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DOE OSTI2013

OpenSQUID: A Flexible Open-Source Software Framework for the Control of SQUID Electronics

We report commercially available computer-controlled SQUID electronics are usually delivered with software providing a basic user interface for adjustment of SQUID tuning parameters, such as bias current, flux offset, and feedback loop settings. However, in a research context it would often be useful to be able to modify this code and/or to have full control over all these parameters from researcher-written software. In the case of the STAR Cryoelectronics PCI/PFL family of SQUID control electronics, the supplied software contains modules for automatic tuning and noise characterization, but does not provide an interface for user code. On the other hand, the Magnicon SQUIDViewer software package includes a public application programming interface (API), but lacks auto-tuning and noise characterization features. To overcome these and other limitations, we are developing an "open-source" framework for controlling SQUID electronics which should provide maximal interoperability with user software, a unified user interface for electronics from different manufacturers, and a flexible platform for the rapid development of customized SQUID auto-tuning and other advanced features. Finally, we have completed a first implementation for the STAR Cryoelectronics hardware and have made the source code for this ongoing project available to the research community on SourceForge (http://opensquid.sourceforge.net) under the GNU public license.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

LANL Contributions to pyiron: An integrated development environment for computational materials science

To support and accelerate the development of simulation protocols in atomistic modelling, we introduce an integrated development environment (IDE) for computational materials science called pyiron (http://pyiron.org). The pyiron IDE combines a web based source code editor, a job management system for build automation, and a hierarchical data management solution. The core components of the pyiron IDE are pyiron objects based on an abstract class, which links application structures such as atomistic structures, projects, jobs, simulation protocols and computing resources with persistent storage and an interactive user environment. The simulation protocols within the pyiron IDE are constructed using the Python programming language. To highlight key concepts of this tool as well as to demonstrate its ability to simplify the implementation and testing of simulation protocols we discuss two applications. In these examples we show how pyiron supports the whole life cycle of a typical simulation, seamlessly combines ab initio with empirical potential calculations, and how complex feedback loops can be implemented. While originally developed with focus on ab initio thermodynamics simulations, the concepts and implementation of pyiron are general thus allowing to employ it for a wide range of simulation topics.

Janssen, Jan↗

DOE OSTI2016

Coupling CTF to MPACT for Improved Thermal-Hydraulic Feedback for Transients

As computational power and techniques continue to advance, reactor analysis codes are afforded the opportunity to employ a more detailed physics model. One area where this has manifested is with coupled neutron kinetics and thermal-hydraulics codes for transient analysis, in which the feedback is critical for accurate modeling. The Michigan Parallel Characteristics Transport (MPACT) code is a 3-D method of characteristics neutron transport code capable of generating sub-pin level power distributions being developed by the University of Michigan through the Consortium for Advanced Simulation of LWRs (CASL) program. Currently, MPACT handles thermal-hydraulic feedback with an internal 1-D radial heat transfer model assuming constant moderator temperature. While this relatively simple treatment of thermal-hydraulic feedback has been shown to accurately model transients where Doppler feedback is the dominant feedback mechanism, coupling MPACT to a detailed thermal-hydraulic code will greatly expand the range of transient problems that can be accurately modeled. COBRA-TF (CTF) is a 3-D two-phase flow, subchannel thermal-hydraulics code maintained by Penn State University through CASL. CTF is based upon the Semi-Implicit Method for Pressure-Linked Equations, and it is especially well suited to model heat transfer and fluid flow phenomena associated with a nuclear reactor through a wide range of conditions. We present an initial effort coupling MPACT to CTF for transients, which provides a wider range of transient problems that can be modeled with increased accuracy. We have successfully coupled the thermal-hydraulics code CTF to the neutronics code MPACT for transient calculations by implicit and Crank-Nicolson methods, which have been demonstrated with single pin and 3x3 configurations. This capability extends the ability of MPACT to accurately model transients through a wider range of conditions than the existing thermal-hydraulic feedback, which is severely limited by the assumption of constant moderator temperature and density. By employing CTF for the thermal- hydraulic feedback, the transient physics can be described more completely at minimal computational expense. (authors)

42 ENGINEERING↗

DOE OSTI2015

SU-E-T-157: CARMEN: A MatLab-Based Research Platform for Monte Carlo Treatment Planning (MCTP) and Customized System for Planning Evaluation

Purpose: Although there exist several radiotherapy research platforms, such as: CERR, the most widely used and referenced; SlicerRT, which allows treatment plan comparison from various sources; and MMCTP, a full MCTP system; it is still needed a full MCTP toolset that provides users complete control of calculation grids, interpolation methods and filters in order to “fairly” compare results from different TPSs, supporting verification with experimental measurements. Methods: This work presents CARMEN, a MatLab-based platform including multicore and GPGPU accelerated functions for loading RT data; designing treatment plans; and evaluating dose matrices and experimental data.CARMEN supports anatomic and functional imaging in DICOM format, as well as RTSTRUCT, RTPLAN and RTDOSE. Besides, it contains numerous tools to accomplish the MCTP process, managing egs4phant and phase space files.CARMEN planning mode assist in designing IMRT, VMAT and MERT treatments via both inverse and direct optimization. The evaluation mode contains a comprehensive toolset (e.g. 2D/3D gamma evaluation, difference matrices, profiles, DVH, etc.) to compare datasets from commercial TPS, MC simulations (i.e. 3ddose) and radiochromic film in a user-controlled manner. Results: CARMEN has been validated against commercial RTPs and well-established evaluation tools, showing coherent behavior of its multiple algorithms. Furthermore, CARMEN platform has been used to generate competitive complex treatment that has been published in comparative studies. Conclusion: A new research oriented MCTP platform with a customized validation toolset has been presented. Despite of being coded with a high-level programming language, CARMEN is agile due to the use of parallel algorithms. The wide-spread use of MatLab provides straightforward access to CARMEN’s algorithms to most researchers. Similarly, our platform can benefit from the MatLab community scientific developments as filters, registration algorithms etc. Finally, CARMEN arises the importance of grid and filtering control in treatment plan comparison.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Developing and testing capabilities for simulating cases with heterogeneous land/water surfaces in a novel atmospheric large eddy simulation code

Large eddy simulations (LES) are the primary computational tool used to simulate high Reynolds number three-dimensional turbulent flows. In the context of earth system sciences, particularly atmospheric science, LES are uniquely able to resolve the scales of atmospheric motion that are key for building process-level understanding of boundary layer turbulence, atmosphere-surface interaction, clouds, and cloud-aerosol-chemistry interaction, and are a core limited-area modeling capability. Increasing demands are being placed on LES code bases as growing high performance computing resources allow LES to address a wider range of scientific problems. In addition, LES are emerging as a source of high-quality machine learning training data. These demands necessitate an agile and extensible code base that allows the model to quickly adapt to emergent needs. However, LES have largely relied on legacy Fortran code bases that lack flexibility. A new, Python-based LES capability called Predicting INteractions of Aerosol and Clouds in Large Eddy Simulation (PINACLES) has been developed as part of the Department of Energy’s Earth System Model Development (ESMD) program area’s Enabling Aerosol-cloud interactions at Global convection-permitting scalES (EAGLES) project. PINACLES was developed from the ground up with a philosophy of maximizing scientific throughput, by attempting to optimize for both model throughput and software extensibility. The initial development of PINACLES delivered a state-of-the-art idealized LES capability solving the non-hydrostatic anelastic equations of motion with doubly periodic boundary conditions and idealized homogenous surface boundary conditions. Here we provide a final report on the outcomes of a fiscal year 2021 Seed Laboratory Directed Research Project that extended PINACLES in two key ways. First, PINACLES was coupled to a state-of-the-art land surface model enabling it to simulate spatially inhomogeneous land-atmosphere interactions that are known to control key atmospheric processes. Second, the dynamical core of PINACLES was modified to permit non-periodic boundary conditions. This model enhancement enables simulation of realistic cases with boundary conditions prescribed from atmospheric reanalysis and enables nested simulations conducted on a hierarchy of computational domains with increasing resolution. Together, these extensions to PINACLES make it a formidable modeling capability and expand its potential application to diverse components of DOE’s atmospheric science portfolio.

42 ENGINEERING↗

DOE OSTI2012

System Advisor Model, SAM 2011.12.2: General Description

This document describes the capabilities of the U.S. Department of Energy and National Renewable Energy Laboratory's System Advisor Model (SAM), Version 2011.12.2, released on December 2, 2011. SAM is software that models the cost and performance of renewable energy systems. Project developers, policy makers, equipment manufacturers, and researchers use graphs and tables of SAM results in the process of evaluating financial, technology, and incentive options for renewable energy projects. SAM simulates the performance of solar, wind, geothermal, biomass, and conventional power systems. The financial model can represent financing structures for projects that either buy and sell electricity at retail rates (residential and commercial) or sell electricity at a price determined in a power purchase agreement (utility). Advanced analysis options facilitate parametric, sensitivity, and statistical analyses, and allow for interfacing SAM with Microsoft Excel or with other computer programs. SAM is available as a free download at http://sam.nrel.gov. Technical support and more information about the software are available on the website.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2015

WE-D-BRA-04: Online 3D EPID-Based Dose Verification for Optimum Patient Safety

Purpose: To develop an online 3D dose verification tool based on EPID transit dosimetry to ensure optimum patient safety in radiotherapy treatments. Methods: A new software package was developed which processes EPID portal images online using a back-projection algorithm for the 3D dose reconstruction. The package processes portal images faster than the acquisition rate of the portal imager (∼ 2.5 fps). After a portal image is acquired, the software seeks for “hot spots” in the reconstructed 3D dose distribution. A hot spot is in this study defined as a 4 cm{sup 3} cube where the average cumulative reconstructed dose exceeds the average total planned dose by at least 20% and 50 cGy. If a hot spot is detected, an alert is generated resulting in a linac halt. The software has been tested by irradiating an Alderson phantom after introducing various types of serious delivery errors. Results: In our first experiment the Alderson phantom was irradiated with two arcs from a 6 MV VMAT H&N treatment having a large leaf position error or a large monitor unit error. For both arcs and both errors the linac was halted before dose delivery was completed. When no error was introduced, the linac was not halted. The complete processing of a single portal frame, including hot spot detection, takes about 220 ms on a dual hexacore Intel Xeon 25 X5650 CPU at 2.66 GHz. Conclusion: A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for various kinds of gross delivery errors. The detection of hot spots was proven to be effective for the timely detection of these errors. Current work is focused on hot spot detection criteria for various treatment sites and the introduction of a clinical pilot program with online verification of hypo-fractionated (lung) treatments.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-F-P-09: A Global Medical Physics Collaboration for Implementation of Modern Radiotherapy in Botswana

Purpose: The global burden of cancer is considerable, particularly in low and middle-income countries. Massachusetts General Hospital (MGH) and Botswana-Harvard AIDS Institute have partnered with the oncology community and government of Botswana to form BOTSOGO (BOTSwana Oncology Global Outreach) to address the rising burden of cancer in Botswana. Currently, radiation therapy (RT) is only available at a single linear accelerator (LINAC) in Gaborone Private Hospital (GPH). BOTSOGO worked to limit the absence of RT during a LINAC upgrade and ensure a safe transition to modern radiotherapy techniques. Methods: The existing Elekta Precise LINAC was decommissioned in November 2015 and replaced with a new Elekta VERSA-HD with IMRT/VMAT/CBCT capability. Upgraded treatment planning and record-and-verify systems were also installed. Physicists from GPH and MGH collaborated during an intensive on-site visit in Botswana during the commissioning process. Measurements were performed using newly purchased Sun Nuclear equipment. Photon beams were matched with an existing model to minimize the time needed for beam modeling and machine down time. Additional remote peer review was also employed. Independent dosimetry was performed by irradiating OSLDs, which were subsequently analyzed at MGH. Results: Photon beam quality agreed with reference data within 0.2%. Electron beam data agreed with example clinical data within 3%. Absolute dose calibration was performed using both IAEA and AAPM protocols. Absolute dose measurements with OSLDs agreed within 5%. Quentry cloud-based software was installed to facilitate remote review of treatment plans. Patient treatments resumed in February 2016. The time without RT was reduced, therefore likely resulting in reduced patient morbidity/mortality. Conclusion: A global physics collaboration was utilized to commission a modern LINAC in a resource-constrained setting. This can be a useful model in other areas with limited resources. Further use of technology and on-site exchanges will facilitate the introduction of more advanced techniques in Botswana. We acknowledge funding support from the AAPM International Educational Activities Committee and the NCI Federal Share Proton Beam Program Income Grant.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-G-TeP2-04: Comprehensive Machine Isocenter Evaluation with Separation of Gantry, Collimator, and Table Variables

Purpose: To develop and demonstrate application of a method that characterizes deviation of linac x-ray beams from the centroid of the volumetric radiation isocenter as a function of gantry, collimator, and table variables. Methods: A set of Winston-Lutz ball-bearing images was used to determine the gantry radiation isocenter as the midrange of deviation values resulting from gantry and collimator rotation. Also determined were displacement of table axis from gantry isocenter and recommended table axis adjustment. The method, previously reported, has been extended to include the effect of collimator walkout by obtaining measurements with 0 and 180 degree collimator rotation for each gantry angle. Twelve images were used to characterize the volumetric isocenter for the full range of available gantry, collimator, and table rotations. Results: Three Varian True Beam, two Elekta Infinity and four Versa HD linacs at five institutions were tested using identical methodology. Varian linacs exhibited substantially less deviation due to head sag than Elekta linacs (0.4 mm vs. 1.2 mm on average). One linac from each manufacturer had additional isocenter deviation of 0.3 to 0.4 mm due to jaw instability with gantry and collimator rotation. For all linacs, the achievable isocenter tolerance was dependent on adjustment of collimator position offset, transverse position steering, and alignment of the table axis with gantry isocenter, facilitated by these test results. The pattern and magnitude of table axis wobble vs. table angle was reproducible and unique to each machine. Conclusion: This new method provides a comprehensive set of isocenter deviation values including all variables. It effectively facilitates minimization of deviation between beam center and target (ball-bearing) position. This method was used to quantify the effect of jaw instability on isocenter deviation and to identify the offending jaw. The test is suitable for incorporation into a routine machine QA program. Software development was performed by Radiological Imaging Technology, Inc.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Tri-Lab Co-Design Milestone: In-Depth Performance Portability Analysis of Improved Integrated Codes on Advanced Architecture.

This milestone is a tri-lab deliverable supporting ongoing Co-Design efforts impacting applications in the Integrated Codes (IC) program element Advanced Technology Development and Mitigation (ATDM) program element. In FY14, the trilabs looked at porting proxy application to technologies of interest for ATS procurements. In FY15, a milestone was completed evaluating proxy applications in multiple programming models and in FY16, a milestone was completed focusing on the migration of lessons learned back into production code development. This year, the co-design milestone focuses on extracting the knowledge gained and/or code revisions back into production applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Release on the Virtual Test Bed of an MSRE thermal hydraulics model

The nuclear industry is taking leaps in innovations with companies seeking a sustainable energy future through advanced nuclear reactors. The \gls{DOE}’s \gls{neams} program seeks to substantiate and bolster the deployment of advanced reactors through flexible multifidelity, multiphysics simulations of advanced nuclear reactors. Applications like SAM for one-dimensional systems thermal-hydraulics, and Pronghorn for multidimensional coarse mesh thermal-hydraulics, are geared to support innovations in industry by facilitating design, optimization, and licensing of advanced nuclear reactors. Coupling systems thermal-hydraulics and computational fluid dynamics codes can be difficult as the pressure coupling converges slowly; however, it is important to obtain the desired accuracy in each part of the primary loop. The authors of this model created an \gls{odc}~\cite{Mau23} approach to coupling SAM and Pronghorn. Leveraging this coupling technique, a \gls{msre} model was developed and released to the \gls{neams}/\gls{nric} \gls{vtb}. The \gls{msre} was chosen to be modeled because of the wealth of experimental data available and because of the strong physics coupling between the core and primary circuit \cite{doi:10.13182/NT8-2-118}. This document contextualizes the history of the \gls{msre}, describes the thermal hydraulics models used, and detail the implementation of multidimensional thermal-hydraulics and system codes based on the \gls{odc} method~\cite{Penn} for the \gls{msre} model. Finally, this document presents how other modelers could apply the SAM-Pronghorn \gls{odc} for other advanced reactor models. Current item is the set of slides for ANS Winter 23. The release of the model and the ANS summary have already been approved

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Release on the Virtual Test Bed of an MSRE thermal hydraulics model

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Field Work Proposal ERKJ358: Black-box training for scientific machine learning models (Final Report)

The overarching goal of this project is to develop a scalable black-box training capability for scientific machine learning (SciML) problems that are non-trainable with existing automatic differentiation (AD)-based algorithms. AD assumes that a loss function can be decomposed into a sequence of elementary operations whose derivatives are known. This assumption is violated when the loss function includes a black-box physical model (e.g., a legacy simulator). The current strategy, converting a black-box simulator to an AD-enabled code via differential programming, is inflexible and time-, labor-consuming. Thus, black-box optimization is a main workhorse for training SciML models, e.g., in scientific reinforcement learning, hyper-parameter fine tuning, designing SciML models with adversarial robustness, etc.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Advancing the Theory of Nuclear Data Evaluations [Abstract]

We present recent advances in the R-matrix formalism as well as the Bayesian evaluation framework for improved nuclear data evaluations. The advances in the R matrix formalism include: 1) direct processes, 2) doorway, as well as multistep, processes, and 3) various forms of the Reich-Moore approximation for eliminated capture channels. Furthermore, to address unreasonably small posterior uncertainties often encountered in nuclear data evaluations of large data sets using the conventional form of the Bayes’ theorem, we introduce imperfections (of the data or the model) as a formal evaluation tool for taming the evaluated uncertainties in harmony with Bayes’ theorem. These theoretical advances were motivated by the nuclear data evaluations of differential resolved resonance cross section data using the code SAMMY, as well as the integral benchmark experiments using the SCALE code system, being performed at Oak Ridge National Laboratory for the Nuclear Criticality Safety Program. Some pedagogical applications of the new formalism, as well as a snapshot of the SAMMY modernization efforts, will be presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2014

SU-E-T-323: The FLUKA Monte Carlo Code in Ion Beam Therapy

Purpose: Monte Carlo (MC) codes are increasingly used in the ion beam therapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code demands accurate and reliable physical models for the transport and the interaction of all components of the mixed radiation field. This contribution will address an overview of the recent developments in the FLUKA code oriented to its application in ion beam therapy. Methods: FLUKA is a general purpose MC code which allows the calculations of particle transport and interactions with matter, covering an extended range of applications. The user can manage the code through a graphic interface (FLAIR) developed using the Python programming language. Results: This contribution will present recent refinements in the description of the ionization processes and comparisons between FLUKA results and experimental data of ion beam therapy facilities. Moreover, several validations of the largely improved FLUKA nuclear models for imaging application to treatment monitoring will be shown. The complex calculation of prompt gamma ray emission compares favorably with experimental data and can be considered adequate for the intended applications. New features in the modeling of proton induced nuclear interactions also provide reliable cross section predictions for the production of radionuclides. Of great interest for the community are the developments introduced in FLAIR. The most recent efforts concern the capability of importing computed-tomography images in order to build automatically patient geometries and the implementation of different types of existing positron-emission-tomography scanner devices for imaging applications. Conclusion: The FLUA code has been already chosen as reference MC code in many ion beam therapy centers, and is being continuously improved in order to match the needs of ion beam therapy applications. Parts of this work have been supported by the European FP7 project ENVISION (grant agreement no. 241851)

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2017

Light Water Reactor Sustainability Program RAVEN modifications supporting optimization under the MOOSE framework

The aim of this report is to describe the activities that have been performed under the RAVEN project for a better and more optimized integration of the current RAVEN code capabilities and the MOOSE framework.

42 ENGINEERING↗

DOE OSTI2019

FPChecker

CUDA is the programming model used to program NVIDIA GPUs, which are widely used in DOE supercomputers. FPChecker allows programmers to detect and fix hidden exceptions in the floating-point computations that CUDA executes. When a floating-point exception occurs (e.g., division by zero), GPUs cannot catch these errors. FPChecker intercepts each floating-point operations (addition, subtraction, multiplication and division) and reports to users where exceptions occur (file and line of code).

Laguna Peralta, Ignacio↗

DOE OSTI2018

Nek5000 Simulations on Turbulent Coolant Flow in a Fuel Assembly Experiment - AREVA/ANL collaboration for advancing CFD tools

The NEAMS program aims to develop an integrated multi physics simulation capability “pellet to plant” for the design and analysis of future generations of nuclear power plants. In particular, the Reactor Product Line code suite’s multi resolution hierarchy is being designed to ultimately span the full range of length and time scales present in relevant reactor design and safety analyses, as well as scale from desktop to petaflop computing platforms.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗