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At least 55 records · Page 3

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part I

This two-part article series provides a generalized description of the scattering geometry of Bragg coherent diffraction imaging (BCDI) experiments, the shear distortion effects inherent in the 3D image obtained from presently used methods and strategies to mitigate this distortion. Part I starts from fundamental considerations to present the general real-space coordinate transformation required to correct this shear, in a compact operator formulation that easily lends itself to implementation with available software packages. Such a transformation, applied as a final post-processing step following phase retrieval, is crucial for arriving at an undistorted, correctly oriented and physically meaningful image of the 3D crystalline scatterer. As the relevance of BCDI grows in the field of materials characterization, the available sparse literature that addresses the geometric theory of BCDI and the subsequent analysis methods are generalized here. This geometrical aspect, specific to coherent Bragg diffraction and absent in 2D transmission CDI experiments, gains particular importance when it comes to spatially resolved characterization of 3D crystalline materials in a reliable nondestructive manner. This series of articles describes this theory, from the diffraction in Bragg geometry to the corrections needed to obtain a properly rendered digital image of the 3D scatterer. Part I of this series provides the experimental BCDI community with the general form of the 3D real-space distortions in the phase-retrieved object, along with the necessary post-retrieval correction method. Part II builds upon the geometric theory developed in Part I with the formalism to correct the shear distortions directly on an orthogonal grid within the phase-retrieval algorithm itself, allowing more physically realistic constraints to be applied. Taken together, Parts I and II provide the X-ray science community with a set of generalized BCDI shear-correction techniques crucial to the final rendering of a 3D crystalline scatterer and for the development of new BCDI methods and experiments.

36 MATERIALS SCIENCE↗

High-Resolution Imaging of Unstained Polymer Materials

Electron microscopy has played an important role in polymer characterization. Traditionally, electron diffraction is used to study crystalline polymers while transmission electron microscopy is used to study microphase separation in stained block copolymers and other multiphase systems. We describe developments that eliminate the barrier between these two approaches - it is now possible to image polymer crystals with atomic resolution. The focus of this Review is on high-resolution imaging (30 Å and smaller) of unstained polymers. Recent advances in hardware allow for capturing numerous (as many as 105) low-dose images from an unperturbed specimen; beam damage is a significant barrier to high-resolution electron microscopy of polymers. Machine-learning-based software is then used to sort and average the images to retrieve pristine structural information from a collection of noisy images. Acknowledging the heterogeneity in polymer samples prior to averaging is essential. Molecular conformations in a wide range of amphiphilic block copolymers, polymerized ionic liquids, and conjugated polymers can be gleaned from two-dimensional projections (2D), three-dimensional (3D) tomograms, and four-dimensional (4D) scanning transmission electron microscopy (STEM) data sets where 2D diffraction patterns are taken as a function of position. Some methods such as phase contrast STEM have been used to image closely related materials such as metal-organic frameworks but not polymers. With improvements in hardware and software, such methods may soon be applied to polymers. Our goal is to provide a comprehensive understanding of the strategies toward the high-resolution imaging of radiation sensitive polymer materials at different length scales.

36 MATERIALS SCIENCE↗

Towards scanning nanostructure X-ray microscopy

This article demonstrates spatial mapping of the local and nanoscale structure of thin film objects using spatially resolved pair distribution function (PDF) analysis of synchrotron X-ray diffraction data. This is exemplified in a lab-on-chip combinatorial array of sample spots containing catalytically interesting nanoparticles deposited from liquid precursors using an ink-jet liquid-handling system. A software implementation is presented of the whole protocol, including an approach for automated data acquisition and analysis using the atomic PDF method. The protocol software can handle semi-automated data reduction, normalization and modeling, with user-defined recipes generating a comprehensive collection of metadata and analysis results. By slicing the collection using included functions, it is possible to build images of different contrast features chosen by the user, giving insights into different aspects of the local structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Symmetry-mode analysis for local structure investigations using pair distribution function data

Symmetry-adapted distortion modes provide a natural way of describing distorted structures derived from higher-symmetry parent phases. Structural refinements using symmetry-mode amplitudes as fit variables have been used for at least ten years in Rietveld refinements of the average crystal structure from diffraction data; more recently, this approach has also been used for investigations of the local structure using real-space pair distribution function (PDF) data. Here, the value of performing symmetry-mode fits to PDF data is further demonstrated through the successful application of this method to two topical materials: TiSe2, where a subtle but long-range structural distortion driven by the formation of a charge-density wave is detected, and MnTe, where a large but highly localized structural distortion is characterized in terms of symmetry-lowering displacements of the Te atoms. Here, the analysis is performed using fully open-source code within the DiffPy framework via two packages developed for this work: isopydistort, which provides a scriptable interface to the ISODISTORT web application for group theoretical calculations, and isopytools, which converts the ISODISTORT output into a DiffPy-compatible format for subsequent fitting and analysis. These developments expand the potential impact of symmetry-adapted PDF analysis by enabling high-throughput analysis and removing the need for any commercial software.

36 MATERIALS SCIENCE↗

EXTENDED VERSION OF SOFTWARE POLYLAUE

(SF-24-031) Software PolyLaue, having ANL OPEN SOURCE LICENSE, will be extended by KITWARE, INC. New functionality, including file manager, visualizer and mapping routine will substantially improve the procedure to identify single-crystals across compression with Laue diffraction technique.

Popov, DmitryYu↗

Spinteract: a program to refine magnetic interactions to diffuse scattering data

Magnetic diffuse scattering—the broad magnetic scattering features observed in neutron-diffraction data above a material's magnetic ordering temperature—provides a rich source of information about the material's magnetic Hamiltonian. However, this information has often remained under-utilised due to a lack of available computer software that can fit values of magnetic interaction parameters to such data. Here, an open-source computer program, Spinteract, is presented, which enables straightforward refinement of magnetic interaction parameters to powder and single-crystal magnetic diffuse scattering data. Here, the theory and implementation of this approach are summarised. Examples are presented of refinements to published experimental diffuse-scattering data sets for the canonical antiferromagnet MnO and the highly-frustrated classical spin liquid Gd 3 Ga 5 O 12 . Guidelines for data collection and refinement are outlined, and possible developments of the approach are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Metal-organic chemical vapor deposition of MgGeN2 films on GaN and sapphire

MgGeN2 films were synthesized using metal-organic chemical vapor deposition on GaN/c-sapphire templates and c-plane sapphire substrates. Energy-dispersive x-ray spectroscopy was used to estimate the cation composition ratios. To mitigate magnesium evaporation, the films were grown at pyrometer temperature 745 °C with a wafer rotation speed of 1000 rpm. Growth rates were determined by fitting energy-dispersive x-ray spectroscopy spectra to film thicknesses using NIST DTSA-II software. The thickness estimates determined by this method were consistent with scanning transmission electron microscopy measurements done for selected samples. Scanning electron microscopy images revealed faceted surfaces indicative of a tendency toward three-dimensional growth. X-ray diffraction spectra confirmed that the films were highly crystalline and exhibited preferential orientation in alignment with the substrate. Atomic force microscopy measurements show that film thicknesses are consistent across samples grown on both GaN templates and sapphire substrates, with typical roughnesses around 10 nm. Transmittance spectra of films grown on double-side-polished sapphire substrates yielded band gaps of 4.28 ± 0.06 eV for samples exhibiting close-to-ideal stoichiometry. Comparison of the measured spectra with ab initio calculations are in good agreement both near the bandgap and at higher energies where excitation is into higher-lying bands. These findings provide insight into the growth and characterization of MgGeN2, contributing to the development of this material for potential applications in optoelectronics and power electronics.

Hu, Chenxi (ORCID:0000000236299660)↗

Impact of Controlled Storage Conditions on the Hydrolysis and Surface Morphology of Amorphous-UO 3

The hydration and morphological effects of amorphous (A)-UO 3 following storage under varying temperature and relative humidity have been investigated. This study provides valuable insight into U-oxide speciation following aging, the U-oxide quantitative morphological data set, and, overall, the characterization of nuclear material provenance. A-UO 3 was synthesized via the washed uranyl peroxide synthetic route and aged based on a 3-factor circumscribed central composite design of experiment. Target aging times include 2.57, 7.00, 14.0, 21.0, and 25.4 days, temperatures of 5.51, 15.0, 30.0, 45.0, and 54.5 °C, and relative humidities of 14.2, 30.0, 55.0, 80.0, and 95.8% were examined. Following aging, crystallographic changes were quantified via powder X-ray diffraction and an internal standard Rietveld refinement method was used to confirm the hydration of A-UO 3 to crystalline schoepite phases. The particle morphology from scanning electron microscopy images was quantified using both the Morphological Analysis of MAterials software and machine learning. Results from the machine learning were processed via agglomerative hierarchical clustering analysis to distinguish trends in morphological attributes from the aging study. Significantly hydrated samples were found to have a much larger, plate-like morphology in comparison to the unaged controls. Predictive modeling via a response surface methodology determined that while aging time, temperature, and relative humidity all have a quantifiable effect on A-UO 3 crystallographic and morphological changes, relative humidity has the most significant impact.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Focused Ion Beam Tomography of Alloy 617 Corroded in Molten Chloride Salt

Materials qualification of reactor structural materials is a critical step in rapid implementation of advanced nuclear reactor technologies, particularly to assess the corrosion performance in these designs. Accelerated qualification of reactor structural materials requires incorporating powerful computational toolsets, such as phase field modelling in the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework, to predict the evolution of structural materials due to corrosion. Accordingly, computational toolsets will require experimental data generated at appropriate length scales to validate accuracy. Focused ion beam (FIB) provides a high degree of control over manipulation of materials for analytical purposes, including capturing data on the evolution in the microstructure and elemental composition of materials at the mesoscale, an appropriate length scale for phase field modelling of intergranular diffusion phenomena using the MOOSE framework. For instance, the FEI Helios G4 UX dual beam plasma FIB microscope at the Irradiated Materials Characterization Laboratory (IMCL) is capable of backscatter diffraction (EBSD) and energy-dispersive x-ray spectroscopy (EDS) documenting the evolution in the microstructure and elemental composition, respectively. The Helios can perform EDS and EBSD three-dimensionally (3D) using tomography, which is then combined using different software packages to visualize 3D volumes correlating elemental composition to microstructural data. The purpose of this investigation was to develop a streamlined characterization and data processing workflow for 3D tomography studies on the FEI Helios G4 plasma FIB. The investigation is segmented into three parts: 1) Optimizing the data collection workflow, 2) identifying appropriate data processing and visualization software (i.e. DREAM.3D, MIPAR, and VGStudioMax), and 3) establishing an infrastructure for public release. The optimization of the data collection workflow is in collaboration with members of the U220 department to setup formal training on the tomography operation of the G4, through ThermoFisher Scientific, and exploring DREAM.3D, MIPAR, and VGStudioMax data processing/visualization software packages. VGStudioMax currently demonstrates the most promise for future use. Optimization of the data collection and processing workflow is still ongoing. A collaboration with INL High Performance Computing (HPC) established an open-source license for expediting the public release of FIB tomography datasets through HPC. FIB tomography data generated by the G4 will provide comprehensive data for validating 3D phase field mesoscale modelling tools within the MOOSE framework for accelerated qualification of reactor structural materials.

Copeland-Johnson, Trishelle↗

BraggNN : fast X-ray Bragg peak analysis using deep learning

X-ray diffraction based microscopy techniques such as high-energy diffraction microscopy (HEDM) rely on knowledge of the position of diffraction peaks with high precision. These positions are typically computed by fitting the observed intensities in detector data to a theoretical peak shape such as pseudo-Voigt. As experiments become more complex and detector technologies evolve, the computational cost of such peak-shape fitting becomes the biggest hurdle to the rapid analysis required for real-time feedback in experiments. To this end, we propose BraggNN, a deep-learning based method that can determine peak positions much more rapidly than conventional pseudo-Voigt peak fitting. When applied to a test dataset, peak center-of-mass positions obtained from BraggNN deviate less than 0.29 and 0.57 pixels for 75 and 95% of the peaks, respectively, from positions obtained using conventional pseudo-Voigt fitting (Euclidean distance). When applied to a real experimental dataset and using grain positions from near-field HEDM reconstruction as ground-truth, grain positions using BraggNN result in 15% smaller errors compared with those calculated using pseudo-Voigt. Recent advances in deep-learning method implementations and special-purpose model inference accelerators allow BraggNN to deliver enormous performance improvements relative to the conventional method, running, for example, more than 200 times faster on a consumer-class GPU card with out-of-the-box software.

36 MATERIALS SCIENCE↗

Modeling Tree Foliage for Microwave Radar Transparency Study

The motivation for this report is to discuss and present some realistic tree models employed in computational electromagnetics (EM) simulations to study foliage penetration (FOPEN) at Ku-band. The detail obtained in these trees is unprecedented in FOPEN modeling since many studies in this area focus on lower frequencies where precise tree parameters are not required due to the associated large wavelengths relative to the tree dimensions. The focus of this study is in the Ku-band range where the wavelength is notably smaller and the details of the trees have more of an influence on EM waves (i.e. scattering, attenuating, reflecting, diffracting etc.). Therefore, explicit tree parameters are modeled. Also, moderate foliage is of most interest because with less dense foliage t here is a higher percentage of Ku-band transmission. The EM wave and foliage interaction s are simulated with the computational electromagnetics (CEM) Altair FEKO software. The realistic tree model s implemented for simulations are created in the computer-aided design (CAD) software Arbaro and the module CADFEKO that is offered in FEKO. Details of these tree models are provided, and EM simulation results will be discussed in a follow-on report

59 BASIC BIOLOGICAL SCIENCES↗

Accelerator physics at NSLS-II: research accomplishments in 2020

NSLS-II accelerator physicists provide scientific support for user operations, as well as for improvements and developments of the accelerator systems. This work includes optimization of the NSLS-II performance with high beam current and low vertical emittance, improvement of the beam stability, development of new software tools for operations and beam studies. The accelerator physicists productively worked on a number of research activities such as the conceptual design of NSLS-II accelerator upgrade; design and optimization of advanced low-emittance lattices; development of novel methods to study nonlinear beam dynamics; ultrafast electron diffraction and microscopy. The physicists also contributed to the BNL electron-ion collider project, to the APS and ALS upgrade projects. Research accomplishments achieved in 2020, are summarized in this report.

43 PARTICLE ACCELERATORS↗

Serial crystallography with multi-stage merging of thousands of images

KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences.

36 MATERIALS SCIENCE↗

High-Energy X-Ray Diffraction Microscopy in Materials Science

High-energy diffraction microscopy (HEDM) is an implementation of three-dimensional X-ray diffraction microscopy. HEDM yields maps of internal crystal orientation fields, strain states, grain shapes and locations as well as intragranular orientation distributions, and grain boundary character. Because it is nondestructive in hard materials, notably metals and ceramics, HEDM has been used to study responses of these materials to external fields including high temperature and mechanical loading. Currently available sources and detectors lead to a spatial resolution of ~1 μm and an orientation resolution of <0.1°. With the penetration characteristic of high energies ( E ≥ 50 keV), sample cross-section dimensions of ~1 mm can be studied in materials containing elements across much of the Periodic Table. This review describes hardware and software associated with HEDM as well as examples of applications. Overall, these applications include studies of grain growth, recrystallization, texture development, orientation gradients, deformation twinning, annealing twinning, plastic deformation, and additive manufacturing. We also describe relationships to other X-ray-based methods as well as prospects for further development.

36 MATERIALS SCIENCE↗

Coherent diffraction imaging in the undergraduate laboratory

We present an undergraduate optics instructional laboratory designed to teach skills relevant to a broad range of modern scientific and technical careers. In this laboratory project, students image a custom aperture using coherent diffraction imaging, while learning principles and skills related to digital image processing and computational imaging, including multidimensional Fourier analysis, iterative phase retrieval, noise reduction, finite dynamic range, and sampling considerations. After briefly reviewing these imaging principles, we describe the required experimental materials and setup for this project. Our experimental apparatus is both inexpensive and portable, and a software application we developed for interactive data analysis is freely available.

Porter, J. Nicholas↗

New Developments and Capabilities Within WEC-Sim

WEC-Sim is an open-source software for simulating wave energy converters and has been actively developed and applied since its initial release in 2014 to simulate a wide variety of device archetypes. WEC-Sim is developed jointly by the National Renewable Energy Laboratory and Sandia National Laboratories within the MATLAB/SIMULINK environment. A general wave-to-wire model begins with a deployment site resource characterization, which is used to complete the hydrodynamic simulation of wave energy converters (WEC), with the power generation profile imported to a grid simulator to understand the influence on the local electrical network. While modeling the entire wave-to-wire is difficult and encompasses multiple time scales and physics, WEC-Sim is focused on the hydrodynamics simulation to predict, analyze, and optimize WEC dynamics and power performance. WEC-Sim simulations are performed in the time domain based on the radiation and diffraction method using hydrodynamics coefficients derived from boundary element method (BEM)-based frequency-domain potential flow solvers (e.g., WAMIT, NEMOH, Capytaine, or ANSYS-AQWA). With this level of modeling fidelity, WEC-Sim can handle floating body hydrodynamics, mechanical and electrical power generation methods, advanced control implementation, mooring systems, and other unique applications such as desalination. Additional WEC-Sim functionalities include pre-built Simulink blocks and MATLAB scripts that can simulate a wide range of floating systems and the corresponding auxiliary subsystems. The developers of WEC-Sim continue to release new versions of the software, at least annually, with the latest release in September 2022. These releases include bug fixes, updates to software documentation, as well as new features to expand WEC-Sim's capabilities to model a wide range of WEC concepts. This publication will highlight the new features added to WEC-Sim between versions 4.1.0 to 5.0.1, which spans a 2-year period from June 2020 to September 2022. New features described here include topics such as continuous integration checks, revised Morison Element and nonlinear hydro implementations, run directly from Simulink (required for hardware-in-the-loop execution), BEMIO updates to import Capytaine BEM hydrodynamics, addition of cable blocks, and new wave visualization features.

TIDAL AND WAVE POWER↗

New Developments and Capabilities Within WEC-Sim: Preprint

WEC-Sim is an open-source software for simulating wave energy converters, which has been actively developed and applied since its initial release in 2014 to simulate a wide variety of device archetypes. WEC-Sim is developed jointly by the National Renewable Energy Laboratory (NREL) and Sandia National Laboratories (Sandia) within the MATLAB/SIMULINK environment. A general wave-to-wire model begins with a deployment site resource characterization, which is used to complete the hydrodynamic simulation of wave energy converters (WEC), with the power generation profile imported to a grid simulator to understand the influence on the local electrical network. While modeling the entire wave-to-wire is difficult and encompasses multiple time scales and physics, WEC-Sim is focused on the hydrodynamics simulation to predict, analyze, and optimize WEC dynamics and power performance. WEC-Sim simulations are performed in the time domain based on the radiation and diffraction method using hydrodynamics coefficients derived from boundary element method (BEM)-based frequency-domain potential flow solvers (e.g., WAMIT, NEMOH, Capytaine, or ANSYS-AQWA). With this level of modeling fidelity, WEC-Sim can handle floating body hydrodynamics, mechanical and electrical power generation methods, advanced control implementation, mooring systems, and other unique applications such as desalination. Additional WEC-Sim functionalities include pre-built Simulink blocks and MATLAB scripts that can simulate a wide range of floating systems and the corresponding auxiliary subsystems. The developers of WEC-Sim continue to release new versions of the software, at least annually, with our latest release in September 2022. These releases include bug fixes, updates to software documentation, as well as new features to expand WEC-Sim's capabilities to model a wide range of WEC concepts. This publication will highlight the new features added to WEC-Sim between versions 4.1.0 to 5.0.1 which spans over a two year period from June 2020 to September 2022. New features to be described will include topics such as continuous integration checks, revised Morison Element and nonlinear hydro implementations, run directly from Simulink (required for hardware-in-the-loop execution), BEMIO updates to import Capytaine BEM hydrodynamics, addition of cable blocks, and new wave visualization features.

TIDAL AND WAVE POWER↗