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At least 127 records · Page 7

Chiral population analysis: a real space visualization of X-ray circular dichroism

The microscopic understanding of probing and controlling molecular chirality is of considerable interest. Numerous spectroscopic techniques are capable of monitoring molecular asymmetry and its consequences, ranging from the infrared to the X-ray regime. Resonant X-rays have long been used to investigate local atomic sites within molecules thanks to the localized nature of core electronic transitions. These techniques can be used to determine the extent to which chirality is a local versus a delocalized property. However, how to systematically partition dichroic contributions from the point of view of electronic structure simulations remains an open question. Here, we introduce the concept of chiral population analysis that connects chirality to the atomic orbital picture. In analogy with Mulliken population analysis, which assigns charges to atomic orbitals, chiral populations allow the dichroic response to be distributed among the participating atomic orbitals. This decomposition can be further visualized in real space by representing it in terms of isosurface plots, providing an intuitive way to connect the dichroic response to its origins. Thus chiral population analysis can be particularly useful to assess the extent to which a given electronic transition is sensitive to chirality as a local or global feature of the molecular geometry.

36 MATERIALS SCIENCE↗

Distributed Augmentation, Hypersweeps, and Branch Decomposition of Contour Trees for Scientific Exploration

Contour trees describe the topology of level sets in scalar fields and are widely used in topological data analysis and visualization. A main challenge of utilizing contour trees for large-scale scientific data is their computation at scale using highperformance computing. To address this challenge, recent work has introduced distributed hierarchical contour trees for distributed computation and storage of contour trees. However, effective use of these distributed structures in analysis and visualization requires subsequent computation of geometric properties and branch decomposition to support contour extraction and exploration. In this work, we introduce distributed algorithms for augmentation, hypersweeps, and branch decomposition that enable parallel computation of geometric properties, and support the use of distributed contour trees as query structures for scientific exploration. Finally, we evaluate the parallel performance of these algorithms and apply them to identify and extract important contours for scientific visualization.

97 MATHEMATICS AND COMPUTING↗

Distributed Resources for the Earth System Grid Federation (ESGF) Advanced Management (DREAM). Final Report

Distributed Resources for the Earth System Grid Federation (ESGF) Advanced Management (DREAM) is a proposed system that will enable data from an infinite number of diverse sources to be organized and accessed from anywhere using any handheld or other computer device. The approach offers a powerful roadmap for the creation and integration of a unified knowledge base of an entire ecosystem, including its many geophysical, geographical, social, political, agricultural, energy, transportation, and cyber aspects. The resulting aggregation of data has the potential to generate an informational universe of unprecedented size that has never before been possible due to the prohibitive costs, managerial complexity, and technical barriers associated with ever-changing exponential-growth data flows. We envision that DREAM will accelerate discovery by enabling climate researchers, among other types of researchers, to manage, analyze, and visualize data from earth-scale measurements and simulations. DREAM’s success will be built on proven components that leverage existing services and resources. A key building block for DREAM will be the ESGF, chaired by Dean N. Williams. Expanding on the existing ESGF, the project will ensure that the access, storage, movement, and analysis of the large quantities of data that are processed and produced by diverse science projects can be dynamically distributed with proper resource management. Much of the Office of Science data is currently generated by multiple stand-alone facilities. DREAM can collect data accumulated from these facilities and incorporate it into a fully integrated network accessible from anywhere in the world. The result is a completely new paradigm shift for data management, analysis, and visualization enabling researchers to: Manage their calculations, data, tools, and research results; Ensure that all data are sharable, reproducible and (re)usable—accompanied by appropriate metadata describing its provenance, syntax, and semantics at creation; Advance application performance by selectively adapting APIs and services in response to scientific requirements and architectural complexities; and Provide scalable interactive resource management—navigate data and metadata at multiple levels, provide architecture-aware data integration, analysis and visualization tools. We will engage closely with DOE, NASA, and NOAA science groups working at the leading edge of computing. These engagements—in domains such as biology, climate, and hydrology—will allow us to advance disciplinary science goals and inform our development of technologies that can accelerate discovery across DOE more broadly. We will advertise and promote our technologies via dedicated workshops, tutorials, and sessions at conferences, stand-alone events with broad inter-disciplinary invitation, and engagements with leadership facilities.

54 ENVIRONMENTAL SCIENCES↗

ECP ST Capability Assessment Report (CAR) for VTK-m (FY20)

The ECP/VTK-m project is providing the core capabilities to perform scientific visualization on Exascale architectures. The ECP/VTK-m project fills the critical feature gap of performing visualization and analysis on processors like graphics-based processors. The results of this project will be delivered in tools like ParaView, Vislt, and Ascent as well as in stand-alone form. Moreover, these projects are depending on this ECP effort to be able to make effective use of ECP architectures. One of the biggest recent changes in high-performance computing is the increasing use of accelerators. Accelerators contain processing cores that independently are inferior to a core in a typical CPU, but these cores are replicated and grouped such that their aggregate execution provides a very high computation rate at a much lower power. Current and future CPU processors also require much more explicit parallelism. Each successive version of the hardware packs more cores into each processor, and technologies like hyper threading and vector operations require even more parallel processing to leverage each core's full potential. VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures. The ECP/VTK-m project is building up the VTK-m codebase with the necessary visualization algorithm implementations that run across the varied hardware platforms to be leveraged at the Exascale. We will be working with other ECP projects, such as ALPINE, to integrate the new VTK-m code into production software to enable visualization on our HPC systems.

97 MATHEMATICS AND COMPUTING↗

Interactively Assessing Disentanglement in GANs

Abstract Generative adversarial networks (GAN) have witnessed tremendous growth in recent years, demonstrating wide applicability in many domains. However, GANs remain notoriously difficult for people to interpret, particularly for modern GANs capable of generating photo‐realistic imagery. In this work we contribute a visual analytics approach for GAN interpretability, where we focus on the analysis and visualization of GAN disentanglement. Disentanglement is concerned with the ability to control content produced by a GAN along a small number of distinct, yet semantic, factors of variation. The goal of our approach is to shed insight on GAN disentanglement, above and beyond coarse summaries, instead permitting a deeper analysis of the data distribution modeled by a GAN. Our visualization allows one to assess a single factor of variation in terms of groupings and trends in the data distribution, where our analysis seeks to relate the learned representation space of GANs with attribute‐based semantic scoring of images produced by GANs. Through use‐cases, we show that our visualization is effective in assessing disentanglement, allowing one to quickly recognize a factor of variation and its overall quality. In addition, we show how our approach can highlight potential dataset biases learned by GANs.

Jeong, Sangwon↗

Visualizing metagenomic and metatranscriptomic data: A comprehensive review

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

59 BASIC BIOLOGICAL SCIENCES↗

NOODLES [SWR-22-78]

NOODLES is a protocol specification for collaborative visualization. It allows software tools of any type to participate in an analysis or visualization session. Use cases include, but are not limited to, distributed analysis, workflow interoperability, computational steering, etc.

Brunhart-Lupo, Nicholas↗

PyKrev: A Python Library for the Analysis of Complex Mixture FT-MS Data

In this study, we present PyKrev, a Python library for the analysis of complex mixture Fourier transform mass spectrometry (FT-MS) data. PyKrev is a comprehensive suite of tools for analysis and visualization of FT-MS data after formula assignment has been performed. These comprise formula manipulation and calculation of chemical properties, intersection analysis between multiple lists of formulas, calculation of chemical diversity, assignment of compound classes to formulas, multivariate analysis, and a variety of visualization tools producing van Krevelen diagrams, class histograms, PCA score, and loading plots, biplots, scree plots, and UpSet plots. The library is showcased through analysis of hot water green tea extracts and Scotch whisky FT-ion cyclotron resonance-MS data sets. PyKrev addresses the lack of a single, cohesive toolset for researchers to perform FT-MS analysis in the Python programming environment encompassing the most recent data analysis techniques used in the field.

47 OTHER INSTRUMENTATION↗

Introducing NOODLES: Collaborative Visualization in a Flavorful Package

We introduce NOODLES, a lightweight collaborative visualization and analysis protocol. NOODLES was developed to enable new scientific workflows while enhancing existing pipelines. Using a technology-minimal approach to strengthen applicability, this protocol allows researchers to tie disparate software together as well as making domain specific visualizations accessible across various platforms and form factors. In this talk we discuss background, challenges, and gaps in the current tool landscape that lead to the development of the protocol. We then describe the design of the protocol and present several use cases to demonstrate the efficacy of NOODLES in addressing complex visualization challenges and how it co-exists with existing tools. We conclude by outlining in-progress work and potential avenues for future development within the NOODLES framework.

collaborative analysis↗

Sub-pilot-scale Production of High-Value Products from U.S. Coals

Investigators from the University of Utah, University of Wyoming and Marshall University pursued a program to study the conversion of raw coal to high-value products of carbon fiber and silicon carbide. Team members also developed an initial framework for a data portal that can incorporate laboratory data on coal processing and product quality, and also work with tools for machine learning for data analysis, data visualization and economic assessment. Experimental R&D efforts focused on the conversion of raw coal to coal tar and other byproducts, and the resulting tar intermediates were upgraded to form anisotropic and isotropic pitch materials. These pitch materials were produced from coal using both thermal (pyrolysis) and chemical (mild solvolysis liquefaction) decomposition of raw coal. Four different coals were studied: Utah bituminous coal (Sufco), Wyoming PRB coal (Black Thunder), Illinois bituminous coal (Illinois #6), and West Virginia bituminous coal (Flying Eagle). Both metallurgical-grade coking coals and lower-grade steam coals were investigated, and controlled secondary gas-phase reactions were used during a two-stage pyrolysis process to induce cracking and condensation reactions among the pyrolytic tar species. This approach successfully improved the performance of the lower grade coals for yielding pitch materials, with properties more consistent with a commercial-grade pitch that had previously demonstrated success for quality carbon fiber production. The use of waste plastic materials was also studied, to help improve physical and chemical characteristics of the intermediate tars and final pitch product; in particular, for lowering the pitch softening point to an acceptable level for melt spinning carbon fiber. Mild solvolysis liquefaction was also used as a method for producing pitch for carbon fiber production. As expected, significantly higher pitch yields were obtained using this approach, and waste plastic materials were also successfully used to reduce pitch softening point to an acceptable level. The plastic materials were also utilized to create a solvent for the mild solvolysis process, and this plastic-derived solvent was shown to provide results consistent with more expensive commercial chemical solvents, and could thus avoid the need for costly recovery and recycle of a liquefaction solvent. Additional experimental R&D focused on the production of silicon carbide (β-SiC) from the residual char byproduct from pitch production, and also on the production of carbon fiber from the anisotropic pitch. SiC was successfully synthesized using a mixture of residual char and sandstone at a ratio of 1:1. Reaction temperature and residence time were optimized and yielded a product purity of 81%. For carbon fiber production, the most successful pitch samples were obtained from the mild solvolysis liquefaction approach, combined with the use of a plastic (HDPE)-derived solvent. Fiber properties improved over time as laboratory fiber production methodologies improved, and final yields of carbon fiber were obtained with a diameter of 12.14 ± 1.10 um, Modulus of 173.73 ± 15.25 GPa, and Tensile Strength of 1.04 ± 0.10 GPa. A proof-of-concept Modern Community Research Data Portal (MCRDP) was developed and deployed for coal and coal-derived pitch characterization, with the full support of (i) remote web-based access, (ii) distributed analysis, (iii) interactive visualization and exploration, (iv) shared and long-term data access, (v) advanced query capabilities and (vi) real-time collaboration. The Coal to Products Data Portal “coaltoproducts.org” provides researchers with space to store and share data within a project, tools for analyzing and understanding data for scientific investigation, and the ability to publish data to the broader community for reproducibility. The portal leverages the Material Commons 2.0 (MC) platform developed by the Center for PRedictive Integrated Structural Materials Science (PRISMS) of the University of Michigan, to achieve long-term longevity of data collections and, more importantly, collaborative science. A number of data visualization tools were also assessed and implemented for interrogating the experimental and modeling data. The machine learning portion of this project analyzed datasets from two different coal conversion processes performed on a diverse set of coal samples from both the coal pyrolysis experiments and the solvent liquefaction experiments. The work was initiated by exploring standard regression models on the pyrolysis data, aiming to understand the impact of sample characteristics and processing conditions on key product metrics. Over the course of the project, the focus expanded to include a variety of machine learning tools, delving into both supervised and unsupervised learning methods. Models tested on the pyrolysis data included linear, ridge, lasso, elastic-net, Gaussian process, random forest regression, and AutoSklearn, and the approach was continually refined to enhance predictive accuracy and model interpretability. Similar techniques were applied to the liquefaction data with an additional focus on feature engineering. Along with mesophase content, additional outputs of interest were the pitch yield, softening point, and QI content. Insights derived from these analyses are crucial in determining the factors influencing the quality and yield of coal-derived products. As the work progressed, the research evolved from foundational model comparisons to analyses of random forests, decision paths, and feature importance scores. A thorough market analysis was performed to examine the prospects of coal-based carbon fibers. The best opportunities for coal come from its lower and more stable price relative to petroleum, particularly for subbituminous coals, which is the primary advantage that a coal refinery may have over a petroleum refinery. Before a commercial CTP production facility can be modeled, however, several things need to be understood regarding the nature of the would-be coal refinery. These include the technology to be deployed, the size of facility, the volume(s) of co-product(s), and the waste and emissions profile of the plant. The volume of co-products and waste may be substantial and will require separate market analysis to ensure viability. In the near-term, the importance of coal tar pitch, in the form of carbon pitch, to the aluminum and steel industries is likely to overshadow the alternative use of this material as an input for carbon fiber. The importance of steel and aluminum in building materials, and the need for carbon materials in their manufacturing, will ensure that demand for these products remains for the long run. In addition, carbon fiber may also be the best substitute for steel and aluminum well into the future. While society will eventually be able to shift production of much of its electricity needs to renewables, it will not be able to shift away from fossil fuels for production of high-strength construction and vehicular materials. Demand for carbon fiber is expected to increase quickly, but the volume of carbon fiber and the amount of coal that would be needed to produce even a sizeable share of this market may still be relatively small compared to current coal production. Thus, other coal-based products like graphene, graphite, carbon foams, resins, and carbon-based building products will play important roles in sustaining coal production as coal-fired power generation continues to decline.

01 COAL, LIGNITE, AND PEAT↗

Netostat: analyzing dynamic flow patterns in high-speed networks

Understanding flow traffic patterns in networks, such as the Internet or service provider networks, is crucial to improving their design and building them robustly. However, as networks grow and become more complex, it is increasingly cumbersome and challenging to study how the many flow patterns, sizes and the continually changing source-destination pairs in the network evolve with time. Here, we present Netostat, a visualization-based network analysis tool that uses visual representation and a mathematics framework to study and capture flow patterns, using graph theoretical methods such as clustering, similarity and difference measures. Netostat generates an interactive graph of all traffic patterns in the network, to isolate key elements that can provide insights for traffic engineering. We present results for U.S. and European research networks, ESnet and GEANT, demonstrating network state changes, to identify major flow trends, potential points of failure, and bottlenecks.

97 MATHEMATICS AND COMPUTING↗

VTAnDeM: A python toolkit for simultaneously visualizing phase stability, defect energetics, and carrier concentrations of materials

Phase stability, defect formation energies, and carrier concentrations are closely interrelated features of semiconductors. Due to their joint dependence on the multidimensional chemical potential space, it is challenging to quantitatively establish patterns between these quantities in a given semiconductor, especially when the semiconductor is comprised of multiple elements. To enable synchronous visualization and analysis of these complementary material properties and their interdependence, we developed the Visualization Toolkit for Analyzing Defects in Materials (VTAnDeM). This python-based toolkit allows users to interactively explore how defect formation energies and carrier concentrations vary across the composition and chemical potential spaces of multicomponent semiconductors. Here, we illustrate the computational workflow that employs VTAnDeM as a post-processing tool for first-principles calculations and describe the data organization and theory underlying the visualization scheme. Furthermore, we believe that this software will serve as a useful tool for simultaneously visualizing the often complex and non-intuitive chemical potential – defect – carrier concentration phase space of semiconductors.

36 MATERIALS SCIENCE↗

Towards elastic in situ analysis for high-performance computing simulations

In situ analysis and visualization have grown increasingly popular for enabling direct access to data from high-performance computing (HPC) simulations. As a simulation progresses and interesting physical phenomena emerge, however, the data produced may become increasingly complex, and users may need to dynamically change the type and scale of in situ analysis tasks being carried out and consequently adapt the amount of resources allocated to such tasks. To date, none of the production in situ analysis frameworks offer such an elasticity feature, and for good reason: the assumption that the number of processes could vary during run time would force developers to rethink software and algorithms at every level of the in situ analysis stack. In this paper we present Colza, a data staging service with elastic in situ visualization capabilities. We demonstrate the use of Colza with the Deep Water Impact and the AMR-Wind simulations, coupling them with the ParaView Catalyst and Ascent in situ libraries, and show that Colza enables dynamic rescaling of these widely-used frameworks with no interruption to the simulation or staging service. Here, we highlight the challenges of enabling such elasticity, which requires overcoming these frameworks' reliance on MPI, using distinct engineering approaches, namely dependency injection and dependency overload. To the best of our knowledge, this work is the first to enable elastic in situ visualization capabilities for HPC applications on top of existing production analysis tools.

97 MATHEMATICS AND COMPUTING↗

Collaborative: in situ visual analytics technologies for extreme scale combustion simulations

This project aims to drastically enhance the usability of in situ analysis and visualization for extreme-scale scientific simulations. Current exascale computing capabilities promise to offer greater predictive ability of simulations and to further push the frontiers of science and technology. However, to validate the simulation output at extreme scale, examine the modeled phenomena, and discover previously unknowns from the output data, the output must be reduced or transformed in situ as it is being generated during the simulation such that the amount of data to examine and store is kept to a minimum. Such in situ approaches allow us to process and analyze the data and any embedded geometry to an extent that would be prohibitively expensive, if not impossible, to perform as a post hoc task. While in situ processing has been demonstrated to be a feasible and promising approach, its full potential has not yet been leveraged. In this project, we have developed comprehensive enhancements to in situ technology based on probability distributions in data. Our research focuses on jointly developing new ways of interacting with massive statistical samples while creatively utilizing new state-of-the-art computational resources to push the boundaries of in situ exploration. Moreover, we have developed new time-dependent techniques to enable previously unattainable capabilities in areas such as intelligent simulation steering and precise feature identification. We have experimentally studied our design and implementation at NERSC and OLCF, and are able to leverage existing in situ infrastructures whenever possible. While the exemplar in this project is combustion, many other fields for which turbulent transport is important, e.g., fusion, climate, astrophysics among others, encounter similar issues as simulations scale up to the exascale. This project shows its potential to generate high impact on DOE missions since the resulting technology promises to improve scientists’ ability to rapidly and correctly interpret and tune extreme-scale simulations, leading to new scientific understanding and advancements.

97 MATHEMATICS AND COMPUTING↗

Visualization Quality Assessment

Understanding how inaccuracies in visualizations affect users’ perception and understanding of scientific data is hard. Inaccuracies in visualizations are quite common and could arise from a range of sources such as errors in the original dataset arising from compression artifacts, errors in the capturing device, noise during transmission of the data, effects due to the algorithm being used to convert data to visualization images, images generated from neural networks, and sources we have yet to discover. Many image quality assessment metrics have been developed to quantify image errors. However, these are usually focused on “natural images” rather than visualizations of scientific data. Common image quality assessment metrics (IQAs) include MSE, PSNR, perceptual metrics such SSIM, FSIM as well as perceptual metrics using deep learning approaches. However, a critical part of understanding how errors are perceived by humans, and subsequently developing more accurate quality assessment metrics, is through user evaluation studies. The goal of this software is to develop a visualization quality assessment (VQA) process that will enable the generation of VQAs that can be used to quantify errors in scientific data visualizations. The VQA development process will include software to support user evaluation experimental design, analysis of visualization differences against standard quality metrics, and the ability to develop additional VQA metrics specific to scientific visualization images.

Grosset, Andre↗

TListSpectrum

TListSpectrum is a C++ class developed inside the CERN high-energy physics analysis C++ framework ROOT. This class structure was developed to assist in the processing, visualization, and analysis of list-mode or time-stamped radiation spectroscopy data. The class structure currently contains parsing and functionality to synthesize list-mode data from CAEN and Mirion Lynx radiation spectroscopy digital acquisition systems along with feature functionality to post-process data sets and build coincident data sets from the instrument.

Pierson, Bruce↗

Performance analysis and data reduction for exascale scientific workflows

Chimbuko is the first in situ, scalable, workflow-level performance analysis tool for trace-level analysis and visualization of application performance. This tool was developed by the Co-design Center for Online Data Analysis and Reduction and funded by the U.S. Department of Energy’s Exascale Computing Project. We provide a detailed description of Chimbuko’s architecture and illustrate our online and offline visualization with multiple use cases. We also present results for the deployment and scalability of the tool as applied to a high-energy physics workflow running at large scale on the Frontier supercomputer.

97 MATHEMATICS AND COMPUTING↗