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We propose an unconditionally energy-stable, orthonormality-preserving, component-wise splitting iterative scheme for the Kohn-Sham gradient flow based model in the electronic structure calculation. We first study the scheme discretized in time but still continuous in space. The component-wise splitting iterative scheme changes one wave function at a time, similar to the Gauss-Seidel iteration for solving a linear equation system. At the time step n , the orthogonality of the wave function being updated to other wave functions is preserved by projecting the gradient of the Kohn-Sham energy onto the subspace orthogonal to all other wave functions known at the current time, while the normalization of this wave function is preserved by projecting the gradient of the Kohn-Sham energy onto the subspace orthogonal to this wave function at t n + 1 / 2. The unconditional energy stability is nontrivial, and it comes from a subtle treatment of the two-electron integral as well as a consistent treatment of the two projections. Rigorous mathematical derivations are presented to show our proposed scheme indeed satisfies the desired properties. We then study the fully-discretized scheme, where the space is further approximated by a conforming finite element subspace. For the fully-discretized scheme, not only the preservation of orthogonality and normalization (together we called orthonormalization) can be quickly shown using the same idea as for the semi-discretized scheme, but also the highlight property of the scheme, i.e., the unconditional energy stability can be rigorously proven. The scheme allows us to use large time step sizes and deal with small systems involving only a single wave function during each iteration step. Several numerical experiments are performed to verify the theoretical analysis, where the number of iterations is indeed greatly reduced as compared to similar examples solved by the Kohn-Sham gradient flow based model in the literature. • This paper proposes a novel and efficient numerical scheme for the Kohn-Sham gradient flow based model. • The scheme is an unconditionally energy-stable, orthonormality-preserving, component-wise splitting iterative scheme. • The scheme does not modify the original energy, allows large time step sizes, and solves small systems at each time step. • The rigorous proof is presented in the paper. • Several numerical examples are illustrated to verify the theoretical analysis. [ABSTRACT FROM AUTHOR]

The Anderson acceleration method is an algorithm for accelerating the convergence of fixed-point iterations, including the Picard method. Anderson acceleration was first proposed in 1965 and, for some years, has been used successfully to accelerate the convergence of self-consistent field iterations in electronic-structure computations. Recently, the method has attracted growing attention in other application areas and among numerical analysts. Compared with a Newton-like method, an advantage of Anderson acceleration is that there is no need to form the Jacobian matrix. Thus the method is easy to implement. In this paper, an Anderson-accelerated Picard method is employed to solve the three-temperature energy equations, which are a type of strong nonlinear radiation-diffusion equations. Two strategies are used to improve the robustness of the Anderson acceleration method. One strategy is to adjust the iterates when necessary to satisfy the physical constraint. Another strategy is to monitor and, if necessary, reduce the matrix condition number of the least-squares problem in the Anderson-acceleration implementation so that numerical stability can be guaranteed. Numerical results show that the Anderson-accelerated Picard method can solve the three-temperature energy equations efficiently. Compared with the Picard method without acceleration, Anderson acceleration can reduce the number of iterations by at least half. A comparison between a Jacobian-free Newton–Krylov method, the Picard method, and the Anderson-accelerated Picard method is conducted in this paper. [ABSTRACT FROM AUTHOR]

Abstract In this paper, we construct an efficient numerical scheme for full-potential electronic structure calculations of periodic systems. In this scheme, the computational domain is decomposed into a set of atomic spheres and an interstitial region, and different basis functions are used in different regions: radial basis functions times spherical harmonics in the atomic spheres and plane waves in the interstitial region. These parts are then patched together by discontinuous Galerkin (DG) method. Our scheme has the same philosophy as the widely used (L)APW methods in materials science, but possesses systematically spectral convergence rate. We provide a rigorous a priori error analysis of the DG approximations for the linear eigenvalue problems, and present some numerical simulations in electronic structure calculations. [ABSTRACT FROM AUTHOR]

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature. [ABSTRACT FROM AUTHOR]

The paper presents two ways of improving the Jacobi–Davidson method for calculating the eigenvalues and eigenvectors described by eight-band k · p model for quantum dots and other low dimensional structures. First, the method is extended by the application of time reversal symmetry operator. This extension allows efficient calculations of the twofold degeneracy present in the multiband k · p model and other interior eigenvalues. Second, the preconditioner for the indefinite matrix which comes from the discretization of the eight band k · p Hamiltonian is presented. The construction of this preconditioner is based on physical considerations about energy band structure in the k · p model. On the basis of two real examples, it is shown that the preconditioner can significantly shorten the time needed to calculate the interior eigenvalues, despite the fact that the memory usage of the preconditioner and Hamiltionian is comparable. Finally, some technical details for implementing the eight band k · p Hamiltonian and the eigensolver are provided. [ABSTRACT FROM AUTHOR]

In this paper, we propose a parallel orbital-updating based optimization method for electronic structure calculations. With our method, the solution of the minimization problem for the Kohn-Sham energy functional with respect to N orbitals is replaced by the solution of N independent minimization problems for the energy functional with respect to one orbital and the orthogonalization of the N updated orbitals. This new method allows a two-level parallelization. This feature makes our approach has a great advantage in large scale parallel computing. The numerical experiments show that our new method is reliable and efficient. Hence, our new method has a great potential for large scale electronic structure calculations on modern supercomputers. • Propose a parallel orbital-updating based optimization approach for KS model. • The new approach has a feature of two-level parallelization. • Provide two practical parallel orbital-updating based optimization algorithms. • Numerical experiments show that these new algorithms are reliable and efficient. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, a framework of using h-adaptive finite element method for the Kohn–Sham equation on the tetrahedron mesh is presented. The Kohn–Sham equation is discretized by the finite element method, and the h-adaptive technique is adopted to optimize the accuracy and the efficiency of the algorithm. The locally optimal block preconditioned conjugate gradient method is employed for solving the generalized eigenvalue problem, and an algebraic multigrid preconditioner is used to accelerate the solver. A variety of numerical experiments demonstrate the effectiveness of our algorithm for both the all-electron and the pseudo-potential calculations. [Copyright &y& Elsevier]

Abstract: Hydrocarbon systems have been intensively studied via numerical methods, including electronic structure computations, molecular dynamics and Monte Carlo simulations. Typically, these methods require an initial structural model (atomic positions and types, topology, etc.) that may be produced using scripts and/or modeling tools. For many systems, however, these building methods may be ineffective, as the user may have to specify the positions of numerous atoms while maintaining structural plausibility. In this paper, we present an interactive physically-based modeling tool to construct structural models of hydrocarbon systems. As the user edits the geometry of the system, atomic positions are also influenced by the Brenner potential, a well-known bond-order reactive potential. In order to be able to interactively edit systems containing numerous atoms, we introduce a new adaptive simulation algorithm, as well as a novel algorithm to incrementally update the forces and the total potential energy based on the list of updated relative atomic positions. The computational cost of the adaptive simulation algorithm depends on user-defined error thresholds, and our potential update algorithm depends linearly with the number of updated bonds. This allows us to enable efficient physically-based editing, since the computational cost is decoupled from the number of atoms in the system. We show that our approach may be used to effectively build realistic models of hydrocarbon structures that would be difficult or impossible to produce using other tools. [Copyright &y& Elsevier]

Abstract: In this paper, we consider band structure calculations governed by the Helmholtz or Maxwell equations in piecewise homogeneous periodic materials. Methods based on boundary integral equations are natural in this context, since they discretize the interface alone and can achieve high order accuracy in complicated geometries. In order to handle the quasi-periodic conditions which are imposed on the unit cell, the free-space Green’s function is typically replaced by its quasi-periodic cousin. Unfortunately, the quasi-periodic Green’s function diverges for families of parameter values that correspond to resonances of the empty unit cell. Here, we bypass this problem by means of a new integral representation that relies on the free-space Green’s function alone, adding auxiliary layer potentials on the boundary of the unit cell itself. An important aspect of our method is that by carefully including a few neighboring images, the densities may be kept smooth and convergence rapid. This framework results in an integral equation of the second kind, avoids spurious resonances, and achieves spectral accuracy. Because of our image structure, inclusions which intersect the unit cell walls may be handled easily and automatically. Our approach is compatible with fast-multipole acceleration, generalizes easily to three dimensions, and avoids the complication of divergent lattice sums. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, we investigate a novel approach based on the combination of Tucker-type and canonical tensor decomposition techniques for the efficient numerical approximation of functions and operators in electronic structure calculations. In particular, we study applicability of tensor approximations for the numerical solution of Hartree–Fock and Kohn–Sham equations on 3D Cartesian grids. We show that the orthogonal Tucker-type tensor approximation of electron density and Hartree potential of simple molecules leads to low tensor rank representations. This enables an efficient tensor-product convolution scheme for the computation of the Hartree potential using a collocation-type approximation via piecewise constant basis functions on a uniform grid. Combined with the Richardson extrapolation, our approach exhibits convergence in the grid-size . Moreover, this requires storage, where r denotes the Tucker rank of the electron density with , almost uniformly in n. For example, calculations of the Coulomb matrix and the Hartree–Fock energy for the molecule, with a pseudopotential on the C atom, achieved accuracies of the order of hartree with a grid-size n of several hundreds. Since the tensor-product convolution in 3D is performed via 1D convolution transforms, our scheme markedly outperforms the 3D-FFT in both the computing time and storage requirements. [Copyright &y& Elsevier]

Abstract: In this paper we present several mathematical models that can be used to create approximate solutions of the three-dimensional Schroedinger–Poisson equation in layered semiconductor devices. A general algorithmic strategy that can be used to create efficient solution procedures for each of these models is described. Computational results demonstrating the accuracy and efficiency that can be obtained with the use of these models is presented. [Copyright &y& Elsevier]

Abstract: The paper is concerned with algorithms for computing several extreme eigenpairs of Hermitian problems based on the conjugate gradient method. We analyse computational strategies employed by various algorithms of this kind reported in the literature and identify their limitations. Our criticism is illustrated by numerical tests on a set of problems from electronic structure calculations and acoustics. [Copyright &y& Elsevier]

• New variational method for periodic electronic eigenvalue problems with Coulomb singularities. • Faster plane-wave convergence with a priori bounds. • Theoretical convergence rates validated by numerical tests. In solid-state physics, energies of crystals are usually computed with a plane-wave discretization of Kohn-Sham equations. However the presence of Coulomb singularities requires the use of large plane-wave cut-offs to produce accurate numerical results. In this paper, an analysis of the plane-wave convergence of the eigenvalues of periodic linear Hamiltonians with Coulomb potentials using the variational projector-augmented wave (VPAW) method is presented. In the VPAW method, an invertible transformation is applied to the original eigenvalue problem, acting locally in balls centered at the singularities. In this setting, a generalized eigenvalue problem needs to be solved using plane-waves. We show that cusps of the eigenfunctions of the VPAW eigenvalue problem at the positions of the nuclei are significantly reduced. These eigenfunctions have however a higher-order derivative discontinuity at the spheres centered at the nuclei. By balancing both sources of error, we show that the VPAW method can drastically improve the plane-wave convergence of the eigenvalues with a minor additional computational cost. Numerical tests are provided confirming the efficiency of the method to treat Coulomb singularities. [ABSTRACT FROM AUTHOR]

Abstract: The electronic charge density is the central quantity in density functional theory. It can be expressed as the diagonal elements of the density matrix in its real space representation, which can be computed by a recursion method based on the Trotter formula. This allows for an orbital free computation of the charge density in the Kohn Sham formalism at finite temperature whose numeric complexity increases linearly with the size of the system (that is, an order N method). No assessment of the numerical properties such an approach has been presented yet, and this paper aims to analyze its convergence properties. In particular, we wish to understand its convergence properties as a function of the number of recursion steps, to establish an error estimate in order to devise a stopping criterion, and to analyze the “locality properties” of the method which is necessary to make it an order N method. We illustrate the assessment with numerical tests performed for the free electron gas and for Helium at a density and high temperature relevant to shock physics. [Copyright &y& Elsevier]

Abstract: A new direct constrained optimization algorithm for minimizing the Kohn–Sham (KS) total energy functional is presented in this paper. The key ingredients of this algorithm involve projecting the total energy functional into a sequence of subspaces of small dimensions and seeking the minimizer of total energy functional within each subspace. The minimizer of a subspace energy functional not only provides a search direction along which the KS total energy functional decreases but also gives an optimal “step-length” to move along this search direction. Numerical examples are provided to demonstrate that this new direct constrained optimization algorithm can be more efficient than the self-consistent field (SCF) iteration. [Copyright &y& Elsevier]