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At least 577 records · Page 32

Experiences with Porting the FLASH Code to Ookami, an HPE Apollo 80 A64FX Platform

We present initial experiences with running the community simulation code FLASH, developed at the University of Chicago for multi-scale multi-physics applications, on Ookami, a technology testbed featuring the A64FX processor developed by Fujitsu. Our effort focused largely on running FLASH “right out of the box” to see which combinations of compilers and software implementations (e.g. MPI) allowed the code to run with minimal modification. FLASH was one application in a larger effort to deploy Ookami; it served as a test for different versions of newly installed software, and as a cornerstone for the FAQ page of the Ookami website. Here, we report on our results with different compilers and other software, along with our initial scaling results and attempts to utilize the A64FX’s SVE instructions and NUMA architecture. We found that FLASH readily ran with different compilers and MPI implementations, and showed the expected good scaling with no turning. However, more work must be done to fully take advantage of the A64FX’s architectural features and produce a significant speedup for FLASH on Ookami.

79 ASTRONOMY AND ASTROPHYSICS↗

Recent Development of the Two-Stroke Engine. II - Design Features: Design Features - 2

Completing the first paper dealing with charging methods and arrangements, the present paper discusses the design forms of two-stroke engines. Features which largely influence piston running are: (a) The shape and surface condition of the sliding parts. (b) The cylinder and piston materials. (c) Heat conditions in the piston, and lubrication. There is little essential difference between four-stroke and two-stroke engines with ordinary pistons. In large engines, for example, are always found separately cast or welded frames in which the stresses are taken up by tie rods. Twin piston and timing piston engines often differ from this design. Examples can be found in many engines of German or foreign make. Their methods of operation will be dealt with in the third part of the present paper, which also includes the bibliography. The development of two-stroke engine design is, of course, mainly concerned with such features as are inherently difficult to master; that is, the piston barrel and the design of the gudgeon pin bearing. Designers of four-stroke engines now-a-days experience approximately the same difficulties, since heat stresses have increased to the point of influencing conditions in the piston barrel. Features which notably affect this are: (a) The material. (b) Prevailing heat conditions.

Zeman, J.↗

Camellia: A Rapid Development Framework for Finite Element Solvers

We report the discontinuous Petrov–Galerkin (DPG) methodology of Demkowicz and Gopalakrishnan guarantees the optimality of the finite element solution in a user-controllable energy norm, and provides several features supporting adaptive schemes. The approach provides stability automatically; there is no need for carefully derived numerical fluxes (as in DG schemes) or for mesh-dependent stabilization terms (as in stabilized methods). In this paper, we focus on features of Camellia that facilitate implementation of new DPG formulations; chief among these is a rich set of features in support of symbolic manipulation, which allow, e.g., bilinear formulations in the code to appear much as they would on paper. Many of these features are general in the sense that they can also be used in the implementation of other finite element formulations. In fact, because DPG’s requirements are essentially a superset of those of other finite element methods, Camellia provides built-in support for most common methods. We believe, however, that the combination of an essentially “hands-free” finite element methodology as found in DPG with the rapid development features of Camellia are particularly winsome, so we focus on use cases in this class. In addition to the symbolic manipulation features mentioned above, Camellia offers support for one-irregular adaptive meshes in 1D, 2D, 3D, and space-time. It provides a geometric multigrid preconditioner particularly suited for DPG problems, and supports distributed parallel execution using MPI. For its load balancing and distributed data structures, Camellia relies on packages from the Trilinos project, which simplifies interfacing with other computational science packages. Camellia also allows loading of standard mesh formats through an interface with the MOAB package. Camellia includes support for static condensation to eliminate element-interior degrees of freedom locally, usually resulting in substantial reduction of the cost of the global problem. Finally, we include a discussion of the variational formulations built into Camellia, with references to those formulations in the literature, as well as an MPI performance study.

97 MATHEMATICS AND COMPUTING↗

The Land Surface Data Toolkit (LDT v7.2) - A Data Fusion Environment for Land Data Assimilation Systems

The effective applications of land surface models (LSMs) and hydrologic models pose a varied set of data input and processing needs, ranging from ensuring consistency checks to more derived data processing and analytics. This article describes the development of the Land surface Data Toolkit (LDT), which is an integrated framework designed specifically for processing input data to execute LSMs and hydrological models. LDT not only serves as a preprocessor to the NASA Land Information System (LIS), which is an integrated framework designed for multi-model LSM simulations and data assimilation (DA) integrations, but also as a land-surface-based observation and DA input processor. It offers a variety of user options and inputs to processing datasets for use within LIS and stand-alone models. The LDT design facilitates the use of common data formats and conventions. LDT is also capable of processing LSM initial conditions and meteorological boundary conditions and ensuring data quality for inputs to LSMs and DA routines. The machine learning layer in LDT facilitates the use of modern data science algorithms for developing data-driven predictive models. Through the use of an object-oriented framework design, LDT provides extensible features for the continued development of support for different types of observational datasets and data analytics algorithms to aid land surface modeling and data assimilation.

droughts and floods↗

Optimization Methodology of Pebble Bed HTGR Start-Up and Running-in Strategy

In recent years interest in advanced reactor technologies has increased significantly. However, the methods used for analysis of traditional nuclear reactors are insufficient to consider all the different and varied advanced reactor designs without further development. One promising advanced reactor design is the pebble bed reactor (PBR). PBRs possess unique operational and fuel cycle features that require the development of specific analysis methodologies to adequately design and analyze the systems. There is a need in PBR research for a capability to analyze and optimize the process of transitioning from the start-up reactor core to the equilibrium core (known as the “running-in” of the reactor). The start-up of a PBR and the transition to the equilibrium core is a complex, multi-physics challenge that has not yet been well researched and has many opportunities for design, analysis, and optimization of the process. In this research, a methodology is defined to consider the potential strategies in PBR start-up and run-in to the equilibrium core. Multiple candidate software are considered, and their pros and cons are discussed for the PBR-specific application in the methodology. A preliminary software selection for the physics engine is made, and initial verification of key modules is performed. Software to support optimization of the reactor run-in strategies through reduced order modeling (ROM) and machine learning are considered. Challenges for a full implementation of the methodology are discussed. Additional code selections and verification of models relevant to the application are needed before full demonstration of the methodology can be achieved and an optimal strategy determined.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

FUN3D Grid Refinement and Adaptation Studies for the Ares Launch Vehicle

This paper presents grid refinement and adaptation studies performed in conjunction with computational aeroelastic analyses of the Ares crew launch vehicle (CLV). The unstructured grids used in this analysis were created with GridTool and VGRID while the adaptation was performed using the Computational Fluid Dynamic (CFD) code FUN3D with a feature based adaptation software tool. GridTool was developed by ViGYAN, Inc. while the last three software suites were developed by NASA Langley Research Center. The feature based adaptation software used here operates by aligning control volumes with shock and Mach line structures and by refining/de-refining where necessary. It does not redistribute node points on the surface. This paper assesses the sensitivity of the complex flow field about a launch vehicle to grid refinement. It also assesses the potential of feature based grid adaptation to improve the accuracy of CFD analysis for a complex launch vehicle configuration. The feature based adaptation shows the potential to improve the resolution of shocks and shear layers. Further development of the capability to adapt the boundary layer and surface grids of a tetrahedral grid is required for significant improvements in modeling the flow field.

Bartels, Robert E.↗

SU-F-T-139: Meeting the Challenges of Quality Control in the TOPAS Monte Carlo Simulation Toolkit for Proton Therapy

Purpose: Monte Carlo particle transport simulation (MC) codes have become important tools in proton therapy and biology, both for research and practice. TOPAS is an MC toolkit serving users worldwide (213 licensed users at 95 institutions in 21 countries). It provides unprecedented ease in 4D placement of geometry components, beam sources and scoring through its user-friendly and reproducible parameter file interface. Quality control (QC) of stochastic simulation software is inherently difficult, and the versatility of TOPAS introduces additional challenges. But QC is vital as the TOPAS development team implements new features, addresses user feedback and reacts to upgrades of underlying software (i.e. Geant4). Methods: Whenever code is committed to our repository, over 50 separate module tests are automatically triggered via a continuous integration service. They check that the various module options execute successfully and that their results are statistically consistent with previous reference values. Prior to each software release, longer end-to-end tests automatically validate TOPAS against experimental data and a TOPAS benchmark. These include simulating multiple properties of spread-out Bragg peaks, validating nuclear models, and searching for differences in patient simulations. Results: Continuous integration has proven effective in catching regressions at the time they are introduced, particularly when implementing new features that involve refactoring code (e.g. multithreading and ntuple output). Code coverage statistics highlight untested portions of code and guide development of new tests. The various end-to-end tests demonstrate that TOPAS accurately describes the physics of proton therapy within clinical tolerances. Conclusion: The TOPAS QC strategy of frequent short tests and pre-release long tests has led to a more reliable tool. However, the versatility of TOPAS makes it difficult to predict how users might combine different modules, and so QC ultimately remains a partnership between the developer and the user. This work was funded by National Cancer Institute grant R01 CA 140735.

60 APPLIED LIFE SCIENCES↗

Predicting the High-Temperature Oxidation Response of Nickel Superalloys Using CALPHAD-Enhanced Machine Learning

Structural materials such as Ni-based superalloys used in high-temperature power cycles are routinely exposed to toxic environments including high temperature and pressure, aqueous and gas corrosion, etc. Here, we present a physics-informed machine learning approach to predict the oxidation response of diverse Ni-superalloys. First, a high-fidelity experimental dataset is curated from typical oxidation mass-change experiments in air, covering 25+ elements and different physical behavior such as parabolic growth, non-parabolic growth, and oxide spallation. Second, the dataset is featurized using thermophysical, chemical, and mechanical properties obtained from high-throughput CALPHAD calculations. Third, several machine learning models are developed to identify key features related to mass-change characteristics and model the mass-change curve for various alloys. Finally, the model is deployed to rapidly screen over a new composition space and down-select candidate alloys with high oxidation resistance for experimental validation.

CALPHAD↗

Data Science Meets Physical Organic Chemistry

At the heart of synthetic chemistry is the holy grail of predictable catalyst design. In particular, researchers involved in reaction development in asymmetric catalysis have pursued a variety of strategies toward this goal. This is driven by both the pragmatic need to achieve high selectivities and the inability to readily identify why a certain catalyst is effective for a given reaction. While empiricism and intuition have dominated the field of asymmetric catalysis since its inception, enantioselectivity offers a mechanistically rich platform to interrogate catalyst-structure response patterns that explain the performance of a particular catalyst or substrate. In the early stages of an asymmetric reaction development campaign, the overarching mechanism of the reaction, catalyst speciation, the turnover limiting step, and many other details are unknown or posited based on related reactions. Considering the unclear details leading to a successful reaction, initial enantioselectivity data are often used to intuitively guide the ultimate direction of optimization. However, if the conditions of the Curtin-Hammett principle are satisfied, then measured enantioselectivity can be directly connected to the ensemble of diastereomeric transition states (TSs) that lead to the enantiomeric products, and the associated free energy difference between competing TSs (ΔΔ G ‡ = - RT ln[( S )/( R )], where ( S ) and ( R ) represent the concentrations of the enantiomeric products). We, and others, speculated that this important piece of information can be leveraged to guide reaction optimization in a quantitative way. Although traditional linear free energy relationships (LFERs), such as Hammett plots, have been used to illuminate important mechanistic features, we sought to develop data science derived tools to expand the power of LFERs in order to describe complex reactions frequently encountered in modern asymmetric catalysis. Specifically, we investigated whether enantioselectivity data from a reaction can be quantitatively connected to the attributes of reaction components, such as catalyst and substrate structural features, to harness data for asymmetric catalyst design. In this context, we developed a workflow to relate computationally derived features of reaction components to enantioselectivity using data science tools. The mathematical representation of molecules can incorporate many aspects of a transformation, such as molecular features from substrate, product, catalyst, and proposed transition states. Statistical models relating these features to reaction outputs can be used for various tasks, such as performance prediction of untested molecules. Perhaps most importantly, statistical models can guide the generation of mechanistic hypotheses that are embedded within complex patterns of reaction responses. Overall, merging traditional physical organic experiments with statistical modeling techniques creates a feedback loop that enables both evaluation of multiple mechanistic hypotheses and future catalyst design. In this Account, we highlight the evolution and application of this approach in the context of a collaborative program based on chiral phosphoric acid catalysts (CPAs) in asymmetric catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular simulation using transfer-learned potentials for the disordered nanoscale structure of nitrogen-doped nanoporous carbons

Machine learning (ML)-based molecular dynamics (MD) simulations of the formation of a class of N-doped nanoporous carbons are performed to assess their disordered partially graphitized nanoscale structure. The study is motivated by the effectiveness of so-called nitrogen assembly carbons (NACs) for catalysis applications. Benchmark simulations for pure-C disordered graphitic systems reveal the importance of reliably capturing the vdW component of the potentials in order to accurately describe the tendency for layering of disordered graphene-like sheets. In our modeling, this is achieved by a transfer learning strategy incorporating features of the energetics from the optB88-vdW DFT functional into potentials initially trained with a less expensive functional, thereby providing a superior description of the pure-C systems. Generation from MD simulations of realistic partially graphitized structures is significantly more challenging for N-doped versus for pure C systems. However, such structures are achieved by a tailored MD simulation protocol mimicking the experimental synthesis process and in particular incorporating an annealing and subsequent quenching stages. Simulated PXRD patterns effectively reproduce the features of experimental observations for NACs, including the appearance of a prominent but broad (002) peak at around 25, and the development of another weaker feature associated with in-layer ordering of mixed C-N graphene-like sheets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Physics-informed machine learning to predict solvatochromic parameters of designer solvents with case studies in CO 2 and lignin dissolution

The polarity of solvents plays a critical role in various research applications, particularly in their solubilities. Polarity is conveniently characterized by the Kamlet-Taft parameters that is, the hydrogen bonding acidity (α), the basicity (β), and the polarizability (π*). Obtaining Kamlet-Taft parameters is very important for designer solvents, namely ionic liquids (ILs) and deep eutectic solvents (DESs). However, given the unlimited theoretical number of combinations of ionic pairs in ILs and hydrogen-bond donor/acceptor pairs in DESs, experimental determination of their Kamlet-Taft parameters is impractical. To address this, the present study developed two different machine learning (ML) algorithms to predict Kamlet-Taft parameters for designer solvents using quantum chemically derived input features. The ML models developed in the present study showed accurate predictions with high R 2 and low RMSE values. Further, in the context of present interest in the circular bioeconomy, the relationship between the basicities and acidities of designer solvents and their ability to dissolve lignin and carbon dioxide (CO 2 ) is discussed. Our method thus guides the design of effective solvents with optimal Kamlet-Taft parameter values dissolving and converting biomass and CO 2 into valuable chemicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analyzing Software Specifications for Mode Confusion Potential

Increased automation in complex systems has led to changes in the human controller's role and to new types of technology-induced human error. Attempts to mitigate these errors have primarily involved giving more authority to the automation, enhancing operator training, or changing the interface. While these responses may be reasonable under many circumstances, an alternative is to redesign the automation in ways that do not reduce necessary or desirable functionality or to change functionality where the tradeoffs are judged to be acceptable. This paper describes an approach to detecting error-prone automation features early in the development process while significant changes can still be made to the conceptual design of the system. The information about such error-prone features can also be useful in the design of the operator interface, operational procedures, or operator training.

Nancy G. Leveson↗

Web-based Decision Support System Tools: the Soil and Water Assessment Tool Online Visualization and Analyses (SWATOnline) and NASA Earth Observation Data Downloading and Reformatting Tool (NASAaccess)

The current influx of climate related information required scientists to communicate their findings to decision makers in governments, disaster preparedness organizations, and the general public. The Soil and Water Assessment Tool (SWAT) is a powerful modelling tool that allows scientists to simulate many of the physical processes involved in the water cycle. This article presents the design, methods and development efforts to overcome some of the limitations of the previously developed SWAT visualization software programs by creating a set of modular web applications that can be duplicated, customized, and run. Moreover, this article features a web application development tool for climate data retrieval. The NASAaccess fetches, extracts and reformats climate data from the National Aeronautics and Space Administration servers and outputs data compatible with hydrological models. This work has the potential to increase the SWAT's model impact on non-technically trained stakeholders and decision makers charged with water and climate management.

Tethys↗

Cost reduction by integration of the assurance technologies.

It is shown how the cost of applying assurance disciplines to the development of complex systems can be reduced by integrating the mechanics of system engineering and system management into a 'Development Risk Control System'. The essential features of the integration process are examined. A 'Development Risk Management Model' is described, and the use of the model to integrate and thereby reduce the cost of other assurance disciplines is discussed and illustrated.

Ball, L. W.↗

A study of the utilization of ERTS-1 data from the Wabash River Basin

The author has identified the following significant results. Nine projects are defined, five ERTS data applications experiments and four supporting technology tasks. The most significant applications results were achieved in the soil association mapping, earth surface feature identification, and urban land use mapping efforts. Four soil association boundaries were accurately delineated from ERTS-1 imagery. A data bank has been developed to test surface feature classifications obtained from ERTS-1 data. Preliminary forest cover classifications indicated that the number of acres estimated tended to be greater than actually existed by 25%. Urban land use analysis of ERTS-1 data indicated highly accurate classification could be obtained for many urban catagories. The wooded residential category tended to be misclassified as woods or agricultural land. Further statistical analysis revealed that these classes could be separated using sample variance.

Landgrebe, D. A.↗

DRiFT - Release 2.1.0: Organic Scintillators and Gas Detectors

DRiFT (a Detector Response Function Toolkit) is LANL-developed software that post-processes output from the extensively validated radiation transport code, MCNP, and generates realistic nuclear instrumentation response. DRiFT is designed to be flexible, enabling users to specify detector type and many experimental settings, as well as accommodating the addition of their own desired features. The focus of this release is on organic scintillator, gas detector, and associated capabilities, while semiconductor features are still under development. Organic scintillators are widely used in the areas of nuclear safeguards and nuclear non-proliferation efforts. DRiFT has several diagnostic and detector physics features relevant to detailed scintillator simulations including: tracking source particle information, scintillation light production, the effects of PMT quantum efficiency and gain, and digitizer settings. Users can select responses from many scintillator and PMT types supported natively by DRiFT, or add their own by following the instructions in this document. DRiFT also has several diagnostic and detector physics features relevant to neutron gas detector simulations including: gas detector wall effects, inactive areas at the end of detector tubes, and effects of a preamplifier. We acknowledge that DRiFT is under active development, bug reports and general questions and comments should be directed to Madison Andrews, madison@lanl.gov. This manual is divided into four parts: I) An overview of DRiFT, including how to obtain and install the executable, II) A description of the detector physics related to scintillators available, III) a description of more general DRiFT features the user may find useful, and IV) a description of the test suite and examples made available with the code release.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Radiomics-based prediction of microsatellite instability in colorectal cancer at initial computed tomography evaluation

Purpose: To predict microsatellite instability (MSI) status of colon cancer on preoperative CT imaging using radiomic analysis. Methods: This retrospective study involved radiomic analysis of preoperative CT imaging of patients who underwent resection of stage II–III colon cancer from 2004 to 2012. A radiologist blinded to MSI status manually segmented the tumor region on CT images. 254 Intensity-based radiomic features were extracted from the tumor region. Three prediction models were developed with (1) only clinical features, (2) only radiomic features, and (3) “combined” clinical and radiomic features. Patients were randomly separated into training (n = 139) and test (n = 59) sets. The model was constructed from training data only; the test set was reserved for validation only. Model performance was evaluated using AUC, sensitivity, specificity, PPV, and NPV. Results: Of the total 198 patients, 134 (68%) patients had microsatellite stable tumors and 64 (32%) patients had MSI tumors. The combined model performed slightly better than the other models, predicting MSI with an AUC of 0.80 for the training set and 0.79 for the test set (specificity = 96.8% and 92.5%, respectively), whereas the model with only clinical features achieved an AUC of 0.74 and the model with only radiomic features achieved an AUC of 0.76. The model with clinical features alone had the lowest specificity (70%) compared with the model with radiomic features alone (95%) and the combined model (92.5%). Conclusions: Preoperative prediction of MSI status via radiomic analysis of preoperative CT adds specificity to clinical assessment and could contribute to personalized treatment selection.

62 RADIOLOGY AND NUCLEAR MEDICINE↗