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DOE OSTI2015

Using ASCEM modeling and visualization to inform stakeholders of contaminant plume evolution and remediation efficacy at F-Basin Savannah river, SC - 15156

Communication with stakeholders, regulatory agencies, and the public is an essential part of implementing different remediation and monitoring activities, and developing site closure strategies at contaminated sites. Modeling of contaminant plume evolution plays a critical role in estimating the benefit, cost, and risk of particular options. At the same time, effective visualization of monitoring data and modeling results are particularly important for conveying the significance of the results and observations. In this paper, we present the results of the Advanced Simulation Capability for Environmental Management (ASCEM) project, including the discussion of the capabilities of newly developed ASCEM software package, along the its application to the F-Area Seepage Basins located in the U.S. Department of Energy Savannah River Site (SRS). ASCEM software includes state-of-the-art numerical methods for simulating complex flow and reactive transport, as well as various tool-sets such as a graphical user interface (GUI), visualization, data management, uncertainty quantification, and parameter estimation. Using this software, we have developed an advanced visualization of tritium plume migration coupled with a data management system, and simulated a three-dimensional model of flow and plume evolution on a high-performance computing platform. We evaluated the effect of engineered flow barriers on a nonreactive tritium plume, through advanced plume visualization and modeling of tritium plume migration. In addition, we developed a geochemical reaction network to describe complex geochemical processes at the site, and evaluated the impact of coupled hydrological and geochemical heterogeneity. These results are expected to support SRS's monitoring activities and operational decisions. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2015

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3) Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2014

WE-D-9A-06: Open Source Monitor Calibration and Quality Control Software for Enterprise Display Management

Purpose: Medical display monitor calibration and quality control present challenges to medical physicists. The purpose of this work is to demonstrate and share experiences with an open source package that allows for both initial monitor setup and routine performance evaluation. Methods: A software package, pacsDisplay, has been developed over the last decade to aid in the calibration of all monitors within the radiology group in our health system. The software is used to calibrate monitors to follow the DICOM Grayscale Standard Display Function (GSDF) via lookup tables installed on the workstation. Additional functionality facilitates periodic evaluations of both primary and secondary medical monitors to ensure satisfactory performance. This software is installed on all radiology workstations, and can also be run as a stand-alone tool from a USB disk. Recently, a database has been developed to store and centralize the monitor performance data and to provide long-term trends for compliance with internal standards and various accrediting organizations. Results: Implementation and utilization of pacsDisplay has resulted in improved monitor performance across the health system. Monitor testing is now performed at regular intervals and the software is being used across multiple imaging modalities. Monitor performance characteristics such as maximum and minimum luminance, ambient luminance and illuminance, color tracking, and GSDF conformity are loaded into a centralized database for system performance comparisons. Compliance reports for organizations such as MQSA, ACR, and TJC are generated automatically and stored in the same database. Conclusion: An open source software solution has simplified and improved the standardization of displays within our health system. This work serves as an example method for calibrating and testing monitors within an enterprise health system.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Flexible and Effective Object Tiering for Heterogeneous Memory Systems

Computing platforms that package multiple types of memory, each with their own performance characteristics, are quickly becoming mainstream. To operate efficiently, heterogeneous memory architectures require new data management solutions that are able to match the needs of each application with an appropriate type of memory. As the primary generators of memory usage, applications create a great deal of information that can be useful for guiding memory management, but the community still lacks tools to collect, organize, and leverage this information effectively. To address this gap, this work introduces a novel software framework that collects and analyzes object-level information to guide memory tiering. The framework includes tools to monitor the capacity and usage of individual data objects, routines that aggregate and convert this information into tier recommendations for the host platform, and mechanisms to enforce these recommendations according to user-selected policies. Moreover, the developed tools and techniques are fully automatic, work on standard Linux systems, and do not require modification or recompilation of existing software. Using this framework, this study evaluates and compares the impact of a variety of design choices for memory tiering, including different policies for prioritizing objects for the fast memory tier as well as the frequency and timing of migration events. In conclusion, the results, collected on a modern Intel platform with conventional DDR4 SDRAM as well as Intel Optane NVRAM, show that guiding data tiering with object-level information can enable significant performance and efficiency benefits compared with standard hardware- and software-directed data-tiering strategies for a diverse set of memory-intensive workloads.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Simulation of Isotopic Concentrations and Gamma Spectra from Dynamic Fission Sources

A tool was developed to rapidly generate synthetic gamma-ray spectra to evaluate safeguards material control and accounting methods for liquid-fueled molten salt reactors. Molten salt reactor operations pose unique challenges to nuclear safeguards methods and protocols compared to deployed reactors designs (e.g., light water reactors). This research evaluates the use of gamma-ray spectroscopy to monitor fission product isotopic flow through a reactor model to understand expected operations and investigate changes to the spectra with material diversion scenarios. The large design space of molten salt reactors (e.g., liquid-fueled, liquid-cooled, online separations) could potentially lead to many measurement points within the reactor system. The developed analytical tool generates and evaluates synthetic gamma-ray spectra from dynamic reactor simulations by extracting isotopic inventory to generate source terms. An implementation in the Gamma Detector Response and Analysis Software (GADRAS) Application Program Interface (API) uses the source terms, a model of the reactor component, a detector response function, and measurement plan to quickly generate and analyze spectra. Prospective measurements are then evaluated in the more accurate but slower Geant4 simulations. Utilization of the developed modeling tool and analysis of the subsequent spectra enables optimization of collimation, shielding requirements, and expected count rates that are used to determine key measurement points in the modeled reactor design.

O'Brien, Sean↗

DOE OSTI2021

User Guide to the Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software (V.1.0)

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the initial software release as ADDER v1.0.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

User Guide to the Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software (V.1.01)

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the software release referred to as ADDER v1.0.1. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software for Depletion and Fuel Management

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the software release referred to as ADDER v1.1.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software for Depletion and Fuel Management

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the software release referred to as ADDER v1.1.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2016

OPENSTUDIO® [SWR-07-40]

OpenStudio® is a cross-platform (Windows, Mac, and Linux) collection of software tools to support whole building energy modeling using EnergyPlus and advanced daylight analysis using Radiance. OpenStudio is an open source (LGPL) project to facilitate community development, extension, and private sector adoption. OpenStudio includes graphical interfaces along with a Software Development Kit (SDK). In addition to the graphical interface, OpenStudio allows building researchers and software developers to quickly get started through its multiple entry levels, including access through C++, Ruby, and C#. Users can leverage the Ruby interface to create OpenStudio Measures that can be easily shared and applied to OpenStudio Models. OPENSTUDIO® IS A REGISTERED TRADEMARK OF ALLIANCE FOR SUSTAINABLE ENERGY, LLC, THE MANAGER AND OPERATOR OF THE NATIONAL RENEWABLE ENERGY LABORATORY.

Ball, Brian↗

DOE OSTI2018

Developing an Interactive Data Visualization Tool to Assess the Impact of Decision Support on Clinical Operations

Due to mandates from recent legislation, clinical decision support (CDS) software is being adopted by radiology practices across the country. This software provides imaging study decision support for referring providers at the point of order entry. CDS systems produce a large volume of data, providing opportunities for research and quality improvement. In order to better visualize and analyze trends in this data, an interactive data visualization dashboard was created using a commercially available data visualization platform. Following the integration of a commercially available clinical decision support product into the electronic health record, a dashboard was created using a commercially available data visualization platform (Tableau, Seattle, WA). Data generated by the CDS were exported from the data warehouse, where they were stored, into the platform. This allowed for real-time visualization of the data generated by the decision support software. The creation of the dashboard allowed the output from the CDS platform to be more easily analyzed and facilitated hypothesis generation. Integrating data visualization tools into clinical decision support tools allows for easier data analysis and can streamline research and quality improvement efforts.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2020

Should Sea-Ice Modeling Tools Designed for Climate Research Be Used for Short-Term Forecasting?

In theory, the same sea-ice models could be used for both research and operations, but in practice, differences in scientific and software requirements and computational and human resources complicate the matter. Although sea-ice modeling tools developed for climate studies and other research applications produce output of interest to operational forecast users, such as ice motion, convergence, and internal ice pressure, the relevant spatial and temporal scales may not be sufficiently resolved. For instance, sea-ice research codes are typically run with horizontal resolution of more than 3 km, while mariners need information on scales less than 300 m. Certain sea-ice processes and coupled feedbacks that are critical to simulating the Earth system may not be relevant on these scales; and therefore, the most important model upgrades for improving sea-ice predictions might be made in the atmosphere and ocean components of coupled models or in their coupling mechanisms, rather than in the sea-ice model itself. This paper discusses some of the challenges in applying sea-ice modeling tools developed for research purposes for operational forecasting on short time scales, and highlights promising new directions in sea-ice modeling.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Livermore tomography tools: Accurate, fast, and flexible software for tomographic science

Livermore Tomography Tools (LTT) is a customizable scientific software package that enables a broad range of research and development efforts into computed tomography (CT). Here, it was developed to process x-ray and neutron CT data accurately and rapidly from raw detector counts to reconstructed volumes with the flexibility to handle many special cases. LTT fulfills long-term CT software goals to provide quantitatively accurate results reported in physical units (e.g., mm -1 or cm -1 ) while exploiting all available computational advantages to maximize speed. Written in C/C++ with support for multiple CPUs and GPUs, LTT runs on many computing platforms (Linux/Unix, Windows, and Mac; laptops to supercomputers). As a result, LTT can:process data acquired from various custom-built and commercially available CT scanners, model and simulate x-ray and neutron interactions to encourage algorithm prototyping, and allow for rapid insertion of the latest algorithms.We describe LTT’s software architecture, user interfaces, and its 88 algorithms (as of this writing) for pre-processing, reconstruction, post-processing, and simulation that support many scanner geometries (parallel-, fan-, cone-beam, and custom). Several applications are presented that illustrate LTT’s accuracy, speed, and flexibility relative to other solutions.

36 MATERIALS SCIENCE↗

DOE OSTI2014

TU-C-BRE-11: 3D EPID-Based in Vivo Dosimetry: A Major Step Forward Towards Optimal Quality and Safety in Radiation Oncology Practice

Purpose: To develop a 3D in vivo dosimetry method that is able to substitute pre-treatment verification in an efficient way, and to terminate treatment delivery if the online measured 3D dose distribution deviates too much from the predicted dose distribution. Methods: A back-projection algorithm has been further developed and implemented to enable automatic 3D in vivo dose verification of IMRT/VMAT treatments using a-Si EPIDs. New software tools were clinically introduced to allow automated image acquisition, to periodically inspect the record-and-verify database, and to automatically run the EPID dosimetry software. The comparison of the EPID-reconstructed and planned dose distribution is done offline to raise automatically alerts and to schedule actions when deviations are detected. Furthermore, a software package for online dose reconstruction was also developed. The RMS of the difference between the cumulative planned and reconstructed 3D dose distributions was used for triggering a halt of a linac. Results: The implementation of fully automated 3D EPID-based in vivo dosimetry was able to replace pre-treatment verification for more than 90% of the patient treatments. The process has been fully automated and integrated in our clinical workflow where over 3,500 IMRT/VMAT treatments are verified each year. By optimizing the dose reconstruction algorithm and the I/O performance, the delivered 3D dose distribution is verified in less than 200 ms per portal image, which includes the comparison between the reconstructed and planned dose distribution. In this way it was possible to generate a trigger that can stop the irradiation at less than 20 cGy after introducing large delivery errors. Conclusion: The automatic offline solution facilitated the large scale clinical implementation of 3D EPID-based in vivo dose verification of IMRT/VMAT treatments; the online approach has been successfully tested for various severe delivery errors.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-C-202-03: A Tool for Automatic Calculation of Delivered Dose Variation for Off-Line Adaptive Therapy Using Cone Beam CT

Purpose: Monitoring the delivered dose is an important task for the adaptive radiotherapy (ART) and for determining time to re-plan. A software tool which enables automatic delivered dose calculation using cone-beam CT (CBCT) has been developed and tested. Methods: The tool consists of four components: a CBCT Colleting Module (CCM), a Plan Registration Moduel (PRM), a Dose Calculation Module (DCM), and an Evaluation and Action Module (EAM). The CCM is triggered periodically (e.g. every 1:00 AM) to search for newly acquired CBCTs of patients of interest and then export the DICOM files of the images and related registrations defined in ARIA followed by triggering the PRM. The PRM imports the DICOM images and registrations, links the CBCTs to the related treatment plan of the patient in the planning system (RayStation V4.5, RaySearch, Stockholm, Sweden). A pre-determined CT-to-density table is automatically generated for dose calculation. Current version of the DCM uses a rigid registration which regards the treatment isocenter of the CBCT to be the isocenter of the treatment plan. Then it starts the dose calculation automatically. The AEM evaluates the plan using pre-determined plan evaluation parameters: PTV dose-volume metrics and critical organ doses. The tool has been tested for 10 patients. Results: Automatic plans are generated and saved in the order of the treatment dates of the Adaptive Planning module of the RayStation planning system, without any manual intervention. Once the CTV dose deviates more than 3%, both email and page alerts are sent to the physician and the physicist of the patient so that one can look the case closely. Conclusion: The tool is capable to perform automatic dose tracking and to alert clinicians when an action is needed. It is clinically useful for off-line adaptive therapy to catch any gross error. Practical way of determining alarming level for OAR is under development.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2013

Validating the Melusine Gamma Spectroscopy Tool

This technical report describes testing to evaluate the gamma spectroscopy tool, Melusine, under development by Pacific Northwest National Laboratory. The goal was to verify that the software can successfully be used to provide accurate results and statistical uncertainties for the detection of isotopes of interest and their activities. Of special interest were spectra similar to those produced by radionuclide stations that contribute to the Comprehensive Nuclear Test Ban Treaty Organization’s International Monitoring System. Two data sets were used to test Melusine’s capabilities. The first was the result of a multi-lab calibration effort based on neutron activations produced at the University of California at Davis. The second was taken from the Proficiency Test Exercises conducted by the CTBTO directly in 2005. In 37 of 42 cases, Melusine produced results in agreement with the best answer presently available, in most cases with calculated uncertainties comparable to or better than competing analyses. In fact, Melusine technically provided one more result than CTBTO’s PTE analyses that agreed with the “book answer” (Monte Carlo simulation). Despite these promising results, the Melusine software is still under development. Effort is especially needed to simplify its analysis process, improve stability, and provide user documentation. Some significant analysis tasks require further vetting, such as those to address summing effects. However, our test results indicate that Melusine’s calculations as presently implemented are sound and can be used to reliably analyze spectra from the CTBTO’s radionuclide stations.

CTBTO↗

DOE OSTI2017

Advanced Scientific Computing Research Exascale Requirements Review. An Office of Science review sponsored by Advanced Scientific Computing Research, September 27-29, 2016, Rockville, Maryland

The widespread use of computing in the American economy would not be possible without a thoughtful, exploratory research and development (R&D) community pushing the performance edge of operating systems, computer languages, and software libraries. These are the tools and building blocks — the hammers, chisels, bricks, and mortar — of the smartphone, the cloud, and the computing services on which we rely. Engineers and scientists need ever-more specialized computing tools to discover new material properties for manufacturing, make energy generation safer and more efficient, and provide insight into the fundamentals of the universe, for example. The research division of the U.S. Department of Energy’s (DOE’s) Office of Advanced Scientific Computing and Research (ASCR Research) ensures that these tools and building blocks are being developed and honed to meet the extreme needs of modern science. See also http://exascaleage.org/ascr/ for additional information.

97 MATHEMATICS AND COMPUTING↗