and Python-based user interface. Thus far, test pressures of 270 atm, blast pressures of 730 atm, and temperatures approaching 10 000 K have been achieved. The extreme limitations of this facility allow for emission spectroscopy to be performed during the oxidation of fuel mixtures, e.g., alkanes diluted in argon and carbon dioxide. Ignition delay times were determined and compared to simulations using chemical kinetic mechanisms. The design, experimental procedures, processes of analysis, and uncertainty determination are outlined, and typical pressure profiles are compared with a new gas dynamics solver and empirical correlations developed across multiple shock tube facilities. Preliminary reactive mixture analyses are included with further investigation of the mixtures outlined.
47 OTHER INSTRUMENTATION↗
GPAW: An open Python package for electronic structure calculations
We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe–Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn–Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Design of an experimental breeder reactor run 138B reactor physics benchmark evaluation management application
Reactor Monte Carlo simulations present numerous challenges including input file generation and processing output files for relevant results. Creating an input file for a heterogeneous core is further complicated when using depleted fuel. Performing perturbations to geometry and material characteristics exacerbates the challenge due to human errors if the input files are manually generated. The difficulty of generating input files is often encountered during the process of performing a reactor physics benchmark evaluation. These challenges were encountered in this study when performing a reactor physics benchmark evaluation for the Experimental Breeder Reactor II (EBR-II), a sodium cooled fast reactor. The EBR-II Monte Carlo input file uses more than 1,000 unique material specifications and ~8,000 regions. To address the input file generation challenge, a computer application was designed to automate the input file generation process. The application utilizes user input from a graphical user interface in conjunction with spreadsheets containing material and geometric data to generate Monte Carlo input files. The application, called MICKA, was used to generate input files to support the reactor physics benchmark evaluation for EBR-II. This paper describes the reactor configuration and provides information about the application design and capabilities for addressing challenges often encountered in reactor physics benchmark evaluations.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
A non-intrusive parallel-in-time approach for simultaneous optimization with unsteady PDEs
This paper presents a non-intrusive framework for integrating existing unsteady partial differential equation (PDE) solvers into a parallel-in-time simultaneous optimization algorithm. The time-parallelization is provided by the non-intrusive software library XBraid [Parallel multigrid in time, software available at http://llnl.gov/casc/xbraid], which applies an iterative multigrid reduction technique to the time domain of existing time-marching schemes for solving unsteady PDEs. Its general user-interface has been extended in [S. Günther, N.R. Gauger, and J.B. Schroder, A non-intrusive parallel-in-time adjoint solver with the XBraid library, Comput. Vis. Sci. 19 (2018), pp. 85–95. Available at arXiv, math.OC/1705.00663] for computing adjoint sensitivities such that gradients of output quantities with respect to design changes can be computed parallel-in-time alongside with the primal PDE solution. In this paper, the primal and adjoint XBraid iterations are embedded into a simultaneous optimization framework, namely the One-shot method. In this method, design updates towards optimality are employed after each state and adjoint update such that optimality and feasibility of the design and the PDE solution are reached simultaneously. Finally, the time-parallel optimization method is validated on an advection-dominated flow control problem which shows significant speedup over a classical time-serial optimization algorithm.
97 MATHEMATICS AND COMPUTING↗