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At least 919 records · Page 51

NCCS High Performance GMRES Mixed Precision

HPG-MxP is a software package that performs a fixed number of multigrid preconditioned (using a Gauss-Seidel smoother) Generalized minimal residual (PGMRES) iterations in order to solve a possibly nonsymmetric large sparse linear system of equations. It is designed to be a benchmark to measure a computer's performance for sparse linear algebra workloads typical in scientific computing while allowing the use of mixed precision methods. The solution is required to have convergence characteristics and accuracy similar to double precision GMRES. It is based on the High Performance Conjugate Gradient Benchmark (HPCG) which restricts all implementations to use only the IEEE double precision format (FP64). The original implementation (https://github.com/hpg-mxp/hpg-mxp) was written by Ichitaro Yamazaki, Jennifer Loe, Christian Glusa, Sivasankaran Rajamanickam, Piotr Luszczek, and Jack Dongarra. Please refer to that repository for documentation on the original implementation. This version is maintained by the National Center for Computational Sciences at Oak Ridge National Laboratory. It is highly scalable and optimized for Oak Ridge Leadership Computing Facility (OLCF) systems, particularly Frontier.

Kashi, Aditya [Oak Ridge National Laboratory (ORNL↗

Supporting information for Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

In this work, we use few-shot learning to segment the body and vein architecture of P. trichocarpa leaves from high-resolution scans obtained in the UC Davis common garden. Leaf and vein segmentation are formulated as separate tasks, in which convolutional neural networks (CNNs) are used to iteratively expand partial segmentations until reaching stopping criteria. Our leaf and vein segmentation approaches use just 50 and 8 manually traced images for training, respectively, and are applied to a set of 2,634 top and bottom leaf scans. We show that both methods achieve high segmentation accuracy, in some cases exceeding even human-level segmentation. The leaf and vein segmentations are subsequently used to extract 68 morphological traits using traditional open-source image processing tools, which are validated using real-world physical measurements. For a biological perspective, we perform a genome-wide association study using the vein density trait to discover novel genetic architectures associated with multiple physiological processes relating to leaf development and function. In addition to sharing all of the few-shot learning code (see https://github.com/jlager/few-shot-leaf-segmentation), we are releasing all images, manual segmentations, model predictions, 68 extracted leaf phenotypes, and a new set of SNPs called against the v4 P. trichocarpa genome for 1,419 genotypes. The data folder includes all images, ground truth segmentations, predicted segmentations, and extracted leaf traits. All images encode the sample ID in the file name by indicating the treatment, block, row, position, and leaf side, respectively. For example, the file, C_1_1_2_bot.jpeg, indicates the control treatment, block 1, row 1, position 2, and the bottom side of the leaf. Tabulated results include position IDs as well as the corresponding genotype IDs. The images folder includes the 2,906 high-resolution leaf scans taken in the field. The leaf_masks folder includes 50 ground truth segmentations used for training the leaf tracing algorithm. The leaf_preds folder includes the 2,906 predicted segmentations from the leaf tracing algorithm. The vein_masks folder includes 8 ground truth segmentations used for training the vein growing algorithm. The vein_preds folder includes the 1,453 predicted segmentations from the vein growing algorithm. The vein_probs folder includes the 1,453 predicted probability maps from the vein growing algorithm before thresholding. The genomes folder includes the set of SNPs called against the v4 P. trichocarpa genome for 1,419 genotypes with a README file detailing the steps taken. The results folder includes: (i) raw values of the 68 predicted leaf traits in digital_traits.tsv, (ii) manually measured values of petiole length and width in manual_traits.tsv, (iii) thin plate spline (TPS) adjusted values of the vein density trait in vein_density_tps_adj.tsv, (iv) best linear unbiased prediction (BLUP) adjusted values of the vein density trait in vein_density_blups.tsv, and (v) GWAS results for the vein density trait, including chromosome positions and corresponding P values, in gwas_results.csv.

09 BIOMASS FUELS↗

Double-real corrections to color singlet decay in a parton-shower inspired scheme

We introduce a local infrared subtraction method for next-to-next-to-leading order QCD calculations in color singlet decays, with counterterms based on scalar radiators and pure splitting functions. Overlapping singularities in the multipole radiation pattern are disentangled by partial fractioning, and the kinematics mapping corresponds to iterated next-to-leading order kinematics. We verify that the double-real remainder to $e^+e^-\to\;q\bar{q}$ is rendered finite in the single and double unresolved limits and investigate the numerical convergence of the Monte-Carlo integral. We compute the phase-space integrals of the scalar counterterms in the back-to-back configuration, both analytically and with the help of numerical techniques based on sector decomposition.

Campbell, John M. [Fermilab]↗

Microscale mechanical modeling of deformable geomaterials with dynamic contacts based on the numerical manifold method

Abstract Micromechanical modeling of geomaterials is challenging because of the complex geometry of discontinuities and potentially large number of deformable material bodies that contact each other dynamically. In this study, we have developed a numerical approach for micromechanical analysis of deformable geomaterials with dynamic contacts. In our approach, we detect contacts among multiple blocks with arbitrary shapes, enforce different contact constraints for three different contact states of separated, bonded, and sliding, and iterate within each time step to ensure convergence of contact states. With these features, we are able to simulate the dynamic contact evolution at the microscale for realistic geomaterials having arbitrary shapes of grains and interfaces. We demonstrate the capability with several examples, including a rough fracture with different geometric surface asperity characteristics, settling of clay aggregates, compaction of a loosely packed sand, and failure of an intact marble sample. With our model, we are able to accurately analyze (1) large displacements and/or deformation, (2) the process of high stress accumulated at contact areas, (3) the failure of a mineral cemented rock samples under high stress, and (4) post-failure fragmentation. The analysis highlights the importance of accurately capturing (1) the sequential evolution of geomaterials responding to stress as motion, deformation, and high stress; (2) large geometric features outside the norms (such as large asperities and sharp corners) as such features can dominate the micromechanical behavior; and (3) different mechanical behavior between loosely packed and tightly packed granular systems.

58 GEOSCIENCES↗

A computationally-efficient method for flamelet calculations

A new open-source code for the simulation of the diffusion flamelet equations is proposed. Emphasis is placed on using an approximate Jacobian to reduce the computational cost of the matrix operations. Performance of the proposed solvers is tested by performing flamelet calculations with kinetic mechanisms of varying sizes. For the unity Lewis number equations, the present iterative Newton solver using an approximate Jacobian greatly outperforms direct Newton solvers using exact Jacobians. The computation cost scales linearly with the number of species, leading to a reduction in solution times by two orders of magnitude for mechanisms containing thousands of species. The applicability of the Jacobian approximations to the solution of the non-unity Lewis number flamelet equations is assessed. The approximations are generally inadequate to solve the full non-unity Lewis number equations but can be used in some applications depending on the balance of terms in the flamelet equations. As an example, the flamelet solver is applied to the study of sooting tendencies in laminar co-flow diffusion flames where modified non-unity Lewis number flamelet equations, previously shown to accurately reproduce experimentally-measured Yield Sooting Indices (YSI), are solved. Here, the accelerated flamelet solver is well suited for sensitivity analysis and uncertainty quantification with large detailed kinetic mechanisms, tasks for which the computational cost was previously prohibitive.

42 ENGINEERING↗

Scalable Simulation of Pressure Gradient-Driven Transport of Rarefied Gases in Complex Permeable Media Using Lattice Boltzmann Method

Accurate representations of slip and transitional flow regimes present a challenge in the simulation of rarefied gas flow in confined systems with complex geometries. In these regimes, continuum-based formulations may not capture the physics correctly. This work considers a regularized multi-relaxation time lattice Boltzmann (LB) method with mixed Maxwellian diffusive and halfway bounce-back wall boundary treatments to capture flow at high Kn. The simulation results are validated against atomistic simulation results from the literature. We examine the convergence behavior of LB for confined systems as a function of inlet and outlet treatments, complexity of the geometry, and magnitude of pressure gradient and show that convergence is sensitive to all three. The inlet and outlet boundary treatments considered in this work include periodic, pressure, and a generalized periodic boundary condition. Compared to periodic and pressure treatments, simulations of complex domains using a generalized boundary treatment conserve mass but require more iterations to converge. Convergence behavior in complex domains improves at higher magnitudes of pressure gradient across the computational domain, and lowering the porosity deteriorates the convergence behavior for complex domains.

42 ENGINEERING↗

Three-dimensional cooperative inversion of airborne magnetic and gravity gradient data using deep-learning techniques

Using multiple geophysical methods has become a prevailing approach in numerous geophysical applications to investigate subsurface structures and parameters. These multimethod-based exploration strategies have the potential to greatly diminish uncertainties and ambiguities encountered during geophysical data analysis and interpretation. One of the applications is the cooperative inversion of airborne magnetic and gravity gradient data for the interpretation of data obtained in mineral, oil and gas, and geothermal explorations. In this paper, a unified cooperative inversion framework is designed by combining the standard separate inversions with a deep neural network (DNN), which serves as the link between different types of data. A well-trained DNN takes the separately inverted susceptibility and density models as the inputs and provides improved models that will be used as the initial models of deterministic inversions. A two-round iteration strategy is adopted to guarantee the reasonability of the recovered models and overall efficiency of the inversion. In addition, this deep-learning (DL)-based framework demonstrates excellent generalization abilities when tested on models that are entirely distinct from the training data sets. The framework can easily incorporate multiphysics without necessitating any structural changes to the network. Synthetic experiments validate that our DL-based method outperforms conventional separate inversions and cross-gradient-based joint inversion in view of the accuracy of the recovered models and inversion efficiency. Successful application to field data further verifies the effectiveness of our DL-based method.

Geochemistry & Geophysics↗

Autonomous fabrication of tailored defect structures in 2D materials using machine learning-enabled scanning transmission electron microscopy

Materials with tailored quantum properties can be engineered from atomic-scale assembly techniques, but existing methods often lack the agility and accuracy to precisely and intelligently control the manufacturing process. Here, we demonstrate a fully autonomous approach for fabricating atomic-level defects using electron beams in scanning transmission electron microscopy (STEM) that combines advanced machine learning and automated beam control. As a proof of concept, we achieved controlled fabrication of MoS-nanowire (MoS-NW) edge structures by iterative and targeted exposure of MoS 2 monolayer to a focused electron beam to selectively eject sulfur atoms, utilizing high-angle annular dark-field (HAADF) imaging for feedback-controlled monitoring of structural evolution of defects. A machine learning framework combining a random forest model and a convolutional neural network (CNN) was developed to decode the HAADF image and accurately identify atomic positions and species. This atomic-level information was then integrated into an autonomous decision-making platform, which applied predefined fabrication strategies to instruct beam control about atomic sites to be ejected. The selected sites were subsequently exposed to a localized electron beam using an FPGA-controlled scan routine with precise control over beam positioning and duration. While the MoS-NW edge structures produced exhibit promising mechanical and electronic properties, the proposed methods to build the autonomous fabrication framework is material-agnostic and can be extended to other 2D materials for the creation of diverse defect structures and heterostructures beyond Mo S2 .

Engineering↗

Calibration of parallel bond parameters in bonded particle models via physics-informed adaptive moment optimisation

This study proposes an automated calibration procedure for bond parameters in bonded discrete element modelling. By exploring the underlying physical correlations between microscopic parameters of bonds and macroscopic strength parameters of the continuum to be modelled, the microscopic shear strength and tensile strength are identified as independent variables for calibration purpose. Then a physics-informed iterative scheme is proposed to automatically approximate the bond parameters by viewing the micro-macro relation as an implicitly defined mathematical mapping function. As a result of highly non-convex features of this implicit mapping, the adaptive moment estimation (Adam), which is especially suitable for problems with noisy gradients, is adopted as the basic iterative scheme, in conjunction with other numerical techniques to approximately evaluate the partial derivatives involved. The whole procedure offers a simple and effective framework for bond parameter calibration. Finally, a numerical example of SiC ceramic is provided for validation. By compared with some existing calibration methods, the proposed method shows significant advantages in terms of calibration efficiency and accuracy.

42 ENGINEERING↗

mpfit: a robust method for fitting atomic resolution images with multiple Gaussian peaks

The standard technique for sub-pixel estimation of atom positions from atomic resolution scanning transmission electron microscopy images relies on fitting intensity maxima or minima with a two-dimensional Gaussian function. While this is a widespread method of measurement, it can be error prone in images with non-zero aberrations, strong intensity differences between adjacent atoms or in situations where the neighboring atom positions approach the resolution limit of the microscope. Here we demonstrate mpfit, an atom finding algorithm that iteratively calculates a series of overlapping two-dimensional Gaussian functions to fit the experimental dataset and then subsequently uses a subset of the calculated Gaussian functions to perform sub-pixel refinement of atom positions. Based on both simulated and experimental datasets presented in this work, this approach gives lower errors when compared to the commonly used single Gaussian peak fitting approach and demonstrates increased robustness over a wider range of experimental conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geometry Optimization for a Quadrupole Resonator at Jefferson Lab

The quadrupole resonator (QPR) is a sample characterization tool to measure the RF properties of superconducting materials using the calorime-try method at different temperatures, magnetic fields, and frequencies. Such resonators are cur-rently operating at CERN and HZB but suffer from Lorentz force detuning and modes overlap-ping, resulting in higher uncertainties in surface resistance measurement. Using the two CERN's QPR model iterations, the geometry was opti-mized via electromagnetic and mechanical simu-lations to eliminate these issues. The new QPR version was modelled for an increasing range of magnetic fields. The magnetic field is concentrat-ed at the center of the sample to reduce the un-certainty in surface resistance measurements sig-nificantly. This paper discusses the QPR geome-try optimization for the new version of QPR, which is now progressing toward fabrication.

Bira, S.↗

Neural Networks for Nuclear Reactions in MAESTROeX

We demonstrate the use of neural networks to accelerate the reaction steps in the MAESTROeX stellar hydrodynamics code. A traditional MAESTROeX simulation uses a stiff ODE integrator for the reactions; here, we employ a ResNet architecture and describe details relating to the architecture, training, and validation of our networks. Our customized approach includes options for the form of the loss functions, a demonstration that the use of parallel neural networks leads to increased accuracy, and a description of a perturbational approach in the training step that robustifies the model. We test our approach on millimeter-scale flames using a single-step, 3-isotope network describing the first stages of carbon fusion occurring in Type Ia supernovae. We train the neural networks using simulation data from a standard MAESTROeX simulation, and show that the resulting model can be effectively applied to different flame configurations. This work lays the groundwork for more complex networks, and iterative time-integration strategies that can leverage the efficiency of the neural networks.

79 ASTRONOMY AND ASTROPHYSICS↗

An Optimization-Based Law of Mass Action Precipitation/Dissolution Model

Rare earth elements (REE) and many other critical minerals are necessary for the manufacturing of modern everyday technologies, including microchips, batteries and electric motors. Recovery of these materials typically involves aqueous systems which can be modeled as chemical equilibrium problems. One common method for solving these problems is the law of mass action approach (LMA), where a system of non-linear equations involving the equilibrium constants is solved. However, despite being theoretically simple, these problems are in practice very difficult to solve. Currently, the use of iterative heuristics based on saturation indices to decide on which species and reactions to include in the calculations is the state of the art to arrive at a solution. Here, we present an optimization-based alternative to solve chemical equilibria problems involving precipitation/dissolution reactions without the need for such heuristics. Our approach is first validated against the LMA software MINTEQ and PHREEQC for a number of case studies, and then applied to a novel REE recovery process reported in the literature. Overall, our approach was found to have close agreement with MINTEQ and PHREEQC, and we were able to successfully replicate the reported yield and purity for the published REE process.

42 ENGINEERING↗

A Flexible Power Method for Solving Infinite Dimensional Tensor Eigenvalue Problems

We propose a flexible power method for computing the leftmost, i.e., algebraically smallest, eigenvalue of an infinite dimensional tensor eigenvalue problem, $H x = \lambda x$, where the infinite dimensional symmetric matrix $H$ exhibits a translational invariant structure. We assume the smallest eigenvalue of $H$ is simple and apply a power iteration of $e^{-H}$ with the eigenvector represented in a compact way as a translational invariant infinite Tensor Ring (iTR). Hence, the infinite dimensional eigenvector can be represented by a finite number of iTR cores of finite rank. In order to implement this power iteration, we use a small parameter $t$ so that the infinite matrix-vector operation $e^{-Ht}x$ can efficiently be approximated by the Lie product formula, also known as Suzuki--Trotter splitting, and we employ a low rank approximation through a truncated singular value decomposition on the iTR cores in order to keep the cost of subsequent power iterations bounded. We also use an efficient way for computing the iTR Rayleigh quotient and introduce a finite size iTR residual which is used to monitor the convergence of the Rayleigh quotient and to modify the timestep $t$. In this paper, we discuss 2 different implementations of the flexible power algorithm and illustrate the automatic timestep adaption approach for several numerical examples.

Beeumen, Roel Van↗

First results of Ne shattered pellet injection for mitigating plasma disruption with full metal wall in EAST tokamak

Disruption mitigation poses a significant and unresolved challenge for ITER and future fusion reactor devices. To mitigate the effect of plasma disruption, a Shattered Pellet Injection (SPI) system has been developed and the first rapid shutdown experiments have been successfully performed in the Experimental Advanced Superconducting Tokamak with full metal wall. The experiments confirmed the system’s capability to inject 5 mm diameter neon (Ne) pellets at velocities ranging from 100 to 400 m s −1 , with a maximum injected quantity of 13.2 Pa m 3 . Compared to unmitigated disruptions, the total radiation power was significantly higher with the respective use of SPI and Massive Gas Injection (MGI). Additionally, the radiation distribution and divertor heat flux were compared between SPI and MGI methods. The results demonstrated that SPI exhibited shorter cooling time, stronger core radiation and more uniform poloidal radiation distribution compared to MGI, indicating deeper deposition using SPI. Furthermore, during plasma shutdown, the electron temperature and peak heat flux near outer divertor strike points were reduced by 40% and 50% respectively, with SPI, in comparison to MGI. These findings serve as a valuable reference for implementing SPI technology as the baseline approach for disruption mitigation in ITER.

EAST↗

Computational methods based on density functional theory for reactions and processes involving electronic spin (Final Technical Report)

This award supports one post-doctoral researcher for 1.5 years. Publications that acknowledge this grant: Refs. 1–14. Refs. 3,10,12 assess current methodology for the evaluation of magnetic exchange couplings in transition metal complexes. In particular, Ref. 10 validates the use of an approximate (non-iterative) Green’s function approach for the calculation of magnetic exchange couplings and will be the foundation for Thrust 2 in this proposal. Refs. 3 and 12 focus on widely used density functional approaches based on the standard energy differences methodology for the particular case of oxo-bridged Fe(III) complexes. Refs. 2,4–7,11 apply current methodologies to problems of practical interest in molecular magnetism. Ref. 13 presents a methodology to explicitly simulate the dynamics of open quantum systems within density functional theory (DFT) calculations based on the Liouville-von Neumann equation of motion for quantum systems driven out-of-equilibrium. Ref. 8 uses non-collinear spin DFT to explain the mechanical behavior of magnetic mono-atomic Pt wires produced in break-junction experiments in the presence of a magnetic field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Density Matrix Implementation of the Fermi–Löwdin Orbital Self-Interaction Correction Method

The Fermi–Löwdin orbital self-interaction correction (FLOSIC) method effectively provides a transformation from canonical orbitals to localized Fermi–Löwdin orbitals which are used to remove the self-interaction error in the Perdew–Zunger (PZ) framework. This transformation is solely determined by a set of points in space, called Fermi–Löwdin descriptors (FODs), and the occupied canonical orbitals or the density matrix. In this work, we provide a detailed workflow for the implementation of the FLOSIC method for removal of self-interaction error in DFT calculations in an orbital-by-orbital basis that takes advantage of the unitary invariant nature of the FLOSIC method. In this way, it is possible to cast the self-consistent energy minimization at fixed FODs in the same manner than standard Kohn–Sham with one additional term in the Kohn–Sham Hamiltonian that introduces the PZ self-interaction correction. Each energy minimization iteration is divided in two substeps, one for the density matrix and one for the FODs. Expressions for the effective Kohn–Sham matrix and FOD gradients are provided such that its implementation is suitable for most electronic structure codes. Here, we analyze the convergence characteristics of the algorithm and present applications for the evaluation of NMR shielding constants and real-time time-dependent DFT simulations based on the Liouville–von Neumann equation to calculate excitation energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stochastic Optimization to Find Optimum Beginning-of-Life Core Configuration of Stable Salt Reactor with Online Refueling

A stochastic optimization method has been developed to find an optimum equilibrium cycle core configuration of the waste-burning stable salt reactor, which is a fast-spectrum molten salt reactor with frequent online refueling. An optimum core configuration was determined with the goal of minimizing radial power peaking. Because of the vast number of potential candidate core configurations, stochastic optimization was applied based on simulated annealing and an additional acceleration method, which screened out unpromising core configurations. It has been demonstrated that the developed stochastic optimization method successfully finds the optimal core configuration regardless of the initial guess and outperforms the gradient descent approach. In addition, it has been observed that the use of a so-called out-in core configuration as the initial guess speeds up convergence of the iterative solution more than five times. Based on the searched optimum equilibrium cycle core configuration, new beginning-of-life (BOL) core configurations have been developed. In conclusion, the new BOL core configurations will be used in developing optimum refueling strategies.

Moltex static salt reactor↗