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DOE OSTI2018

Women in Science: Fermilab computing analyst Margherita Vittone-Wiersma

With February 11 marking the International Day of Women and Girls in Science, female physicists, engineers and computer scientists from CERN and Fermilab share their experiences of building careers in science. Margherita Vittone-Wiersma came to Fermilab as a physicist in February 1985. Together with a group of researchers from Italy's Institute of Nuclear Physics, she began a new experiment called E687. But she soon learned that she preferred working on data acquisition and the many methods to store and access the huge amount of data coming out of science experiments. What was once mere megabytes of data is now terabytes of information - and experimental physicists need to be able to retrieve stored data and monitor data coming from the detectors in real-time. "It's been an incredible change in scale of the amount of data that is handled by computers and has to be analyzed by the physicists," she says. Margherita migrated from physics to her new role in computing through lots of hands-on learning and classes in different programming languages and software development offered at Fermilab. She officially joined the lab's computing division in 1989. "It's a great experience to work with the physicists," she says. Together physicists and computing experts iterate over tools "to make sure that everything is working the way they expect. It's very rewarding." Credits: Video production - Fermilab Creative Services Music Copyright: Universal Production Music Astral Light Chevalier Idea originally conceived by Tanya Levshina, Fermilab and Maria Dimou, CERN.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2025

An open-source hybrid unstructured mesh - CAD fusion multiphysics analysis workflow in SALAMANDER

Plasma facing components in fusion devices will endure extreme neutron and heat fluxes. To facilitate their design using simulation tools, the open-source Fusion Module, Fusion ENergy Integrated multiphys-X (FENIX) framework is being developed to model these components with a high-fidelity multi-physics multi-dimensional approach. It can iteratively resolve couplings between all the physics at play, from neutron radiation, to thermomechanics, to near-wall plasma dynamics. This framework is based on the Multiphysics Object Oriented Simulation Environment (MOOSE), which is developed by a collaboration of US National Laboratories since 2008, for advanced nuclear, geomechanics simulations and other applications. FENIX couples numerous simulation tools, including OpenMC, the Tritium Migration Analysis Program v8, the NekRS CFD software, and most MOOSE modules. For the coupling of radiation transport and other physics, FENIX supports a hybrid workflow between Computer Assisted Design (CAD) and unstructured mesh geometries. The CAD can be generated from skinning the unstructured mesh, to enable a coarse geometry for efficient particle transport, but still resolving the local material compositions and temperature gradients. Neutron transport is performed using DAGMC on the CAD, and Cardinal, integrated in FENIX, maps tallied quantities, such as the heat deposition or the tritium generation rates, from a tally volumetric mesh to the other physics’ unstructured mesh. This coupling was exercised on a simplified tokamak geometry, coupling neutron transport with the heat conduction equation, and on a monoblock divertor problem, coupling additionally with tritium migration. Mesh convergence studies highlight the importance of the mapping conservativeness. Coupling with thermo-mechanics is further enabled by the generalization of the approach to moving meshes. The presentation will include these coupled analysis as well as an update on status of the FENIX framework.

70 - PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

A tool and a methodology to use macros for abstracting variations in code for different computational demands

Scientific software used on high-performance computing platforms is in a phase of transformation because of the combined increase in the heterogeneity and complexity of models and hardware platforms. Having separate implementations for different platforms can easily lead to combinatorial explosions; therefore, the computational science community has been looking for mechanisms to express code through abstractions that can be specialized for different platforms. Most existing approaches use template meta-programming in C++, and are, therefore language specific. Here, we have developed a tool that uses customized expansion of macros to mimic some of C++ behavior in other languages. It enables unification of any code variants that may be necessary to run efficiently on different target architectures and different computational environments through use of macros with multiple alternative definitions and ability to arbitrate on definition selection for expansion. Combined with two other tools, a custom runtime, and a user specified recipe translator, our custom macroprocessor becomes a part of an overall performance portability solution that does not depend on any specific programming language. We also use macros as code-shorthand that lets code snippets become building blocks that allow variations in control flow to explore performance options. We demonstrate use of macros in Flash-X, a multiphysics multicomponent code with many Fortran legacy components derived from an earlier community code FLASH.

Heterogenous computing↗

DOE OSTI2015

Transmission Planning Analysis Tool

Developed to solve specific problem: Assist transmission planning for regional transfers in interconnected power systems. This work was originated in a study for the U.S. Department of State, to recommend transmission reinforcements for the Central American regional system that interconnects 6 countries. Transmission planning analysis is currently performed by engineers with domain-specific and system-specific knowledge without a unique methodology. The software codes of this disclosure assists engineers by defining systematic analysis procedures to help identify weak points and make decisions on transmission planning of regional interconnected power systems. Transmission Planning Analysis Tool groups PSS/E results of multiple AC contingency analysis and voltage stability analysis and QV analysis of many scenarios of study and arrange them in a systematic way to aid power system planning engineers or transmission operators in effective decision-making process or in the offline study environment.

Vyakaranam, Bharat↗

DOE OSTI2017

Solving Complex Radioactive Decay Chains for Future Assessment and Cleanup Decisions - 17046

In support of U.S. Environmental Protection Agency's on-line calculators for risk and dose assessment, a decay chain tool was developed to address the need to understand how radionuclide activity changes with time as the activity measured in the past will be different from current and future levels. When a radionuclide decays, its activity decreases exponentially as a function of time transforming into a different atom - a decay product. The atoms keep transforming to new decay products until they reach a stable state and are no longer radioactive. The series of decay products created to reach this balance is called the decay chain. For radionuclide chains, the daughter products can have significant implications in dosimetry and remediation. Thus, risk assessors evaluating sites with radioactive contamination need to plan for future progeny ingrowth, in addition to sampled radionuclides. These are important considerations for risk quantification during the characterization and cleanup plans, particularly when sampling may have occurred years before the remediation cleanup work begins. If a radionuclide half-life and current activity are known, then hand-calculating the future activity is straightforward. However, calculating the ingrowth of progeny quickly becomes cumbersome for longer chains such as the Thorium-232 decay series. For the more complex chains where many daughters are formed, possibly with multiple branches, this calculation involves solving a complex set of simultaneous differential equations known as the Bateman Equation. The Decay Chain Activity Projection Tool calculates the activity of radionuclides and their progeny as a function of time. This tool currently uses a combination of Perl, JavaScript, Plot.ly, and jQuery to automatically construct the radionuclide decay chains, solve the resulting Bateman Equation, and provide the user with tabular solution output and plots. Additional software may be used as development advances. The risk assessor can then use the data for exposure assessment and cleanup decisions without further costly sampling. The benefits of providing this calculator are to prevent overestimation of risk due to decay of the parent isotope and to avoid underestimation of risk due to ingrowth of progeny more toxic than the parent. Graphs are provided to show the simultaneous decay rates and ingrowth, as well as tabular output at time-point T and all the decay half-life intervals. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

TEMWizard pyCHIP.gui

TEMWizard pyCHIP.gui is used to visualize intermediate and final results from Atomap, an open-source software tool for determining the position and other features of atomic columns in transmission electron microscopy images. Also known as pyCHIP.gui.

Spurgeon, Steven R.↗

DOE OSTI2021

Roles of Dynamic State Estimation in Power System Modeling, Monitoring and Operation

—Power system dynamic state estimation (DSE) remains an active research area. This is driven by the absence of accurate models, the increasing availability of fast-sampled, time synchronized measurements, and the advances in the capability, scalability, and affordability of computing and communications. This paper discusses the advantages of DSE as compared to static state estimation, and the implementation differences between the two, including the measurement configuration, modeling framework and support software features. The important roles of DSE are discussed from modeling, monitoring and operation aspects for today’s synchronous machine dominated systems and the future power electronics-interfaced generation systems. Several examples are presented to demonstrate the benefits of DSE on enhancing the operational robustness and resilience of 21st century power system through time critical applications. Future research directions are identified and discussed, paving the way for developing the next generation of energy management systems.

Zhao, Junbo↗

DOE OSTI2016

SU-F-I-14: 3D Breast Digital Phantom for XACT Imaging

Purpose: The X-ray induced acoustic computed tomography (XACT) is a new imaging modality which combines X-ray contrast and high ultrasonic resolution in a single modality. Using XACT in breast imaging, a 3D breast volume can be imaged by only one pulsed X-ray radiation, which could dramatically reduce the imaging dose for patients undergoing breast cancer screening and diagnosis. A 3D digital phantom that contains both X-ray properties and acoustic properties of different tissue types is indeed needed for developing and optimizing the XACT system. The purpose of this study is to offer a realistic breast digital phantom as a valuable tool for improving breast XACT imaging techniques and potentially leading to better diagnostic outcomes. Methods: A series of breast CT images along the coronal plane from a patient who has breast calcifications are used as the source images. A HU value based segmentation algorithm is employed to identify breast tissues in five categories, namely the skin tissue, fat tissue, glandular tissue, chest bone and calcifications. For each pixel, the dose related parameters, such as material components and density, and acoustic related parameters, such as frequency-dependent acoustic attenuation coefficient and bandwidth, are assigned based on tissue types. Meanwhile, other parameters which are used in sound propagation, including the sound speed, thermal expansion coefficient, and heat capacity are also assigned to each tissue. Results: A series of 2D tissue type image is acquired first and the 3D digital breast phantom is obtained by using commercial 3D reconstruction software. When giving specific settings including dose depositions and ultrasound center frequency, the X-ray induced initial pressure rise can be calculated accordingly. Conclusion: The proposed 3D breast digital phantom represents a realistic breast anatomic structure and provides a valuable tool for developing and evaluating the system performance for XACT.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Enhancing User Customization through Novel Software Architecture for Utility Scale Solar Siting Software

There is a need for a spatial decision support application that allows users to create customized metrics for comparing proposed locations of a new solar installation. This document discusses how PVMapper was designed to overcome the customization problem through the development of loosely coupled spatial and decision components in a JavaScript plugin architecture. This allows the user to easily add functionality and data to the system. The paper also explains how PVMapper provides the user with a dynamic and customizable decision tool that enables them to visually modify the formulas that are used in the decision algorithms that convert data to comparable metrics. The technologies that make up the presentation and calculation software stack are outlined. This document also explains the architecture that allows the tool to grow through custom plugins created by the software users. Some discussion is given on the difficulties encountered while designing the system.

14 SOLAR ENERGY↗

DOE OSTI2013

Roadmap Document for Pacific Northwest National Laboratory Contribution to the Open Modeling Framework

The Cooperative Research Network (CRN) of the National Rural Electric Cooperative Association (NRECA) has identified GridLAB-D as a tool that would provide significant benefit to its member utilities. However, they have also noted that the complexity of the tool would be a significant barrier for adoption. As can often happen in complex simulation environments, as the available capabilities and flexibility increases, the usability of the software decreases except for a few “power” users; this is not unique to GridLAB-D. While GridLAB-D has expanded to a considerable user base, with a few notable exceptions (e.g., American Electric Power) most users are focused on research and development. As a result, NRECA/CRN has proposed an Open Modeling Framework (OMF) designed to make the capabilities of GridLAB-D, and other advanced grid tools, available via a web interface. This will allow utility users to access many of the capabilities of GridLAB-D, with little to no knowledge of the tool itself. Other components will be layered over the simulation engines to provide the user with business support functions, allowing full business case scenarios to be created from the technical data generated within the simulations. Because of the open availability and potential national benefit of the OMF, PNNL has been tasked with supporting NRECA/CRN’s development of the tool, with a focus on incorporating GridLAB-D within the OMF structure and expanding GridLAB-D capabilities to support OMF functions. The GridLAB-D enhancements will be provided first to the OMF developers, but will also be delivered to the wider GridLAB-D community after validation via the community repository. This report is intended to provide a roadmap for the intended enhancements to be delivered by PNNL. Seven tasks were identified in cooperation with NRECA/CRN – each is briefly discussed, including potential outcomes and deadlines.

distribution↗

DOE OSTI2016

MDSplus quality improvement project

MDSplus is a data acquisition and analysis system used worldwide predominantly in the fusion research community. Development began 29 years ago on the OpenVMS operating system. Since that time there have been many new features added and the code has been ported to many different operating systems. There have been contributions to the MDSplus development from the fusion community in the way of feature suggestions, feature implementations, documentation and porting to different operating systems. The bulk of the development and support of MDSplus, however, has been provided by a relatively small core developer group of three or four members. Given the size of the development team and the large number of users much more effort was focused on providing new features for the community than on keeping the underlying code and documentation up to date with the evolving software development standards. To ensure that MDSplus will continue to provide the needs of the community in the future, the MDSplus development team along with other members of the MDSplus user community has commenced on a major quality improvement project. The planned improvements include changes to software build scripts to better use GNU Autoconf and Automake tools, refactoring many of the source code modules using new language features available in modern compilers, using GNU MinGW-w64 to create MS Windows distributions, migrating to a more modern source code management system, improvement of source documentation as well as improvements to the www.mdsplus.org web site documentation and layout, and the addition of more comprehensive test suites to apply to MDSplus code builds prior to releasing installation kits to the community. This paper should lead to a much more robust product and establish a framework to maintain stability as more enhancements and features are added. Finally, this paper will describe these efforts that are either in progress or planned for the near future.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

ProteoSign: an end-user online differential proteomics statistical analysis platform

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a userfriendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ ProteoSign.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

GRIDAPPSD/GOSS-GridAPPS-D

GridAPPS-D provides a method for developers to run their new applications on a real-time simulator with extensive modeling and tool support. GridAPPS-D is built around standard data models like the CIM. It readily interfaces to existing software products, which may also 1) use components of GridAPPS-D and 2) supplement or replace the built-in distribution simulator, facilitating the deployment of new ADMS applications to existing software products.

Allwardt, Craig↗

DOE OSTI2014

Situational Awareness Geospatial Application (iSAGA)

Situational Awareness Geospatial Application (iSAGA) is a geospatial situational awareness software tool that uses an algorithm to extract location data from nearly any internet-based, or custom data source and display it geospatially; allows user-friendly conduct of spatial analysis using custom-developed tools; searches complex Geographic Information System (GIS) databases and accesses high resolution imagery. iSAGA has application at the federal, state and local levels of emergency response, consequence management, law enforcement, emergency operations and other decision makers as a tool to provide complete, visual, situational awareness using data feeds and tools selected by the individual agency or organization. Feeds may be layered and custom tools developed to uniquely suit each subscribing agency or organization. iSAGA may similarly be applied to international agencies and organizations.

Sher, Benjamin↗

DOE OSTI2022

Coupling Subsurface and Above-Surface Models for Optimizing the Design of Borefields and District Heating and Cooling Systems

Accurate dynamic energy simulation is important for the design and sizing of district heating and cooling systems with geothermal heat exchange for seasonal energy storage. Current modeling approaches in building and district energy simulation tools typically consider heat conduction through the ground between boreholes without flowing groundwater. While detailed simulation tools for subsurface heat and mass transfer exist, these fall short in simulating above-surface energy systems. To support the design and operation of such systems, the study developed a coupled model including a software package for building and district energy simulation, and software for detailed heat and mass transfer in the subsurface. For the first, it uses the open-source Modelica Buildings Library, which includes dynamic simulation models for building and district energy and control systems. For the heat and mass transfer in the soil, it uses the TOUGH simulator. The TOUGH family of codes can model heat and multi-phase, multi-component mass transport for a variety of fluid systems, as well as chemical reactions, in fractured porous media. The study validated the coupled modeling approach by comparing the simulation results with one from the g-function based ground response model. It then looked into effects when the water table and the regional groundwater flow are considered in the ground, from the perspective of heat exchange between borehole and ground, and the electrical consumption of the district heating and cooling systems. To access the simulation models, please find the links in the submission: -- For coupled approach validation: see model Buildings.Fluid.Geothermal.Borefields.Examples.BorefieldsWithTough and Buildings.Examples.DistrictReservoirNetworks.Examples.Reservoir3Variable_TOUGH from the "Modelica Building Library" resource, branch issue1495_tough_interface, commit a2667c0. -- For the study of the effect of water table: see model Buildings.Examples.DistrictReservoirNetworks.Examples.Reservoir3Variable_TOUGH from he "Modelica Building Library" resource, branch issue1495_tough_interface_moreIO, commit 760de49. -- For the study of the effect of regional groundwater flow: see Buildings.Examples.DistrictReservoirNetworks.Examples.Reservoir3Variable_TOUGH from he "Modelica Building Library" resource, branch issue1495_tough_interface_moreIO_3D, commit c2a2d2a. The coupling interface script "GrounResponse.py" can be found from the above links in the folder Buildings/Resources/Python-Sources. Also, the needed files for TOUGH simulation are in the folder Buildings/Resources/Python-Sources/ToughFiles that can be accessed through the above links. A brief description of these files is given below; detailed specifications for the first three files may be found in the TOUGH3 Users Guide (Jung et al., 2018) https://tough.lbl.gov/documentation/tough-manuals/. (1) INCON - initial conditions for each grid block (2) INFILE - main input file with material properties and control parameters (3) MESH - description of the computational grid (4) readsave - Modelica/TOUGH interface program: read the final output of TOUGH simulation after TOUGH time step and prepare for transfer to Modelica for next Modelica time step (5) readsave.inp - input parameters for program readsave (6) writeincon - Modelica/TOUGH interface program: write the output of Modelica after Modelica time step and prepare for transfer to TOUGH as initial conditions for the next TOUGH step (7) writeincon.inp - input parameters for program writeincon

15 GEOTHERMAL ENERGY↗

DOE OSTI2013

Benefits of Daily File Analysis

Data analysis is an integral part of the Second Line of Defense (SLD) program to ensure that radiation monitoring equipment is operating effectively. Oak Ridge National Laboratory (ORNL) has developed the Desktop Analysis Reporting Tool (DART), which allows SLD users to easily analyze daily file data and to determine the state of health of the monitors. Currently, SLD analysts at ORNL use the DART software to review radiation portal monitor (RPM) data and to generate reports that provide findings to SLD country, project, and sustainability managers.

DART↗

DOE OSTI2020

Total Measurement Uncertainty in Neutron Coincidence Multiplicity Analysis

Neutron multiplicity counting is the most commonly used nondestructive assay technique for determining the plutonium mass within containers of scrap PuO 2 or mixed oxide (MOX). In multiplicity analysis, the 240 Pu eff mass, leakage multiplication, and alpha ratio (the ratio of [α, n]-to-spontaneous fission neutron production) are the three primary unknown sample properties. They must be determined simultaneously. To solve for these three unknowns in a multiplicity assay, three measured values are needed: the singles, doubles, and triples neutron count rates. While the analysis is limited to solving for three unknowns, there are many additional factors that impact the observed count rates and contribute to the measurement uncertainty. In this study we investigate the various uncertainty contributors for the multiplicity analysis through a combination of traditional uncertainty propagation techniques supplemented by Monte Carlo simulations to address the dependences not explicitly expressed by the point source model. Uncertainties arising from counting statistics, calibration parameters, calibration method, nuclear data, and various material characteristics (isotopic abundances, chemical form, density, and impurities) are considered. A Total Measurement Uncertainty (TMU) estimate is then developed from these uncertainty contributors. This study is confined to multiplicity analysis of items commonly encountered in international safeguards applications. That is, the study focused on Pu oxides and MOX materials for the masses ranging up to 4000 grams total Pu. Multiplicity measurements were simulated using MCNP V6 based on the Plutonium Scrap Multiplicity Counter (PSMC), Epithermal Multiplicity Counter (ENMC), Pyrochemical Multiplicity Counter, and Large Epithermal Multiplicity Counter (LEMC) for this study; however, this report focuses on the parameterization of the uncertainties for the PSMC. The performance differences between the PSMC and the other multiplicity counting systems are relatively small, primarily manifesting in the impact on measurement precision so that the evaluation developed for the PSMC can be applied to the other multiplicity counting systems. Finally an analysis tool, the Multiplicity TMU Estimator, was developed from this study to serve as an aid for evaluation of the total measurement uncertainty of multiplicity assay results obtained from the commonly used INCC acquisition and analysis software.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Multi-Physics Topology Optimization for Dual Flow Heat Exchangers

Current heat exchanger (HX) designs are subjected to strict constraints pertaining to their manufacturability through conventional lengthy and expensive processes consisting of subtractive, forming and brazing processes. Therefore, existing HXs are typically restricted to the classical and rather simple geometries, such as plate-fin or shell-tube geometries, with lower efficiency and larger size. To increase HX efficiencies, novel designs are needed. Recent advances in topology optimization (TO) and additive manufacturing (AM) offer significant flexibility in design and fabrication of complex geometries, with potentially superior thermo-mechanical performance and high-power density. On the other hand, there is no commercially available software tool that addresses the combined coupling of structural, fluid dynamics, and thermal with multiple materials (hot and cold streams, solid, and void space) in TO of HXs. The goal of this project is to develop a multi-physics multi-phase TO approach to enhance the performance of HXs. The optimized design will be additively manufactured and tested in a physical environment to quantify its performance.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗