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At least 577 records · Page 32

PDE-constrained high-order mesh optimization

Here, we present a novel framework for PDE-constrained r-adaptivity of high-order meshes. The proposed method formulates mesh movement as an optimization problem, with an objective function defined as a convex combination of a mesh quality metric and a measure of the accuracy of the PDE solution obtained via finite element discretization. The proposed formulation achieves optimized, well-defined high-order meshes by integrating mesh quality control, PDE solution accuracy, and robust gradient regularization. We adopt the Target-Matrix Optimization Paradigm to control geometric properties across the mesh, independent of the PDE of interest. To incorporate the accuracy of the PDE solution, we introduce error measures that control the finite element discretization error. The implicit dependence of these error measures on the mesh nodal positions is accurately captured by adjoint sensitivity analysis. Additionally, a convolution-based gradient regularization strategy is used to ensure stable and effective adaptation of high-order meshes. We demonstrate that the proposed framework can improve mesh quality and reduce the error by up to 10 times for the solution of Poisson and linear elasto-static problems. The approach is general with respect to the dimensionality, the order of the mesh, the types of mesh elements, and can be applied to any PDE that admits well-defined adjoint operators.

Computer science↗

F-Hash: Feature-Based Hash Design for Time-Varying Volume Visualization via Multi-Resolution Tesseract Encoding

Interactive time-varying volume visualization is challenging due to its complex spatiotemporal features and sheer size of the dataset. Recent works transform the original discrete time-varying volumetric data into continuous Implicit Neural Representations (INR) to address the issues of compression, rendering, and super-resolution in both spatial and temporal domains. However, training the INR takes a long time to converge, especially when handling large-scale time-varying volumetric datasets. In this work, we proposed F-Hash, a novel feature-based multi-resolution Tesseract encoding architecture to greatly enhance the convergence speed compared with existing input encoding methods for modeling time-varying volumetric data. The proposed design incorporates multi-level collision-free hash functions that map dynamic 4D multi-resolution embedding grids without bucket waste, achieving high encoding capacity with compact encoding parameters. Our encoding method is agnostic to time-varying feature detection methods, making it a unified encoding solution for feature tracking and evolution visualization. Experiments show the F-Hash achieves state-of-the-art convergence speed in training various time-varying volumetric datasets for diverse features. We also proposed an adaptive ray marching algorithm to optimize the sample streaming for faster rendering of the time-varying neural representation.

deep learning↗

An Optimized Multicolor Point-Implicit Solver for Unstructured Grid Applications on Graphics Processing Units

In the field of computational fluid dynamics, the Navier-Stokes equations are often solved using an unstructuredgrid approach to accommodate geometric complexity. Implicit solution methodologies for such spatial discretizations generally require frequent solution of large tightly-coupled systems of block-sparse linear equations. The multicolor point-implicit solver used in the current work typically requires a significant fraction of the overall application run time. In this work, an efficient implementation of the solver for graphics processing units is proposed. Several factors present unique challenges to achieving an efficient implementation in this environment. These include the variable amount of parallelism available in different kernel calls, indirect memory access patterns, low arithmetic intensity, and the requirement to support variable block sizes. In this work, the solver is reformulated to use standard sparse and dense Basic Linear Algebra Subprograms (BLAS) functions. However, numerical experiments show that the performance of the BLAS functions available in existing CUDA libraries is suboptimal for matrices representative of those encountered in actual simulations. Instead, optimized versions of these functions are developed. Depending on block size, the new implementations show performance gains of up to 7x over the existing CUDA library functions.

Zubair, Mohammad↗

Continuously differentiable PIC shape functions for triangular meshes

In this study, a new class of continuously-differentiable shape functions is developed and applied to two-dimensional electrostatic PIC simulation on an unstructured simplex (triangle) mesh. It is shown that troublesome aliasing instabilities are avoided for cold plasma simulation in which the Debye length is as small as 0.01 cell sizes. These new shape functions satisfy all requirements for PIC particle shape. They are non-negative, have compact support, and partition unity. They are given explicitly by cubic expressions in the usual triangle logical (areal) coordinates. The shape functions are not finite elements because their structure depends on the topology of the mesh, in particular, the number of triangles neighboring each mesh vertex. Nevertheless, they may be useful as approximations to solution of other problems in which continuity of derivatives is required or desired.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An exploratory study of a finite difference method for calculating unsteady transonic potential flow

A method for calculating transonic flow over steady and oscillating airfoils was developed by Isogai. The full potential equation is solved with a semi-implicit, time-marching, finite difference technique. Steady flow solutions are obtained from time asymptotic solutions for a steady airfoil. Corresponding oscillatory solutions are obtained by initiating an oscillation and marching in time for several cycles until a converged periodic solution is achieved. The method is described in general terms and results for the case of an airfoil with an oscillating flap are presented for Mach numbers 0.500 and 0.875. Although satisfactory results are obtained for some reduced frequencies, it is found that the numerical technique generates spurious oscillations in the indicial response functions and in the variation of the aerodynamic coefficients with reduced frequency. These oscillations are examined with a dynamic data reduction method to evaluate their effects and trends with reduced frequency and Mach number. Further development of the numerical method is needed to eliminate these oscillations.

Bennett, R. M.↗

On the molecular correlations that result in field-dependent conductivities in electrolyte solutions

Employing recent advances in response theory and nonequilibrium ensemble reweighting, we study the dynamic and static correlations that give rise to an electric field-dependent ionic conductivity in electrolyte solutions. We consider solutions modeled with both implicit and explicit solvents, with different dielectric properties, and at multiple concentrations. Implicit solvent models at low concentrations and small dielectric constants exhibit strongly field-dependent conductivities. We compare these results to Onsager-Wilson theory of the Wien effect, which provides a qualitatively consistent prediction at low concentrations and high static dielectric constants but is inconsistent away from these regimes. The origin of the discrepancy is found to be increased ion correlations under these conditions. Explicit solvent effects act to suppress nonlinear responses, yielding a weakly field-dependent conductivity over the range of physically realizable field strengths. By decomposing the relevant time correlation functions, we find that the insensitivity of the conductivity to the field results from the persistent frictional forces on the ions from the solvent. Our findings illustrate the utility of nonequilibrium response theory in rationalizing nonlinear transport behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit

In this study, molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. As a result, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.

97 MATHEMATICS AND COMPUTING↗

On the use of wall functions as boundary conditions for two-dimensional separated compressible flows

A new and improved wall function method for compressible turbulent flows has been developed and tested. This method is applicable to attached and separated flows, to both high- and low-Reynolds number flows, and to flows with adiabatic and nonadiabatic surfaces. This wall function method has been applied to the Launder-Spalding k-epsilon two-equation model of turbulence. The tests consist of comparisons of calculated and experimental results for: (1) an axisymmetrical transonic shock-wave/boundary-wave interaction flow at low Reynolds number in an adiabatic tube, (2) an axisymmetrical high-Reynolds number transonic flow over a nonadiabatic bump, and (3) a two-dimensional supersonic high-Reynolds number flow on a nonadiabatic deflected flap. Each of these experiments had significant regions of flow separation. The calculations are performed with an implicit algorithm that solves the Reynolds-averaged Navier-Stokes equations. It is shown that the results obtained agree very well with the data for the complex compressible flows tested.

Viegas, J. R.↗

Inter-Domain Fusion for Enhanced Intrusion Detection in Power Systems: An Evidence Theoretic and Meta-Heuristic Approach

False alerts due to misconfigured or compromised intrusion detection systems (IDS) in industrial control system (ICS) networks can lead to severe economic and operational damage. However, research using deep learning to reduce false alerts often requires the physical and cyber sensor data to be trustworthy. Implicit trust is a major problem for artificial intelligence or machine learning (AI/ML) in cyber-physical system (CPS) security, because when these solutions are most urgently needed is also when they are most at risk (e.g., during an attack). To address this, the Inter-Domain Evidence theoretic Approach for Inference (IDEA-I) is proposed that reframes the detection problem as how to make good decisions given uncertainty. Specifically, an evidence theoretic approach leveraging Dempster–Shafer (DS) combination rules and their variants is proposed for reducing false alerts. A multi-hypothesis mass function model is designed that leverages probability scores obtained from supervised-learning classifiers. Using this model, a location-cum-domain-based fusion framework is proposed to evaluate the detector’s performance using disjunctive, conjunctive, and cautious conjunctive rules. The approach is demonstrated in a cyber-physical power system testbed, and the classifiers are trained with datasets from Man-In-The-Middle attack emulation in a large-scale synthetic electric grid. For evaluating the performance, we consider plausibility, belief, pignistic, and general Bayesian theorem-based metrics as decision functions. To improve the performance, a multi-objective-based genetic algorithm is proposed for feature selection considering the decision metrics as the fitness function. Finally, we present a software application to evaluate the DS fusion approaches with different parameters and architectures.

42 ENGINEERING↗

A structural model of the adaptive human pilot

A compensatory tracking model of the human pilot is offered which attempts to provide a more realistic representation of the human's signal processing structure than that which is exhibited by pilot models currently in use. Two features of the model distinguish it from other representations of the human pilot. First, proprioceptive information from the control stick or manipulator constitutes one of the major feedback paths in the model, providing feedback of vehicle output rate due to control activity. Implicit in this feedback loop is a model of the vehicle dynamics which is valid in and beyond the region of crossover. Second, error-rate information is continuously derived and independently but intermittently controlled. An output injected remnant model is offered and qualitatively justified on the basis of providing a measure of the effect of inaccuracies such as time variations in the pilot's internal model of the controlled element dynamics. The data from experimental tracking tasks involving five different controlled element dynamics and one nonideal viewing condition were matched with model generated describing functions and remnant power spectral densities.

Hess, R. A.↗

An unconditionally stable, time-implicit algorithm for solving the one-dimensional Vlasov–Poisson system

The development of an implicit, unconditionally stable, numerical method for solving the Vlasov–Poisson system in one dimension using a phase-space grid is presented. The algorithm uses the Crank–Nicolson discretization scheme and operator splitting allowing for direct solution of the finite difference equations. This method exactly conserves particle number, enstrophy and momentum. A variant of the algorithm which does not use splitting also exactly conserves energy but requires the use of iterative solvers. This algorithm has no dissipation and thus fine-scale variations can lead to oscillations and the production of negative values of the distribution function. We find that overall, the effects of negative values of the distribution function are relatively benign. We consider a variety of test cases that have been used extensively in the literature where numerical results can be compared with analytical solutions or growth rates. We examine higher-order differencing and construct higher-order temporal updates using standard composition methods.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ANALYTICAL THEORY FOR THE INITIAL MASS FUNCTION. III. TIME DEPENDENCE AND STAR FORMATION RATE

The present paper extends our previous theory of the stellar initial mass function (IMF) by including time dependence and by including the impact of the magnetic field. The predicted mass spectra are similar to the time-independent ones with slightly shallower slopes at large masses and peak locations shifted toward smaller masses by a factor of a few. Assuming that star-forming clumps follow Larson-type relations, we obtain core mass functions in good agreement with the observationally derived IMF, in particular, when taking into account the thermodynamics of the gas. The time-dependent theory directly yields an analytical expression for the star formation rate (SFR) at cloud scales. The SFR values agree well with the observational determinations of various Galactic molecular clouds. Furthermore, we show that the SFR does not simply depend linearly on density, as is sometimes claimed in the literature, but also depends strongly on the clump mass/size, which yields the observed scatter. We stress, however, that any SFR theory depends, explicitly or implicitly, on very uncertain assumptions like clump boundaries or the mass of the most massive stars that can form in a given clump, making the final determinations uncertain by a factor of a few. Finally, we derive a fully time dependent model for the IMF by considering a clump, or a distribution of clumps accreting at a constant rate and thus whose physical properties evolve with time. In spite of its simplicity, this model reproduces reasonably well various features observed in numerical simulations of converging flows. Based on this general theory, we present a paradigm for star formation and the IMF.

79 ASTRONOMY AND ASTROPHYSICS↗

Vibrational heat-bath configuration interaction with semistochastic perturbation theory using harmonic oscillator or VSCF modals

Vibrational heat-bath configuration interaction (VHCI)—a selected configuration interaction technique for vibrational structure theory—has recently been developed in two independent works [J. H. Fetherolf and T. C. Berkelbach, J. Chem. Phys. 154, 074104 (2021); A. U. Bhatty and K. R. Brorsen, Mol. Phys. 119, e1936250 (2021)], where it was shown to provide accuracy on par with the most accurate vibrational structure methods with a low computational cost. Here, we eliminate the memory bottleneck of the second-order perturbation theory correction using the same (semi)stochastic approach developed previously for electronic structure theory. This allows us to treat, in an unbiased manner, much larger perturbative spaces, which are necessary for high accuracy in large systems. Stochastic errors are easily controlled to be less than 1 cm−1. We also report two other developments: (i) we propose a new heat-bath criterion and an associated exact implicit sorting algorithm for potential energy surfaces expressible as a sum of products of one-dimensional potentials; (ii) we formulate VHCI to use a vibrational self-consistent field (VSCF) reference, as opposed to the harmonic oscillator reference configuration used in previous reports. Our tests are done with quartic and sextic force fields, for which we find that with VSCF, the minor improvements to accuracy are outweighed by the higher computational cost associated the matrix element evaluations. We expect VSCF-based VHCI to be important for more general potential representations, for which the harmonic oscillator basis function integrals are no longer analytic.

Chemistry↗

A Mixed-Method Design Approach for Empirically Based Selection of Unbiased Data Annotators

Implicit bias embedded in the annotated data is by far the greatest impediment in the effectual use of supervised machine learning models in tasks involving race, ethics, and geopolitical polarization. For societal good and demonstrable positive impact on wider society, it is paramount to carefully select data annotators and rigorously validate the annotation process. Current approaches to selecting annotators are not sufficiently grounded in scientific principles and are limited at the policy-guidance level, thereby rendering them unusable for machine learning practitioners. This work proposes a new approach based on the mixed-methods design that is functional, adaptable, and simpler to implement in selecting unbiased annotators for any machine learning problem. By demonstrating it on a real-world geopolitical problem, we also identified and ranked key inane profile characteristics towards an empirically-based selection of unbiased data annotators.

Thakur, Gautam Malviya↗

Conservative DG method for the micro-macro decomposition of the Vlasov–Poisson–Lenard–Bernstein model

The micro-macro (mM) decomposition approach is considered for the numerical solution of the Vlasov– Poisson–Lenard–Bernstein (VPLB) system, which is relevant for plasma physics applications. In the mM approach, the kinetic distribution function is decomposed as $f$ = $\mathscr{E}$[$ρ_f$] + g , where $\mathscr{E}$ is a local equilibrium distribution, depending on the macroscopic moments $ρ_f$ = $∫_{\mathbb{R}}$ $efdv$ = $\langle$$ef$$\rangle$$_{\mathbb{R}}$, where e = (1, $v$, $\frac{1}{2}$ $v^2$) T , and $g$, the microscopic distribution, is defined such that $\langle$$eg$$\rangle$$_{\mathbb{R}}$ = 0. We aim to design numerical methods for the mM decomposition of the VPLB system, which consists of coupled equations for $ρ_f$ and $g$. To this end, we use the discontinuous Galerkin (DG) method for phase-space discretization, and implicit-explicit (IMEX) time integration, where the phase-space advection terms are integrated explicitly and the collision operator is integrated implicitly. We give special consideration to ensure that the resulting mM method maintains the $\langle$$eg$$\rangle$$_{\mathbb{R}}$ = 0 constraint, which may be necessary for obtaining (i) satisfactory results in the collision dominated regime with coarse velocity resolution, and (ii) unambiguous conservation properties. The constraint-preserving property is achieved through a consistent discretization of the equations governing the micro and macro components. Here, we present numerical results that demonstrate the performance of the mM method. The mM method is also compared against a corresponding DG-IMEX method solving directly for $f$.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Repeated cascade theory of homogeneous turbulence.

The problem of turbulent spectrum engenders two coupled hierarchies: one originates from the development of stress, leading to a transfer function, and the other from the development of an eddy viscosity. In order to incorporate physical roles among scales, the turbulent velocity fluctuation is decomposed into a series of ranks in the increasing order of randomness, contributing successively to energy or stress, eddy viscosity, relaxation frequency, and higher-rank frequencies in the memory chain. As a result, the first hierarchy mentioned above becomes closed at the quadrupole correlation. The second hierarchy governs the eddy viscosities of different ranks, related to relaxation frequencies of such ranks, in the form of a memory chain. It is cut off by an implicit viscous mechanism. For zero wind gradient, the spectrum in the inertial subrange recovers the Kolmogoroff k to the minus 5/3 law with a numerical constant 1.58, in good agreement with experiments. For a strong wind gradient, the spectrum in the production subrange has a k to the minus 1 law.

Tchen, C. M.↗

brulilo, Version 0.x

brulilo is a Python package for building and evolving thermonuclear reaction networks, such as those used in astrophysical explosion calculations. It is very much a current work in progress, and much of the intended functionality is still under development. The main goal of brulilo is an easy-to-use code for quick calculations or post-processing, as well as a learning tool to test various implementations of solvers on both CPUs and GPUs. Currently, brulilo parses an input text file that specifies the reactions to be included in the network. The notation of the inputs are in the typical astrophysical notation; i.e. hydrogen burning to deuterium in the sun, "p + p + e --> d + neutrino", is given as "p(p,)d." Each reaction is added to a list comprising the reaction network, and once completed, the network contains a list of all isotopes and reactions involved. brulilo then parses publicly available nuclear data (binding energy, spin, partition function data, etc.) for each isotope from the WebNucleo group's data at nucleo.ces.clemson.edu. Fits to reaction rate data for each reaction are obtained from the publicly available data provided by the Joint Institute for Nuclear Astrophysics' Reaclib database. Reverse reactions are calculated from detailed balance. The reaction network then consists of a sparse system of mathematically stiff ordinary differential equations (ODEs). Physically, "stiffness" here means that there are some reaction rates that are occurring much faster than others; the ratio of the fast to slow often being greater than 10^15 in astrophysics. Numerical integration of such systems typically involves implicit integration schemes, which brulilo will leverage from the scientific computing Python package, Numpy, as well as implement its own. There has recently been work from researchers at Oak Ridge National Lab who have found good results from applying quasi-equilibrium and quasi-asymptotic conditions to the stiff system of ODEs, which effectively remove some of the stiffness and allow for efficient explicit integration techniques to be used. The original intent of brulilo was to implement these stiffness-alleviating techniques with explicit integrators and compare the performance to traditional implicit integrations of the full stiff system. This is still underway, as the code is very much in an alpha-release state. Furthermore, explicit integrators are often much easier to parallelize than their implicit counterparts. brulilo will implement parallelization of these techniques, leveraging both the Python implementation of MPI, mpi4py, as well as highly parallelized versions targeted at GPUs with PyOpenCL and/or PyCUDA.

Malone, Chris↗

Fierro Version 2.x

FIERRO is a parallel C++ code designed to simulate fluid mechanics, heat transfer, and solid mechanics in two- and three-dimensional space. FIERRO is written to run on homogeneous (CPU) and heterogeneous (CPU+GPU) high performance computing machines. Fierro can aid a) modeling and design efforts that have historically relied on commercial implicit and explicit finite element codes, b) numerical methods research, c) manufacturing research, and d) computer science research. The code contains diverse numerical methods to solve the governing physics equations for both quasi-static and dynamic problems. Mathematical optimization solvers are coupled to the numerical methods to research topology and shape optimization that has application to additive manufacturing, and to create novel numerical approaches. Phase-field methods with micromechanical solvers are provided to simulate microstructure formation and evolution in manufacturing processes. The micromechanical solvers can also help research efforts create continuum-scale constitutive models for solids, as a function of the microstructure, in situ in a calculation or in a stand-alone manner. No physical data exists within the code.

Morgan, Nathaniel↗