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At least 397 records · Page 22

On the asymptotic preserving property of the unified gas kinetic scheme for the diffusion limit of linear kinetic models

The unified gas kinetic scheme (UGKS) of K. Xu et al. (2010) [37], originally developed for multiscale gas dynamics problems, is applied in this paper to a linear kinetic model of radiative transfer theory. While such problems exhibit purely diffusive behavior in the optically thick (or small Knudsen) regime, we prove that UGKS is still asymptotic preserving (AP) in this regime, but for the free transport regime as well. Moreover, this scheme is modified to include a time implicit discretization of the limit diffusion equation, and to correctly capture the solution in case of boundary layers. Contrary to many AP schemes, this method is based on a standard finite volume approach, it does neither use any decomposition of the solution, nor staggered grids. Several numerical tests demonstrate the properties of the scheme.

97 MATHEMATICS AND COMPUTING↗

Second order symmetry-preserving conservative Lagrangian scheme for compressible Euler equations in two-dimensional cylindrical coordinates

In applications such as astrophysics and inertial confinement fusion, there are many three-dimensional cylindrical-symmetric multi-material problems which are usually simulated by Lagrangian schemes in the two-dimensional cylindrical coordinates. For this type of simulation, a critical issue for the schemes is to keep spherical symmetry in the cylindrical coordinate system if the original physical problem has this symmetry. In the past decades, several Lagrangian schemes with such symmetry property have been developed, but all of them are only first order accurate. In this paper, we develop a second order cell-centered Lagrangian scheme for solving compressible Euler equations in cylindrical coordinates, based on the control volume discretizations, which is designed to have uniformly second order accuracy and capability to preserve one-dimensional spherical symmetry in a two-dimensional cylindrical geometry when computed on an equal-angle-zoned initial grid. The scheme maintains several good properties such as conservation for mass, momentum and total energy, and the geometric conservation law. Several two-dimensional numerical examples in cylindrical coordinates are presented to demonstrate the good performance of the scheme in terms of accuracy, symmetry, non-oscillation and robustness. The advantage of higher order accuracy is demonstrated in these examples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A mesh partitioning algorithm for preserving spatial locality in arbitrary geometries

Highlights: •An algorithm for partitioning computational meshes is proposed. •The Morton order space-filling curve is modified to achieve improved locality. •A spatial locality metric is defined to compare results with existing approaches. •Results indicate improved performance of the algorithm in complex geometries. -- Abstract: A space-filling curve (SFC) is a proximity preserving linear mapping of any multi-dimensional space and is widely used as a clustering tool. Equi-sized partitioning of an SFC ignores the loss in clustering quality that occurs due to inaccuracies in the mapping. Often, this results in poor locality within partitions, especially for the conceptually simple, Morton order curves. We present a heuristic that improves partition locality in arbitrary geometries by slicing a Morton order curve at points where spatial locality is sacrificed. In addition, we develop algorithms that evenly distribute points to the extent possible while maintaining spatial locality. A metric is defined to estimate relative inter-partition contact as an indicator of communication in parallel computing architectures. Domain partitioning tests have been conducted on geometries relevant to turbulent reactive flow simulations. The results obtained highlight the performance of our method as an unsupervised and computationally inexpensive domain partitioning tool.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An asymptotic-preserving scheme for the semiconductor Boltzmann equation toward the energy-transport limit

We design an asymptotic-preserving scheme for the semiconductor Boltzmann equation which leads to an energy-transport system for electron mass and energy as mean free path goes to zero. As opposed to the classical drift-diffusion limit where the stiff collisions are all in one scale, new difficulties arise in the two-scale stiff collision terms because the simple BGK penalization [15] fails to drive the solution to the correct limit. We propose to set up a spatially dependent threshold on the penalization of the stiffer collision operator such that the evolution of the solution resembles a Hilbert expansion at the continuous level. Formal asymptotic analysis and numerical results confirm the efficiency and accuracy of our scheme.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An asymptotic preserving unified gas kinetic scheme for frequency-dependent radiative transfer equations

This paper presents an extension of previous work (Sun et al., 2015 [22]) of the unified gas kinetic scheme (UGKS) for the gray radiative transfer equations to the frequency-dependent (multi-group) radiative transfer system. Different from the gray radiative transfer equations, where the optical opacity is only a function of local material temperature, the simulation of frequency-dependent radiative transfer is associated with additional difficulties from the frequency-dependent opacity. For the multiple frequency radiation, the opacity depends on both the spatial location and the frequency. For example, the opacity is typically a decreasing function of frequency. At the same spatial region the transport physics can be optically thick for the low frequency photons, and optically thin for high frequency ones. Therefore, the optical thickness is not a simple function of space location. In this paper, the UGKS for frequency-dependent radiative system is developed. The UGKS is a finite volume method and the transport physics is modeled according to the ratio of the cell size to the photon's frequency-dependent mean free path. When the cell size is much larger than the photon's mean free path, a diffusion solution for such a frequency radiation will be obtained. On the other hand, when the cell size is much smaller than the photon's mean free path, a free transport mechanism will be recovered. In the regime between the above two limits, with the variation of the ratio between the local cell size and photon's mean free path, the UGKS provides a smooth transition in the physical and frequency space to capture the corresponding transport physics accurately. The seemingly straightforward extension of the UGKS from the gray to multiple frequency radiation system is due to its intrinsic consistent multiple scale transport modeling, but it still involves lots of work to properly discretize the multiple groups in order to design an asymptotic preserving (AP) scheme in all regimes. The current scheme is tested in a few frequency-dependent radiation problems, and the results are compared with the solutions from the well-defined implicit Monte Carlo (IMC) method. The UGKS is much more efficient than IMC, and the computational times of both schemes for all test cases are listed. The UGKS seems to be the first discrete ordinate method (DOM) for the accurate capturing of multiple frequency radiative transport physics from ballistic particle motion to the diffusive wave propagation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An asymptotic-preserving stochastic Galerkin method for the radiative heat transfer equations with random inputs and diffusive scalings

In this paper, we develop an Asymptotic-Preserving (AP) stochastic Galerkin scheme for the radiative heat transfer equations with random inputs and diffusive scalings. In this problem the random inputs arise due to uncertainties in cross section, initial data or boundary data. We use the generalized polynomial chaos based stochastic Galerkin (gPC-SG) method, which is combined with the micro–macro decomposition based deterministic AP framework in order to handle efficiently the diffusive regime. For linearized problem we prove the regularity of the solution in the random space and consequently the spectral accuracy of the gPC-SG method. We also prove the uniform (in the mean free path) linear stability for the space-time discretizations. Several numerical tests are presented to show the efficiency and accuracy of proposed scheme, especially in the diffusive regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A stochastic asymptotic-preserving scheme for a kinetic-fluid model for disperse two-phase flows with uncertainty

In this paper we consider a kinetic-fluid model for disperse two-phase flows with uncertainty. We propose a stochastic asymptotic-preserving (s-AP) scheme in the generalized polynomial chaos stochastic Galerkin (gPC-sG) framework, which allows the efficient computation of the problem in both kinetic and hydrodynamic regimes. The s-AP property is proved by deriving the equilibrium of the gPC version of the Fokker–Planck operator. The coefficient matrices that arise in a Helmholtz equation and a Poisson equation, essential ingredients of the algorithms, are proved to be positive definite under reasonable and mild assumptions. The computation of the gPC version of a translation operator that arises in the inversion of the Fokker–Planck operator is accelerated by a spectrally accurate splitting method. Numerical examples illustrate the s-AP property and the efficiency of the gPC-sG method in various asymptotic regimes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Dissipation-preserving spectral element method for damped seismic wave equations

This article describes the extension of the conformal symplectic method to solve the damped acoustic wave equation and the elastic wave equations in the framework of the spectral element method. The conformal symplectic method is a variation of conventional symplectic methods to treat non-conservative time evolution problems, which has superior behaviors in long-time stability and dissipation preservation. To reveal the intrinsic dissipative properties of the model equations, we first reformulate the original systems in their equivalent conformal multi-symplectic structures and derive the corresponding conformal symplectic conservation laws. We thereafter separate each system into a conservative Hamiltonian system and a purely dissipative ordinary differential equation system. Based on the splitting methodology, we solve the two subsystems respectively. The dissipative one is cheaply solved by its analytic solution. While for the conservative system, we combine a fourth-order symplectic Nyström method in time and the spectral element method in space to cover the circumstances in realistic geological structures involving complex free-surface topography. The Strang composition method is adopted thereby to concatenate the corresponding two parts of solutions and generate the completed conformal symplectic method. A relative larger Courant number than that of the traditional Newmark scheme is found in the numerical experiments in conjunction with a spatial sampling of approximately 5 points per wavelength. A benchmark test for the damped acoustic wave equation validates the effectiveness of our proposed method in precisely capturing dissipation rate. The classical Lamb problem is used to demonstrate the ability of modeling Rayleigh wave in elastic wave propagation. More comprehensive numerical experiments are presented to investigate the long-time simulation, low dispersion and energy conservation properties of the conformal symplectic methods in both the attenuating homogeneous and heterogeneous media.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Compatible, energy conserving, bounds preserving remap of hydrodynamic fields for an extended ALE scheme

From the very origins of numerical hydrodynamics in the Lagrangian work of von Neumann and Richtmyer [83], the issue of total energy conservation as well as entropy production has been problematic. Because of well known problems with mesh deformation, Lagrangian schemes have evolved into Arbitrary Lagrangian–Eulerian (ALE) methods [39] that combine the best properties of Lagrangian and Eulerian methods. Energy issues have persisted for this class of methods. We believe that fundamental issues of energy conservation and entropy production in ALE require further examination. The context of the paper is an ALE scheme that is extended in the sense that it permits cyclic or periodic remap of data between grids of the same or differing connectivity. The principal design goals for a remap method then consist of total energy conservation, bounded internal energy, and compatibility of kinetic energy and momentum. We also have secondary objectives of limiting velocity and stress in a non-directional manner, keeping primitive variables monotone, and providing a higher than second order reconstruction of remapped variables. Particularly, the new contributions fall into three categories associated with: energy conservation and entropy production, reconstruction and bounds preservation of scalar and tensor fields, and conservative remap of nonlinear fields. Our paper presents a derivation of the methods, details of implementation, and numerical results for a number of test problems. The methods requires volume integration of polynomial functions in polytopal cells with planar facets, and the requisite expressions are derived for arbitrary order.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Moment preserving constrained resampling with applications to particle-in-cell methods

The Moment Preserving Constrained Resampling (MPCR) algorithm for particle resampling is introduced and applied to particle-in-cell (PIC) methods to increase simulation accuracy, reduce compute cost, and/or avoid numerical instabilities. The general algorithm partitions the system space into smaller subsets and resamples the distribution within each subset. Further, the algorithm is designed to conserve any number of particle and grid moments with a high degree of accuracy (i.e. machine accuracy). The effectiveness of MPCR is demonstrated with several numerical tests, including a use-case study in gyrokinetic fusion plasma simulations. Finally, the computational cost of MPCR is negligible compared to the cost of particle evolution in PIC methods, and the tests demonstrate that periodic particle resampling yields a significant improvement in the accuracy and stability of the results.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

An asymptotic-preserving 2D-2P relativistic Drift-Kinetic-Equation solver for runaway electron simulations in axisymmetric tokamaks

We propose an asymptotic-preserving (AP), uniformly convergent numerical scheme for the relativistic collisional Drift-Kinetic Equation (rDKE) to simulate runaway electrons in axisymmetric toroidal magnetic field geometries typical of tokamak devices. The approach is derived from an exact Green's function solution with numerical approximations of quantifiable impact, and results in a simple, two-step operator-split algorithm, consisting of a collisional Eulerian step, and a Lagrangian orbit-integration step with analytically prescribed kernels. The AP character of the approach is demonstrated by analysis of the dominant numerical errors, as well as by numerical experiments. We demonstrate the ability of the algorithm to provide accurate answers regardless of plasma collisionality on a circular axisymmetric tokamak geometry.

97 MATHEMATICS AND COMPUTING↗

Structure-preserving neural networks for the regularized entropy-based closure of a linear, kinetic, radiative transport equation

The main challenge of large-scale numerical simulation of radiation transport is the high memory and computation time requirements of discretization methods for kinetic equations. In this work, we derive and investigate a neural network-based approximation to the entropy-based closure method to accurately compute the solution of the multi-dimensional moment system with a low memory footprint and competitive computational time. We extend methods developed for the standard entropy-based closure to the regularized entropy-based closures. The main idea is to interpret structure-preserving neural network approximations of the regularized entropy-based closure as a two-stage approximation to the original entropy-based closure. We conduct a numerical analysis of this approximation and investigate optimal parameter choices. Our numerical experiments demonstrate that the method has a much lower memory footprint than traditional methods with competitive computation times and simulation accuracy. The code and all trained networks are provided on GitHub.

entropy closure↗

Asymptotic-preserving semi-implicit finite volume scheme for extended magnetohydrodynamics

A Finite Volume (FV) scheme is developed for solving the extended magnetohydrodynamic (XMHD) equations, yielding accurate results in the ideal, resistive, and Hall MHD limits. This is accomplished by first re-writing the XMHD equations such that it allows the algorithm to retain the use of ideal MHD Riemann solvers and the constrained transport method to preserve divergence-free magnetic fields. Incorporation of electron inertia and displacement current introduces additional numerical stiffness which motivates a semi-implicit FV scheme that re-formulates the XMHD model as a relaxation system. The equations are then advanced in time using an explicit 2nd-order Runge–Kutta scheme with operator splitting applied to the implicit source term updates at each sub-stage. For additional numerical stability, a density-dependent slope limiter is implemented to increase flux diffusivity at low density regions where non-ideal effects become significant. The algorithm is subsequently implemented in a scalable adaptive mesh refinement (AMR) framework. As the new algorithm retains many aspects of the ideal MHD formulations, it asymptotes naturally to the ideal MHD limit. Moreover, it shows promising results at the resistive and Hall MHD limits. This is verified against reference test problems for ideal, resistive and Hall MHD.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dynamic in-situ imaging of methane hydrate formation and self-preservation in porous media

Here we present the results of dynamic in-situ 3D X-ray imaging of methane hydrates microstructure during methane hydrate formation and dissociation in sand samples. Short scanning times and high resolution provided by synchrotron X-rays allowed for better understanding of water movement and different types of gas-hydrate formation. Complementing previous observations, we conclude that the process of gas-hydrate formation is accompanied by the water movements caused by cryogenic water suction that happens in sequences of short fast movements with longer equilibrium states in between (when the water is immobile). Based on the 3D microstructure we identified two distinct types of gas-hydrate formation: (i) into the gas pockets and (ii) inside water volumes. For both mechanisms we do not see problems in gas or water supply to support the gas-hydrate formation. The rate of dissociation in the self-preservation mode (pressure drop at negative temperatures) appears to be different for these two types of gas hydrates. This means that the history of the gas-hydrate formation may influence its behaviour at the dissociation stage (e.g. gas-hydrate production).

58 GEOSCIENCES↗

Preservation of high glycolytic phenotype by establishing new acute lymphoblastic leukemia cell lines at physiologic oxygen concentration

Cancer cells typically exhibit increased glycolysis and decreased mitochondrial oxidative phosphorylation, and they continue to exhibit some elevation in glycolysis even under aerobic conditions. However, it is unclear whether cancer cell lines employ a high level of glycolysis comparable to that of the original cancers from which they were derived, even if their culture conditions are changed to physiologically relevant oxygen concentrations. From three childhood acute lymphoblastic leukemia (ALL) patients we established three new pairs of cell lines in both atmospheric (20%) and physiologic (bone marrow level, 5%) oxygen concentrations. Cell lines established in 20% oxygen exhibited lower proliferation, survival, expression of glycolysis genes, glucose consumption, and lactate production. Interestingly, the effects of oxygen concentration used during cell line initiation were only partially reversible when established cell cultures were switched from one oxygen concentration to another for eight weeks. These observations indicate that ALL cell lines established at atmospheric oxygen concentration can exhibit relatively low levels of glycolysis and these levels are semi-permanent, suggesting that physiologic oxygen concentrations may be needed from the time of cell line initiation to preserve the high level of glycolysis commonly exhibited by leukemias in vivo. - Highlights: • Establishing new ALL cell lines in 5% oxygen resulted in higher glycolytic expression and function. • Establishing new ALL cell lines in 5% oxygen resulted in higher proliferation and lower cell death. • The divergent metabolic phenotypes selected in 5% and 20% oxygen are semi-permanent.

60 APPLIED LIFE SCIENCES↗

A structure-preserving machine learning framework for accurate prediction of structural dynamics for systems with isolated nonlinearities

The nonlinearities present in structural systems are often found in isolated regions within the structure, such as those containing joints or interfaces. However, despite the localized nature of these nonlinearities their presence serves to couple together the modes of the underlying linear system and significantly complicate the development of appropriate reduced-order models; the localized nonlinearities have a global effect on the dynamics of the system. Further, in the presence of evolving structural health the nonlinearities can arise from accumulating damage, with dynamics distinct from those observed in the healthy state. The present work develops a data-driven formulation to identify and include the contributions of the isolated nonlinearities on the dynamics of the underlying linear structure. A novel coordinate separation is developed that decomposes those nonlinearities restricted to the isolated subdomain from the known linear system defined over the entire domain, and the influence of the isolated nonlinearities is reintroduced as an appropriately identified traction at the boundary of the isolated subdomain, referred to as the deviatoric force. In the region exterior to the nonlinear subdomain the response of the ideal linear system recovers that of the original nonlinear system. In this work, the deviatoric force component is predicted using a structure-preserving multilayer perceptron, based only on measured responses at the boundary of the isolated subdomain. Therefore introduction of the perceptron is able to bypass the direct numerical simulation of the nonlinearities within the isolated subdomain. This approach is illustrated through a simple structural system in which an interior region contains cubic nonlinearities and hysteretic damping. Once trained, the machine learning system is able to accurately predict the deviatoric force so that the ideal system recovers the response of the original system in the region outside the isolated nonlinear subdomain. Moreover, the data-driven approach is able to accurately predict the response when the system is subject to differing initial conditions and external excitation without the need for retraining, so that the proposed approach provides a robust description of the structural dynamics of the overall system.

Machine learning↗

Classical Optimal Control for Energy Minimization Based On Diffeomorphic Modulation under Observable-Response-Preserving Homotopy

In this work, we introduce the so-called “Classical Optimal Control Optimization” (COCO) method for global energy minimization based on the implementation of the diffeomorphic modulation under observable-response-preserving homotopy (DMORPH) gradient algorithm. A probe particle with time-dependent mass $m(t;β)$ and dipole $μ(r,t;β)$ is evolved classically on the potential energy surface $V(r)$ coupled to an electric field $E(t;β)$, as described by the time-dependent density of states represented on a grid, or otherwise as a linear combination of Gaussians generated by the k-means clustering algorithm. Control parameters $β$ defining $m(t;β), μ(r,t;β),$ and $E(t;β)$ are optimized by following the gradients of the energy with respect to $β,$ adapting them to steer the particle toward the global minimum energy configuration. We find that the resulting COCO algorithm is capable of resolving near-degenerate states separated by large energy barriers and successfully locates the global minima of golf potentials on flat and rugged surfaces, previously explored for testing quantum annealing methodologies and the quantum optimal control optimization (QuOCO) method. Preliminary results show successful energy minimization of multidimensional Lennard-Jones clusters. Beyond the analysis of energy minimization in the specific model systems investigated, we anticipate COCO should be valuable for solving minimization problems in general, including optimization of parameters in applications to machine learning and molecular structure determination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Preserving Symmetry and Degeneracy in the Localized Orbital Scaling Correction Approach

Symmetry is a fundamental concept that plays a critical role in many chemical and physical phenomena and processes, which highlights the importance of theoretical methods to correctly handle symmetry. The recently developed localized orbital scaling correction (LOSC1) shows great improvement on the description of band gaps, photoemission spectra, and dissociation limits of cationic species. However, issues remain with LOSC1 in dealing with the symmetry and degeneracy of electronic states, which are also relevant to other methods using localization. In this work, we utilize a new method that deals with the physical-space and the energy-space localization on an equal footing. The resulting localized orbitals, i.e., orbitalets, are able to maintain more symmetry and the desired state degeneracy, which is important in calculating the electronic structure of both molecules and periodic bulk systems. Furthermore, the curvature matrix is redefined to improve potential energy curves for systems with stretched bonds, while retaining the correct dissociation limits. This new approach, termed LOSC2, includes only two fitting parameters. It maintains accuracy similar to that of LOSC1 over many properties, while overcoming LOSC1’s deficiencies in symmetry and degeneracy. Our tests have shown that LOSC2 orbitalets possess the full- or subgroup of molecular symmetry if allowed, which preserves the state degeneracy. Tests on differently sized planar annulenes, odd-numbered allenes, and triphenylene again verify that LOSC2 is able to maintain the state degeneracy, while LOSC1 cannot. Finally, all the tests demonstrate the advantage of LOSC2 in the calculation of molecular systems and its potential for application to periodic bulk systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗