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At least 415 records · Page 23

Validation of the TOPAS Monte Carlo toolkit for HDR brachytherapy simulations

The goal of this work is to validate the user-friendly Geant4-based Monte Carlo toolkit TOol for PArticle Simulation (TOPAS) for brachytherapy applications. Brachytherapy simulations performed with TOPAS were systematically compared with published TG-186 reference data. The photon emission energy spectrum, the air-kerma strength, and the dose-rate constant of the model-based dose calculation algorithm (MBDCA)-WG generic Ir-192 source were extracted. For dose calculations, a track-length estimator was implemented. Additionally, the four Joint AAPM/ESTRO/ABG MBDCA-WG test cases were evaluated through histograms of the local and global dose difference volumes. A prostate, a palliative lung, and a breast case were simulated. For each case, the dose ratio map, the histogram of the global dose difference volume, and cumulative dose-volume histograms were calculated. The air-kerma strength was (9.772 ± 0.001) × 10 -8 U Bq -1 (within 0.3% of the reference value). The dose-rate constant was 1.1107 ± 0.0005 cGy h -1 U -1 (within 0.01% of the reference value). For all cases, at least 96.9% of voxels had a local dose difference within [-1%, 1%] and at least 99.9% of voxels had a global dose difference within [-0.1%, 0.1%]. The implemented track-length estimator scorer was more efficient than the default analog dose scorer by a factor of 237. For all clinical cases, at least 97.5% of voxels had a global dose difference within [-1%, 1%]. Dose-volume histograms were consistent with the reference data. TOPAS was validated for high-dose-rate brachytherapy simulations following the TG-186 recommended approach for MBDCAs. Built on top of Geant4, TOPAS provides broad access to a state-of-the-art Monte Carlo code for brachytherapy simulations.

59 BASIC BIOLOGICAL SCIENCES↗

US Department of Energy, Office of Science High Performance Computing Facility Operational Assessment 2021: Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory’s (ORNL’s) Leadership Computing Facility (OLCF) continues to surpass its operational target goals of supporting users; delivering fast, reliable computational ecosystems; creating innovative solutions for high-performance computing (HPC) needs; contributing to the community to build the next generation HPC workforce, and managing risks, safety, and security associated with operating some of the most powerful computers in the world. The results can be seen in the cutting-edge science conducted by users and the praise from the research community. Calendar year (CY) 2021 saw continued excellence in research supported by the OLCF’s leadership-class computing resources, including Summit (the nation’s most powerful supercomputer), the global scratch file system Alpine, the Scalable Protected Infrastructure (SPI), the Exploratory Visualization Environment for Research in Science and Technology (EVEREST), and the archival mass-storage resource High-Performance Storage System (HPSS). While maintaining access and exceptional user support for Summit, the OLCF continued to make progress on the installation and deployment of Frontier, which will be the nation’s first exascale system when it comes online at the start of CY 2023. Users have already begun running and optimizing scientific codes on Crusher, the OLCF test and development system equipped with Frontier’s architecture. Throughout the year, the OLCF maintained a strong culture of operational excellence, including risk management, workplace safety, and cybersecurity. The OLCF’s rigorous risk management strategy anticipated and mitigated risks, and at this time there are no high-priority operational risks. Similarly, ORNL and the OLCF were committed to operating under the US Department of Energy’s (DOE’s) safety regulations that ensure a safe workplace. Technical staff tracked and monitored existing threats and vulnerabilities within the OLCF while continually developing tools and practices to enhance operations without increasing the facility’s risk. CY 2021 was filled with outstanding results and accomplishments, including a very high rating from users on overall satisfaction for the eighth consecutive year; a tremendous number of node hours delivered to 1,671 researchers on Summit; and the successful delivery of the allocation split of roughly 60%, 20%, and 20% of core-hours offered for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE), Advanced Scientific Computing Research Leadership Computing Challenge (ALCC), and Director’s Discretionary (DD) programs, respectively (Section 2). COVID-19 research remained a focus in 2021, and the ALCC and DD programs allocated over 1 million Summit hours to the COVID-19 High Performance Computing Consortium. These accomplishments, coupled with the high utilization rates (i.e., overall and capability usage), represent the fulfillment of the promise of leadership class machines: efficient facilitation of leadership-class computational applications.

97 MATHEMATICS AND COMPUTING↗

Naval Ship Counter Measure Capability (Final Report) [Slides]

Task 1: RUNQUIC.py was modified to add options 4 and 5, which run only the QUIC-PLUME and QUICPRESSURE codes without rerunning QUIC-URB. Task 2: We have verified that the RUNQUIC.py produces a WPC file to facilitate the interface with the CONTAM model. Task 3: RUNQUIC.py is now compatible with Python 3.8 and above. Task 4: The CMWD capability has been added QUIC-PLUME, which uses two new input files: QP_countermeasures.inp and QP_grounddep.inp. This first controls the efficiency of the CMWD system and when it is turned on and off and the second makes it possible to turn of tracking of surface deposition on the ocean surface. Task 5: This report was written for this task. Additionally, we are updating the QUIC Start Guide and RUNQUIC.py Guide, which will be made available once they have gone through the publication review process. Task 6: We performed a literature review on models for inertial deposition on the upwind faces of obstacles. We identified a model that was compatible with QUIC’s existing deposition model and implemented a first draft of this model in QUIC-PLUME. We have performed some preliminary qualitative testing, which shows the expected behavior. Further quantitative testing to fully validate the inertial deposition model.

97 MATHEMATICS AND COMPUTING↗

Accelerating detector simulations with Celeritas: Profiling and performance optimizations

Celeritas is a GPU-optimized Monte Carlo (MC) particle transport code designed to meet the growing computational demands of next-generation high energy physics (HEP) experiments. It provides efficient simulation of electromagnetic (EM) physics processes in complex geometries with magnetic fields, detector hit scoring, and seamless integration into Geant4-driven applications to offload EM physics to GPUs. Recent efforts have focused on performance optimizations and expanding profiling capabilities. This paper presents some key advancements, including the integration of the Perfetto system profiling tool for detailed performance analysis and the development of track-sorting methods to improve computational efficiency.

Lund, Amanda [Argonne National Laboratory (ANL)]↗

Modelling dust transport in DIII-D with DTOKS-Upgrade

Comprehensive upgrades to the dust transport code Dust in TOKamaks (DTOKS) that extend the plasma-dust interaction model are presented and compared with recent measurements of dust transport in DIII-D. Simulations incorporating variation in physical properties of graphite dust with temperature and size in a stationary plasma background suggest a substantial decrease in lifetimes due principally to thermal expansion. The trajectories of 53 dust grains identified from analysis of visible camera data taken across two similar shots were used to measure the dust particle velocity distributions. Dust tracks terminated mostly at the outer divertor strike point having a mean observation time of 2.1 ± 0.4 ms. Stochastic modelling of 200 graphite dust particles in the DIII-D tokamak performed with DTOKS-U using plasma simulations generated by OEDGE found similar behaviour, with particles ablating rapidly after acquiring a positive charge in the region close to the outer strike point, creating an acute source of neutral carbon atoms. The simulated mean lifetime, 11 ± 2 ms, showed approximate agreement with experimental observation when corrected by accounting for dust visibility and ignoring the longest trajectories 1.5 ± 0.2 ms. Synthetic diagnostic data generated from coupling the results of DTOKS-U with the visualisation software Calcam offers a powerful new tool for validation of simulations and predictive calculations of dust dynamics.

Physics↗

Large-scale atomistic calculations of clusters in intense x-ray pulses

Here, we present the methodology of our recently developed Monte-Carlo/ Molecular-Dynamics method for studying the fundamental ultrafast dynamics induced by high-fluence, high-intensity x-ray free electron laser (XFEL) pulses in clusters. The quantum nature of the initiating ionization process is accounted for by a Monte Carlo method to calculate probabilities of electronic transitions, including photo absorption, inner-shell relaxation, photon scattering, electron collision and recombination dynamics, and thus track the transient electronic configurations explicitly. The freed electrons and ions are followed by classical particle trajectories using a molecular dynamics algorithm. These calculations reveal the surprising role of electron-ion recombination processes that lead to the development of nonuniform spatial charge density profiles in x-ray excited clusters over femtosecond timescales. In the high-intensity limit, it is important to include the recombination dynamics in the calculated scattering response even for a 2- fs pulse. We also demonstrate that our numerical codes and algorithms can make e!cient use of the computational power of massively parallel supercomputers to investigate the intense-field dynamics in systems with increasing complexity and size at the ultrafast timescale and in non-linear x-ray interaction regimes. In particular, picosecond trajectories of XFEL clusters with attosecond time resolution containing millions of particles can be e!ciently computed on upwards of 262,144 processes.

74 ATOMIC AND MOLECULAR PHYSICS↗

Machine learning for photovoltaic single axis tracker fault detection and classification

More than 81% of the annual capacity of utility-scale photovoltaic (PV) power plants in the U.S. use single-axis trackers (SATs) due to SATs delivering 4% in capacity factor on average over fixed-array systems. However, SATs are subject to faults, such as software misconfigurations and mechanical failures, resulting in suboptimal tracking. If left undetected, the overall power yield of the PV power plant is reduced significantly. Minimizing downtime and ensuring efficient operation of SATs requires robust detection and diagnosis mechanisms for SAT faults. We present a machine learning framework for implementing real-time SAT fault detection and classification. Our implementation of the proposed framework reliably identifies measurements taken from a test PV system undergoing emulated SAT faults relative to state-of-the-art algorithms and produces nearly zero false positives on our testing days. Code and data are available at https://pvpmc.sandia.gov/tools.

Fault classification↗

Assessment of Different Discrete Particle Methods Ability To Predict Gas-Particle Flow in a Small-Scale Fluidized Bed

Several discrete particle methods exist in the open literature to simulate fluidized bed systems, such as discrete element method (DEM), time driven hard sphere (TDHS), coarse-grained particle method (CGPM), coarse grained hard sphere (CGHS), and multi-phase particle-in-cell (MP-PIC). These different approaches usually solve the fluid phase in a Eulerian fixed frame of reference and the particle phase using the Lagrangian method. The first difference between these models lies in tracking either real particles or lumped parcels. The second difference is in the treatment of particle-particle interactions: by calculating collision forces (DEM and CGPM), using momentum conservation laws (TDHS and CGHS), or based on particle stress model (MP-PIC). These major model differences lead to a wide range of results accuracy and computation speed. However, these models have never been compared directly using the same experimental dataset. In this research, a small-scale fluidized bed is simulated with these methods using the same open-source code MFIX. The results indicate that modeling the particle-particle collision by TDHS increases the computation speed while maintaining good accuracy. Also, lumping few particles in a parcel increases the computation speed with little loss in accuracy. However, modeling particle-particle interactions with solids stress leads to a big loss in accuracy with a little increase in computation speed. The MP-PIC method predicts an unphysical particle-particle overlap, which results in incorrect voidage distribution and incorrect overall bed hydrodynamics. Based on this study, we recommend using the CGHS method for fluidized bed simulations due to its computational speed that rivals that of MPPIC while maintaining a much better accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

UQpy: A general purpose Python package and development environment for uncertainty quantification

In this paper, we present the UQpy software toolbox, an open-source Python package for general uncertainty quantification (UQ) in mathematical and physical systems. The software serves as both a user-ready toolbox that includes many of the latest methods for UQ in computational modeling and a convenient development environment for Python programmers advancing the field of UQ. The paper presents an introduction to the software's architecture and existing capabilities, divided in the code in a set of modules centered around different UQ tasks such as sampling methods, generation of random processes and random fields, probabilistic inverse modeling, reliability analysis, surrogate modeling, and active learning. The paper also highlights the importance of the RunModel module, which is used to drive simulations in the uncertainty analyses performed in UQpy. This module conveniently allows the user to define computational models directly in Python, or to run simulations from a third-party software in serial or in parallel. To illustrate the various capabilities, two examples are tracked throughout the paper and analyzed repeatedly for various UQ tasks. The first is a Python model solving a nonlinear structural dynamics problem, used to illustrate UQpy's capabilities in sampling and forward propagation of high dimensional random vectors (stochastic processes), and probabilistic inference. The second model is a third-party Abaqus finite element model solving the thermomechanical response of a beam structure. This example is used to illustrate UQpy's capabilities in variance reduction sampling techniques, reliability analysis, surrogate modeling and active learning techniques.

97 MATHEMATICS AND COMPUTING↗

OccuTherm: Occupant Thermal Comfort Inference using Body Shape Information

Thermal comfort is a decisive factor for the well-being, productivity, and overall satisfaction of commercial building occupants. Many commercial building automation systems either use a fixed zone-wide temperature set-point for all occupants or they rely on extensive sensor deployments with frequent online interaction with occupants. This results in inadequate comfort levels or significant training effort from users, respectively. However, the increasing ubiquity of cheap, depth-based occupancy tracking systems has enabled an improvement in inferential capabilities. We propose the novel system OccuTherm to model thermal comfort of occupants. We conducted a laboratory study with 77 participants to collect data for the implementation of a thermal comfort model that derives thermal comfort using the human body shape. Based on the comparison with model baselines and ablations, we show that our approach infers thermal comfort of individuals with 60 % accuracy when body shape information is taken into account; 6 % more than state-of-the-art approaches. We make our code, mobile app, datasets, and models freely available.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Structural basis of R-loop recognition by the S9.6 monoclonal antibody

R-loops are ubiquitous, dynamic nucleic-acid structures that play fundamental roles in DNA replication and repair, chromatin and transcription regulation, as well as telomere maintenance. The DNA-RNA hybrid–specific S9.6 monoclonal antibody is widely used to map R-loops. Here, we report crystal structures of a S9.6 antigen-binding fragment (Fab) free and bound to a 13-bp hybrid duplex. We demonstrate that S9.6 exhibits robust selectivity in binding hybrids over double-stranded (ds) RNA and in categorically rejecting dsDNA. S9.6 asymmetrically recognizes a compact epitope of two consecutive RNA nucleotides via their 2'-hydroxyl groups and six consecutive DNA nucleotides via their backbone phosphate and deoxyribose groups. Recognition is mediated principally by aromatic and basic residues of the S9.6 heavy chain, which closely track the curvature of the hybrid minor groove. These findings reveal the molecular basis for S9.6 recognition of R-loops, detail its binding specificity, identify a new hybrid-recognition strategy, and provide a framework for S9.6 protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Demonstration and Automation of Reflected Target Optical Measurement for Heliostats

Accurate optical surfaces are a primary driver of concentrated solar power plant performance. Errors in pointing and tracking mirrors, the canting of individual mirror facets, and the surface slope of the mirror itself can be caused by errors during assembly, transportation, wind loading, gravity, and many other sources. The tools that exist to measure these error sources today largely rely on fringe deflectometry (SOFAST, QDec, others), or photogrammetry with targets attached to the mirror surface. Since 2022, NREL has been developing a measurement method called the Reflected Target Non-intrusive Assessment (ReTNA) system. This system differs from most established methods in that we perform deflectometry with a pattern of coded targets, identified in space with photogrammetry. Reflected target systems have several advantages over traditional fringe deflectometry systems. Firstly, they can be operated in bright or ambient lighting, a challenge for fringe systems that use a projector and screen. Reflected target systems also can use a much lighter and less expensive target than projector-based systems. Lastly, 2D slope measurement can be solved from a single image, which leads to several advantages for accommodating faster measurements and smaller sized targets. These advantages make ReTNA particularly well-suited for applications where there are space or lighting constraints, like performing heliostat quality assurance on an assembly line. It's also useful when a lightweight, flexible system is needed, like for heliostat developers to quickly measure a new heliostat design at different orientations, to observe gravitational effects on the mirror surface shape. In the last year, significant improvements were made to this tool to make it more useful for these applications. These improvements were focused around validation of the ReTNA measurement system, and automation of the setup and measurement process. First, we present an improved ReTNA layout, for use on the heliostat assembly line. Next, we detail the various changes to the ReTNA software and computer vision methods to automate data collection in this new setup, and lessons learned from this process. The goal with this new setup is to perform a full heliostat surface characterization without removing the mirror from the assembly line. Lastly, we share results from several ReTNA validation studies undertaken over the last year. These include repeated ReTNA measurement on demonstration mirror facets, comparisons with other optical measurement tools, and some studies aimed at quantifying the uncertainty of ReTNA measurement under various constraints (mirror-target spacing, camera resolution, etc.). These results are compared with 2024 HelioCon performance targets, and our planned next steps for the ReTNA measurement system are presented.

CSP↗

yProv4ML: Effortless provenance tracking for machine learning systems

The rapid growth in interest in deep learning and foundation models (FMs) in particular, has attracted the attention of a diverse range of researchers thanks to their generalization ability. However, the advent of these techniques has also brought to light the lack of transparency and rigor in the way development is pursued. In particular, the inability to determine the number of epochs and other hyperparameters in advance presents challenges in identifying the best model. To address this challenge, machine learning frameworks such as MLFlow can automate the collection of this type of information. However, these tools capture data using proprietary formats and pose little attention to lineage. This paper proposes yProv4ML, a framework that captures provenance information generated during machine learning processes in PROV-JSON format, with minimal code modification.

Machine learning↗

Improvements to PVWatts for Fixed and One-Axis Tracking Systems

This work presents improvements to the widely used NREL PVWatts photovoltaic system energy model to improve modeling accuracy for typical fixed and one axis system designs. The aim is to calculate losses in the PV system assuming typical modern system design practices, while maintaining simplicity by keeping the required set of input parameters small. These improvements allow users to more credibly and quickly evaluate competing system designs in early stage feasibility. Common submodels for module cover, spectral, snow, tracker, transformer, plant controller, and self-shading losses, in addition to a bifacial gain option, are incorporated into the PVWatts model, and are shown to improve PVWatts' system performance prediction capabilities without major impact to ease of use. We anticipate including these improvements in a future release of NREL's open source PVWatts code, and some of the features may become available in the System Advisor Model (SAM) desktop software as well as the popular PVWatts web application.

14 SOLAR ENERGY↗

Ensemble‐Based, Large‐Eddy Reconstruction of Wind Turbine Inflow in a Near‐Stationary Atmospheric Boundary Layer Through Generative Artificial Intelligence

ABSTRACT To validate the second‐by‐second dynamics of turbines in field experiments, it is necessary to accurately reconstruct the winds going into the turbine. Current time‐resolved inflow reconstruction techniques estimate wind behavior in unobserved regions using relatively simple spectral‐based models of the atmosphere. Here, we develop a technique for time‐resolved inflow reconstruction that is rooted in a large‐eddy simulation model of the atmosphere. Our “large‐eddy reconstruction” technique blends observations and atmospheric model information through a diffusion model machine learning algorithm, allowing us to generate probabilistic ensembles of reconstructions for a single 10‐min observational period. Our generated inflows can be used directly by aeroelastic codes or as inflow boundary conditions in a large‐eddy simulation. We verify the second‐by‐second reconstruction capability of our technique in three synthetic field campaigns, finding positive Pearson correlation coefficient values () between ground‐truth and reconstructed streamwise velocity, as well as smaller positive correlation coefficient values for unobserved fields (spanwise velocity, vertical velocity, and temperature). We validate our technique in three real‐world case studies by driving large‐eddy simulations with reconstructed inflows and comparing to independent inflow measurements. The reconstructions are visually similar to measurements, follow desired power spectra properties, and track second‐by‐second behavior ().

17 WIND ENERGY↗

HDTS 2017.0 Testing and verification document

This report is a continuation of the series of Hunter Dose Tracking System (HDTS) Quality Assurance documents including (Foley and Powell, 2010; Dixon, 2012). In this report we have created a suite of automated test cases and a system to analyze the results of those tests as well as documented the methodology to ensure the field system performs within specifications. The software test cases cover all of the functions and interactions of functions that are practical to test. With the developed framework, if software defects are discovered, it will be easy to create one or more test cases to reproduce the defect and ensure that code changes correct the defect. These tests con rm HDTS version 2017.0 performs according to its specifications and documentation and that its performance meets the needs of its users at the Savannah River Site.

97 MATHEMATICS AND COMPUTING↗

Three-phase Interstellar Medium in Galaxies Resolving Evolution with Star Formation and Supernova Feedback (TIGRESS): Algorithms, Fiducial Model, and Convergence

We introduce TIGRESS, a novel framework for multi-physics numerical simulations of the star-forming interstellar medium (ISM) implemented in the Athena MHD code. The algorithms of TIGRESS are designed to spatially and temporally resolve key physical features, including: (1) the gravitational collapse and ongoing accretion of gas that leads to star formation in clusters; (2) the explosions of supernovae (SNe), both near their progenitor birth sites and from runaway OB stars, with time delays relative to star formation determined by population synthesis; (3) explicit evolution of SN remnants prior to the onset of cooling, which leads to the creation of the hot ISM; (4) photoelectric heating of the warm and cold phases of the ISM that tracks the time-dependent ambient FUV field from the young cluster population; (5) large-scale galactic differential rotation, which leads to epicyclic motion and shears out overdense structures, limiting large-scale gravitational collapse; (6) accurate evolution of magnetic fields, which can be important for vertical support of the ISM disk as well as angular momentum transport. We present tests of the newly implemented physics modules, and demonstrate application of TIGRESS in a fiducial model representing the solar neighborhood environment. We use a resolution study to demonstrate convergence and evaluate the minimum resolution Δx required to correctly recover several ISM properties, including the star formation rate, wind mass-loss rate, disk scale height, turbulent and Alfvénic velocity dispersions, and volume fractions of warm and hot phases. For the solar neighborhood model, all these ISM properties are converged at Δx⩽8 pc.

79 ASTRONOMY AND ASTROPHYSICS↗