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Implicit and coupled fluid plasma solver with adaptive Cartesian mesh and its applications to non-equilibrium gas discharges

In this work, we present a new fluid plasma solver with adaptive Cartesian mesh (ACM) based on a full-Newton (nonlinear, implicit) scheme for non-equilibrium gas discharge plasma. The electrons and ions are described using drift-diffusion approximation coupled to Poisson equation for the electric field. The electron-energy transport equation is solved to account for electron thermal conductivity, Joule heating, and energy loss of electrons in collisions with neutral species. The rate of electron-induced ionization is a function of electron temperature and could also depend on electron density (important for plasma stratification). The ion and gas temperature are kept constant. The transport equations are discretized using a non-isothermal Scharfetter-Gummel scheme to resolve possible large temperature gradients in the sheaths. We demonstrate the new solver for simulations of direct current (DC) and radiofrequency (RF) discharges. The implicit treatment of the coupled equations allows using large time steps. The full-Newton method (FNM) enables fast nonlinear convergence at each time step, offering significantly improved simulation efficiency. We discuss the selection of time steps for solving different plasma problems. The new solver enables solving several problems we could not solve before with existing software: two- and three-dimensional structures of the entire DC discharges including cathode and anode regions, electric field reversals and double-layer formation, the normal cathode spot and an anode ring, moving striations in diffuse and constricted DC discharges, and standing striations in RF discharges. The developed FNM-ACM technique offers many benefits for tackling the disparity of gas discharge plasma systems' time scales and nonlinearity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry

Abstract Motivation Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required. Results We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing. Availability and implementation https://github.com/PNNL-Comp-Mass-Spec/AutoCCS. Supplementary information Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).

47 OTHER INSTRUMENTATION↗

WinGridder-A graphic grid generator for TOUGH2 simulators (WinGridder) v3.0

WINGRIDDER V3.0 is a Windows-based software for designing and generating numerical grids for numerical simulators that are based on the "integral finite difference" or the "control volume" numerical scheme (e.g., TOUGH2, Pruess et al., 1996). The user can design and generate grid that properly represents the stratigraphic features, inclined faults, and repository. WINGRIDDER V3.0 is an upgrade from WINGRIDDER V2.0. This revision includes testable requirements as listed in the Requirements Document (RD), 10024-RD-3.0-00, Section 2. With new features, WINGRIDDER V3.0 adds the ability to generate a multiple-interactive-continuum (MINC) grid.

Pan, Lehua↗

OpenStudio® HPXML workflow [SWR-25-13]

OpenStudio-HPXML allows running residential EnergyPlus™ simulations using an HPXML file for the building description. It is intended to be used by user interfaces or other automated software workflows that automatically produce the HPXML file. OpenStudio-HPXML can accommodate a wide range of different building technologies and geometries. End-to-end simulations typically run in 3-10 seconds, depending on complexity, computer platform and speed, etc. For more information on running simulations, generating HPXML files with the appropriate inputs to run EnergyPlus, etc., please visit the documentation linked below. https://openstudio-hpxml.readthedocs.io/en/latest

Horowitz, Scott↗

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

59 BASIC BIOLOGICAL SCIENCES↗

Increasing the resilience and security of the United States' power infrastructure

The United States' power infrastructure is aging, underfunded, and vulnerable to cyber attack. Emerging smart grid technologies may take some of the burden off of existing systems and make the grid as a whole more efficient, reliable, and secure. The Pacific Northwest National Laboratory (PNNL) is funding research into several aspects of smart grid technology and grid security, creating a software simulation tool that will allow researchers to test power infrastructure control and distribution paradigms by utilizing different smart grid technologies to determine how the grid and these technologies react under different circumstances. Understanding how these systems behave in real-world conditions will lead to new ways to make our power infrastructure more resilient and secure. Demonstrating security in embedded systems is another research area PNNL is tackling. Many of the systems controlling the U.S. critical infrastructure, such as the power grid, lack integrated security and the aging networks protecting them are becoming easier to attack.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Monitoring and Control of Chemical Composition of InGaN Layers During MOCVD

This Department of Energy SBIR Phase II grant targets the inefficiency of the epitaxial processes used to deposit wide band-gap semiconductor thin films that are an essential part of the next generation high-brightness LEDs for solid state lighting. Non-uniformity of the layers over a single wafer and non-repeatability over the wafers in a single batch, separate batches and separate reactors are some of the primary source of reduced manufacturing yield. The team performed extensive research, development and validation of an in-situ spectroscopic optical monitoring and epitaxial process control system. The system monitors the LED thin films as they grow on the individual wafers inside the epitaxial reactor, records the signal in a broad spectral range and processes the information to retrieve essential film quality parameters and their variation over a single wafer, all the wafers in a batch and multiple batches. A novel software algorithm is implemented, which performs real-time spectral pattern recognition and displays any abnormalities or differences in the deposition, which is used by the engineer to optimize the epitaxial process. The project resulted in the optimization of the LED film growth and improvement of its uniformity and repeatability, reducing the cost of the final LED devices.

36 MATERIALS SCIENCE↗

Advanced Reactors-Intermediate Heat Exchanger (IHX) Coupling: Theoretical Modeling and Experimental Validation

The overall goal of the research project was to model the behavior of the advanced reactorintermediate heat exchange system and to develop advanced control techniques for off-normal conditions. The specific objectives defined for the project were: 1. To develop the steady-state thermal hydraulic design of the intermediate heat exchanger (IHX); 2. To develop mathematical models to describe the advanced nuclear reactor-IHX-chemical process/power generation coupling during normal and off-normal operations, and to simulate models using multiphysics software; 3. To develop control strategies using genetic algorithm or neural network techniques and couple these techniques with the multiphysics software; 4. To validate the models experimentally The project objectives were accomplished by defining and executing four different tasks corresponding to these specific objectives. The first task involved selection of IHX candidates and developing steady state designs for those. The second task involved modeling of the transient and offnormal operation of the reactor-IHX system. The subsequent task dealt with the development of control strategies and involved algorithm development and simulation. The last task involved experimental validation of the thermal hydraulic performances of the two prototype heat exchangers designed and fabricated for the project at steady state and transient conditions to simulate the coupling of the reactor- IHX-process plant system. The experimental work utilized the two test facilities at The Ohio State University (OSU) including one existing High-Temperature Helium Test Facility (HTHF) and the newly developed high-temperature molten salt facility.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Reproducibility and Variability of I/O Performance on BG/Q: Lessons Learned from a Data Aggregation Algorithm

Reading and writing data efficiently from different tiers of storage is necessary for most scientific simulations to achieve good performance at scale. Many software solutions have been developed to decrease the I/O bottleneck. One wellknown strategy, in the context of collective I/O operations, is the two-phase I/O scheme. This strategy consists of selecting a subset of processes to aggregate contiguous pieces of data before performing reads/writes. In our previous work, we implemented the two-phase I/O scheme with a MPI-based topology-aware algorithm. Our algorithm showed very good performance at scale compared to the standard I/O libraries such as POSIX I/O and MPI I/O. However, the algorithm had several limitations hindering a satisfying reproducibility of our experiments. In this paper, we extend our work by 1) identifying the obstacles we face to reproduce our experiments and 2) discovering solutions that reduce the unpredictability of our results.

97 MATHEMATICS AND COMPUTING↗

SIRIUS: Science-Driven Data Management for Multi-Tiered Storage

The data sets being generated by large applications on very large-scale systems are increasing in both size and complexity. At the same time, there are new ways available to store and access these data sets. The goal in this project is to develop software that applications can use to make use of new and existing storage technologies in more sophisticated ways. One challenge in scientific data management is handling ‘hot’ vs ‘cold’ data. Data that is hot is data that is needed (or will be needed soon) in order for the program to continue progressing, while cold data is either output (and so will not be need further during the life of the program) or will not be needed until significantly later in the program’s run. Hot data should be stored in a way that allows fast access. On most systems, economic factors lead to an inverse relationship between storage performance and storage capacity and so fast access storage is limited. This makes it important to correctly place hot and cold data and avoid cold data unnecessarily consuming precious resources. In this reporting period, we addressed this challenge in various ways and at various levels. Data management frameworks offer only limited control to applications in how data is stored. We have added software capabilities for seamlessly moving data between layers of the storage technology using promote and demote functions to existing software frameworks. This gives direct control to applications in deciding what priority data receives. Additionally, we integrated different storage layer management frameworks in order to allow data to be exchanged and moved between storage layers in a consistent way across the application. Further, applications are not always able to directly decide what storage level makes sense for a given piece of data without an understanding of the underlying storage technologies. Data storage frameworks are often positioned to make these sorts of decisions in service of the application. We have added machine-learning based capabilities to data staging frameworks in order to make intelligent decisions about where data should be stored given learning about patterns in previous usage of similar data.

97 MATHEMATICS AND COMPUTING↗

The Uniform Methods Project: Smart Thermostat Evaluation Protocol

A smart thermostat is an internet-connected device that controls home heating, ventilation, and air-conditioning (HVAC) equipment and can automatically adjust temperature set points to optimize performance and achieve energy savings. Smart thermostat features often include two way communication, occupancy detection (such as geofencing and occupancy sensors), schedule learning, and seasonal optimization algorithms. Smart thermostats can control most conventional HVAC systems, including central air conditioners, heat pumps, and forced air furnaces. Several types of residential utility programs offer smart thermostats as replacements measures. Working with smart thermostat vendors, utilities can offer separate optimization programs to produce energy savings beyond those achieved by installing a smart thermostat. From an evaluation perspective, smart thermostat programs have several noteworthy features. First, the energy savings from a smart thermostat may change over the life of the device. As a smart thermostat is connected to the internet, original equipment manufacturers can update the thermostat software to improve the thermostat's energy efficiency. Likewise, users can adjust the thermostat settings and schedules over time in response to changes in weather, thermal comfort, energy prices, or preferences for energy efficiency. Additionally, many thermostat manufacturers offer seasonal optimization programs that recommend changes or make minor, automated adjustments to the thermostat settings to improve energy efficiency. These opt-in programs are now standard offerings for many smart thermostat manufacturers and provided at no additional cost to users. The potential for software updates and continuous optimization and the evolving nature of user interactions mean future energy savings may differ from first-year savings and the energy savings of smart thermostats may need to be evaluated more than once. Second, smart thermostats often have small unit energy savings relative to a home's total energy consumption, especially in comparison to whole- home retrofit programs. This can make it difficult to detect the smart thermostat savings in billing or advanced metering infrastructure (AMI) meter consumption data. For example, as cooling loads in many regions average about 20% of annual electricity consumption, smart thermostat savings of 10% of cooling energy use would equate to a 2% reduction in home electricity consumption. Evaluators should use regression analysis of whole-home billing consumption or advanced metering infrastructure (AMI) meter consumption data to evaluate smart thermostat savings because, as explained at greater length below , these data are usually available to evaluators and regression can control for the impacts of weather and other potentially confounding factors on a home's energy consumption. Finally, as with other energy efficiency programs, participation in smart thermostat programs is self-selective. As discussed at greater length below , smart thermostat participants tend to be, among other things, younger, higher-income, and more likely to adopt electric vehicles (EVs) and internet connected devices than nonparticipants. These differences are often unobservable to the evaluator and correlated with a home's energy consumption, creating the potential for bias in estimating savings. Due to the small unit savings of thermostats, errors and biases from self-selection that may not be very consequential when evaluating a whole- home retrofits (e.g., ±2% of home electricity consumption) can have a major impact when evaluating the savings and cost-effectiveness of smart thermostat programs. A percentage point change in the estimated savings could affect the cost-effectiveness of a program. This means it is important for evaluators to assess and to minimize the potential for error from selection bias in estimating smart thermostat program savings. The Uniform Methods Project provides model protocols for determining energy savings and demand reductions that result from specific energy efficiency measures implemented through state and utility programs. In most cases, the measure protocols are based on a particular option identified by the International Performance Verification and Measurement Protocol ; however, this work provides a more detailed approach to implementing that option. Each chapter is written by technical experts in collaboration with their peers, reviewed by industry experts, and subject to public review and comment. The UMP protocols can be used by utilities, program administrators, public utility commissions, evaluators, and other stakeholders for both program planning and evaluation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Shallow Marine High-Resolution 3D Seismics for Above-Zone CO2 Monitoring: A Case Study in Offshore Japan

Shallow marine high-resolution 3D (HR3D) seismic utilizes a novel seismic acquisition technology for imaging fine geological features not revealed by conventional 3D surveys. HR3D technology has been previously used for shallow subsurface studies, however is rarely implemented for monitoring injected fluids, and has not previously been used to monitor an active CO2 storage project. In this study, we for the first time demonstrate the acquisition, processing and initial interpretation of a HR3D seismic survey in Tomakomai, offshore Japan, where a large-scale CO2 storage project is being undertaken. As a seismic monitoring tool, the HR3D survey images the geologic overburden (< 1000 ms), aiming to detect potential CO2 leakage pathways above the injection reservoir. The HR3D acquisition system comprises a 210 in3 GI air gun and 4 streamers that are 25 m in length with 10 m inline separation. Each streamer has 8 channels with a 3.125 m group interval, yielding a very small final bin size of 3 x 3 m. The short offset and low-fold coverage of the HR3D data creates new challenges in seismic data processing, which demands a different data processing workflow tailored to the HR3D acquisition. We present a data processing workflow involving multiple software processing packages, which tackled high-resolution related static issues and significantly reduced various noise elements. Dip-steering and structural filtering were employed on the stacked volume to further enhance the lateral coherence and to remove random noise and suppress acquisition footprints. The final volume shows flat and coherent above-zone stratigraphy, suggesting a good seal quality above the CO2 reservoir. The successful implementation of HR3D acquisition and the customized processing workflow verify the feasibility of HR3D seismics for the above- zone monitoring of offshore CO2 injection and storage projects.

Feng, Ye Erickson↗

SHALLOW MARINE HIGH-RESOLUTION 3D SEISMICS FOR ABOVE- ZONE CO2MONITORING: A CASE STUDY IN OFFSHORE JAPAN

Shallow marine high-resolution 3D (HR3D) seismic utilizes a novel seismic acquisition technology for imaging fine geological features not revealed by conventional 3D surveys. HR3D technology has been previously used for shallow subsurface studies, however is rarely implemented for monitoring injected fluids, and has not previously been used to monitor an active CO2 storage project. In this study, we for the first time demonstrate the acquisition, processing and initial interpretation of a HR3D seismic survey in Tomakomai, offshore Japan, where a large-scale CO2 storage project is being undertaken. As a seismic monitoring tool, the HR3D survey images the geologic overburden (< 1000 ms), aiming to detect potential CO2 leakage pathways above the injection reservoir. The HR3D acquisition system comprises a 210 in3 GI air gun and 4 streamers that are 25 m in length with 10 m inline separation. Each streamer has 8 channels with a 3.125 m group interval, yielding a very small final bin size of 3 x 3 m. The short offset and low-fold coverage of the HR3D data creates new challenges in seismic data processing, which demands a different data processing workflow tailored to the HR3D acquisition. We present a data processing workflow involving multiple software processing packages, which tackled high-resolution related static issues and significantly reduced various noise elements. Dip-steering and structural filtering were employed on the stacked volume to further enhance the lateral coherence and to remove random noise and suppress acquisition footprints. The final volume shows flat and coherent above-zone stratigraphy, suggesting a good seal quality above the CO2 reservoir. The successful implementation of HR3D acquisition and the customized processing workflow verify the feasibility of HR3D seismics for the above-zone monitoring of offshore CO2 injection and storage projects.

Feng, Ye E.↗

Fault Response of Distributed Energy Resources Considering the Requirements of IEEE 1547-2018

Inverter-based DER responses to faults on the electric power system are different than those of conventional generators and are often poorly understood. Inverter fault responses are largely software-defined, within physics-based constraints. DERs are regulated by standards and grid codes that also constrain their responses. Though fault response of DERs will vary widely, for any DER following any particular standard, a pattern of fault response can be synthesized by observing that particular standard. In this paper, the recently published IEEE 1547-2018 is examined to explore the general fault response of any DER that follows IEEE 1547-2018. Additionally, an IEEE 1547-2018 compliant inverter model is developed and tested in simulation to find the fault response, and that response is compared with the fault response of a commercial off-the-shelf inverter.

41 EE - Solar Energy Technologies Office (EE-4S)↗

HOPP - Hybrid Optimization and Performance Platform

The Hybrid Optimization and Performance Platform, HOPP, is a wind + solar + battery + X design software for optimizing co-located, utility-scale hybrid plants down to the component level for different markets and technoeconomic objectives. Key technology and financial inputs to the HOPP model that inform the objective to be optimized are presented. The layout and performance integration is combined with optimal dispatch and full financial modeling within an optimization framework. With an example scenario, optimal sizing and layout results are shown in a sensitivity analysis of prices for two hybrid configurations.

batteries↗

PSI/J: A Portable Interface for Submitting, Monitoring, and Managing Jobs

It is generally desirable for high-performance computing (HPC) applications to be portable between HPC systems, for example to make use of more performant hardware, make effective use of allocations, and to co-locate compute jobs with large datasets. Unfortunately, moving scientific applications between HPC systems is challenging for various reasons, most notably that HPC systems have different HPC schedulers. We introduce PSI/J, a job management abstraction API intended to simplify the construction of software components and applications that are portable over various HPC scheduler implementations. We argue that such a system is both necessary and that no viable alternative currently exists. We analyze similar notable APIs and attempt to determine the factors that influenced their evolution and adoption by the HPC community. We base the design of PSI/J on that analysis. We describe how PSI/J has been integrated in three workflow systems and one application, and also show via experiments that PSI/J imposes minimal overhead.

Hategan, Mihael↗

TH-E-209-03: Development of An In-House CT Dose Monitoring and Management System Based On Open-Source Software Resources -- Pearls and Pitfalls

Radiation dose monitoring solutions have opened up new opportunities for medical physicists to be more involved in modern clinical radiology practices. In particular, with the help of comprehensive radiation dose data, data-driven protocol management and informed case follow up are now feasible. Significant challenges remain however and the problems faced by medical physicists are highly heterogeneous. Imaging systems from multiple vendors and a wide range of vintages co-exist in the same department and employ data communication protocols that are not fully standardized or implemented making harmonization complex. Many different solutions for radiation dose monitoring have been implemented by imaging facilities over the past few years. Such systems are based on commercial software, home-grown IT solutions, manual PACS data dumping, etc., and diverse pathways can be used to bring the data to impact clinical practice. The speakers will share their experiences with creating or tailoring radiation dose monitoring/management systems and procedures over the past few years, which vary significantly in design and scope. Topics to cover: (1) fluoroscopic dose monitoring and high radiation event handling from a large academic hospital; (2) dose monitoring and protocol optimization in pediatric radiology; and (3) development of a home-grown IT solution and dose data analysis framework. Learning Objectives: Describe the scope and range of radiation dose monitoring and protocol management in a modern radiology practice Review examples of data available from a variety of systems and how it managed and conveyed. Reflect on the role of the physicist in radiation dose awareness.

60 APPLIED LIFE SCIENCES↗

Evaluation of the OpenCL AES Kernel using the Intel FPGA SDK for OpenCL

The OpenCL standard is an open programming model for accelerating algorithms on heterogeneous computing system. OpenCL extends the C-based programming language for developing portable codes on different platforms such as CPU, Graphics processing units (GPUs), Digital Signal Processors (DSPs) and Field Programmable Gate Arrays (FPGAs). The Intel FPGA SDK for OpenCL is a suite of tools that allows developers to abstract away the complex FPGA-based development flow for a high-level software development flow. Users can focus on the design of hardware-accelerated kernel functions in OpenCL and then direct the tools to generate the low-level FPGA implementations. The approach makes the FPGA-based development more accessible to software users as the needs for hybrid computing using CPUs and FPGAs are increasing. It can also significantly reduce the hardware development time as users can evaluate different ideas with high-level language without deep FPGA domain knowledge. In this report, we evaluate the performance of the kernel using the Intel FPGA SDK for OpenCL and Nallatech 385A FPGA board. Compared to the M506 module, the board provides more hardware resources for a larger design exploration space. The kernel performance is measured with the compute kernel throughput, an upper bound to the FPGA throughput. The report presents the experimental results in details. The Appendix lists the kernel source code.

97 MATHEMATICS AND COMPUTING↗