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Electron tomography imaging methods with diffraction contrast for materials research

Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) enable the visualization of three-dimensional (3D) microstructures ranging from atomic to micrometer scales using 3D reconstruction techniques based on computed tomography algorithms. This 3D microscopy method is called electron tomography (ET) and has been utilized in the fields of materials science and engineering for more than two decades. Although atomic resolution is one of the current topics in ET research, the development and deployment of intermediate-resolution (non-atomic-resolution) ET imaging methods have garnered considerable attention from researchers. This research trend is probably not irrelevant due to the fact that the spatial resolution and functionality of 3D imaging methods of scanning electron microscopy (SEM) and X-ray microscopy have come to overlap with those of ET. In other words, there may be multiple ways to carry out 3D visualization using different microscopy methods for nanometer-scale objects in materials. From the above standpoint, this review paper aims to (i) describe the current status and issues of intermediate-resolution ET with regard to enhancing the effectiveness of TEM/STEM imaging and (ii) discuss promising applications of state-of-the-art intermediate-resolution ET for materials research with a particular focus on diffraction contrast ET for crystalline microstructures (superlattice domains and dislocations) including a demonstration of in situ dislocation tomography.

36 MATERIALS SCIENCE↗

SCALE Newsletter (Number 52, Spring 2020)

SCALE Newsletter is published by the Reactor and Nuclear Systems Division of the Oak Ridge National Laboratory. This issue, number 52 from Spring of 2020, holds information about the current state, planned updates, and previews of the SCALE system designed and maintained by ORNL staff. This issue contains employee spotlights for Dr. Kursat Bekar as well as Dr. Andrew M. Holcomb and displays data and charts from new/updated features of SCALE such as new data libraries, Fulcrum 3D visualizations, and interactions with ENDF/B-VIII.0 data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Influence of flowability, casting time and formwork geometry on fiber orientation and mechanical properties of UHPFRC

In this study, fiber orientation in ultra-high-performance fiber-reinforced-concrete (UHPFRC) with different formwork geometry was evaluated using visualization model concrete and via analysis involving 3D visualization based on X-ray computed tomography (CT). Differences in fiber orientation in the height direction were first reviewed. Furthermore, the influence of flowability and casting time on the fiber orientation and mechanical properties of UHPFRC were examined. The results indicated that flowability dictates eventual fiber orientation in parts close to the surfaces of formwork. The use of UHPFRC with superior flowability results in more fibers being oriented parallel to the longitudinal direction of slabs in comparison to UHPFRC with inferior flowability. It was also found that flowability and casting time can have strong influences on the mechanical properties of UHPFRC. Residual flexural strength after initial cracking exhibited perfect linear dependence on the effective number of fibers at fracture planes.

36 MATERIALS SCIENCE↗

Phase 1 Development Report for the SESSA Toolkit.

The Site Exploitation System for Situational Awareness ( SESSA ) tool kit , developed by Sandia National Laboratories (SNL) , is a comprehensive de cision support system for crime scene data acquisition and Sensitive Site Exploitation (SSE). SESSA is an outgrowth of another SNL developed decision support system , the Building R estoration Operations Optimization Model (BROOM), a hardware/software solution for data acquisition, data management, and data analysis. SESSA was designed to meet forensic crime scene needs as defined by the DoD's Military Criminal Investigation Organiza tion (MCIO) . SESSA is a very comprehensive toolki t with a considerable amount of database information managed through a Microsoft SQL (Structured Query Language) database engine, a Geographical Information System (GIS) engine that provides comprehensive m apping capabilities, as well as a an intuitive Graphical User Interface (GUI) . An electronic sketch pad module is included. The system also has the ability to efficiently generate necessary forms for forensic crime scene investigations (e.g., evidence submittal, laboratory requests, and scene notes). SESSA allows the user to capture photos on site, and can read and generate ba rcode labels that limit transcription errors. SESSA runs on PC computers running Windows 7, but is optimized for touch - screen tablet computers running Windows for ease of use at crime scenes and on SSE deployments. A prototype system for 3 - dimensional (3 D) mapping and measur e ments was also developed to complement the SESSA software. The mapping system employs a visual/ depth sensor that captures data to create 3D visualizations of an interior space and to make distance measurements with centimeter - level a ccuracy. Output of this 3D Model Builder module provides a virtual 3D %22walk - through%22 of a crime scene. The 3D mapping system is much less expensive and easier to use than competitive systems. This document covers the basic installation and operation of th e SESSA tool kit in order to give the user enough information to start using the tool kit . SESSA is currently a prototype system and this documentation covers the initial release of the tool kit . Funding for SESSA was provided by the Department of Defense (D oD), Assistant Secretary of Defense for Research and Engineering (ASD(R&E)) Rapid Fielding (RF) organization. The project was managed by the Defense Forensic Science Center (DFSC) , formerly known as the U.S. Army Criminal Investigation Laboratory (USACIL) . ACKNOWLEDGEMENTS The authors wish to acknowledge the funding support for the development of the Site Exploitation System for Situational Awareness (SESSA) toolkit from the Department of Defense (DoD), Assistant Secretary of Defense for Research and Engineering (ASD(R&E)) Rapid Fielding (RF) organization. The project was managed by the Defense Forensic Science Center (DFSC) , formerly known as the U.S. Army Criminal Investigation Laboratory (USACIL). Special thanks to Mr. Garold Warner, of DFSC, who served as the Project Manager. Individuals that worked on the design, functional attributes, algorithm development, system arc hitecture, and software programming include: Robert Knowlton, Brad Melton, Robert Anderson, and Wendy Amai.

Knowlton, Robert G.↗

Sandia MEMS Visualization Tools v. 3.0

This is a revision to the Sandia MEMS Visualization Tools. It replaces all previous versions. New features in this version: Support for AutoCAD 2014 and 2015 . This CD contains an integrated set of electronic files that: a) Provides a 2D Process Visualizer that generates cross-section images of devices constructed using the SUMMiT V fabrication process. b) Provides a 3D Visualizer that generates 3D images of devices constructed using the SUMMiT V fabrication process. c) Provides a MEMS 3D Model generator that creates 3D solid models of devices constructed using the SUMMiT V fabrication process. While there exists some files on the CD that are used in conjunction with software package AutoCAD , these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.

Yarberry, Victor↗

Visualization of electronic density

An atom’s volume depends on its electronic density. Although this density can only be evaluated exactly for hydrogen-like atoms, there are many excellent numerical algorithms and packages to calculate it for other materials. 3D visualization of charge density is challenging, especially when several molecular/atomic levels are intertwined in space. We explore several approaches to 3D charge density visualization, including the extension of an anaglyphic stereo visualization application based on the AViz package to larger structures such as nanotubes. We will describe motivations and potential applications of these tools for answering interesting questions about nanotube properties.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

LiDAR-Based Point Cloud Data Processing

The presentation includes the procedures of utilizing LiDAR-based point cloud data in WebGL applications, such as capturing data, processing data, importing point cloud into Unity software, and improving application performance. It uses IRC BLD 603 Lab B-12 as an example. It'll be presented at Viz n Learn workshop which is a collaboration series between INL's Applied Visualization Laboratory (AVL) and University of Wyoming (UW)'s Shell 3D Visualization center. Each session will highlight 2 projects from each institution monthly, followed by discussion on areas of collaborative interest and action.

3D↗

3D Virtual Simulation for Radiation Safety and Survey Training

3D virtual technologies have been widely used in remote training. Training integrated with 3D visualization technologies can enhance students’ engagement and reduce cost. The Applied Visualization Lab collaborates with College of Eastern Idaho on creating a 3D desktop application that simulate a pipe environment for radiation safety and survey training. Students can learn to perform radiation and contamination surveys remotely on their desktop. This simulation provides random scenarios, guided instructions, user interactions, and visual and sound feedback. It will promote utilizing virtual training for education outreach and minimize radiation and contamination exposure during the training.

3D↗

3D Virtual Simulation for Radiation Safety and Survey Training

3D virtual technologies have been widely used in remote training. Training integrated with 3D visualization technologies can enhance students’ engagement and reduce cost. The Applied Visualization Lab collaborates with College of Eastern Idaho on creating a 3D desktop application that simulate a pipe environment for radiation safety and survey training. Students can learn to perform radiation and contamination surveys remotely on their desktop. This simulation provides random scenarios, guided instructions, user interactions, and visual and sound feedback. It will promote utilizing virtual training for education outreach and minimize radiation and contamination exposure during the training.

3D↗

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↗

Real-space texture and pole-figure analysis using the 3D pair distribution function on a platinum thin film

An approach is described for studying texture in nanostructured materials. The approach implements the real-space texture pair distribution function (PDF), txPDF, laid out by Gong & Billinge {(2018). arXiv:1805.10342 [cond-mat]}. It is demonstrated on a fiber-textured polycrystalline Pt thin film. The approach uses 3D PDF methods to reconstruct the orientation distribution function of the powder crystallites from a set of diffraction patterns, taken at different tilt angles of the substrate with respect to the incident beam, directly from the 3D PDF of the sample. A real-space equivalent of the reciprocal-space pole figure is defined in terms of interatomic vectors in the PDF and computed for various interatomic vectors in the Pt film. Furthermore, it is shown how a valid isotropic PDF may be obtained from a weighted average over the tilt series, including the measurement conditions for the best approximant to the isotropic PDF from a single exposure, which for the case of the fiber-textured film was in a nearly grazing incidence orientation of ∼10°. Finally, an open-source Python software package, FouriGUI , is described that may be used to help in studies of texture from 3D reciprocal-space data, and indeed for Fourier transforming and visualizing 3D PDF data in general.

3D pair distribution functions↗

Advances in reactor physics education: Visualization of reactor parameters

Modern computer codes allow detailed neutron transport calculations. In combination with advanced 3D visualization software capable of treating large amounts of data in real time they form a powerful tool that can be used as a convenient modern educational tool for reactor operators, nuclear engineers, students and specialists involved in reactor operation and design. Visualization is applicable not only in education and training, but also as a tool for fuel management, core analysis and irradiation planning. The paper treats the visualization of neutron transport in different moderators, neutron flux and power distributions in two nuclear reactors (TRIGA type research reactor and a typical PWR). The distributions are calculated with MCNP and CORD-2 computer codes and presented using Amira software. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry

Visualizing 3D molecular structures is crucial to understanding and predicting their chemical behavior. However, static 2D hand-drawn skeletal structures remain the preferred method of chemical communication. Here, we combine cutting-edge technologies in augmented reality (AR), machine learning, and computational chemistry to develop MolAR, an open-source mobile application for visualizing molecules in AR directly from their hand-drawn chemical structures. Users can also visualize any molecule or protein directly from its name or protein data bank ID and compute chemical properties in real time via quantum chemistry cloud computing. MolAR provides an easily accessible platform for the scientific community to visualize and interact with 3D molecular structures in an immersive and engaging way.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Can Electrical Resistance Tomography be used for imaging unsaturated moisture flow in cement-based materials with discrete cracks?

Previously, it has been shown that Electrical Resistance Tomography (ERT) can be used for monitoring moisture flow in undamaged cement-based materials. In this work, we investigate whether ERT could be used for imaging three-dimensional (3D) unsaturated moisture flow in cement-based materials that contain discrete cracks. Novel computational methods based on the so-called absolute imaging framework are developed and used in ERT image reconstructions, aiming at a better tolerance of the reconstructed images with respect to the complexity of the conductivity distribution in cracked material. ERT is first tested using specimens with physically simulated cracks of known geometries, and corroborated with numerical simulations of unsaturated moisture flow. Next, specimens with loading-induced cracks are imaged; here, ERT reconstructions are evaluated qualitatively based on visual observations and known properties of unsaturated moisture flow. Results indicate that ERT is a viable method of visualizing 3D unsaturated moisture flow in cement-based materials with discrete cracks. - Highlights: • 3D EIT is developed to visualize water ingress in cracked mortar. • Mortar with different size discrete cracks are used. • The EIT results are corroborated with numerical simulations. • EIT results accurately show the temporal and spatial variation of water content. • EIT is shown to be a viable method to monitor flow in cracks and matrix.

36 MATERIALS SCIENCE↗

RECONSTRUCTING THE SUBSURFACE THREE-DIMENSIONAL MAGNETIC STRUCTURE OF A SOLAR ACTIVE REGION USING SDO/HMI OBSERVATIONS

A solar active region (AR) is a three-dimensional (3D) magnetic structure formed in the convection zone, whose property is fundamentally important for determining the coronal structure and solar activity when emerged. However, our knowledge of the detailed 3D structure prior to its emergence is rather poor, largely limited by the low cadence and sensitivity of previous instruments. Here, using the 45 s high-cadence observations from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we are able for the first time to reconstruct a 3D data cube and infer the detailed subsurface magnetic structure of NOAA AR 11158, and to characterize its magnetic connectivity and topology. This task is accomplished with the aid of the image-stacking method and advanced 3D visualization. We find that the AR consists of two major bipoles or four major polarities. Each polarity in 3D shows interesting tree-like structure, i.e., while the root of the polarity appears as a single tree-trunk-like tube, the top of the polarity has multiple branches consisting of smaller and thinner flux tubes which connect to the branches of the opposite polarity that is similarly fragmented. The roots of the four polarities align well along a straight line, while the top branches are slightly non-coplanar. Our observations suggest that an active region, even appearing highly complicated on the surface, may originate from a simple straight flux tube that undergoes both horizontal and vertical bifurcation processes during its rise through the convection zone.

79 ASTRONOMY AND ASTROPHYSICS↗

Pole Figure Explorer v. 1.8

This software is employed for 3D visualization of X-ray diffraction (XRD) data with functionality for slicing, reorienting, isolating and plotting of 2D color contour maps and 3D renderings of large datasets. The program makes use of the multidimensionality of textured XRD data where diffracted intensity is not constant over a given set of angular positions (as dictated by the three defined dimensional angles of phi, chi, and two-theta). Datasets are rendered in 3D with intensity as a scaler which is represented as a rainbow color scale. A GUI interface and scrolling tools along with interactive function via the mouse allow for fast manipulation of these large datasets so as to perform detailed analysis of diffraction results with full dimensionality of the diffraction space.

Van Benthem, Mark H.↗

Remotely Teleoperating a Humanoid Robot to Perform Fine Motor Tasks with Virtual Reality - 18446

In this paper, we describe our ongoing work to develop cooperative control of NASA's R5 Valkyrie humanoid robot for performing dexterous manipulation tasks inside gloveboxes commonly found in many nuclear facilities. These tasks can be physically demanding and provide some element of risk to the operator when done by a person in situ. For example, if a glove is ruptured, the operator could be exposed to radioactive material. In many cases, the operator has low visibility and is unable to reach the entire task space, requiring the use of additional tools located inside the glovebox. Such tasks include cleaning particulate from inside the glovebox via sweeping or vacuuming, separating a specific amount of a compound to be weighed on a scale, or grasping and manipulating objects inside the glovebox. There is potential to move the operator to a nearby, safe location and instead place a humanoid robot in the potentially hazardous environment. However, teleoperating a humanoid robot to perform dexterous tasks at a comparable level to a human hand remains a difficult problem. Previous work for controlling humanoid robots often involves one or more operators using a standard 2D display with a mouse and keyboard as controllers. Successful interfaces use sensor fusion to provide information to the operator for increased situation awareness, but these designs have limitations. Gaining proper situation awareness by visualizing 3D information on a 2D screen requires time and increases the cognitive load on the user. Instead, if the operator is able to visualize and control the robot properly in three dimensions, it can increase situation and task awareness, reduce task time, reduce the chance of mistakes, and increase the likelihood of overall task success. We propose a two-part system that combines an HTC Vive virtual reality headset with either the Vive handheld controllers, or the Manus VR wearable gloves as the primary control. The operator wears the headset in a remote location and can visualize a reconstruction of the glovebox, created live by sensor scans from the robot and with sensors located inside the glovebox for a perspective traditionally unavailable to operators. By using the controllers or gloves to control the humanoid robots hands directly, they can plan actions in the virtual reconstruction. When the operator is satisfied with the plan, the actions are sent to the real robot. To test this system we have created a mockup of a glovebox that is accessible by Valkyrie, as well as several tasks that are a subsample of the tasks that might be required when working in a real glovebox. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗