Ab initio framework for systems with helical symmetry: theory, numerical implementation and applications to torsional deformations in nanostructures

We formulate and implement Helical DFT -- a self-consistent first principles simulation method for nanostructures with helical symmetries. Such materials are well represented in all of nanotechnology, chemistry and biology, and are expected to be associated with unprecedented material properties. We rigorously demonstrate the existence and completeness of special solutions to the single electron problem for helical nanostructures, called helical Bloch waves. We describe how the Kohn-Sham Density Functional Theory equations for a helical nanostructure can be reduced to a fundamental domain with the aid of these solutions. A key component in our mathematical treatment is the definition and use of a helical Bloch-Floquet transform to perform a block-diagonalization of the Hamiltonian in the sense of direct integrals. We develop a symmetry-adapted finite-difference strategy in helical coordinates to discretize the governing equations, and obtain a working realization of the proposed approach. We verify the accuracy and convergence properties of our numerical implementation through examples. Finally, we employ Helical DFT to study the properties of zigzag and chiral single wall black phosphorus (i.e., phosphorene) nanotubes. We use our simulations to evaluate the torsional stiffness of a zigzag nanotube ab initio. Additionally, we observe an insulator-to-metal-like transition in the electronic properties of this nanotube as it is subjected to twisting. We also find that a similar transition can be effected in chiral phosphorene nanotubes by means of axial strains. Notably, self-consistent ab initio simulations of this nature are unprecedented and well outside the scope of any other systematic first principles method in existence. We end with a discussion on various future avenues and applications

A spectral scheme for Kohn-Sham density functional theory of clusters

Starting from the observation that one of the most successful methods for solving the Kohn-Sham equations for periodic systems -- the plane-wave method -- is a spectral method based on eigenfunction expansion, we formulate a spectral method designed towards solving the Kohn-Sham equations for clusters. This allows for efficient calculation of the electronic structure of clusters (and molecules) with high accuracy and systematic convergence properties without the need for any artificial periodicity. The basis functions in this method form a complete orthonormal set and are expressible in terms of spherical harmonics and spherical Bessel functions. Computation of the occupied eigenstates of the discretized Kohn-Sham Hamiltonian is carried out using a combination of preconditioned block eigensolvers and Chebyshev polynomial filter accelerated subspace iterations. Several algorithmic and computational aspects of the method, including computation of the electrostatics terms and parallelization are discussed. We have implemented these methods and algorithms into an efficient and reliable package called ClusterES (Cluster Electronic Structure). A variety of benchmark calculations employing local and non-local pseudopotentials are carried out using our package and the results are compared to the literature. Convergence properties of the basis set are discussed through numerical examples. Computations involving large systems that contain thousands of electrons are demonstrated to highlight the efficacy of our methodology. The use of our method to study clusters with arbitrary point group symmetries is briefly discussed.Comment: Manuscript submitted (with revisions) to Journal of Computational Physic

Periodic Pulay method for robust and efficient convergence acceleration of self-consistent field iterations

Pulay's Direct Inversion in the Iterative Subspace (DIIS) method is one of the most widely used mixing schemes for accelerating the self-consistent solution of electronic structure problems. In this work, we propose a simple generalization of DIIS in which Pulay extrapolation is performed at periodic intervals rather than on every self-consistent field iteration, and linear mixing is performed on all other iterations. We demonstrate through numerical tests on a wide variety of materials systems in the framework of density functional theory that the proposed generalization of Pulay's method significantly improves its robustness and efficiency.Comment: Version 2 (with minor edits from version 1

Solution of the Schrodinger equation for quasi-one-dimensional materials using helical waves

We formulate and implement a spectral method for solving the Schrodinger equation, as it applies to quasi-one-dimensional materials and structures. This allows for computation of the electronic structure of important technological materials such as nanotubes (of arbitrary chirality), nanowires, nanoribbons, chiral nanoassemblies, nanosprings and nanocoils, in an accurate, efficient and systematic manner. Our work is motivated by the observation that one of the most successful methods for carrying out electronic structure calculations of bulk/crystalline systems -- the plane-wave method -- is a spectral method based on eigenfunction expansion. Our scheme avoids computationally onerous approximations involving periodic supercells often employed in conventional plane-wave calculations of quasi-one-dimensional materials, and also overcomes several limitations of other discretization strategies, e.g., those based on finite differences and atomic orbitals. We describe the setup of fast transforms to carry out discretization of the governing equations using our basis set, and the use of matrix-free iterative diagonalization to obtain the electronic eigenstates. Miscellaneous computational details, including the choice of eigensolvers, use of a preconditioning scheme, evaluation of oscillatory radial integrals and the imposition of a kinetic energy cutoff are discussed. We have implemented these strategies into a computational package called HelicES (Helical Electronic Structure). We demonstrate the utility of our method in carrying out systematic electronic structure calculations of various quasi-one-dimensional materials through numerous examples involving nanotubes, nanoribbons and nanowires. We also explore the convergence, accuracy and efficiency of our method. We anticipate that our method will find numerous applications in computational nanomechanics and materials science

Density functional theory method for twisted geometries with application to torsional deformations in group-IV nanotubes

We present a real-space formulation and implementation of Kohn-Sham Density Functional Theory suited to twisted geometries, and apply it to the study of torsional deformations of X (X = C, Si, Ge, Sn) nanotubes. Our formulation is based on higher order finite difference discretization in helical coordinates, uses ab intio pseudopotentials, and naturally incorporates rotational (cyclic) and screw operation (i.e., helical) symmetries. We discuss several aspects of the computational method, including the form of the governing equations, details of the numerical implementation, as well as its convergence, accuracy and efficiency properties. The technique presented here is particularly well suited to the first principles simulation of quasi-one-dimensional structures and their deformations, and many systems of interest can be investigated using small simulation cells containing just a few atoms. We apply the method to systematically study the properties of single-wall zigzag and armchair group-IV nanotubes, as they undergo twisting. For the range of deformations considered, the mechanical behavior of the tubes is found to be largely consistent with isotropic linear elasticity, with the torsional stiffness varying as the cube of the nanotube radius. Furthermore, for a given tube radius, this quantity is seen to be highest for carbon nanotubes and the lowest for those of tin, while nanotubes of silicon and germanium have intermediate values close to each other. We also describe different aspects of the variation in electronic properties of the nanotubes as they are twisted. In particular, we find that akin to the well known behavior of armchair carbon nanotubes, armchair nanotubes of silicon, germanium and tin also exhibit bandgaps that vary periodically with imposed rate of twist, and that the periodicity of the variation scales in an inverse quadratic manner with the tube radius

Symmetry-adapted real-space density functional theory for cylindrical geometries: Application to large group-IV nanotubes

We present a symmetry-adapted real-space formulation of Kohn-Sham density functional theory for cylindrical geometries and apply it to the study of large X (X=C, Si, Ge, Sn) nanotubes. Specifically, starting from the Kohn-Sham equations posed on all of space, we reduce the problem to the fundamental domain by incorporating cyclic and periodic symmetries present in the angular and axial directions of the cylinder, respectively. We develop a high-order finite-difference parallel implementation of this formulation, and verify its accuracy against established plane-wave and real-space codes. Using this implementation, we study the band structure and bending properties of X nanotubes and Xene sheets, respectively. Specifically, we first show that zigzag and armchair X nanotubes with radii in the range 1 to 5 nm are semiconducting, other than the armchair and zigzag type III carbon variants, for which we find a vanishingly small bandgap, indicative of metallic behavior. In particular, we find an inverse linear dependence of the bandgap with respect to the radius for all nanotubes, other than the armchair and zigzag type III carbon variants, for which we find an inverse quadratic dependence. Next, we exploit the connection between cyclic symmetry and uniform bending deformations to calculate the bending moduli of Xene sheets in both zigzag and armchair directions, while considering radii of curvature up to 5 nm . We find Kirchhoff-Love type bending behavior for all sheets, with graphene and stanene possessing the largest and smallest moduli, respectively. In addition, other than graphene, the sheets demonstrate significant anisotropy, with larger bending moduli along the armchair direction. Finally, we demonstrate that the proposed approach has very good parallel scaling and is highly efficient, enabling ab initio simulations of unprecedented size for systems with a high degree of cyclic symmetry. In particular, we show that even micron-sized nanotubes can be simulated with modest computational effort. Overall, the current work opens an avenue for the efficient ab initio study of 1D nanostructures with large radii as well as 1D/2D nanostructures under uniform bending

Two-level Chebyshev filter based complementary subspace method: pushing the envelope of large-scale electronic structure calculations

We describe a novel iterative strategy for Kohn-Sham density functional theory calculations aimed at large systems (> 1000 electrons), applicable to metals and insulators alike. In lieu of explicit diagonalization of the Kohn-Sham Hamiltonian on every self-consistent field (SCF) iteration, we employ a two-level Chebyshev polynomial filter based complementary subspace strategy to: 1) compute a set of vectors that span the occupied subspace of the Hamiltonian; 2) reduce subspace diagonalization to just partially occupied states; and 3) obtain those states in an efficient, scalable manner via an inner Chebyshev-filter iteration. By reducing the necessary computation to just partially occupied states, and obtaining these through an inner Chebyshev iteration, our approach reduces the cost of large metallic calculations significantly, while eliminating subspace diagonalization for insulating systems altogether. We describe the implementation of the method within the framework of the Discontinuous Galerkin (DG) electronic structure method and show that this results in a computational scheme that can effectively tackle bulk and nano systems containing tens of thousands of electrons, with chemical accuracy, within a few minutes or less of wall clock time per SCF iteration on large-scale computing platforms. We anticipate that our method will be instrumental in pushing the envelope of large-scale ab initio molecular dynamics. As a demonstration of this, we simulate a bulk silicon system containing 8,000 atoms at finite temperature, and obtain an average SCF step wall time of 51 seconds on 34,560 processors; thus allowing us to carry out 1.0 ps of ab initio molecular dynamics in approximately 28 hours (of wall time).Comment: Resubmitted version (version 2

Bicrystallography-informed Frenkel-Kontorova model for interlayer dislocations in strained 2D heterostructures

In recent years, van der Waals (vdW) heterostructures and homostructures, which consist of stacks of two-dimensional (2D) materials, have risen to prominence due to their association with exotic quantum phenomena. Atomistic scale relaxation effects play an extremely important role in the electronic scale quantum physics of these systems. We investigate such structural relaxation effects in this work using atomistic and mesoscale models, within the context of twisted bilayer graphene -- a well-known heterostructure system that features moire patterns arising from the lattices of the two graphene layers. For small twist angles, atomic relaxation effects in this system are associated with the natural emergence of interface dislocations or strain solitons, which result from the cyclic nature of the generalized stacking fault energy (GSFE), that measures the interface energy based on the relative movement of the two layers. In this work, we first demonstrate using atomistic simulations that atomic reconstruction in bilayer graphene under a large twist also results from interface dislocations, although the Burgers vectors of such dislocations are considerably smaller than those observed in small-twist systems. To reveal the translational invariance of the heterointerface responsible for the formation of such dislocations, we derive the translational symmetry of the GSFE of a 2D heterostructure using the notions of coincident site lattices (CSLs) and displacement shift complete lattices (DSCLs). The workhorse for this exercise is a recently developed Smith normal form bicrystallography framework. Next, we construct a bicrystallography-informed and frame-invariant Frenkel-Kontorova model, which can predict the formation of strain solitons in arbitrary 2D heterostructures, and apply it to study a heterostrained, large-twist bilayer graphene system

Electronic Structure Prediction of Multi-million Atom Systems Through Uncertainty Quantification Enabled Transfer Learning

The ground state electron density - obtainable using Kohn-Sham Density Functional Theory (KS-DFT) simulations - contains a wealth of material information, making its prediction via machine learning (ML) models attractive. However, the computational expense of KS-DFT scales cubically with system size which tends to stymie training data generation, making it difficult to develop quantifiably accurate ML models that are applicable across many scales and system configurations. Here, we address these fundamental challenges using Bayesian neural networks and employ transfer learning to leverage the multi-scale nature of the training data. Our ML models employ descriptors involving simple scalar products, comprehensively sample system configurations through thermalization, and quantify uncertainty in electron density predictions. We show that our models incur significantly lower data generation costs while allowing confident - and when verifiable, accurate - predictions for a wide variety of bulk systems well beyond training, including systems with defects, different alloy compositions, and at unprecedented, multi-million-atom scales