Data assimilation for unsaturated flow models with restart adaptive probabilistic collocation based Kalman filter
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Man, Jun (ORCID:0000000183740773)↗
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Non-intrusive reduced order modeling of natural convection in porous media using convolutional autoencoders: Comparison with linear subspace techniques
Natural convection in porous media is a highly nonlinear multiphysical problem relevant to many engineering applications (e.g., the process of CO 2 sequestration). Here, we extend and present a non-intrusive reduced order model of natural convection in porous media employing deep convolutional autoencoders for the compression and reconstruction and either radial basis function (RBF) interpolation or artificial neural networks (ANNs) for mapping parameters of partial differential equations (PDEs) on the corresponding nonlinear manifolds. To benchmark our approach, we also describe linear compression and reconstruction processes relying on proper orthogonal decomposition (POD) and ANNs. Further, we present comprehensive comparisons among different models through three benchmark problems. The reduced order models, linear and nonlinear approaches, are much faster than the finite element model, obtaining a maximum speed-up of 7 × 10 6 because our framework is not bound by the Courant–Friedrichs–Lewy condition; hence, it could deliver quantities of interest at any given time contrary to the finite element model. Our model’s accuracy still lies within a relative error of 7% in the worst-case scenario. We illustrate that, in specific settings, the nonlinear approach outperforms its linear counterpart and vice versa. We hypothesize that a visual comparison between principal component analysis (PCA) and t-Distributed Stochastic Neighbor Embedding (t-SNE) could indicate which method will perform better prior to employing any specific compression strategy.
97 MATHEMATICS AND COMPUTING↗
A high-order computational framework for particle-resolved simulations of disperse multiphase flows
This work presents a high-order numerical approach for particle-resolved simulations of disperse multiphase flows, where the Navier-Stokes equations for fluid flow are solved using a high-order spectral element method in the Eulerian framework, and the particle phase is directly simulated with a discrete element method. The coupling between particles and fluids is explicitly handled using an adapted direct-forcing immersed boundary method. Unlike the conventional schemes, a high-order barycentric Lagrange interpolation method and a Gaussian projection kernel are used to ensure accurate momentum exchange between local boundary points and surrounding fluid nodes in the framework of high-order fluid solver. Benchmark tests of increasing complexity are conducted to demonstrate the accuracy and efficiency of our method. Here, it is found that our approach exhibits an excellent convergence performance, as the fluid element/grid is refined and the number of boundary points increases. Compared to conventional low-order methods, the proposed high-order framework enables the use of substantially larger fluid elements while maintaining high accuracy in modeling fluid-particle interactions, owing to the enhanced resolution of high-order basis functions. Moreover, since the primary unknowns are stored at element or grid nodes, the high-order approach offers improved efficiency in both CPU memory usage and total computational cost.
42 ENGINEERING↗
Dynamic Performance Enhancement for Nonlinear Stochastic Systems Using RBF Driven Nonlinear Compensation with Extended Kalman Filter
In this paper, a novel hybrid control method is proposed to enhance the control performance of the PI based control system for a class of nonlinear and non-Gaussian stochastic dynamic processes with unmeasurable states. Firstly, to enhance the tracking performance of the PI controller where the PI parameters are fixed in many actual control systems, the compensative signal is formed using the extended Kalman filter(EKF) based state estimator and driven by the radial basis function (RBF) neural network based compensator. In addition, the weights of RBF is trained to minimize the entropy criterion of tracking error as the process is subjected to non-Gaussian disturbances. Meanwhile, since the precise statistical property of noises is hard to obtain for many industrial processes, the kernel density estimation (KDE) technique is employed in this paper to estimate the entropy. The convergence of RBF network is discussed and the stability of the resulted closed-loop hybrid control system is analyzed in mean square sense. Finally, a numerical example and a practical system testing are given to illustrate the effectiveness of the proposed control method.
stochastic systems, PI Controller, Entropy, Extend↗
Kinetics-Informed Neural Networks
Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize feed-forward artificial neural networks as basis functions to solve ordinary differential equations (ODEs) constrained by differential algebraic equations (DAEs) that describe microkinetic models (MKMs). We present an algebraic framework for the mathematical description and classification of reaction networks, types of elementary reaction, and chemical species. Under this framework, we demonstrate that the simultaneous training of neural nets and kinetic model parameters in a regularized multi-objective optimization setting leads to the solution of the inverse problem through the estimation of kinetic parameters from synthetic experimental data. We analyze a set of scenarios to establish the extent to which kinetic parameters can be retrieved from transient kinetic data, and assess the robustness of the methodology with respect to statistical noise. Furthermore, this approach to inverse kinetic ODEs can assist in the elucidation of reaction mechanisms based on transient data.
36 MATERIALS SCIENCE↗
PetIGA: A framework for high-performance isogeometric analysis
We present PetIGA, a code framework to approximate the solution of partial differential equations using isogeometric analysis. PetIGA can be used to assemble matrices and vectors which come from a Galerkin weak form, discretized with Non-Uniform Rational B-spline basis functions. We base our framework on PETSc, a high-performance library for the scalable solution of partial differential equations, which simplifies the development of large-scale scientific codes, provides a rich environment for prototyping, and separates parallelism from algorithm choice. We describe the implementation of PetIGA, and exemplify its use by solving a model nonlinear problem. To illustrate the robustness and flexibility of PetIGA, we solve some challenging nonlinear partial differential equations that include problems in both solid and fluid mechanics. Lastly, we show strong scaling results on up to 4096 cores, which confirm the suitability of PetIGA for large scale simulations.
97 MATHEMATICS AND COMPUTING↗
Multiscale topology optimization using neural network surrogate models
In this study, we are concerned with optimization of macroscale elastic structures that are designed utilizing spatially varying microscale metamaterials. The macroscale optimization is accomplished using gradient-based nonlinear topological optimization. But instead of using density as the optimization decision variable, the decision variables are the multiple parameters that define the local microscale metamaterial. This is accomplished using single layer feedforward Gaussian basis function networks as a surrogate models of the elastic response of the microscale metamaterial. The surrogate models are trained using highly resolved continuum finite element simulations of the microscale metamaterials and hence are significantly more accurate than analytical models e.g. classical beam theory. Because the derivative of the surrogate model is important for sensitivity analysis of the macroscale topology optimization, a neural network training procedure based on the Sobolev norm is described. Since the SIMP method is not appropriate for spatially varying lattices, an alternative method is developed to enable creation of void regions. Lastly, the efficacy of this approach is demonstrated via several examples in which the optimal graded metamaterial outperforms a traditional solid structure.
42 ENGINEERING↗
Modeling strong discontinuities in the material point method using a single velocity field
We propose a new way to include strong velocity discontinuities in the material point method (MPM). We use the recent idea of damage gradient partitioning to dynamically determine whether or not deformed locations of material points are on the same side of a discontinuity as each node of a finite element discretization of the Eulerian velocity field. Velocity basis functions associated with the finite element nodes are then altered to ensure that their contributions to discontinuous components of the velocity are supported only at points assigned to the same side of the discontinuity. The partitioning of material points relative to each finite element node eliminates the need for indexing partitions, and accommodates discontinuities that do not partition material into disjoint bodies (e.g., propagating cracks). By building velocity discontinuities directly into the approximation space, sliding contact, separation, and multi-body interaction are possible within a single velocity field. The methodology avoids the need to track contact surfaces, construct and evolve explicit cracks, or use multiple velocity fields. Several numerical examples are computed to support these claims. The examples are also compared to the conventional MPM, demonstrating the method’s superiority in dealing with sliding contact and separation.
42 ENGINEERING↗
A configurational force for adaptive re-meshing of gradient-enhanced poromechanics problems with history-dependent variables
Here, we introduce a mesh-adaption framework that employs a multi-physical configurational force and Lie algebra to capture multiphysical responses of fluid-infiltrating geological materials while maintaining the efficiency of the computational models. To resolve sharp gradients of both displacement and pore pressure, we introduce an energy-estimate-free re-meshing criterion by extending the configurational force theory to consider the energy dissipation due to the fluid diffusion and the gradient-dependent plastic flow. To establish new equilibria after remeshing, the local tensorial history-dependent variables at the integration points are first decomposed into spectral forms. Then, the principal values and directions are projected onto smooth fields interpolated by the basis function of the finite element space via the Lie-algebra mapping. Our numerical results indicate that this Lie algebra operator in general leads to a new trial state closer to the equilibrium than the ones obtained from the tensor component mapping approach. A new configurational force for dissipative fluid-infiltrating porous materials that exhibit gradient-dependent plastic flow is introduced such that the remeshing may accommodate the need to resolve the sharp pressure gradient as well as the strain localization. The predicted responses are found to be not influenced by the mesh size due to the micromorphic regularization, while the adaptive meshing enables us to capture the width of deformation bands without the necessity of employing fine mesh everywhere in the domain.
42 ENGINEERING↗
Galerkin formulations of isogeometric shell analysis: Alleviating locking with Greville quadratures and higher-order elements
Here we propose new quadrature schemes that asymptotically require only four in-plane points for Reissner–Mindlin shell elements and nine in-plane points for Kirchhoff–Love shell elements in B-spline and NURBS-based isogeometric shell analysis, independent of the polynomial degree p of the elements. The quadrature points are Greville abscissae associated with pth-order B-spline basis functions whose continuities depend on the specific Galerkin formulations, and the quadrature weights are calculated by solving a linear moment fitting problem in each parametric direction. The proposed shell element formulations are shown through numerical studies to be rank sufficient and to be free of spurious modes. The studies reveal comparable accuracy, in terms of both displacement and stress, compared with fully integrated spline-based shell elements, while at the same time reducing storage and computational cost associated with forming element stiffness and mass matrices and force vectors. The high accuracy with low computational cost makes the proposed quadratures along with higher-order spline bases, in particular polynomial orders, p = 5 and 6, good choices for alleviating membrane and shear locking in shells.
42 ENGINEERING↗
A hybrid meshfree discretization to improve the numerical performance of peridynamic models
Efficient and accurate calculation of spatial integrals is of major interest in the numerical implementation of peridynamics (PD). The standard way to perform this calculation is a particle-based approach that discretizes the strong form of the PD governing equation. This approach has rapidly been adopted by the PD community since it offers some advantages. Additionally, it is computationally cheaper than other available schemes, can conveniently handle material separation, and effectively deals with nonlinear PD models. Nevertheless, PD models are still computationally very expensive compared with those based on the classical continuum mechanics theory, particularly for large-scale problems in three dimensions. This results from the nonlocal nature of the PD theory which leads to interactions of each node of a discretized body with multiple surrounding nodes. Here, we propose a new approach to significantly boost the numerical efficiency of PD models. We propose a discretization scheme that employs a simple collocation procedure and is truly meshfree; i.e., it does not depend on any background integration cells. In contrast to the standard scheme, the proposed scheme requires a much smaller set of neighboring nodes (keeping the same physical length scale) to achieve a specific accuracy and is thus computationally more efficient. Our new scheme is applicable to the case of linear PD models and within neighborhoods where the solution can be approximated by smooth basis functions. Therefore, to fully exploit the advantages of both the standard and the proposed schemes, a hybrid discretization is presented that combines both approaches within an adaptive framework. The high performance of the developed framework is illustrated by several numerical examples, including brittle fracture and corrosion problems in two and three dimensions.
42 ENGINEERING↗
Two-body potential model based on cosine series expansion for ionic materials
There is a method to construct a two-body potential model for ionic materials with a Fourier series basis and we examine it. For this method, the coefficients of cosine basis functions are uniquely determined by solving simultaneous linear equations to minimize the sum of weighted mean square errors in energy, force and stress, where first-principles calculation results are used as the reference data. As a validation test of the method, potential models for magnesium oxide are constructed. The mean square errors appropriately converge with respect to the truncation of the cosine series. This result mathematically indicates that the constructed potential model is sufficiently close to the one that is achieved with the non-truncated Fourier series and demonstrates that this potential virtually provides minimum error from the reference data within the two-body representation. The constructed potential models work appropriately in both molecular statics and dynamics simulations, especially if a two-step correction to revise errors expected in the reference data is performed, and the models clearly outperform two existing Buckingham potential models that were tested. Moreover, the good agreement over a broad range of energies and forces with first-principles calculations should enable the prediction of materials behavior away from equilibrium conditions, such as a system under irradiation.
36 MATERIALS SCIENCE↗
CASM — A software package for first-principles based study of multicomponent crystalline solids
CASM is a software package that enables first-principles based studies of crystalline materials. It has been designed to treat coupled chemical, mechanical, vibrational, and magnetic degrees of freedom to determine ground state and finite temperature properties of crystals. The symmetry of the underlying parent crystal structure is used to enumerate perturbations of the parent crystal structure and generate derivative structures which can be input to first-principles calculations in order to explore the ground state energy landscape. CASM algorithmically constructs cluster expansions that fully couple discrete and continuous degrees of freedom, and generates highly efficient code to evaluate the cluster expansion basis functions. Widely used machine learning methods are integrated for fitting expansion coefficients to first-principle calculations. The fully parameterized cluster expansions can be combined with (kinetic) Monte Carlo methods to calculate finite temperature thermodynamic and kinetic properties. CASM Alloy Manager identifies distinct parent crystal structures in an alloy system, creating individual projects for each, and integrating the results. The integrated infrastructure facilitates the linkage between first-principles statistical mechanics predictions with higher length scale computational methods, such as phase field simulations. In conclusion, CASM projects are designed to be easy to share in repositories, to re-use, and to extend to include additional chemical species or types of degrees of freedom.
36 MATERIALS SCIENCE↗
Parallel derivative-free optimization for simulation-based design of behind-the-meter energy systems
In this work, the integrated design and dispatch of behind-the-meter or distributed resources (e.g. stationary battery storage and solar PV generation) is considered. A simulation-based framework is employed, generating high-fidelity results with closed-loop predictive control at a fine resolution, at the expense of high computational cost (several minutes to a few hours per design point). To address this challenge, parallel derivative-free design methods are considered. Four methods are compared, including state-of-the-art surrogate-based methods (Radial-Basis Functions and Gaussian processes) and sampling strategies, an evolutionary-based method, and a simple sequential grid refinement method. As a case study, two types of design problem with increasing complexity are considered, namely, the design of behind-the-meter resources (three design variables) and the inclusion of grid capacity (four design variables). The second yields a constrained design problem for which violations can only be determined after solving the computationally expensive simulation. For the three-dimensional case, all methods present a good performance, achieving a solution within 1% of the optimum after the first iteration, with the sequential grid refinement exhibiting the fastest convergence and achieving the best final objective value. This indicates that the parallel evaluation of multiple sampling points may be more important than the choice of method for small decision spaces. For the four-dimensional constrained case, the Genetic Algorithm presents the best tradeoff between performance and computational effort, while the rough objective function terrain generated by constraint violation penalties reduces the performance of surrogate-based methods. Contour plots with flat regions indicate flexibility in the optimal design and highlight the importance of characterizing the solution space.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Residual estimation for grid modification in wall-modeled large eddy simulation using unstructured high-order methods
Here, the accuracy and computational cost of a large eddy simulation are highly dependent on the computational grid. Building optimal grids manually from a priori knowledge is not feasible in most practical use cases; instead, solution-adaptive strategies can provide a robust and cost-efficient method to generate a grid with the desired accuracy. We adapt the residual estimation algorithm developed by Toosi and Larsson for Discontinuous Galerkin Spectral Elements Methods (DGSEM) to guide the grid-adaptation process. The core of the method is the computation of the estimated modeling residual using the polynomial basis functions used in DGSEM, and the averaging of the estimated residual over each element. The final method is assessed in multiple channel flow test cases and for the transonic flow over an airfoil, in both cases making use of mortar interfaces between elements with hanging nodes. The method is found to be robust and reliable, and to provide solutions on grids with significantly fewer elements at comparable accuracy compared to when using human-generated grids.
97 MATHEMATICS AND COMPUTING↗
Massively parallel and linear-scaling algorithm for second-order Moller–Plesset perturbation theory applied to the study of supramolecular wires
Here, we present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide–Expand–Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide–Expand–Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, where X is either OpenMP or OpenACC. We demonstrate strong and weak scalability of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the “resolution of the identity second-order Moller–Plesset perturbation theory” (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24 440 basis functions and 91 280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods.
97 MATHEMATICS AND COMPUTING↗
High-order finite element method for atomic structure calculations
We introduce featom, an open source code that implements a high-order finite element solver for the radial Schrödinger, Dirac, and Kohn-Sham equations. The formulation accommodates various mesh types, such as uniform or exponential, and the convergence can be systematically controlled by increasing the number and/or polynomial order of the finite element basis functions. The Dirac equation is solved using a squared Hamiltonian approach to eliminate spurious states. Here, to address the slow convergence of the $κ=±1$ states due to divergent derivatives at the origin, we incorporate known asymptotic forms into the solutions. We achieve a high level of accuracy (10 -8 Hartree) for total energies and eigenvalues of heavy atoms such as uranium in both Schrödinger and Dirac Kohn-Sham solutions. We provide detailed convergence studies and computational parameters required to attain commonly required accuracies. Finally, we compare our results with known analytic results as well as the results of other methods. In particular, we calculate benchmark results for atomic numbers (Z) from 1 to 92, verifying current benchmarks. We demonstrate significant speedup compared to the state-of-the-art shooting solver dftatom. An efficient, modular Fortran 2008 implementation, is provided under an open source, permissive license, including examples and tests, wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Partition of unity finite element method for quantum mechanical materials calculations
The current state of the art for large-scale quantum-mechanical simulations is the planewave (PW) pseudopotential method, as implemented in codes such as VASP, ABINIT, and many others. However, since the PW method uses a global Fourier basis, with strictly uniform resolution at all points in space, it suffers from substantial inefficiencies in calculations involving atoms with localized states, such as first-row and transition-metal atoms, and requires significant nonlocal communications, which limit parallel efficiency. Real-space methods such as finite-differences (FD) and finite-elements (FE) have partially addressed both resolution and parallel-communications issues but have been plagued by one key disadvantage relative to PW: excessive number of degrees of freedom (basis functions) needed to achieve the required accuracies. In this paper, we present a real-space partition of unity finite element (PUFE) method to solve the Kohn–Sham equations of density functional theory. In the PUFE method, we build the known atomic physics into the solution process using partition-of-unity enrichment techniques in finite element analysis. The method developed herein is completely general, applicable to metals and insulators alike, and particularly efficient for deep, localized potentials, as occur in calculations at extreme conditions of pressure and temperature. Full self-consistent Kohn–Sham calculations are presented for LiH, involving light atoms, and CeAl, involving heavy atoms with large numbers of atomic-orbital enrichments. We find that the new PUFE approach attains the required accuracies with substantially fewer degrees of freedom, typically by an order of magnitude or more, than the PW method. As a result, we compute the equation of state of LiH and show that the computed lattice constant and bulk modulus are in excellent agreement with reference PW results, while requiring an order of magnitude fewer degrees of freedom to obtain.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗