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At least 1,567 records · Page 87

Rapid generation of optimal generalized Monkhorst-Pack grids

In this report computational modeling of the properties of crystalline materials has become an increasingly important aspect of materials research, consuming hundreds of millions of CPU-hours at scientific computing centers around the world each year, if not more. A routine operation in such calculations is the evaluation of integrals over the Brillouin zone. We have previously demonstrated that performing such integrals using generalized Monkhorst-Pack k-point grids can roughly double the speed of these calculations relative to the widely-used traditional Monkhorst-Pack grids. However the generation of optimal generalized Monkhorst-Pack grids is not implemented in most software packages due to the computational cost and difficulty of identifying the best grids. To address this problem, we present new algorithms that allow rapid generation of optimal generalized Monkhorst-Pack grids on the fly. We demonstrate that the grids generated by these algorithms are on average significantly more efficient than those generated using existing algorithms across a range of grid densities. For grids that correspond to a real-space supercell with at least 50 Å between lattice points, which is sufficient to converge density functional theory calculations within 1 meV/atom for nearly all materials, our algorithm finds optimized grids in an average of 0.19 s on a single processing core. To facilitate the widespread adoption of this approach, we present new open-source tools including a library designed for integration with third-party software packages.

36 MATERIALS SCIENCE↗

SU-G-BRC-10: Feasibility of a Web-Based Monte Carlo Simulation Tool for Dynamic Electron Arc Radiotherapy (DEAR)

Purpose: DEAR is a radiation therapy technique utilizing synchronized motion of gantry and couch during delivery to optimize dose distribution homogeneity and penumbra for treatment of superficial disease. Dose calculation for DEAR is not yet supported by commercial TPSs. The purpose of this study is to demonstrate the feasibility of using a web-based Monte Carlo (MC) simulation tool (VirtuaLinac) to calculate dose distributions for a DEAR delivery. Methods: MC simulations were run through VirtuaLinac, which is based on the GEANT4 platform. VirtuaLinac utilizes detailed linac head geometry and material models, validated phase space files, and a voxelized phantom. The input was expanded to include an XML file for simulation of varying mechanical axes as a function of MU. A DEAR XML plan was generated and used in the MC simulation and delivered on a TrueBeam in Developer Mode. Radiographic film wrapped on a cylindrical phantom (12.5 cm radius) measured dose at a depth of 1.5 cm and compared to the simulation results. Results: A DEAR plan was simulated using an energy of 6 MeV and a 3×10 cm{sup 2} cut-out in a 15×15 cm{sup 2} applicator for a delivery of a 90° arc. The resulting data were found to provide qualitative and quantitative evidence that the simulation platform could be used as the basis for DEAR dose calculations. The resulting unwrapped 2D dose distributions agreed well in the cross-plane direction along the arc, with field sizes of 18.4 and 18.2 cm and penumbrae of 1.9 and 2.0 cm for measurements and simulations, respectively. Conclusion: Preliminary feasibility of a DEAR delivery using a web-based MC simulation platform has been demonstrated. This tool will benefit treatment planning for DEAR as a benchmark for developing other model based algorithms, allowing efficient optimization of trajectories, and quality assurance of plans without the need for extensive measurements.

60 APPLIED LIFE SCIENCES↗

Robust wind farm layout optimization

Wake interactions in wind farms cause losses in annual energy production (AEP) on the order of 10%. Wind farm designers optimize the layout of the farm to mitigate wake losses, especially in the dominant site-specific wind directions. As wind turbines and wind farms grow in scale, optimization becomes more complex. Offshore wind farms regularly comprise more than 100 wind turbines and are characterized by complex boundaries due to shipping lanes, neighboring wind farms, and other constraints. Layout optimization methods are broadly split between gradient-based and gradient-free approaches. Gradient-based approaches can converge quickly and perform well for smaller, academic problems but are often sensitive to initial conditions and tuning parameters and require expert knowledge to use. On the other hand, gradient-free approaches can be more robust to problem complexities. We present a robust layout optimization approach based on a random search algorithm. The algorithm is intended for those who are not optimization experts and has few tuning parameters that need specification to achieve satisfactory results. Unlike off-the-shelf methods, which use generally available, non-domain-specific optimization routines that accept as inputs an optimization function and constraint definitions, this approach takes advantage of the relative computational costs of the different evaluations by evaluating cheaper computations first (boundary and minimum distance constraints) and running expensive AEP evaluations only if all other checks pass. Moreover, an outer genetic algorithm allows multiple solutions to evolve in parallel, enabling rapid solution development on high-performance computers. We discuss the relative ease of selecting necessary tuning parameters and demonstrate the efficacy of the genetic random search on a complex layout problem consisting of placing 70 turbines in a nonconvex and unconnected boundary region.

17 WIND ENERGY↗

Performance optimization, modeling and analysis of sparse matrix-matrix products on multi-core and many-core processors

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is widely used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. Although many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. In this work, we firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. We examine their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. We build the performance model for hash-table and heap-based algorithms, which supports the recipe. A critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix. Finally, we integrate our implementations into a large-scale protein clustering code named HipMCL, accelerating its SpGEMM kernel by up to 10X and achieving an overall performance boost for the whole HipMCL application by 2.6X.

97 MATHEMATICS AND COMPUTING↗

ML-GA

ML-GA is a software that can be used to expedite design optimization process combining machine learning and genetic algorithm approaches. It employs a machine learning (ML) model (any ML algorithm can be incorporated) to predict the quality (merit) of a design from the input parameters. Then, a stochastic global optimization genetic algorithm (GA) is used, with the machine learning model as the objective function, to optimize the input parameters based on the merit function. ML-GA is scalable to higher computational platforms like supercomputers and clusters enabling optimization to be performed in significantly short time frames (e.g., in a day).

PAL, PINAKI↗

High-Performance Sparse Matrix-Matrix Products on Intel KNL and Multicore Architectures

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is vastly used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. While many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. We firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting multi- and many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. We investigate their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. In conclusion, a critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix.

97 MATHEMATICS AND COMPUTING↗

The Kalai-Smorodinsky solution for many-objective Bayesian optimization

An ongoing aim of research in multiobjective Bayesian optimization is to extend its applicability to a large number of objectives. While coping with a limited budget of evaluations, recovering the set of optimal compromise solutions generally requires numerous observations and is less interpretable since this set tends to grow larger with the number of objectives. We thus propose to focus on a specific solution originating from game theory, the Kalai-Smorodinsky solution, which possesses attractive properties. In particular, it ensures equal marginal gains over all objectives. We further make it insensitive to a monotonic transformation of the objectives by considering the objectives in the copula space. A novel tailored algorithm is proposed to search for the solution, in the form of a Bayesian optimization algorithm: sequential sampling decisions are made based on acquisition functions that derive from an instrumental Gaussian process prior. Our approach is tested on four problems with respectively four, six, eight, and nine objectives. The method is available in the R package GPGame available on CRAN at https://cran.r-project.org/package=GPGame.

Game theory↗

Automatic Detection of Clear-Sky Periods Using Ground and Satellite Based Solar Resource Data

Solar resource availability and variability are important aspects of monitoring performance of photovoltaic installations. For example, recent degradation studies have highlighted the importance of considering cloud cover when calculation degradation rates. With this in mind, we present a method for optimizing clear sky detection algorithms given only modeled clear sky irradiance and ground-measured irradiance values. This method is tested on global horizontal irradiance (GHI) data from ground collectors at six sites across the US and was trained against clear sky classifications determined from satellite data. Thirty models were optimized on each individual site at GHI data frequencies of 1, 5, 10, 15, and 30 minutes. The models had an average F 0.5 score of 0.945 +/- .021 on a holdout test set. In comparison, the un-optimized clear sky detection algorithm produced F 0.5 score that averaged to 0.707 +/- 0.187.

14 SOLAR ENERGY↗

Multi-objective Bayesian active learning for MeV-ultrafast electron diffraction

Ultrafast electron diffraction using MeV energy beams(MeV-UED) has enabled unprecedented scientific opportunities in the study of ultrafast structural dynamics in a variety of gas, liquid and solid state systems. Broad scientific applications usually pose different requirements for electron probe properties. Due to the complex, nonlinear and correlated nature of accelerator systems, electron beam property optimization is a time-taking process and often relies on extensive hand-tuning by experienced human operators. Algorithm based efficient online tuning strategies are highly desired. Here, we demonstrate multi-objective Bayesian active learning for speeding up online beam tuning at the SLAC MeV-UED facility. The multi-objective Bayesian optimization algorithm was used for efficiently searching the parameter space and mapping out the Pareto Fronts which give the trade-offs between key beam properties. Such scheme enables an unprecedented overview of the global behavior of the experimental system and takes a significantly smaller number of measurements compared with traditional methods such as a grid scan. This methodology can be applied in other experimental scenarios that require simultaneously optimizing multiple objectives by explorations in high dimensional, nonlinear and correlated systems.

43 PARTICLE ACCELERATORS↗

Broadband Asymmetric Transmission of Linearly Polarized Mid‐Infrared Light Based on Quasi‐3D Metamaterials

Abstract Metamaterials consisting of subwavelength resonators offer an exciting opportunity for realizing asymmetric transmission (AT) of linearly polarized light. However, to date, only moderate/narrow‐band AT responses have been obtained in metadevices based on stacked planar nanostructures. Here, leveraging a combination of a genetic algorithm (GA) based optimization method and a membrane projection lithography (MPL) fabrication approach, a quasi‐3D metamaterial for broadband AT of linearly polarized mid‐infrared light is demonstrated. Facilitated by the customized GA, an efficient exploration of 3D plasmonic meta‐atoms with broken mirror symmetry in the light propagation direction allows the satisfaction of the rigorous conditions for AT of linearly polarized waves over a broad wavelength range. Confirmed by surface current analysis, the observed AT behavior is attributed to the resonant coupling between the plasmonic nanostructures located on the two orthogonal walls of the MPL cavities. Incorporating an advanced inverse‐design method and a state‐of‐art fabrication technique, the methodology used in the present study provides a promising route for exploiting 3D metamaterials with sophisticated functionalities via effectively exploring the high‐dimensional parametric space offered by true 3D meta‐atoms.

Whiting, Eric B.↗

Geothermal-integrated thermally anisotropic building envelope for energy and peak-demand reduction

Buildings consume large amounts of energy for heating and cooling, while peak electricity demand places significant stress on the power grid. This paper presents a reduced-order co-simulation framework and load-oriented supervisory control strategy for a geothermal-integrated thermally anisotropic building envelope with a ground loop (TABE+GL). In TABE+GL, a hydronic loop embedded in the building envelope is directly coupled with a geothermal ground loop, allowing for bidirectional heat exchange between the envelope, the ground, and the indoor environment. A hybrid co-simulation framework was established by coupling a reduced-order resistor–capacitor (RC) thermal network model with EnergyPlus augmented with GHEDesigner modules. The RC model generated feasible heat flux options under three operating modes, and EnergyPlus predicted sensible loads, energy use, and pump energy demand. At each simulation step, a supervisory control algorithm selected the optimal loop configuration and duty factor that maximizes useful TABE geothermal utilization without exceeding the predicted sensible load, thereby avoiding overheating or cooling. Case studies were conducted for Los Angeles, California, Charleston, South Carolina, and Denver, Colorado. Results showed that the proposed framework reduced HVAC electricity consumption by 43%–67%, natural gas use for space heating by 11%–38%, and peak electricity demand by 43%–88%. These results highlight the potential of combining reduced-order envelope modeling, direct geothermal coupling, and load-oriented supervisory control to improve whole building energy performance and reduce peak demand across diverse weather conditions.

Howard, Daniel [Southern Adventist University]↗

MADLens, a python package for fast and differentiable non-Gaussian lensing simulations

Here, we present MADLens a python package for producing non-Gaussian lensing convergence maps at arbitrary source redshifts with unprecedented precision. MADLens is designed to achieve high accuracy while keeping computational costs as low as possible. A MADLens simulation with only particles produces convergence maps whose power agrees with theoretical lensing power spectra up to within the accuracy limits of HaloFit. This is made possible by a combination of a highly parallelizable particle-mesh algorithm, a sub-evolution scheme in the lensing projection, and a machine-learning inspired sharpening step. Further, MADLens is fully differentiable with respect to the initial conditions of the underlying particle-mesh simulations and a number of cosmological parameters. These properties allow MADLens to be used as a forward model in Bayesian inference algorithms that require optimization or derivative-aided sampling. Another use case for MADLens is the production of large, high resolution simulation sets as they are required for training novel deep-learning-based lensing analysis tools. We make the MADLens package publicly available under a Creative Commons License

79 ASTRONOMY AND ASTROPHYSICS↗

Graph-based modeling and simulation of complex systems

We present graph-based modeling abstractions to represent cyber-physical dependencies arising in complex systems. Specifically, we propose an algebraic graph abstraction to capture physical connectivity in complex optimization models and a computing graph abstraction to capture communication connectivity in computing architectures. The proposed abstractions are scalable and are used as the backbone of a Julia-based software package that we call Plasmo.j1. Here, we show how the algebraic graph abstraction facilitates the implementation, analysis, and decomposition of optimization problems and we show how the computing graph abstraction facilitates the implementation of optimization and control algorithms and their simulation in virtual environments that involve distributed, centralized, and hierarchical computing architectures.

97 MATHEMATICS AND COMPUTING↗

Quantifying uncertainty for deep learning based forecasting and flow-reconstruction using neural architecture search ensembles

Classical problems in computational physics such as data-driven forecasting and signal reconstruction from sparse sensors have recently seen an explosion in deep neural network (DNN) based algorithmic approaches. However, most DNN models do not provide uncertainty estimates, which are crucial for establishing the trustworthiness of these techniques in downstream decision making tasks and scenarios. In recent years, ensemble-based methods have achieved significant success for the uncertainty quantification in DNNs on a number of benchmark problems. However, their performance on real-world applications remains under-explored. In this work, we present an automated approach to DNN discovery and demonstrate how this may also be utilized for ensemble-based uncertainty quantification. Specifically, we propose the use of a scalable neural and hyperparameter architecture search for discovering an ensemble of DNN models for complex dynamical systems. We highlight how the proposed method not only discovers high-performing neural network ensembles for our tasks, but also quantifies uncertainty seamlessly. This is achieved by using genetic algorithms and Bayesian optimization for sampling the search space of neural network architectures and hyperparameters. Subsequently, a model selection approach is used to identify candidate models for an ensemble set construction. Afterwards, a variance decomposition approach is used to estimate the uncertainty of the predictions from the ensemble. We demonstrate the feasibility of this framework for two tasks — forecasting from historical data and flow reconstruction from sparse sensors for the sea-surface temperature. In conclusion, we demonstrate superior performance from the ensemble in contrast with individual high-performing models and other benchmarks.

Deep ensembles↗

Excitonic Energy Landscape of the Y16F Mutant of the Chlorobium tepidum Fenna–Matthews–Olson (FMO) Complex: High Resolution Spectroscopic and Modeling Studies

We report high-resolution (low-temperature) absorption, emission, and nonresonant/resonant hole-burned (HB) spectra and results of excitonic calculations using a non-Markovian reduced density matrix theory (with an improved algorithm for parameter optimization in heterogeneous samples) obtained for the Y16F mutant of the Fenna–Matthews–Olson (FMO) trimer from the green sulfur bacterium Chlorobium tepidum. We show that the Y16F mutant is a mixture of FMO complexes with three independent low-energy traps (located near 817, 821, and 826 nm), in agreement with measured composite emission and HB spectra. Two of these traps belong to mutated FMO subpopulations characterized by significantly modified low-energy excitonic states. Hamiltonians for the two major subpopulations (Sub 821 and Sub 817 ) provide new insight into extensive changes induced by the single-point mutation in the vicinity of BChl 3 (where tyrosine Y16 was replaced with phenylalanine F16). The average decay time(s) from the higher exciton state(s) in the Y16F mutant depends on frequency and occurs on a picosecond time scale.

59 BASIC BIOLOGICAL SCIENCES↗

Revealing the Crystalline Architecture of Semicrystalline Ion Exchange Membranes for the Design of Conductive and Durable Alkaline Anion Exchange Membranes

Alkaline anion exchange membrane (AAEM) fuel cells offer a cost-effective alternative to proton exchange membrane (PEM) fuel cells by eliminating the need for expensive precious metal catalysts. In both PEMs and AAEMs, semicrystalline polymers are a common choice, as the crystalline domains can act as mechanical reinforcements that limit swelling and promote mechanical durability in the material. However, spatially resolved characterization of crystalline organization in ion exchange membranes beyond ensemble-averaged X-ray scattering is underrepresented, likely in part due to ionization damage limitations in soft materials. Here, in this study, we resolve the nanometer-size crystallites in semicrystalline ion exchange membranes by applying cryogenic four-dimensional scanning transmission electron microscopy (cryo-4D-STEM) along with data-processing algorithms designed to optimize signals at a low dose to minimize radiation damage. We investigate the effects of synthesis components, including molecular weight and thermal treatment, on a model system of AAEMs in comparison to Nafion, the most commonly used and commercially successful PEM today. We find that excess water uptake in polymer membranes, a property directly associated with weak mechanical durability and with possible negative impacts on ion conductivity, can be reduced by over 30% by varying the polymer's crystalline morphology through changes in synthesis parameters such as molecular weight and thermal history. Our results indicate that this improvement is correlated with smaller crystalline domains with a more homogeneous distribution. More broadly, these results demonstrate how the crystalline architecture of polymer membranes can be tuned through their chemistry and thermal treatment in order to improve their conductivity and durability for commercial fuel cell performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A compact tunable quadrupole lens for brighter and sharper ultra-fast electron diffraction imaging

In this article, we report our proof-of-principle design and experimental commissioning of a broadly tunable and low-cost transverse focusing lens system for MeV-energy electron beams. The lens system based on electromagnetic (EM) quadrupoles has been built as a part of the existing instrument for ultra-fast electron diffraction (UED) experiments at the Accelerator Test Facility II (ATF-II) at Brookhaven National Laboratory (BNL). We experimentally demonstrated the independent control of the size and divergence of the beam with the charge ranging from 1 to 13 pC. The charge density and divergence of the beam at the sample are the most important factors determining the quality of the Bragg-diffraction image (BDI). By applying the Robust Conjugate Directional Search (RCDS) algorithm for online optimization of the quadrupoles, the transverse beam size can be kept constant down to 75 µm from 1 to 13 pC. The charge density is nearly two orders of magnitude higher than the previously achieved value using a conventional solenoid. Using the BDI method we were able to extract the divergence of the beam in real-time and apply it to the emittance measurement for the first time. Our results agree well with simulations and with the traditional quadrupole scan method. The real-time divergence measurement opens the possibility of online optimization of the beam divergence (< 0.2 mrad) at the sample with the increased beam charge. This optimization is crucial for the future development of single-shot ultra-fast electron microscope (UEM). Finally, we demonstrated BDI with significant improvement, up to 3 times higher peak intensity and 2 times sharper Bragg-diffraction peaks at 13 pC. The charge is now limited by the laser power and increasing charge may improve the quality of BDI further. The capability we demonstrated here provides us with opportunities for new sciences using near-parallel, bright and ultrafast electron beams for single-shot imaging, to directly visualize the dynamics of defects and nanostructured materials, or even record molecular movie, which are impossible using present electron-beam technologies.

43 PARTICLE ACCELERATORS↗

Anisotropic colloidal interactions & assembly in AC electric fields

In this work, we match experimental and simulated configurations of anisotropic epoxy colloidal particles in high frequency AC electric fields by identifying analytical potentials for dipole-field and dipole-dipole interactions. We report an inverse Monte Carlo simulation algorithm to determine optimal fits of analytical potentials by matching simulated and experimental distribution functions for non-uniform liquid, liquid crystal, and crystal microstructures in varying amplitude electric fields. Two potentials that include accurate particle volume and dimensions along with a concentration dependent prefactor quantitatively capture experimental observations. At low concentrations, an effective ellipsoidal point dipole potential works well, whereas a novel stretched point dipole potential is found to be suitable at all concentrations, field amplitudes, and degrees of ordering. The simplicity, accuracy, and adjustability of the stretched point dipole potential suggest it can be applied to model field mediated microstructures and assembly of systematically varying anisotropic particle shapes.

42 ENGINEERING↗