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At least 235 records · Page 13

Structure optimization with stochastic density functional theory

Linear-scaling techniques for Kohn–Sham density functional theory are essential to describe the ground state properties of extended systems. Still, these techniques often rely on the localization of the density matrix or accurate embedding approaches, limiting their applicability. In contrast, stochastic density functional theory (sDFT) achieves linear- and sub-linear scaling by statistically sampling the ground state density without relying on embedding or imposing localization. In return, ground state observables, such as the forces on the nuclei, fluctuate in sDFT, making optimizing the nuclear structure a highly non-trivial problem. In this work, we combine the most recent noise-reduction schemes for sDFT with stochastic optimization algorithms to perform structure optimization within sDFT. We compare the performance of the stochastic gradient descent approach and its variations (stochastic gradient descent with momentum) with stochastic optimization techniques that rely on the Hessian, such as the stochastic Broyden–Fletcher–Goldfarb–Shanno algorithm. In conclusion, we further provide a detailed assessment of the computational efficiency and its dependence on the optimization parameters of each method for determining the ground state structure of bulk silicon with varying supercell dimensions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-solution nature of topology optimization and its application in design for additive manufacturing

The purpose of this paper is to introduce the multi-solution nature of topology optimization (TO) as a design tool for additive manufacturing (AM). The sensitivity of topologically optimized parts and manufacturing constraints to the initial starting point of the optimization process leading to structures with equivalent performance is explored. A modified bi-directional evolutionary structural optimization (BESO) code was used as the numerical approach to optimize a cantilever beam problem and reduce the mass by 50 per cent. Several optimized structures with relatively equivalent mechanical performance were generated by changing the initial starting point of the TO algorithm. These optimized structures were manufactured using fused deposition modeling (FDM). The equivalence of strain distribution in FDM parts was tested with the digital image correlation (DIC) technique and compared with that from the modified BESO code.The results confirm that TO could lead to a wide variety of non-unique solutions based on loading and manufacturability constraints. The modified BESO code was able to reduce the support structure needed to build the simple two-dimensional cantilever beam by 15 per cent while keeping the mechanical performance at the same level. Finally, the originality of this paper lies in introduction and application of the multi-solution nature of TO for AM as a design tool for optimizing structures with minimized features in the overhang condition and the need for support structures.

36 MATERIALS SCIENCE↗

LigninGraphs: lignin structure determination with multiscale graph modeling

Lignin is an aromatic biopolymer found in ubiquitous sources of woody biomass. Designing and optimizing lignin valorization processes requires a fundamental understanding of lignin structures. Experimental characterization techniques, such as 2D-heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra, could elucidate the global properties of the polymer molecules. Computer models could extend the resolution of experiments by representing structures at the molecular and atomistic scales. We introduce a graph-based multiscale modeling framework for lignin structure generation and visualization. The framework employs accelerated rejection-free polymerization and hierarchical Metropolis Monte Carlo optimization algorithms. We obtain structure libraries for various lignin feedstocks based on literature and new experimental NMR data for poplar wood, pinewood, and herbaceous lignin. The framework could guide researchers towards feasible lignin structures, efficient space exploration, and future kinetics modeling. Its software implementation in Python, LigninGraphs, is open-source and available on GitHub.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-GPU immersed boundary method hemodynamics simulations

Large-scale simulations of blood flow that resolve the 3D deformation of each comprising cell are increasingly popular owing to algorithmic developments in conjunction with advances in compute capability. Among different approaches for modeling cell-resolved hemodynamics, fluid structure interaction (FSI) algorithms based on the immersed boundary method are frequently employed for coupling separate solvers for the background fluid and the cells within one framework. GPUs can accelerate these simulations; however, both current pre-exascale and future exascale CPU-GPU heterogeneous systems face communication challenges critical to performance and scalability. In this paper, we describe, to our knowledge, the largest distributed GPU-accelerated FSI simulations of high hematocrit cell-resolved flows with over 17 million red blood cells. We compare scaling on a fat node system with six GPUs per node and on a system with a single GPU per node. Through comparison between the CPU- and GPU-based implementations, we identify the costs of data movement in multiscale multi-grid FSI simulations on heterogeneous systems and show it to be the greatest performance bottleneck on the GPU.

97 MATHEMATICS AND COMPUTING↗

Review of structure representation and reconstruction on mesoscale and microscale

Structure representation and reconstruction on mesoscale and microscale is critical in material design, advanced manufacturing and multiscale modeling. Microstructure reconstruction has been applied in different areas of materials science and technology, structural materials, energy materials, geology, hydrology, etc. This review summarizes the microstructure descriptors and formulations used to represent and algorithms to reconstruct structures at microscale and mesoscale. In the stochastic methods using correlation function, different optimization approaches have been adapted for objective function minimization. A variety of reconstruction approaches are compared in efficiency and accuracy.

Microstructure reconstruction, inverse design, mic↗

Multithreaded sparse matrix-matrix multiplication for many-core and GPU architectures

Sparse matrix-matrix multiplication is a key kernel that has applications in several domains such as scientific computing and graph analysis. Several algorithms have been studied in the past for this foundational kernel. In this work, we develop parallel algorithms for sparse matrix-matrix multiplication with a focus on performance portability across different high performance computing architectures. The performance of these algorithms depend on the data structures used in them. We compare different types of accumulators in these algorithms and demonstrate the performance difference between these data structures. Furthermore, we develop a meta-algorithm, kkSpGEMM, to choose the right algorithm and data structure based on the characteristics of the problem. We show performance comparisons on three architectures and demonstrate the need for the community to develop two phase sparse matrix-matrix multiplication implementations for efficient reuse of the data structures involved.

97 MATHEMATICS AND COMPUTING↗

Multi-threaded Sparse Matrix Sparse Matrix Multiplication for Many-Core and GPU Architectures.

Sparse Matrix-Matrix multiplication is a key kernel that has applications in several domains such as scientific computing and graph analysis. Several algorithms have been studied in the past for this foundational kernel. In this paper, we develop parallel algorithms for sparse matrix- matrix multiplication with a focus on performance portability across different high performance computing architectures. The performance of these algorithms depend on the data structures used in them. We compare different types of accumulators in these algorithms and demonstrate the performance difference between these data structures. Furthermore, we develop a meta-algorithm, kkSpGEMM, to choose the right algorithm and data structure based on the characteristics of the problem. We show performance comparisons on three architectures and demonstrate the need for the community to develop two phase sparse matrix-matrix multiplication implementations for efficient reuse of the data structures involved.

97 MATHEMATICS AND COMPUTING↗

Crystallographic variant mapping using precession electron diffraction data

In this work, we developed three methods to map crystallographic variants of samples at the nanoscale by analyzing precession electron diffraction data using a high-temperature shape memory alloy and a VO2 thin film on sapphire as the model systems. The three methods are (I) a user-selecting-reference pattern approach, (II) an algorithm-selecting-reference-pattern approach, and (III) a k-means approach. In the first two approaches, Euclidean distance, Cosine, and Structural Similarity (SSIM) algorithms were assessed for the diffraction pattern similarity quantification. We demonstrated that the Euclidean distance and SSIM methods outperform the Cosine algorithm. We further revealed that the random noise in the diffraction data can dramatically affect similarity quantification. Denoising processes could improve the crystallographic mapping quality. With the three methods mentioned above, we were able to map the crystallographic variants in different materials systems, thus enabling fast variant number quantification and clear variant distribution visualization. The advantages and disadvantages of each approach are also discussed. We expect these methods to benefit researchers who work on martensitic materials, in which the variant information is critical to understand their properties and functionalities.

Crystallographic variant mapping↗

Hybridization of IMC and PID control structures based on filtered GPC using genetic algorithm

Classical and advanced hybridization methods are employed in the control literature to calibrate the tuning parameters of internal model control (IMC) and proportional-integral-derivative (PID) controllers. This paper presents an alternative tuning design for the generalized predictive controller (GPC) that is based on both the positional process model and cost function. The proposed method involves the selection of an integral polynomial weighting filter for reference and output signals to deal with reference tracking, disturbance rejection, model-plant mismatch (MPM), minimum control energy and closed-loop robustness. The filter positional GPC (FP-GPC) obtained is transformed into a two-degree-of-freedom polynomial filtered RST structure and then into filtered internal model control (F-IMC) and PID controllers. Also, a multi-objective optimization based on genetic algorithm is applied to tune the filter parameters. Numerical and experimental essays show the effectiveness of the proposed control methodology.

97 MATHEMATICS AND COMPUTING↗

Observation of η-Al41Sm5 reveals motif-aware structural evolution in Al-Sm alloys

Using an effective genetic algorithm, we uncover the structure of a metastable Al41Sm5 phase that supplements its family sharing similar short-range orders. The phase evolves upon heating an amorphous Al-9.7at.%Sm ribbon, produced by melt-spinning. The dynamical phase selection is discussed with respect to the structural connections between the short-range packing motifs in the amorphous precursor and those observed in the selected phases. This dataset includes information such as the crystal structure of Al41Sm5, the short-range packing motifs, experimental and calculated XRD, formation energy of stable and meta-stable phases in the Al-Sm system.

Ye, Zhou↗

A fourth-order adaptive mesh refinement algorithm for the multicomponent, reacting compressible Navier–Stokes equations

In this study, we present a fourth-order in space and time block-structured adaptive mesh refinement algorithm for the compressible multicomponent reacting Navier–Stokes equations. The algorithm uses a finite-volume approach that incorporates a fourth-order discretisation of the convective terms. The time-stepping algorithm is based on a multi-level spectral deferred corrections method that enables explicit treatment of advection and diffusion coupled with an implicit treatment of reactions. The temporal scheme is embedded in a block-structured adaptive mesh refinement algorithm that includes subcycling in time with spectral deferred correction sweeps applied on levels. Here we present the details of the multi-level scheme paying particular attention to the treatment of coarse–fine boundaries required to maintain fourth-order accuracy in time. We then demonstrate the convergence properties of the algorithm on several test cases including both non-reacting and reacting flows. Finally we present simulations of a vitiated dimethyl ether jet in 2D and a turbulent hydrogen jet in 3D, both with detailed kinetics and transport.

97 MATHEMATICS AND COMPUTING↗

Development of a deep machine learning interatomic potential for metalloid-containing Pd-Si compounds

Interatomic potentials based on neural-network machine learning (ML) approach to address the long-standing challenge of accuracy versus efficiency in molecular-dynamics simulations have recently attracted a great deal of interest. In this work, utilizing Pd-Si system as a prototype, we extend the development of neural-network ML potentials to compounds exhibiting various types of bonding characteristics. The ML potential is trained by fitting to the energies and forces of both liquid and crystal structures first-principles calculations based on density-functional theory (DFT). We show that the generated ML potential captures the structural features and motifs in Pd 82 Si 18 and Pd 75 Si 25 liquids more accurately than the existing interatomic potential based on embedded-atom method (EAM). The ML potential also describes the solid-liquid interface of these systems very well. Moreover, while the existing EAM potential fails to describe the relative energies of various crystalline structures and predict wrong ground-state structures at Pd 3 Si and Pd 9 Si 2 composition, the developed ML potential predicts correctly the ground-state structures from genetic algorithm search. The efficient ML potential with DFT accuracy from our study will provide a promising scheme for accurate atomistic simulations of structures and dynamics of complex Pd-Si system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

ECP Milestone Report WBS 2.3.4.13 ECP/VTK-m FY18Q1 [MS-18/01-03] Multiblock / Gradients / Release STDA05-5.

The FY18Q1 milestone of the ECP/VTK-m project includes the implementation of a multiblock data set, the completion of a gradients filtering operation, and the release of version 1.1 of the VTK-m software. With the completion of this milestone, the new multiblock data set allows us to iteratively schedule algorithms on composite data structures such as assemblies or hierarchies like AMR. The new gradient algorithms approximate derivatives of fields in 3D structures with finite differences. Finally, the release of VTK-m version 1.1 tags a stable release of the software that can more easily be incorporated into external projects.

97 MATHEMATICS AND COMPUTING↗

A new track finding algorithm based on a multi-dimensional extension of the Hough Transform

We introduce a new pattern recognition algorithm for track finding in High Energy Physics Experiments based on an extension of the Hough Transform to multiple dimensions. A remarkable property of this algorithm is that the execution time is simply proportional to the total number of the hits to be processed, making it particularly attractive for high occupancy situations. The algorithm needs to be trained using a sufficiently large set of simulated tracks. The same track finding algorithm can be used for very different detector geometries and only the set of simulated tracks used for training needs to be changed. The particular structure of the algorithm also lends itself naturally to parallel hardware implementations which, combined with its intrinsic flexibility, should provide a most powerful tool for triggering at future colliders.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Time reversal and phase coherent music techniques for super-resolution ultrasound imaging

Systems and methods for super-resolution ultrasound imaging using a windowed and generalized TR-MUSIC algorithm that divides the imaging region into overlapping sub-regions and applies the TR-MUSIC algorithm to the windowed backscattered ultrasound signals corresponding to each sub-region. The algorithm is also structured to account for the ultrasound attenuation in the medium and the finite-size effects of ultrasound transducer elements. A modified TR-MUSIC imaging algorithm is used to account for ultrasound scattering from both density and compressibility contrasts. The phase response of ultrasound transducer elements is accounted for in a PC-MUSIC system.

47 OTHER INSTRUMENTATION↗

Mapping ephemeral stream networks in desert environments using very-high-spatial-resolution multispectral remote sensing

In this paper, understanding the spatial patterns of ephemeral streams is crucial for understanding how hydrologic processes influence the abundance and distribution of wildlife habitats in desert regions. Available methods for mapping ephemeral streams at the watershed scale typically underestimate the size of channel networks. Although remote sensing is an effective means of collecting data and obtaining information on large, inaccessible areas, conventional techniques for extracting channel features are not sufficient in regions that have small topographic gradients and subtle target-background spectral contrast. By using very high resolution multispectral imagery, we developed a new algorithm that applies landscape information to map ephemeral channels in desert regions of the Southwestern United States where utility-scale solar energy development is occurring. Knowledge about landscape features and structures was integrated into the algorithm using a series of spectral transformation and spatial statistical operations to integrate information about landscape features and structures. The algorithm extracted ephemeral stream channels at a local scale, with the result that approximately 900% more ephemeral streams was identified than what were identified by using the U.S. Geological Survey’s National Hydrography Dataset. The accuracy of the algorithm in detecting channel areas was as high as 92%, and its accuracy in delineating channel center lines was 91% when compared to a subset of channel networks that were digitized by using the very high resolution imagery. Although the algorithm captured stream channels in desert landscapes across various channel sizes and forms, it often underestimated stream headwaters and channels obscured by bright soils and sparse vegetation. While further improvement is warranted, the algorithm provides an effective means of obtaining detailed information about ephemeral streams, and it could make a significant contribution toward improving the hydrological modelling of desert environments.

47 OTHER INSTRUMENTATION↗

Distribution System Behind-the-Meter DERs: Estimation, Uncertainty Quantification, and Control

This paper summarizes the three-year technical activities of the IEEE Task Force (TF) on behind-the-meter (BTM) distributed energy resources (DERs): estimation, uncertainty quantification, and control. The potential grid services from BTM DERs are discussed in detail. The paper also reviews the state-of-the-art for BTM DERs visibility, uncertainty quantification, and, optimization and control. Furthermore, different aspects of the market structures associated with BTM DERs are covered, including emerging market and business models. Finally, needs and recommendations are provided for additional areas such as system protection, computing capabilities, algorithm development, market structure design, cyberinfrastructure and security, and hardware and software developments.

behind-the-meter↗

SU-E-J-264: Using Magnetic Resonance Imaging-Derived Features to Quantify Radiotherapy-Induced Normal Tissue Morbidity

Purpose: The aim of this study was to explore the use of Magnetic Resonance Imaging (MRI)-derived features as indicators of Radiotherapy (RT)-induced normal tissue morbidity. We also investigate the relationship between these features and RT dose in four critical structures. Methods: We demonstrate our approach for four patients treated with RT for base of tongue cancer in 2005–2007. For each patient, two MRI scans (T1-weighted pre (T1pre) and post (T1post) gadolinium contrast-enhancement) were acquired within the first six months after RT. The assessed morbidity endpoint observed in 2/4 patients was Grade 2+ CTCAEv.3 trismus. Four ipsilateral masticatory-related structures (masseter, lateral and medial pterygoid, and the temporal muscles) were delineated on both T1pre and T1post and these scans were co-registered to the treatment planning CT using a deformable demons algorithm. For each structure, the maximum and mean RT dose, and six MRI-derived features (the second order texture features entropy and homogeneity, and the first order mean, median, kurtosis, and skewness) were extracted and compared structure-wise between patients with and without trismus. All MRI-derived features were calculated as the difference between T1pre and T1post, ΔS. Results: For 5/6 features and all structures, ΔS diverged between trismus and non-trismus patients particularly for the masseter, lateral pterygoid, and temporal muscles using the kurtosis feature (−0.2 vs. 6.4 for lateral pterygoid). Both the maximum and mean RT dose in all four muscles were higher amongst the trismus patients (with the maximum dose being up to 25 Gy higher). Conclusion: Using MRI-derived features to quantify RT-induced normal tissue complications is feasible. We showed that several features are different between patients with and without morbidity and that the RT dose in all investigated structures are higher amongst patients with morbidity. MRI-derived features, therefore, has the potential to improve predictions of normal tissue morbidity.

60 APPLIED LIFE SCIENCES↗