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NEAMS-Multiphysics MOOSE End Year Framework Activities FY20

The Multiphysics Object Oriented Simulation Environment (MOOSE) is a general finite element package meant for high performance solution of multiphysics problems in science and engineering. In this report, we present additions and enhancements to MOOSE funded by the Nuclear Engineering Advanced Modeling and Simulation (NEAMS) program. NEAMS-funded MOOSE framework library improvements include: expansion of support for multi-level multi-application restart; enhancement of coupling between native MOOSE applications and external libraries; addition of a sparse automatic differentiation (AD) container enabling non-local degree of freedom coupling; block-specific quadrature rules; further development of an eigenvalue executioner; faster setup of periodic boundary conditions; and creation of a mesh meta-data system streamlining simulation startup. Besides developing the framework library, NEAMS funds were used to overhaul a swath of important MOOSE infrastructure in order to substantially improve user experience. These critical infrastructure changes included adapting MOOSE to python 3, improving the test harness to catch race conditions, and most importantly transitioning MOOSE to use Conda, a globally known packaging system, that greatly eases software adoption.

97 MATHEMATICS AND COMPUTING↗

User Manual - HydraGNN v5.0: Distributed Implementation of Multi-Tasking Graph Neural Networks

This document serves as the user manual for HydraGNN v5.0, a scalable graph neural network (GNN) architecture for simultaneous prediction of multiple target properties using multi-task learning (MTL). This version of HydraGNN has been developed primarily to support the development, training, and deployment of predictive graph-based deep learning (DL) models for atomistic materials modeling. HydraGNN is templated over 13 message-passing policies, including invariant models (GIN, PNA, PNAPlus, GAT, MFC, CGCNN, SAGE, SchNet, DimeNet) and equivariant models (EGNN, PNAEq, PAINN, MACE), and supports distributed training via distributed data parallelism (DDP), DeepSpeed, and Fully Sharded Data Parallelism (FSDP) on leadership-class supercomputers. Although HydraGNN can be applied to problems beyond atomistic materials modeling, its current use is confined to homogeneous graphs. Additional capabilities include machine-learned interatomic potentials with energy-conserving forces, General, Powerful, and Scalable Graph Transformer (GraphGPS) global attention, periodic boundary conditions, hyperparameter optimization, mixed-precision training, and uncertainty quantification.

97 MATHEMATICS AND COMPUTING↗

Infinite temperature at zero energy

We construct a family of static, geometrically local Hamiltonians that inherit eigenstate properties of periodically-driven (Floquet) systems. Our construction is a variation of the Feynman-Kitaev clock -- a well-known mapping between quantum circuits and local Hamiltonians -- where the clock register is given periodic boundary conditions. Assuming the eigenstate thermalization hypothesis (ETH) holds for the input circuit, our construction yields Hamiltonians whose eigenstates have properties characteristic of infinite temperature, like volume-law entanglement entropy, across the whole spectrum -- including the ground state. We then construct a family of exactly solvable Floquet quantum circuits whose eigenstates are shown to obey the ETH at infinite temperature. Combining the two constructions yields a new family of local Hamiltonians with provably volume-law-entangled ground states, and the first such construction where the volume law holds for all contiguous subsystems.

FOS: Physical sciences↗

tobac v1.5: introducing fast 3D tracking, splits and mergers, and other enhancements for identifying and analysing meteorological phenomena

There is a continuously increasing need for reliable feature detection and tracking tools based on objective analysis principles for use with meteorological data. Many tools have been developed over the previous 2 decades that attempt to address this need but most have limitations on the type of data they can be used with, feature computational and/or memory expenses that make them unwieldy with larger datasets, or require some form of data reduction prior to use that limits the tool's utility. The Tracking and Object-Based Analysis of Clouds (tobac) Python package is a modular, open-source tool that improves on the overall generality and utility of past tools. A number of scientific improvements (three spatial dimensions, splits and mergers of features, an internal spectral filtering tool) and procedural enhancements (increased computational efficiency, internal regridding of data, and treatments for periodic boundary conditions) have been included in tobac as a part of the tobac v1.5 update. These improvements have made tobac one of the most robust, powerful, and flexible identification and tracking tools in our field to date and expand its potential use in other fields. Future plans for tobac v2 are also discussed.

54 ENVIRONMENTAL SCIENCES↗

Development of neural network force fields for corrosion studies

To fully understand the chemistry and physics of corrosion, novel methods of simulation must be developed. One approach is designing machine learning (ML) algorithms integrated with density functional theory to develop adaptive force fields to gain insight into corrosion behavior namely at the surface of metal oxides. Current methods of modeling corrosion are slow due to the computational cost of resolving both reaction mechanics and mass transport processes. Machine learning methods can be implemented to obtain structure-activity relationships at both the molecular and bulk scale while still retaining the accuracy of density functional theory (DFT) and significantly decreasing the time needed for simulations of complex chemical processes in the various environments of corrosion. Multiscale models are needed for corrosion studies to fully understand its processes not only at the atomic length scale (chemical bonding, energies, and forces), but also at the nano and meso length scales (solid-state physics and material science processes). Current methods of study include DFT, molecular dynamics, and Monte Carlo. The limitation of DFT is that only a small number of atoms or molecules can be simulated at that level of theory. Density functional theory is used to study the electronic structure of atoms and molecules, and calculate the force component of each atom. However, these calculations are limited to about 1000 atoms. Custom periodic boundary conditions (PBC) can be used to describe the various environments and defects that affect the atomic forces to produce a large data set from which a training set can be derived. Machine learning can be utilized to overcome the barrier of modeling macroscopic and multi-scale processes from ab initio calculations through the development of adaptive force fields. Local environments determine the atomic forces of a given system, therefore adaptive force fields must be created to produce reliable quantum mechanical calculations. This can be achieved by developing a learning algorithm that uses the mapped atomic forces or fingerprint as an input to produce energies and magnetic moments as output. A systematic approach was used to begin to build a data set in order to accurately describe the atomic forces in various environments. In Figure 4 below, a simple PBC cell of Fe{sub 2}O{sub 3} was first optimized. A surface optimization was performed next, followed by a hydroxylated surface optimization. Once this calculation has converged, the adsorption of halide species to the hydroxylated surface will be investigated. TensorFlow is an open source platform for machine learning developed by Google. Using a high level application program interface (API) such as Keras allows for building and training ML models easily in a number of different environments and languages. For this project, a neural network was developed within Anaconda in Python. Future Work: Further development of reference data set; Refining neural network and learning algorithm; Fingerprinting atomic environment to enable mapping of atomic force components; Choosing appropriate training set from reference data; Learning from training set and enabling non-linear mapping of training set fingerprints and the atomic forces; Estimation of uncertainty to identify ranges of outside applicability; Testing and analysis of molecular dynamic simulations.

36 MATERIALS SCIENCE↗

A coupled DEM-IMB-LBM model for simulating methane hydrate exploitation involving particle dissolution

The coupled discrete element and lattice Boltzmann method using an immersed moving boundary scheme was extended to simulate methane hydrate exploitation involving mass transport and particle dissolution. In this coupled DEM-IMB-LBM model, a new Dirichlet-type thermal boundary condition is extended to simulate moving curved boundaries with constant concentration. A novel periodic boundary including an efficient searching algorithm for particle contact is proposed to reduce the computational cost and boundary effect. So, this model is validated by two numerical examples: a circular particle with concentration convection-diffusion moving in a horizontal channel and mass transport from a cylinder particle in a simple shear flow. The numerical results obtained from the proposed model agree well with previous studies. To further demonstrate the capacity of the proposed model, simulations of methane hydrate exploitation including two formations in marine sediments are carried out. The numerical results indicate that the coupled DEM-IMB-LBM is not only capable of simulating the dissolution of hydrate particles at the grain level, but also recover the sand erosion and migration process in a fundamental perspective during the methane hydrate exploitation process.

42 ENGINEERING↗

Investigating the relationship between simulation parameters and flow variables in simulating atmospheric gravity waves for wind energy applications

Wind farms, particularly offshore clusters, are becoming larger than ever before. Besides influencing the surface wind flow and the inflow for downstream wind farms, large wind farms can trigger atmospheric gravity waves in the inversion layer and the free atmosphere aloft. Wind-farm-induced gravity waves can cause adverse pressure gradients upstream of the wind farm, which contribute to the global blockage effect, and can induce favorable pressure gradients above and downstream of the wind farm that enhance wake recovery. Numerical modeling is a powerful means of studying these wind-farm-induced atmospheric gravity waves, but it comes with the challenge of handling spurious reflections of these waves from domain boundaries. Typically, approaches which employ radiation boundary conditions and forcing zones are used to avoid these reflections. However, the simulation setup of these approaches relies heavily on ad hoc processes. For instance, the widely used Rayleigh damping method requires ad hoc tuning to produce a setup that may only produce satisfactory results for a particular case. To provide more systematic guidance on setting up realistic simulations of atmospheric gravity waves, we conduct a large-eddy simulation (LES) study of flow over a 2D hill and through a wind farm canopy that explores the optimum domain size and damping layer setup depending on the fundamental parameters which determine the flow characteristics. In this work, we only consider linearly stratified conditions (i.e., no inversion layer), thereby focusing on internal gravity waves in the free atmosphere and their reflections from the domain boundaries. This type of flow is governed by a single Froude number, which dictates most of the internal wave properties, such as wavelength, amplitude, and direction. This, in turn, will dictate the optimum domain size and Rayleigh damping layer setup. We find the effective horizontal and vertical wavelengths (the representative wavelengths of the entire wave spectrum) to be the appropriate length scales to size the domain and damping layer thickness, and the optimal Rayleigh damping coefficient scales with the Brunt–Väisälä frequency. Considering Froude numbers seen in wind farm applications, we propose recommendations to limit the reflections to less than 10 % of the total upward-propagating wave energy. Typically, damping is done at the top boundary, but given the non-periodic lateral boundary conditions of practical wind farm simulation domains, we find that damping the inflow–outflow boundaries is of equal importance to damping the top boundary. The Brunt–Väisälä frequency-normalized damping coefficient should be between 1 and 10. The damping layer thickness should be at least one effective vertical wavelength; damping layers exceeding 1.5 times the vertical wavelength are found to be unnecessary. The domain length and height should accommodate at least one effective horizontal and vertical wavelength, respectively. Moreover, Rayleigh damping does not damp the waves completely, and the non-damped energy might accumulate over the simulation time.

17 WIND ENERGY↗

Physics–Informed Neural Networks of the Saint–Venant Equations for Downscaling a Large–Scale River Model

Large-scale river models are being refined over coastal regions to improve the scientific understanding of coastal processes, hazards and responses to climate change. However, coarse mesh resolutions and approximations in physical representations of tidal rivers limit the performance of such models at resolving the complex flow dynamics near the river-ocean interface, resulting in inaccurate simulations of flood inundation. In this research, we propose a machine learning (ML) framework based on the state-of-the-art physics-informed neural network (PINN) to simulate the downscaled flow at the subgrid scale. First, we demonstrate that PINN is able to assimilate observations of various types and solve the one-dimensional (1-D) Saint-Venant equations (SVE) directly. We perform the flow simulations over a floodplain and along an open channel in several synthetic case studies. The PINN performance is evaluated against analytical solutions and numerical models. Our results indicate that the PINN solutions of water depth have satisfactory accuracy with limited observations assimilated. In the case of flood wave propagation induced by storm surge and tide, a new neural network architecture is proposed based on Fourier feature embeddings that seamlessly encodes the periodic tidal boundary condition in the PINN's formulation. Furthermore, we show that the PINN-based downscaling can produce more reasonable subgrid solutions of the along-channel water depth by assimilating observational data. The PINN solution outperforms the simple linear interpolation in resolving the topography and dynamic flow regimes at the subgrid scale. This study provides a promising path towards improving emulation capabilities in large-scale models to characterize fine-scale coastal processes.

54 ENVIRONMENTAL SCIENCES↗

Eulerian simulations of electrostatic waves in plasmas with a single sign of charge

An Eulerian, numerical simulation is used to model the launching of plasma waves in a non-neutral plasma that is confined in a Penning–Malmberg trap. The waves are launched by applying an oscillating potential to an electrically isolated sector at one end of the conducting cylinder that bounds the confinement region and are received by another electrically isolated sector at the other end of the cylinder. The launching of both Trivelpiece–Gould waves and electron acoustic waves is investigated. Adopting a stratagem, the simulation captures essential features of the finite length plasma, while retaining the numerical advantages of a simulation employing periodic spatial boundary conditions. As a benchmark test of the simulation, the results for launched Trivelpiece–Gould waves of small amplitude are successfully compared to a linearized analytic solution for these fluctuations.

Physics↗

Benchmark estimate of the effect of anthropogenic emissions on the ocean surface

Abstract Investigations into the role of anthropogenic emissions in the occurrence of extreme weather often use a method that compares simulations of atmospheric climate models run under a factual scenario of historical boundary conditions observed during the period of the event against simulations run under a counterfactual scenario of what those boundary conditions might naturally have been over that same period in the absence of anthropogenic emissions. A particular requirement for this experiment design is an accurate estimation of ocean surface boundary conditions for use by the counterfactual natural simulations. Here we use output from the CMIP5 multi‐climate‐model archive to develop a robust estimate of sea surface temperatures and sea ice conditions for use in counterfactual natural simulations, intended as a benchmark estimate to facilitate comparison across climate models and across studies. This development includes tests to ensure that the final estimate is stable from year‐to‐year and stable against other perturbations to the methodology, as well as consideration of the strengths and weaknesses in comparison to other available attributable warming estimates. While this estimate is tailored specifically for the International CLIVAR C20C+ Detection and Attribution Project, it can be used by related projects as well.

Stone, Dáithí A.↗

Effect of boundary conditions on fluctuations of the Bose condensate of interacting atoms

For a gas of trapped interacting atoms forming a Bose condensate, we demonstrate a possibility of a significant influence of the boundary conditions on the statistics of the number of particles in the fundamental mode of the system. The analysis is carried out in the Bogoliubov – Popov low-temperature approximation for model homogeneous cubic traps with periodic or combined periodic and zero boundary conditions. It is shown that the effect of the boundary conditions does not weaken even in the region of parameters corresponding to the relatively strong interaction in the Thomas – Fermi asymptotic case, and does not disappear when proceeding to the thermodynamic limit. (paper)

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Explicit block encodings of boundary value problems for many-body elliptic operators

Simulation of physical systems is one of the most promising use cases of future digital quantum computers. In this work we systematically analyze the quantum circuit complexities of block encoding the discretized elliptic operators that arise extensively in numerical simulations for partial differential equations, including high-dimensional instances for many-body simulations. When restricted to rectangular domains with separable boundary conditions, we provide explicit circuits to block encode the many-body Laplacian with separable periodic, Dirichlet, Neumann, and Robin boundary conditions, using standard discretization techniques from low-order finite difference methods. To obtain high-precision, we introduce a scheme based on periodic extensions to solve Dirichlet and Neumann boundary value problems using a high-order finite difference method, with only a constant increase in total circuit depth and subnormalization factor. We then present a scheme to implement block encodings of differential operators acting on more arbitrary domains, inspired by Cartesian immersed boundary methods. We then block encode the many-body convective operator, which describes interacting particles experiencing a force generated by a pair-wise potential given as an inverse power law of the interparticle distance. This work provides concrete recipes that are readily translated into quantum circuits, with depth logarithmic in the total Hilbert space dimension, that block encode operators arising broadly in applications involving the quantum simulation of quantum and classical many-body mechanics.

Kharazi, Tyler [University of California, Berkeley↗

Spectral properties of three-dimensional Anderson model

The three-dimensional Anderson model represents a paradigmatic model to understand the Anderson localization transition. In this work we first review some key results obtained for this model in the past 50 years, and then study its properties from the perspective of modern numerical approaches. Our main focus is on the quantitative comparison between the level sensitivity statistics and the level statistics. While the former studies the sensitivity of Hamiltonian eigenlevels upon inserting a magnetic flux, the latter studies the properties of unperturbed eigenlevels. We define two versions of dimensionless conductance, the first corresponding to the width of the level curvature distribution relative to the mean level spacing, and the second corresponding to the ratio of the Heisenberg time and the Thouless time obtained from the spectral form factor. We show that both conductances look remarkably similar around the localization transition, in particular, they predict a nearly identical critical point consistent with other well-established measures of the transition. We then study some further properties of those quantities: for level curvatures, we discuss particular similarities and differences between the width of the level curvature distribution and the characteristic energy studied by Edwards and Thouless (1972) in their pioneering work, in which the hopping at one lattice edge is changed from periodic to antiperiodic boundary conditions. In the context of the spectral form factor, we show that at the critical point it enters a broad time-independent regime, in which its value is consistent with the level compressibility obtained from the level variance. Finally, we test the scaling solution of the average level spacing ratio in the crossover regime using the cost function minimization approach introduced recently in Šuntajs et al. (2020). The latter approach seeks for the optimal scaling solution in the vicinity of the crossing point, while at the same time it allows for the crossing point to drift due to finite-size corrections. We find that the extracted transition point and the scaling coefficient agree with those from the literature to high numerical accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Eigenstate thermalization in ( 2 + 1 )-dimensional SU(2) lattice gauge theory

We present preliminary numerical evidence for the hypothesis that the Hamiltonian SU(2) gauge theory discretized on a lattice obeys the eigenstate thermalization hypothesis (ETH). To do so we study three approximations: (a) a linear plaquette chain in a reduced Hilbert space limiting the electric field basis to j = 0 , 1 2 , (b) a two-dimensional honeycomb lattice with periodic or closed boundary condition and the same Hilbert space constraint, and (c) a chain of only three plaquettes but such a sufficiently large electric field Hilbert space ( j ≤ 7 2 ) that convergence of all energy eigenvalues in the analyzed energy window is observed. While an unconstrained Hilbert space is required to reach the continuum limit of SU(2) gauge theory, numerical resource constraints do not permit us to realize this requirement for all values of the coupling constant and large lattices. In each of the three studied cases we check first for random matrix theory (RMT) behavior in the eigenenergy spectrum and then analyze the diagonal as well as the off-diagonal matrix elements between energy eigenstates for a few operators. Within current uncertainties all results for (a), (b) and (c) agree with ETH predictions. Furthermore, we find the off-diagonal matrix elements of the electric energy operator exhibit RMT behavior in frequency windows that are small enough in (b) and (c). To unambiguously establish ETH behavior and determine for which class of operators it applies, an extension of our investigations is necessary. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Direct E&M Field Solver for a Plane Wave without Sources

A three dimensional direct field solver for the electric and magnetic fields using the Finite Difference Time Domain (FDTD) method is described. Example simulations using periodic and absorbing boundary conditions in a vacuum medium for a plane wave propagating in three dimensions are explored and are compared to theory.

97 MATHEMATICS AND COMPUTING↗

Axial magnetic flux amplification in Hall-magnetohydrodynamic simulations of externally magnetized z-pinches

It is shown that externally magnetized gas-puff z-pinches under compression can exhibit robust axial flux amplification under suitable axial boundary conditions. This effect relies upon the Hall term in the generalized Ohm's law to generate azimuthal currents in the presence of a driving axial electric field. Under dynamic compression, the total current tends to flow in a mostly force-free boundary layer, separating the predominately azimuthal field outside the layer and the predominately axial field inside the layer. The effect only appears to occur if the axial boundaries allow for outflow or absorption of electromagnetic energy. The effect is mitigated by imposing either periodic or conducting axial boundary conditions. A semi-analytic equilibrium analysis agrees with steady-state solutions of the time-dependent electron-magnetohydrodynamic equations and provides an estimate of the scaling of the boundary layer as well as suggesting a scenario for the formation of the boundary layer. When operative, the effect can significantly impede plasma compression due to the increase in axial flux that diffuses into the pre-compressed plasma or through the presence of conductors that inhibit movement of the generated axial flux. Several facilities have noted unusual implosion behavior in z-pinch experiments with applied axial fields that does not appear to be explainable within the standard magnetohydrodynamic model. In conclusion, it is suggested that these experiments can be explained by the axial flux amplification and concentration effect

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Technical descriptions of the experimental dynamical downscaling simulations over North America by the CAM–MPAS variable-resolution model

Abstract. Comprehensive assessment of climate datasets is important for communicating model projections and associated uncertainties to stakeholders. Uncertainties can arise not only from assumptions and biases within the model but also from external factors such as computational constraint and data processing. To understand sources of uncertainties in global variable-resolution (VR) dynamical downscaling, we produced a regional climate dataset using the Model for Prediction Across Scales (MPAS; dynamical core version 4.0) coupled to the Community Atmosphere Model (CAM; version 5.4), which we refer to as CAM–MPAS hereafter. This document provides technical details of the model configuration, simulations, computational requirements, post-processing, and data archive of the experimental CAM–MPAS downscaling data. The CAM–MPAS model is configured with VR meshes featuring higher resolutions over North America as well as quasi-uniform-resolution meshes across the globe. The dataset includes multiple uniform- (240 and 120 km) and variable-resolution (50–200, 25–100, and 12–46 km) simulations for both the present-day (1990–2010) and future (2080–2100) periods, closely following the protocol of the North American Coordinated Regional Climate Downscaling Experiment. A deviation from the protocol is the pseudo-warming experiment for the future period, using the ocean boundary conditions produced by adding the sea surface temperature and sea-ice changes from the low-resolution version of the Max Planck Institute Earth System Model (MPI-ESM-LR) in the Coupled Model Intercomparison Project Phase 5 to the present-day ocean state from a reanalysis product. Some unique aspects of global VR models are evaluated to provide background knowledge to data users and to explore good practices for modelers who use VR models for regional downscaling. In the coarse-resolution domain, strong resolution sensitivity of the hydrological cycles exists over the tropics but does not appear to affect the midlatitude circulations in the Northern Hemisphere, including the downscaling target of North America. The pseudo-warming experiment leads to similar responses of large-scale circulations to the imposed radiative and boundary forcings in the CAM–MPAS and MPI-ESM-LR models, but their climatological states in the historical period differ over various regions, including North America. Such differences are carried to the future period, suggesting the importance of the base state climatology. Within the refined domain, precipitation statistics improve with higher resolutions, and such statistical inference is verified to be negligibly influenced by horizontal remapping during post-processing. Limited (≈50 % slower) throughput of the current code is found on a recent many-core/wide-vector high-performance computing system, which limits the lengths of the 12–46 km simulations and indirectly affects sampling uncertainty. Our experience shows that global and technical aspects of the VR downscaling framework require further investigations to reduce uncertainties for regional climate projection.

58 GEOSCIENCES↗

Parametric Instability of Alfvén Waves and Wave Packets in Periodic and Open Systems

The parametric decay instability of Alfvén waves has been widely studied, but few investigations have examined wave packets of finite size and the effect of different boundary conditions on the growth rate. In this paper, we perform a linear analysis of circular and arc-polarized wave trains and wave packets in periodic and open boundary systems in a low- β plasma. We find that both types of wave are 3–5 times more stable in open boundary conditions compared to periodic. Additionally, once the wave packet width ℓ becomes smaller than the system size L , the growth rate decreases nearly with a power law γ ∝ ℓ / L . This study demonstrates that the stability of a pump wave cannot be separated from the laboratory settings, and that the growth rate of daughter waves depends on the conditions downstream and upstream of the pump wave and on the fraction of volume it fills. Our results can explain simulations and experiments of localized Alfvén waves. They also suggest that Alfvénic fluctuations in the solar wind, including sharp impulses known as switchbacks, can be more stable than traditional theory suggests depending on wind conditions.

Alfven waves↗