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In this paper, we present a new high-order discontinuous Galerkin (DG) method, in which neither a penalty parameter nor a stabilization parameter is needed. We refer to this method as penalty-free DG (\PFDG). In this method, the trial and test functions belong to the broken Sobolev space, in which the functions are in general discontinuous on the mesh skeleton and do not meet the Dirichlet boundary conditions. However, a subset can be distinguished in this space, where the functions are continuous and satisfy the Dirichlet boundary conditions, and this subset is called admissible. The trial solution is chosen to lie in an \emph{augmented} admissible subset, in which a small violation of the continuity condition is permitted. This subset is constructed by applying special augmented constraints to the linear combination of finite element basis functions. In this approach, all the advantages of the DG method are retained without the necessity of using stability parameters or numerical fluxes. Several benchmark problems in two dimensions (Poisson equation, linear elasticity, hyperelasticity, and biharmonic equation) on polygonal (triangles, quadrilateral and weakly convex polygons) meshes as well as a three-dimensional Poisson problem on hexahedral meshes are considered. Numerical results are presented that affirm the sound accuracy and optimal convergence of the method in the $L^2$ norm and the energy seminorm.

In this paper, we present a first-order Stress-Hybrid Virtual Element Method (SH-VEM) on six-noded triangular meshes for linear plane elasticity. We adopt the Hellinger--Reissner variational principle to construct a weak equilibrium condition and a stress based projection operator. On applying the divergence theorem to the weak strain-displacement relations, the stress projection operator is expressed in terms of the nodal displacements, which leads to a displacement-based formulation. This stress-hybrid approach assumes a globally continuous displacement field while the stress field is discontinuous across each element. The stress field is initially represented by divergence-free tensor polynomials based on Airy stress functions. However, for flexibility in choosing basis functions, we also present a formulation that uses a penalty term to enforce the element equilibrium conditions. This method is referred to as the Penalty Stress-Hybrid Virtual Element Method (PSH-VEM). Numerical results are presented for PSH-VEM and SH-VEM, and we compare their convergence to the composite triangle FEM and B-bar VEM on benchmark problems in linear elasticity. The SH-VEM converges optimally in the $L^2$ norm of the displacement, energy seminorm, and the $L^2$ norm of hydrostatic stress. Furthermore, the results reveal that PSH-VEM converges in most cases at a faster rate than the expected optimal rate, but it requires the selection of a suitably chosen penalty parameter., Comment: 49 pages, 49 figures

In this paper, we introduce new generalized barycentric coordinates (coined as {\em moment coordinates}) on nonconvex quadrilaterals and convex hexahedra with planar faces. This work draws on recent advances in constructing interpolants to describe the motion of the Filippov sliding vector field in nonsmooth dynamical systems, in which nonnegative solutions of signed matrices based on (partial) distances are studied. For a finite element with $n$ vertices (nodes) in $\mathbb{R}^2$, the constant and linear reproducing conditions are supplemented with additional linear moment equations to set up a linear system of equations of full rank $n$, whose solution results in the nonnegative shape functions. On a simple (convex or nonconvex) quadrilateral, moment coordinates using signed distances are identical to mean value coordinates. For signed weights that are based on the product of distances to edges that are incident to a vertex and their edge lengths, we recover Wachspress coordinates on a convex quadrilateral. Moment coordinates are also constructed on a convex hexahedra with planar faces. We present proofs in support of the construction and plots of the shape functions that affirm its properties.

We introduce \texttt{featom}, an open source code that implements a high-order finite element solver for the radial Schr\"odinger, 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. To address the slow convergence of the $\kappa=\pm1$ 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 Schr\"odinger 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 \texttt{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., Comment: 30 pages, 3 tables, 6 figures, accepted in Elsevier's Computer Physics Communications

In this paper, we propose a robust low-order stabilization-free virtual element method on quadrilateral meshes for linear elasticity that is based on the stress-hybrid principle. We refer to this approach as the Stress-Hybrid Virtual Element Method (SH-VEM). In this method, the Hellinger$-$Reissner variational principle is adopted, wherein both the equilibrium equations and the strain-displacement relations are variationally enforced. We consider small-strain deformations of linear elastic solids in the compressible and near-incompressible regimes over quadrilateral (convex and nonconvex) meshes. Within an element, the displacement field is approximated as a linear combination of canonical shape functions that are $\textit{virtual}$. The stress field, similar to the stress-hybrid finite element method of Pian and Sumihara, is represented using a linear combination of symmetric tensor polynomials. A 5-parameter expansion of the stress field is used in each element, with stress transformation equations applied on distorted quadrilaterals. In the variational statement of the strain-displacement relations, the divergence theorem is invoked to express the stress coefficients in terms of the nodal displacements. This results in a formulation with solely the nodal displacements as unknowns. Numerical results are presented for several benchmark problems from linear elasticity. We show that SH-VEM is free of volumetric and shear locking, and it converges optimally in the $L^2$ norm and energy seminorm of the displacement field, and in the $L^2$ norm of the hydrostatic stress., Comment: 38 pages, 37 figures

The choice of stabilization term is a critical component of the virtual element method (VEM). However, the theory of VEM provides only asymptotic guidance for selecting the stabilization term, which ensures convergence as the mesh size approaches zero, but does not provide a unique prescription for its exact form. Thus, the selection of a suitable stabilization term is often guided by numerical experimentation and analysis of the resulting solution, including factors such as stability, accuracy, and efficiency. In this paper, we establish a new link between VEM and generalized barycentric coordinates, in particular isoparametric finite elements as a specific case. This connection enables the interpretation of the stability as the energy of a particular function in the discrete space, commonly known as the `hourglass mode.' Through this approach, this study sheds light on how the virtual element solution depends on the stabilization term, providing insights into the behavior of the method in more general scenarios., Comment: 18 pages, 9 figures

We introduce a PDE-based node-to-element contact formulation as an alternative to classical, purely geometrical formulations. It is challenging to devise solutions to nonsmooth contact problem with continuous gap using finite element discretizations. We herein achieve this objective by constructing an approximate distance function (ADF) to the boundaries of solid objects, and in doing so, also obtain universal uniqueness of contact detection. Unilateral constraints are implemented using a mixed model combining the screened Poisson equation and a force element, which has the topology of a continuum element containing an additional incident node. An ADF is obtained by solving the screened Poisson equation with constant essential boundary conditions and a variable transformation. The ADF does not explicitly depend on the number of objects and a single solution of the partial differential equation for this field uniquely defines the contact conditions for all incident points in the mesh. Having an ADF field to any obstacle circumvents the multiple target surfaces and avoids the specific data structures present in traditional contact-impact algorithms. We also relax the interpretation of the Lagrange multipliers as contact forces, and the Courant--Beltrami function is used with a mixed formulation producing the required differentiable result. We demonstrate the advantages of the new approach in two- and three-dimensional problems that are solved using Newton iterations. Simultaneous constraints for each incident point are considered., Comment: Paper accepted in "Computational Mechanics"

In this paper, we present and compare four methods to enforce Dirichlet boundary conditions in Physics-Informed Neural Networks (PINNs) and Variational Physics-Informed Neural Networks (VPINNs). Such conditions are usually imposed by adding penalization terms in the loss function and properly choosing the corresponding scaling coefficients; however, in practice, this requires an expensive tuning phase. We show through several numerical tests that modifying the output of the neural network to exactly match the prescribed values leads to more efficient and accurate solvers. The best results are achieved by exactly enforcing the Dirichlet boundary conditions by means of an approximate distance function. We also show that variationally imposing the Dirichlet boundary conditions via Nitsche's method leads to suboptimal solvers., Comment: 22 pages, 45 figures

Physics-Informed Neural Networks (PINNs) are a class of deep learning neural networks that learn the response of a physical system without any simulation data, and only by incorporating the governing partial differential equations (PDEs) in their loss function. While PINNs are successfully used for solving forward and inverse problems, their accuracy decreases significantly for parameterized systems. PINNs also have a soft implementation of boundary conditions resulting in boundary conditions not being exactly imposed everywhere on the boundary. With these challenges at hand, we present first-order physics-informed neural networks (FO-PINNs). These are PINNs that are trained using a first-order formulation of the PDE loss function. We show that, compared to standard PINNs, FO-PINNs offer significantly higher accuracy in solving parameterized systems, and reduce time-per-iteration by removing the extra backpropagations needed to compute the second or higher-order derivatives. Additionally, FO-PINNs can enable exact imposition of boundary conditions using approximate distance functions, which pose challenges when applied on high-order PDEs. Through three examples, we demonstrate the advantages of FO-PINNs over standard PINNs in terms of accuracy and training speedup., Comment: 16 pages, 11 figures, Selected for ML4PS workshop at NeurIPS 2022

We present a higher order stabilization-free virtual element method applied to plane elasticity problems. We utilize a serendipity approach to reduce the total number of degrees of freedom from the corresponding high-order approximations. The well-posedness of the problem is numerically studied via an eigenanalysis. The method is then applied to several benchmark problems from linear elasticity and we show that the method delivers optimal convergence rates in $L^2$ norm and energy seminorm that match theoretical estimates as well as the convergence rates from higher order virtual element methods., Comment: 24 pages, 17 figures. arXiv admin note: text overlap with arXiv:2202.10037

In this paper, we study applications of the virtual element method (VEM) for simulating the deformation of multiphase composites. The VEM is a Galerkin approach that is applicable to meshes that consist of arbitrarily-shaped polygonal and polyhedral (simple and nonsimple) elements. In the VEM, the basis functions are defined as the solution of a local elliptic partial differential equation, and are never explicitly computed in the implementation of the method. The stifness matrix of each element is built by using the elliptic projection operator of the internal virtual work (bilinear form) and it consists of two terms: a consistency term that is exactly computed (linear patch test is satisfied) and a correction term (ensures stability) that is orthogonal to affine displacement fields and has the right scaling. The VEM simplifies mesh generation for a multiphase composite: a stiff inclusion can be modeled using a single polygonal or polyhedral element. Attributes of the virtual element approach are highlighted through comparisons with Voronoi-cell lattice models, which provide discrete representations of material structure. The comparisons involve a suite of two-dimensional linear elastic problems: patch test, axisymmetric circular inclusion problem, and the deformation of a three-phase composite. The simulations demonstrate the accuracy and flexibility of the virtual element method., Comment: 9 pages, 6 figures

We present the construction and application of a first order stabilization-free virtual element method to problems in plane elasticity. Well-posedness and error estimates of the discrete problem are established. The method is assessed on a series of well-known benchmark problems from linear elasticity and numerical results are presented that affirm the optimal convergence rate of the virtual element method in the $L^2$ norm and the energy seminorm., Comment: 38 pages, 11 figures

In this paper, we propose an eXtended Virtual Element Method (X-VEM) for two-dimensional linear elastic fracture. This approach, which is an extension of the standard Virtual Element Method (VEM), facilitates mesh-independent modeling of crack discontinuities and elastic crack-tip singularities on general polygonal meshes. For elastic fracture in the X-VEM, the standard virtual element space is augmented by additional basis functions that are constructed by multiplying standard virtual basis functions by suitable enrichment fields, such as asymptotic mixed-mode crack-tip solutions. The design of the X-VEM requires an extended projector that maps functions lying in the extended virtual element space onto a set spanned by linear polynomials and the enrichment fields. An efficient scheme to compute the mixed-mode stress intensity factors using the domain form of the interaction integral is described. The formulation permits integration of weakly singular functions to be performed over the boundary edges of the element. Numerical experiments are conducted on benchmark mixed-mode linear elastic fracture problems that demonstrate the sound accuracy and optimal convergence in energy of the proposed formulation.

In this paper, we use the first-order virtual element method (VEM) to investigate the effect of shape quality of polyhedra in the estimation of the critical time step for explicit three-dimensional elastodynamic finite element (FE) simulations. Low-quality finite elements are common when meshing realistic complex components, and while tetrahedral meshing technology is generally robust, meshing algorithms cannot guarantee high-quality meshes for arbitrary geometries or for non-water-tight computer-aided design models. For reliable simulations on such meshes, we consider FE meshes with tetrahedral and prismatic elements that have badly-shaped elements$-$tetrahedra with dihedral angles close to $0^\circ$ and $180^\circ$, and slender prisms with triangular faces that have short edges$-$and agglomerate such `bad' elements with neighboring elements to form a larger polyhedral virtual element. On each element, the element-eigenvalue inequality is used to estimate the critical time step. For a suite of illustrative finite element meshes with $\epsilon$ being a mesh-coordinate parameter that leads to poor mesh quality, we show that adopting VEM on the agglomerated polyhedra yield critical time steps that are insensitive as $\epsilon \rightarrow 0$. The significant reduction in solution time on meshes with agglomerated virtual elements vis-$\`a$-vis tetrahedral meshes is demonstrated through explicit dynamics simulations on a tapered beam., Comment: 32 pages, 30 figures

In this paper, we introduce a new approach based on distance fields to exactly impose boundary conditions in physics-informed deep neural networks. The challenges in satisfying Dirichlet boundary conditions in meshfree and particle methods are well-known. This issue is also pertinent in the development of physics informed neural networks (PINN) for the solution of partial differential equations. We introduce geometry-aware trial functions in artifical neural networks to improve the training in deep learning for partial differential equations. To this end, we use concepts from constructive solid geometry (R-functions) and generalized barycentric coordinates (mean value potential fields) to construct $\phi$, an approximate distance function to the boundary of a domain. To exactly impose homogeneous Dirichlet boundary conditions, the trial function is taken as $\phi$ multiplied by the PINN approximation, and its generalization via transfinite interpolation is used to a priori satisfy inhomogeneous Dirichlet (essential), Neumann (natural), and Robin boundary conditions on complex geometries. In doing so, we eliminate modeling error associated with the satisfaction of boundary conditions in a collocation method and ensure that kinematic admissibility is met pointwise in a Ritz method. We present numerical solutions for linear and nonlinear boundary-value problems over domains with affine and curved boundaries. Benchmark problems in 1D for linear elasticity, advection-diffusion, and beam bending; and in 2D for the Poisson equation, biharmonic equation, and the nonlinear Eikonal equation are considered. The approach extends to higher dimensions, and we showcase its use by solving a Poisson problem with homogeneous Dirichlet boundary conditions over the 4D hypercube. This study provides a pathway for meshfree analysis to be conducted on the exact geometry without domain discretization., Comment: 50 pages, 46 figures

This paper introduces the scaled boundary cubature (SBC) scheme for accurate and efficient integration of functions over polygons and two-dimensional regions bounded by parametric curves. Over two-dimensional domains, the SBC method reduces integration over a region bounded by $m$ curves to integration over $m$ regions (referred to as curved triangular regions), where each region is bounded by two line segments and a curve. With proper (counterclockwise) orientation of the boundary curves, the scheme is applicable to convex and nonconvex domains. Additionally, for star-convex domains, a tensor-product cubature rule with positive weights and integration points in the interior of the domain is obtained. If the integrand is homogeneous, we show that this new method reduces to the homogeneous numerical integration scheme; however, the SBC scheme is more versatile since it is equally applicable to both homogeneous and non-homogeneous functions. This paper also introduces several methods for smoothing integrands with point singularities and near-singularities. When these methods are used, highly efficient integration of weakly singular functions is realized. The SBC method is applied to a number of benchmark problems, which reveal its broad applicability and superior performance (in terms of time to generate a rule and accuracy per cubature point) when compared to existing methods for integration., Comment: 41 pages, 24 figures

In this paper, we compute the band structure of one- and two-dimensional phononic composites using the extended finite element method (X-FEM) on structured higher-order (spectral) finite element meshes. On using partition-of-unity enrichment in finite element analysis, the X-FEM permits use of structured finite element meshes that do not conform to the geometry of holes and inclusions. This eliminates the need for remeshing in phononic shape optimization and topology optimization studies. In two dimensions, we adopt rational B{\'e}zier representation of curved (circular) geometries, and construct suitable material enrichment functions to model two-phase composites. A Bloch-formulation of the elastodynamic phononic eigenproblem is adopted. Efficient computation of weak form integrals with polynomial integrands is realized via the homogeneous numerical integration scheme -- a method that uses Euler's homogeneous function theorem and Stokes's theorem to reduce integration to the boundary of the domain. Ghost penalty stabilization is used on finite elements that are cut by a hole. Band structure calculations on perforated (circular holes, elliptical holes, and holes defined as a level set) materials as well as on two-phase phononic crystals are presented that affirm the sound accuracy and optimal convergence of the method on structured, higher-order spectral finite element meshes. Several numerical examples demonstrate the advantages of $p$-refinement made possible by the spectral extended finite element method. In these examples, fourth-order spectral extended finite elements deliver $\mathcal{O}(10^{-8})$ accuracy in frequency calculations with more than thirty-fold fewer degrees-of-freedom when compared to quadratic finite elements.

Using density functional theory calculations, we study doping of a Cr, Mo, and W atom in boron clusters in the size range of 18-24 atoms and report the finding of metal atom encapsulated fullerene-like cage structures with 20 to 24 boron atoms in contrast to a fullerene-like structure of pure boron with 40 atoms. Our results show that bicapped drum-shaped structures are favored for neutral Cr@B$_{18}$, Mo@B$_{20}$, and W@B$_{20}$ clusters whereas a drum-shaped structure is preferred for neutral, cation, and anion of Mo@B$_{18}$ and W@B$_{18}$. Further, we find that B$_{20}$ is the smallest cage for Cr encapsulation, while B$_{22}$ is the smallest symmetric cage for Mo and W encapsulation and it is magic. Symmetric cage structures are also obtained for Mo@B$_{24}$ and W@B$_{24}$. A detailed analysis of the bonding character and molecular orbitals suggests that Cr@B$_{18}$, Cr@B$_{20}$, M@B$_{22}$ (M = Cr, Mo, and W) and M@B$_{24}$ (M = Mo and W) cages are stabilized with 18 $\pi$-bonded valence electrons whereas the drum-shaped M@B$_{18}$ (M = Mo and W) clusters are stabilized by 20 $\pi$-bonded valence electrons. Calculations with PBE0 functional in Gaussian 09 code show that in all cases of neutral clusters there is a large highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap. In some cases the lowest energy isomer of the charged clusters is different from the one for the neutral. We discuss the calculated infrared and Raman spectra for the neutral and cation clusters as well as the electronic structure of the anion clusters. Also we report results for isoelectronic anion and neutral clusters doped with V, Nb, and Ta which are generally similar to those obtained for Mo and W doped clusters. These results would be helpful to confirm the formation of these doped boron clusters experimentally., Comment: 33 pages, 12 figures, Supplementary Information Attached

In this paper, we present a novel nodal integration scheme for meshfree Galerkin methods that draws on the mathematical framework of the virtual element method. We adopt linear maximum-entropy basis functions for the discretization of field variables, although the proposed scheme is applicable to any linear meshfree approximant. In our approach, the weak form integrals are nodally integrated using nodal representative cells that carry the nodal displacements and state variables such as strains and stresses. The nodal integration is performed using the virtual element decomposition, wherein the bilinear form is decomposed into a consistency part and a stability part that ensure consistency and stability of the method. The performance of the proposed nodal integration scheme is assessed through benchmark problems in linear and nonlinear analyses of solids for small displacements and small-strain kinematics. Numerical results are presented for linear elastostatics and linear elastodynamics, and viscoelasticity. We demonstrate that the proposed nodally integrated meshfree method is accurate, converges optimally, and is more reliable and robust than a standard cell-based Gauss integrated meshfree method.

Quantum mechanical calculations require the repeated solution of a Schr\"odinger equation for the wavefunctions of the system. Recent work has shown that enriched finite element methods significantly reduce the degrees of freedom required to obtain accurate solutions. However, time to solution has been adversely affected by the need to solve a generalized eigenvalue problem and the ill-conditioning of associated systems matrices. In this work, we address both issues by proposing a stable and efficient orbital-enriched partition-of-unity method to solve the Schr\"odinger boundary-value problem in a parallelepiped unit cell subject to Bloch-periodic boundary conditions. In our proposed PUM, the three-dimensional domain is covered by overlapping patches, with a compactly-supported, non-negative weight function, that is identically equal to unity over some finite subset of its support associated with each patch. This so-called flat-top property provides a pathway to devise a stable approximation over the whole domain. On each patch, we use $p$-th degree orthogonal polynomials that ensure $p$-th order completeness, and in addition include eigenfunctions of the radial solution of the Schr\"odinger equation. Furthermore, we adopt a variational lumping approach to construct a block-diagonal overlap matrix that yields a standard eigenvalue problem and demonstrate accuracy, stability and efficiency of the method., Comment: 24 pages, 12 figures

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 and finite-elements 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 needed to achieve the required accuracies. 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. 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., Comment: 23 pages, 7 figures

By extending the classical analysis techniques due to Samokish, Faddeev and Faddeeva, and Longsine and McCormick among others, we prove the convergence of preconditioned steepest descent with implicit deflation (PSD-id) method for solving Hermitian-definite generalized eigenvalue problems. Furthermore, we derive a nonasymptotic estimate of the rate of convergence of the \psdid method. We show that with the proper choice of the shift, the indefinite shift-and-invert preconditioner is a locally accelerated preconditioner, and is asymptotically optimal that leads to superlinear convergence. Numerical examples are presented to verify the theoretical results on the convergence behavior of the \psdid method for solving ill-conditioned Hermitian-definite generalized eigenvalue problems arising from electronic structure calculations. While rigorous and full-scale convergence proofs of preconditioned block steepest descent methods in practical use still largely eludes us, we believe the theoretical results presented in this paper sheds light on an improved understanding of the convergence behavior of these block methods., Comment: 20 pages