Explicit synchronous partitioned algorithms for interface problems based on Lagrange multipliers
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97 MATHEMATICS AND COMPUTING↗
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The VTK-m User's Guide (V. 2.2)
High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures. VTK-m supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. VTK-m also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although VTK-m provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction.
97 MATHEMATICS AND COMPUTING↗
Analytical Modeling of Triple-Metal Hetero-Dielectric DG SON TFET
In this paper, a 2-D analytical model of triple-metal hetero-dielectric DG TFET is presented by combining the concepts of triple material gate engineering and hetero-dielectric engineering. Three metals with different work functions are used as both front- and back gate electrodes to modulate the barrier at source/channel and channel/drain interface. In addition to this, front gate dielectric consists of high-K HfO{sub 2} at source end and low-K SiO{sub 2} at drain side, whereas back gate dielectric is replaced by air to further improve the ON current of the device. Surface potential and electric field of the proposed device are formulated solving 2-D Poisson’s equation and Young’s approximation. Based on this electric field expression, tunneling current is obtained by using Kane’s model. Several device parameters are varied to examine the behavior of the proposed device. The analytical model is validated with TCAD simulation results for proving the accuracy of our proposed model.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers
The program VinaMPI has been developed to enable massively large virtual drug screens on leadership-class computing resources, using a large number of cores to decrease the time-to-completion of the screen. VinaMPI is a massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina, and is used to distribute tasks while multithreading is used to speed-up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high-throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time. The code is freely available and downloadable. Lastly, the instructions for downloading and using the code are provided in the Supporting Information.
97 MATHEMATICS AND COMPUTING↗
The thermodynamics of proton hydration and the electrochemical surface potential of water
The free energy change for transferring a single ion across the water liquid/vapor interface includes an electrochemical surface potential contribution. Since this potential is not directly accessible to thermodynamic measurement, several extra-thermodynamic approaches have been employed to infer its sign and magnitude, with a resulting wide spread of values. Here, we examine further the thermodynamics of proton hydration and the electrochemical surface potential of water along three directions: (1) a basic relation of interfacial electrostatics and experimental results on ion distributions near a water/organic interface are employed to infer a solvent contribution to the electrochemical surface potential, (2) a re-analysis is performed of the existing bulk and cluster ion hydration data, and (3) extensive computational modeling is conducted to examine the size dependence of hydration enthalpy differences for the NaF ion pair between the small cluster and the converged bulk limits. The computational studies include classical polarizable models and high-level quantum chemical methods. The new theoretical analysis of existing experimental data and the combined classical/quantum modeling lead to results consistent with our previously derived proton hydration quantities.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Applying uncertainty quantification to multiphase flow computational fluid dynamics
Multiphase computational fluid dynamics plays a major role in design and optimization of fossil fuel based reactors. There is a growing interest in accounting for the influence of uncertainties associated with physical systems to increase the reliability of computational simulation based engineering analysis. The U.S. Department of Energy's National Energy Technology Laboratory (NETL) has recently undertaken an initiative to characterize uncertainties associated with computer simulation of reacting multiphase flows encountered in energy producing systems such as a coal gasifier. The current work presents the preliminary results in applying non-intrusive parametric uncertainty quantification and propagation techniques with NETL's open-source multiphase computational fluid dynamics software MFIX. For this purpose an open-source uncertainty quantification toolkit, PSUADE developed at the Lawrence Livermore National Laboratory (LLNL) has been interfaced with MFIX software. In this study, the sources of uncertainty associated with numerical approximation and model form have been neglected, and only the model input parametric uncertainty with forward propagation has been investigated by constructing a surrogate model based on data-fitted response surface for a multiphase flow demonstration problem. Monte Carlo simulation was employed for forward propagation of the aleatory type input uncertainties. Several insights gained based on the outcome of these simulations are presented such as how inadequate characterization of uncertainties can affect the reliability of the prediction results. Also a global sensitivity study using Sobol' indices was performed to better understand the contribution of input parameters to the variability observed in response variable.
42 ENGINEERING↗
Reactive Flows in Porous Media: Challenges in Theoretical and Numerical Methods
We review theoretical and computational research, primarily from the past 10 years, addressing the flow of reactive fluids in porous media. The focus is on systems where chemical reactions at the solid–fluid interface cause dissolution of the surrounding porous matrix, creating nonlinear feedback mechanisms that can often lead to greatly enhanced permeability. Here, we discuss insights into the evolution of geological forms that can be inferred from these feedback mechanisms, as well as some geotechnical applications such as enhanced oil recovery, hydraulic fracturing, and carbon sequestration. Until recently, most practical applications of reactive transport have been based on Darcy-scale modeling, where averaged equations for the flow and reactant transport are solved. We summarize the successes and limitations of volume averaging, which leads to Darcy-scale equations, as an introduction to pore-scale modeling. Pore-scale modeling is computationally intensive but offers new insights as well as tests of averaging theories and pore-network models. We include recent research devoted to validation of pore-scale simulations, particularly the use of visual observations from microfluidic experiments.
wormhole formation↗
V&V for turbulent mixing in the intermediate asymptotic regime
Turbulent fluid flow interacts nonlinearly with a number of processes, including reactive flow (chemistry), radiation, and the transport of particles embedded in the flow. Subgrid scale modeling of these nonlinear processes is a major challenge to computational science. To this end, turbulent mixing of dissimilar fluids is a driver. Here we study validation issues for a class of turbulent mixing simulations. In previous work, we have obtained agreement between simulation and experiment. The present paper addresses a remaining issue, the role of meniscus related boundary effects for immiscible fluids in the validation process. Validation and even verification has been controversial for turbulent mixing flows, as commonly used numerical models are diffusive and the resulting numerical diffusion modifies the parameters of the problem and its solution. Additionally, numerical diffusion of concentration and temperature is well documented in the scientific literature for Eulerian simulations. Lagrangian simulations, which might appear to avoid this problem, are subject to mesh tangling, ensuing regridding and use of Arbitrary Lagrangian Eulerian codes to substitute for a pure Lagrangian algorithm. In practice, Lagrangian methods are potentially subject to the same numerical diffusion issues when used to study complex interface instabilities.
97 MATHEMATICS AND COMPUTING↗
The Influence of Grain Boundaries on Radiation-Induced Point Defect Production in Materials: A Review of Atomistic Studies
Radiation-induced defects cause severe degradation of materials properties during irradiation that can ultimately cause the material to fail. Consequences of these defects include swelling, embrittlement, and undesirable phase transformations. Nanocrystalline materials, which contain a high density of grain boundaries, have demonstrated enhanced radiation tolerance compared to large grain counterparts under certain conditions. This is because, as has long been recognized, grain boundaries can serve as defect sinks for absorbing and annihilating radiation-induced defects. Increasingly, researchers have examined how grain boundaries influence the direct production of defects during collision cascade, the origin of the radiation-induced defects. In this review article, we analyze the computational studies in this area that have been performed during the past two decades. These studies examine defect production near grain boundaries in metallic, ionic, and covalent systems. It is found that, in most systems, grain boundaries absorb more interstitials than vacancies during the defect production stage. While this is generically true of most boundaries, the detailed interaction between defects and grain boundaries does depend on boundary atomic structure, the stress state near the boundary, cascade-boundary separation, and materials properties. Furthermore, the defect distribution near boundaries is qualitatively different from that in single crystals, with the former often exhibiting larger vacancy clusters and smaller interstitial clusters than the latter. Finally, grain boundaries that are damaged after cascades have occurred exhibit different interaction behavior with defects than their pristine counterparts. Together, these atomistic simulation results provide useful insight for both developing higher-level modeling of defect evolution at long timescales and how interfaces influence radiation damage evolution.
36 MATERIALS SCIENCE↗
Toward Higher Voltage Solid-State Batteries by Metastability and Kinetic Stability Design
The energy density of battery systems is limited largely by the electrochemical window of the electrolyte. Here, the combined thermodynamic and kinetic effects of mechanically induced metastability are shown to greatly widen the operational voltage window of solid-state batteries based on ceramic-sulfide electrolytes. Solid electrolyte voltage stability up to 10 V is achieved with minimal degradation, far beyond the capability of organic liquid electrolytes. Furthermore, combined experiment, ab initio computation, and theoretical modeling identify the nature of mechanically constrained Li 10 GeP 2 S 12 decomposition both within the bulk and at interfaces with cathode materials at very high voltages. Previously unclear kinetic processes are identified that, when properly implemented, can potentially allow solid-state full cells with remarkably high operational voltages.
25 ENERGY STORAGE↗
Modeling deformation and failure in AlSi-polyester abradable sealcoating material using microstructure-based finite element simulation
A plasma-sprayed aluminum-silicon (AlSi)/polyester coating is applied in modern gas turbine engines as an abradable sealcoating to maintain tight clearances between the rotating blades and the static casing. While running the engine, the rotating blades “rub” with the abradable coating, which results in extreme strain rate (up to 10 6 ) dynamics and a high-temperature environment. Due to the difficulty of collecting direct measurements, predictive computational models are important for analyzing the deformation and failure of the abradable material, to help meet the design target of avoiding damage to the blade tip and maintaining high fuel efficiency. In this research, a microstructure-based finite element (FE) computational model was developed to capture the complex mechanical behavior of the AlSi/polyester microstructure. The model is based on a virtual representative-volume-element (RVE) of a metal-polymer microstructure, reconstructed from x-ray computed tomography. It models the plastic deformation of, and damage to, each AlSi and polyester constituents, as well as the failure at their interface. The model was calibrated and validated with uniaxial tension and compression experiments, conducted at two temperatures (298 K and 533 K) at an applied strain rate of 10 3 - 10 4 s -1 . The material exhibited strongly asymmetric tension-compression behavior and a sensitivity to temperature, which was well captured by the model. The model was further applied to investigate changes in mechanical behavior due to variations in constituents’ volume fractions, which provides guidance to the microstructural design of AlSi/polyester abradable materials. The model is expected to facilitate the development of improved abradable materials by bypassing the conventional trial-and-error approach and extensive testing requirements.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Developing A Large Time Step, Robust, and Low Communication Multi-Moment PDE Integration Scheme for Exascale Applications
The Boundary Averaged Multi-moment Constrained finite-Volume (BA-MCV) method is de- rived, explained, and evaluated for 1-D transport to assess accuracy, maximum stable time step (MSTS), oscillations for discontinuous data, and parallel communication burden. The BA-MCV scheme is altered from the original MCV scheme to compute the updates of point wise cell boundary derivatives entirely locally. Then it is altered such that boundary moments are replaced with the interface upwind value. The scheme is stable at a maximum stable CFL (MSCFL) value of one no matter how high-order the scheme is, giving significantly larger time steps than Galerkin methods, for which the MSCFL decreases nearly quadratically with in- creasing order. The BA-MCV method is compared against a SE method at varying order, both using the ADER-DT time discretization. BA-MCV error for a sine wave was comparable to the same order of accuracy for a SE method. The resulting large time step, multi-moment, low communication scheme is of great interest for exascale architectures.
Norman, Matthew R.↗
Condensed Phase Water Molecular Multipole Moments from Deep Neural Network Models Trained on Ab Initio Simulation Data
Ionic solvation phenomena in liquids involve intense interactions in the inner solvation shell. For interactions beyond the first shell, the ion–solvent interaction energies result from the sum of many smaller-magnitude contributions that can still include polarization effects. Deep neural network (DNN) methods have recently found wide application in developing efficient molecular models that maintain near-quantum accuracy. In this work, we extend the DeePMD-kit code to produce accurate molecular multipole moments in the bulk and near interfaces. The new method is validated by comparing the DNN moments with those generated by ab initio simulations. The moments are used to compute the electrostatic potential at the center of a molecular-sized hydrophobic cavity in water. The results show that the fields produced by the DNN models are in quantitative agreement with the AIMD-derived values. These efficient methods will open the door to more accurate solvation models for large solutes such as proteins.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Edge-Enhanced Oxygen Evolution Reactivity at Ultrathin, Au-Supported Fe 2 O 3 Electrocatalysts
Transition metal oxides have gained attention as promising oxygen evolution reaction (OER) electrocatalysts in alkaline electrolytes, but heterogeneities in typical catalyst samples often obscure key structure–property relationships that are essential for developing higher performance materials. Here, we have combined ultrahigh vacuum surface science techniques, electrochemical measurements, and density functional theory (DFT) to quantify structure-dependent OER activity in a series of well-defined electrocatalysts. We describe a direct correlation between the population of Fe edge-site atoms and the OER activity of ultrathin Fe 2 O 3 nanostructures (~0.5 nm apparent height) grown on Au(111) substrates. Hydroxylated Fe atoms residing at edge-sites along the catalyst/support interface were spectroscopically identified as key reaction centers, and these Fe edge-site atoms were estimated to produce OER turnover frequencies approximately 150 times higher than that of Fe atoms on the catalyst surface at an applied potential of 1.8 V vs the reversible hydrogen electrode. Impressively, ultrathin Fe 2 O 3 /Au nanostructures with a high density of catalytically active Fe edge-site atoms outperformed an ultrathin IrOx/Au catalyst at moderate overpotentials. DFT calculations revealed more favorable OER at edge sites along the Fe 2 O 3 /Au interface, with lower predicted overpotentials due to beneficial modification of intermediate binding. Our results demonstrate how a combination of surface science, electrochemistry, and computational modeling can be used to identify key structure–property relationships in a well-defined electrocatalytic system.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Combined Global and Local Approach to Elucidate Spatial Organization of the Mycobacterial ParB-parS Partition Assembly
Combining diverse sets of data at global (size, shape) and local (residue) scales is an emerging trend for elucidating the organization and function of the cellular assemblies. We used such a strategy, combining data from X-ray and neutron scattering with H/D-contrast variation and X-ray footprinting with mass spectrometry, to elucidate the spatial organization of the ParB-parS assembly from Mycobacterium tuberculosis. The ParB-parS participates in plasmid and chromosome segregation and condensation in predivisional bacterial cells. ParB polymerizes around the parS centromere(s) to form a higher-order assembly that serves to recruit cyto-skeletal ParA ATPases and SMC proteins for chromosome segregation. A hybrid model of the ParB-parS was built by combining and correlating computational models with experiment-derived information about size, shape, position of the symmetry axis within the shape, internal topology, DNA-protein interface, exposed surface patches, and prior knowledge. This first view of the ParB-parS leads us to propose how ParB spread on the chromosome to form a larger assembly.
59 BASIC BIOLOGICAL SCIENCES↗
Experiences with user-centered design for the tigres workflow API
Scientific data volumes have been growing exponentially. This has resulted in the need for new tools that enable users to operate on and analyze data. Cyber infrastructure tools, including workflow tools, that have been developed in the last few years has often fallen short if user needs and suffered from lack of wider adoption. User-centered Design (UCD) process has been used as an effective approach to develop usable software with high adoption rates. However, UCD has largely been applied for user-interfaces and there has been limited work in applying UCD to application program interfaces and cyber infrastructure tools. We use an adapted version of UCD that we refer to as Scientist-Centered Design (SCD) to engage with users in the design and development of Tigres, a workflow application programming interface. Tigres provides a simple set of programming templates (e.g., sequence, parallel, split, merge) that can be can used to compose and execute computational and data transformation pipelines. In this paper, we describe Tigres and discuss our experiences with the use of UCD for the initial development of Tigres. Our experience-to-date is that the UCD process not only resulted in better requirements gathering but also heavily influenced the architecture design and implementation details. User engagement during the development of tools such as Tigres is critical to ensure usability and increase adoption.
Ramakrishnan, L↗
A New Method for the Solution of Group Diffusion Equations
Here, the diffusion equations associated with the multigroup, multiregion problem are solved by expansions in eigenfunctions which are solutions of the Helmholtz equation. A determinantal criticality equation is exhibited in which the order of the determinant is independent of the number of groups and which can be solved without recourse to complicated computational procedures. Moreover, the need to fulfill explicitly the requirements that the flux and current associated with each neutron group be continuous across interfaces is eliminated.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
A Look At Topics and Topic Clusters for DOE Laboratories, 1996 - 2021 [Slides]
Beginning in 2018, Elsevier through its Scopus database introduced topics to further refine its classification of publications: Previous classification schemes used concepts such as subject areas, e.g., physics and astronomy, chemistry, computer science, etc.; Topics, in contrast, are much more granular. There are over 96,000 and their titles/contents are very specific, e.g., “Multilayers; Interfaces (materials); Individual layer." Elsevier topic clusters or Clarivate citation topics represent good approaches to examining an institution’s scientific productivity areas. These approaches have the granularity that is not present in the previous categorization approaches used by these databases. The Elsevier topic clusters for the DOE Laboratories do not appear to vary that much over the 1996 – 2021 period. In some cases (ANL, LBNL, LANL, ORNL, and PNNL), there were over 1000 topic clusters at these Laboratories, but a consistent set formed the core of the publication activity. Diversity is viewed as a desirable property of a research portfolio. Examining the balance component of the DOE laboratories, the spread is uneven or not diverse. This may be due to the missions of these laboratories. The balance of a single university was unequal too.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
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