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At least 1,387 records · Page 77

Five years of ForTrilinos ECP

The ForTrilinos subproject of the Exascale Computing Project (ECP) was initiated to bring the capabilities and scalability of the Trilinos numerical solver collection to Fortran scientific application codes. A novel Fortran extension to the Simplified Wrapper and Interface Generator (SWIG) tool, which automatically generates Fortran bindings from existing C/C++ library code, has been applied to key Trilinos solver libraries to generate the new ForTrilinos libraries. SWIG-Fortran has additionally been used to generate new Fortran compatibility layers for additional scientific libraries and applications. This report summarizes the products and impact of the ForTrilinos subproject.

97 MATHEMATICS AND COMPUTING↗

Teaching Computational Reproducibility for Neuroimaging

We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on which the techniques are based. The lectures are often paired with practical workshops in which students run imaging analyses using the graphical interface of specific neuroimaging software packages. Our experience suggests that this combination leaves the student with a superficial understanding of the underlying ideas, and an informal, inefficient, and inaccurate approach to analysis. To address these problems, we based our course around a substantial open-ended group project. This allowed us to teach: (a) computational tools to ensure computationally reproducible work, such as the Unix command line, structured code, version control, automated testing, and code review and (b) a clear understanding of the statistical techniques used for a basic analysis of a single run in an MR scanner. The emphasis we put on the group project showed the importance of standard computational tools for accuracy, efficiency, and collaboration. The projects were broadly successful in engaging students in working reproducibly on real scientific questions. We propose that a course on this model should be the foundation for future programs in neuroimaging. We believe it will also serve as a model for teaching efficient and reproducible research in other fields of computational science.

60 APPLIED LIFE SCIENCES↗

COLUMBUS─An Efficient and General Program Package for Ground and Excited State Computations Including Spin–Orbit Couplings and Dynamics

The COLUMBUS program system provides the tools for performing high-level multireference (MR) computations, including the multireference configuration interaction (MRCI) method and its multireference averaged quadratic coupled cluster (MR-AQCC) extension, allowing computations on a wide range of fascinating atomic and molecular systems, including the treatment of open-shells and complicated excited state phenomena. The inclusion of spin−orbit coupling (SOC) directly within the MRCI step enables the description of systems containing heavy elements, such as lanthanides and actinides, whose properties are strongly influenced by SOC. Analytic energy gradients and nonadiabatic couplings at the correlated MRCI level provide the foundation for a variety of dynamics studies, giving insight into ultrafast photochemistry. New and ongoing method developments in COLUMBUS include the computation of spin densities, improved descriptions of ionic states, enhancements to the AQCC method, and the porting of COLUMBUS to graphical processing units (GPUs). New external interfaces enable an enhanced description of electronic resonances and molecules in strong laser fields. This work highlights these new developments while providing a detailed account of the diverse applications of COLUMBUS in recent years.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

THE THEORETICAL ASTROPHYSICAL OBSERVATORY: CLOUD-BASED MOCK GALAXY CATALOGS

We introduce the Theoretical Astrophysical Observatory (TAO), an online virtual laboratory that houses mock observations of galaxy survey data. Such mocks have become an integral part of the modern analysis pipeline. However, building them requires expert knowledge of galaxy modeling and simulation techniques, significant investment in software development, and access to high performance computing. These requirements make it difficult for a small research team or individual to quickly build a mock catalog suited to their needs. To address this TAO offers access to multiple cosmological simulations and semi-analytic galaxy formation models from an intuitive and clean web interface. Results can be funnelled through science modules and sent to a dedicated supercomputer for further processing and manipulation. These modules include the ability to (1) construct custom observer light cones from the simulation data cubes; (2) generate the stellar emission from star formation histories, apply dust extinction, and compute absolute and/or apparent magnitudes; and (3) produce mock images of the sky. All of TAO’s features can be accessed without any programming requirements. The modular nature of TAO opens it up for further expansion in the future.

79 ASTRONOMY AND ASTROPHYSICS↗

Bias-dependent local structure of water molecules at a metallic interface

Understanding the local structure of water at the interfaces of metallic electrodes is a key issue in aqueous-based electrochemistry. Nevertheless a realistic simulation of such a setup is challenging, particularly when the electrodes are maintained at different potentials. To correctly compute the effect of an external bias potential applied to truly semi-infinite surfaces, we combine Density Functional Theory (DFT) and Non-Equilibrium Green’s Function (NEGF) methods. This framework allows for the out-of-equilibrium calculation of forces and dynamics, and directly correlates to the chemical potential of the electrodes, which is introduced experimentally. In this work, we apply this methodology to study the electronic properties and atomic forces of a water molecule at the interface of a gold surface. We find that the water molecule tends to align its dipole moment with the electric field, and it is either repelled or attracted to the metal depending on the sign and magnitude of the applied bias, in an asymmetric fashion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modulating thermal conductance at ligand/nanocrystal interfaces via oxygen-coordinated ligands

Here, the interfacial thermal conductance (h lig–NC ) between a cadmium selenide (CdSe) nanocrystal (NC) and three related organic ligands—olealdehyde, oleyl alcohol, and oleic acid—was investigated computationally. These ligands have the same carbon backbone but differ in the number and type of oxygen-coordinated headgroups (carbonyl and/or hydroxyl), leading to distinct bonding geometries involving monodentate and bidentate bonds. For a fully encapsulated NC, h lig–NC increases in the order of olealdehyde, oleic acid, and oleyl alcohol ligands. To isolate the contributions of h lig–NC from each headgroup type, the distinct bonding geometries were analyzed. Aldehyde and alcohol ligands, each featuring a single oxygen headgroup (carbonyl or hydroxyl), exhibit similar O–Cd separations and nearly identical h lig–NC per ligand at full surface coverage. However, the hydroxyl group in the alcohol ligand enables a higher ligand grafting density on the NC surface, resulting in a greater overall h lig–NC than the aldehyde-grafted NCs. In contrast, the oleic acid ligand forms multidentate bonds with the NC, leading to a shorter average O–Cd separation and a higher h lig–NC per ligand compared to monodentate bonds. Nevertheless, steric hindrance from the acid ligand's larger headgroup reduces its grafting density relative to alcohol ligands, ultimately resulting in a lower overall h lig–NC .

Wong, Kae-Lin [Zhejiang Univ., Hangzhou (China)] (↗

The structure, composition, and performance impact of a YSZ-GDC interdiffusion layer in solid oxide electrolysis cells

This study provides a combined experimental and computational investigation into the structure and impact of the cation interdiffusion layer that appears at the gadolinium doped ceria (GDC)/yttria stabilized zirconia (YSZ) interface in solid oxide electrolysis cells (SOECs). Scanning transmission electron microscopy (STEM) illustrates that a ∼0.4 μm interdiffusion layer (IDL) with an intermixed cation distribution and fine grain size forms upon sintering. STEM identifies that the interdiffusion layer exists in the cubic fluorite structure despite changes in cation composition. The interdiffusion layer microstructure formed during sintering does not change during SOEC testing at either 1.3V or heightened voltage pulse testing. Modeling predicts that ionic conductivity may decrease in the interdiffusion layer due to Coulombic trapping between mobile oxygen vacancies and excess Gd 3+ acceptor dopants. Yet, the density and continuous nature of the layer should benefit cell stability by substantially reducing the formation of SrZrO 3 , which is corroborated by STEM and Synchrotron X-ray diffraction (XRD). We conclude that the interdiffusion layer acts as a beneficial barrier to Sr diffusion, when operating in a regime where electrolyte void formation is not observed.

organic↗

External beam planning module of Eclipse for external beam radiation therapy

Eclipse is a 3-dimensional (3D) treatment planning system for radiation therapy offered by Varian Medical Systems, Inc. The system has the network connectivity for the electronic transfer of image datasets and digital data communication among different equipment. The scope of this project for this special issue of Medical Dosimetry on 3D treatment planning systems is the assessment of planning tools in the external beam planning module of Eclipse to generate optimized treatment plans for patients undergoing external beam radiation therapy. This treatment planning system is relatively mature to be able to generate (1) simple treatment plans, (2) conformal radiation therapy plans, (3) static intensity-modulated radiation therapy (IMRT) plans, (4) volumetric-modulated arc therapy (VMAT) plans, and (5) treatment plans for electron beam therapy. The treatment planning tools are relatively plentiful to assist in the radiation therapy treatment planning. Some new features have been incorporated in the latest version and are helpful for making high-quality treatment plans. However, the location of the tools is not intuitive, and hence, familiarity with the user interface is essential to the efficient use of the treatment planning system. In addition, there are a number of dose algorithms available for the computation of dose distributions. The understanding of each dose computation algorithm is essential for the optimal use of this treatment planning system.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Computer-Aided Molecular Design of Bis-phosphine Oxide Lanthanide Extractants

Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R 2 (O)P-link-P(O)R 2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theory and the performance of known bis-phosphine oxide extractants. For the case where link is -CH 2 -, evaluation of the ligand geometry provides the first characterization of a steric origin for the ‘anomalous aryl strengthening’ effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Negating interfacial impedance in garnet-based solid-state Li metal batteries

Garnet-type solid-state electrolytes have attracted extensive attention due to their high ionic conductivity, approaching 1 mS cm -1 , excellent environmental stability, and wide electrochemical stability window, from lithium metal to ~6 V. However, to date, there has been little success in the development of high-performance solid-state batteries using these exceptional materials, the major challenge being the high solid–solid interfacial impedance between the garnet electrolyte and electrode materials. In this paper, we effectively address the large interfacial impedance between a lithium metal anode and the garnet electrolyte using ultrathin aluminium oxide (Al 2 O 3 ) by atomic layer deposition. Li 7 La 2.75 Ca 0.25 Zr 1.75 Nb 0.25 O 12 (LLCZN) is the garnet composition of choice in this work due to its reduced sintering temperature and increased lithium ion conductivity. A significant decrease of interfacial impedance, from 1,710 Ω cm 2 to 1 Ω cm 2 , was observed at room temperature, effectively negating the lithium metal/garnet interfacial impedance. Experimental and computational results reveal that the oxide coating enables wetting of metallic lithium in contact with the garnet electrolyte surface and the lithiated-alumina interface allows effective lithium ion transport between the lithium metal anode and garnet electrolyte. Finally, we also demonstrate a working cell with a lithium metal anode, garnet electrolyte and a high-voltage cathode by applying the newly developed interface chemistry.

25 ENERGY STORAGE↗

Electromagnetic levitation containerless processing of metallic materials in microgravity: rapid solidification

Space levitation processing allows researchers to conduct benchmark tests in an effort to understand the physical phenomena involved in rapid solidification processing, including alloy thermodynamics, nucleation and growth, heat and mass transfer, solid/liquid interface dynamics, macro- and microstructural evolution, and defect formation. Supported by ground-based investigations, a major thrust is to develop and refine robust computational tools based on theoretical and applied approaches. This work is accomplished in conjunction with experiments designed for precise model validation with application to a broad range of industrial processes.

42 ENGINEERING↗

Analysis of bipolar membranes for electrochemical CO 2 capture from air and oceanwater

Carbon dioxide (CO 2 ) must be removed from the atmosphere to mitigate the negative effects of climate change. However, the most scalable methods for removing CO 2 from the air require heat from fossil-fuel combustion to produce pure CO 2 and continuously regenerate the sorbent. Bipolar-membrane electrodialysis (BPM-ED) is a promising technology that uses renewable electricity to dissociate water into acid and base to regenerate bicarbonate-based CO 2 capture solutions, such as those used in chemical loops of direct-air-capture (DAC) processes, and in direct-ocean capture (DOC) to promote atmospheric CO 2 drawdown via decarbonization of the shallow ocean. In this study, we develop an experimentally validated 1D model for the electrochemical regeneration of CO 2 from bicarbonate-based carbon capture solutions and seawater using BPM-ED. For DAC, our experimental and computational results demonstrate that pH swings induced by BPM water dissociation drive the formation of CO 2 at the cation-exchange layer|catholyte interface with energy-intensities of less than 150 kJ mol -1 . However, high rates of bubble formation increase energy intensity at current densities >100 mA cm -2 . Correspondingly, accelerating water dissociation catalysis and enacting bubble removal could enable CO 2 recovery at energy intensities <100 kJ mol -1 and current densities >100 mA cm -2 . For DOC, mass transport limitations associated with low carbon concentrations in oceanwater suggest that DOC is best suited for clean production of acid and base usable in downstream processes. Further, these results provide design principles for industrial-scale CO 2 recovery using BPM-ED.

54 ENVIRONMENTAL SCIENCES↗

Influence of baroclinic vorticity production on unsteady drag coefficient in shock–particle interaction

The influence of baroclinic vorticity production on the unsteady drag coefficient in shock–particle interaction is numerically studied in this work. Numerical simulations are performed for shock–particle interaction utilizing a high–resolution axisymmetric solver for the Euler equations that allows for multi-material interface and shock propagation in both the particle and surrounding medium. We consider an aluminum particle in nitromethane and allow for particle deformation. We compute the vorticity production and unsteady drag coefficient as a function of time to explain the complex physical mechanisms that occur during shock–particle interaction. We observe baroclinic vorticity production as the shock propagates over the particle and find that the vorticity is primarily generated at the surface of the particle. After the passage of the shock over the particle, the generated vortex traverses downstream, thus creating a sharpened particle edge and low pressure on the downstream side of the particle, followed by the trapping of the vortex at the particle edge. These mechanisms lead to the generation of a quasi-steady drag force even after the passage of the shock, thus suggesting the importance of baroclinic vorticity production to the unsteady drag coefficient. Finally, we compute the unsteady drag coefficient for various shock Mach numbers and particle ellipticities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

High-speed impact of micron-sized diesel drop trains—Splashing dynamics, secondary droplet formation, and effects of pre-existing film thickness

This work investigates surface impingement of monodispersed diesel drop trains using computational simulations. The three-dimensional simulations include high-speed impact of micrometer-sized fuel drops onto initially dry and wetted stainless steel substrates. The drop size and impact velocity are representative of fuel injection conditions in internal combustion engines (ICEs). The drop trains serve as a simplified representation of fuel spray. To accurately capture the film that naturally develops on initially dry substrates, a dynamic diesel-stainless steel contact angle model was developed using experiments of single drop impact under ICE representative temperature. Simulations are presented for a highly splashing case and the effects of a pre-existing film on splashing dynamics were investigated, including the temporal evolution of splashed mass and film thickness. It was concluded that for thin films, the effect of pre-existing film thickness is less significant than in single drop impingement. Secondary droplet characterization was performed on simulation results, leading to instantaneous and time-averaged distributions of secondary droplet size, velocity magnitude, and trajectory angle. It was found that for each drop impingement, approximately 58% of the splashed mass is from the impinging drop itself, while the remainder of the splashed mass is composed of film liquid. From a high resolution case, details of secondary droplet formation are observed and three distinct phases of secondary droplet formation are identified. The detailed analysis of drop train impingement under engine-relevant conditions serves as a first step toward a robust understanding of fuel impingement and the development of cleaner and more efficient ICEs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Piezo-Antenna: An Electromagnetic-Ultrasonic Data Transfer System

Electronic systems contained within sealed metallic enclosures, such as nuclear waste containers where wire penetration is not an option, require a through-wall data transfer technology to communicate. One such technology utilizes piezoelectric ultrasonic transducers to communicate through the barrier using elastic waves. Currently demonstrated ultrasonic through-wall data communication techniques have relied on having a direct interface with the ultrasonic transducers on either side. Here, this work studies the coupling of an antenna to such an ultrasonic communication system. A computationally efficient model of a piezobarrier ultrasonic communication system and antenna using a simplified antenna model and a transfer matrix piezobarrier model is utilized to perform a representative parameter space search. The system efficiency and bandwidth trends are shown for the system parameters as well as operating frequency. The tradeoff between efficiency and bandwidth is also presented. A system configuration within the parameter space is fabricated and demonstrated to achieve a data rate of up to 100 kb/s.

Antenna↗

SU-F-J-94: Development of a Plug-in Based Image Analysis Tool for Integration Into Treatment Planning

Purpose: To extend the functionality of a commercial treatment planning system (TPS) to support (i) direct use of quantitative image-based metrics within treatment plan optimization and (ii) evaluation of dose-functional volume relationships to assist in functional image adaptive radiotherapy. Methods: A script was written that interfaces with a commercial TPS via an Application Programming Interface (API). The script executes a program that performs dose-functional volume analyses. Written in C#, the script reads the dose grid and correlates it with image data on a voxel-by-voxel basis through API extensions that can access registration transforms. A user interface was designed through WinForms to input parameters and display results. To test the performance of this program, image- and dose-based metrics computed from perfusion SPECT images aligned to the treatment planning CT were generated, validated, and compared. Results: The integration of image analysis information was successfully implemented as a plug-in to a commercial TPS. Perfusion SPECT images were used to validate the calculation and display of image-based metrics as well as dose-intensity metrics and histograms for defined structures on the treatment planning CT. Various biological dose correction models, custom image-based metrics, dose-intensity computations, and dose-intensity histograms were applied to analyze the image-dose profile. Conclusion: It is possible to add image analysis features to commercial TPSs through custom scripting applications. A tool was developed to enable the evaluation of image-intensity-based metrics in the context of functional targeting and avoidance. In addition to providing dose-intensity metrics and histograms that can be easily extracted from a plan database and correlated with outcomes, the system can also be extended to a plug-in optimization system, which can directly use the computed metrics for optimization of post-treatment tumor or normal tissue response models. Supported by NIH - P01 - CA059827.

60 APPLIED LIFE SCIENCES↗

KIVA-hpFE version 1.0.1

KIVA-hpFE is a computer software for solving the physics of multi-species turbulent reactive flow in complex geometries having immersed moving parts. The code is written in Fortran 90/95 and can be used on any computer platform with any popular complier. The code is in 2 versions, a serial version and a parallel version utilizing MPICH2 type Message Passing Interface (MPI or Intel MPI) for solving distributed domains.

Waters, Jiajia↗