Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, result in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as its dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5,000-50,000 processors. We use DGDFT based ab-initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 * 1 edge reconstruction appears in ACPNRs at room temperature.Comment: 9 pages, 5 figure

Projected Commutator DIIS Method for Accelerating Hybrid Functional Electronic Structure Calculations

The commutator direct inversion of the iterative subspace (commutator DIIS or C-DIIS) method developed by Pulay is an efficient and the most widely used scheme in quantum chemistry to accelerate the convergence of self consistent field (SCF) iterations in Hartree-Fock theory and Kohn-Sham density functional theory. The C-DIIS method requires the explicit storage of the density matrix, the Fock matrix and the commutator matrix. Hence the method can only be used for systems with a relatively small basis set, such as the Gaussian basis set. We develop a new method that enables the C-DIIS method to be efficiently employed in electronic structure calculations with a large basis set such as planewaves for the first time. The key ingredient is the projection of both the density matrix and the commutator matrix to an auxiliary matrix called the gauge-fixing matrix. The resulting projected commutator-DIIS method (PC-DIIS) only operates on matrices of the same dimension as the that consists of Kohn-Sham orbitals. The cost of the method is comparable to that of standard charge mixing schemes used in large basis set calculations. The PC-DIIS method is gauge-invariant, which guarantees that its performance is invariant with respect to any unitary transformation of the Kohn-Sham orbitals. We demonstrate that the PC-DIIS method can be viewed as an extension of an iterative eigensolver for nonlinear problems. We use the PC-DIIS method for accelerating Kohn-Sham density functional theory calculations with hybrid exchange-correlation functionals, and demonstrate its superior performance compared to the commonly used nested two-level SCF iteration procedure

DGDFT: A Massively Parallel Method for Large Scale Density Functional Theory Calculations

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) [J. Comput. Phys. 2012, 231, 2140] method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field (SCF) iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. It minimizes the number of degrees of freedom required to represent the solution to the Kohn-Sham problem for a desired level of accuracy. In particular, DGDFT can reach the planewave accuracy with far fewer numbers of degrees of freedom. By using the pole expansion and selected inversion (PEXSI) technique to compute electron density, energy and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of two-dimensional (2D) phosphorene systems with 3,500-14,000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.Comment: 13 pages, 8 figures in J. Chem. Phys. 2015. arXiv admin note: text overlap with arXiv:1501.0503

Interpolative Separable Density Fitting through Centroidal Voronoi Tessellation With Applications to Hybrid Functional Electronic Structure Calculations

The recently developed interpolative separable density fitting (ISDF) decomposition is a powerful way for compressing the redundant information in the set of orbital pairs, and has been used to accelerate quantum chemistry calculations in a number of contexts. The key ingredient of the ISDF decomposition is to select a set of non-uniform grid points, so that the values of the orbital pairs evaluated at such grid points can be used to accurately interpolate those evaluated at all grid points. The set of non-uniform grid points, called the interpolation points, can be automatically selected by a QR factorization with column pivoting (QRCP) procedure. This is the computationally most expensive step in the construction of the ISDF decomposition. In this work, we propose a new approach to find the interpolation points based on the centroidal Voronoi tessellation (CVT) method, which offers a much less expensive alternative to the QRCP procedure when ISDF is used in the context of hybrid functional electronic structure calculations. The CVT method only uses information from the electron density, and can be efficiently implemented using a K-Means algorithm. We find that this new method achieves comparable accuracy to the ISDF-QRCP method, at a cost that is negligible in the overall hybrid functional calculations. For instance, for a system containing $1000$ silicon atoms simulated using the HSE06 hybrid functional on $2000$ computational cores, the cost of QRCP-based method for finding the interpolation points costs $434.2$ seconds, while the CVT procedure only takes $3.2$ seconds. We also find that the ISDF-CVT method also enhances the smoothness of the potential energy surface in the context of \emph{ab initio} molecular dynamics (AIMD) simulations with hybrid functionals

Phase Dynamics in Intrinsic Josephson Junctions and its Electrodynamics

We present a theoretical description of the phase dynamics and its corresponding electrodynamics in a stack of inductively coupled intrinsic Josephson junctions of layered high-$T_c$ superconductors in the absence of an external magnetic field. Depending on the spatial structure of the gauge invariant phase difference, the dynamic state is classified into: state with kink, state without kink, and state with solitons. It is revealed that in the state with phase kink, the plasma is coupled to the cavity and the plasma oscillation is enhanced. In contrast, in the state without kink, the plasma oscillation is weak. It points a way to enhance the radiation of electromagnetic from high-$T_c$ superconductors. We also perform numerical simulations to check the theory and a good agreement is achieved. The radiation pattern of the state with and without kink is calculated, which may serve as a fingerprint of the dynamic state realized by the system. At last, the power radiation of the state with solitons is calculated by simulations. The possible state realized in the recent experiments is discussed in the viewpoint of the theoretical description. The state with kink is important for applications including terahertz generators and amplifiers.Comment: 14 pages, 13 figure

Distance between unitary orbits of normal elements in simple C*-algebras of real rank zero

Let $x, y$ be two normal elements in a unital simple C*-algebra $A.$ We introduce a function $D_c(x, y)$ and show that in a unital simple AF-algebra there is a constant $1>C>0$ such that $$C\cdot D_c(x, y)\le {\rm dist}({\cal U}(x),{\cal U}(y))\le D_c(x,y),$$ where ${\cal U}(x)$ and ${\cal U}(y)$ are the closures of the unitary orbits of $x$ and of $y,$ respectively. We also generalize this to unital simple C*-algebras with real rank zero, stable rank one and weakly unperforated $K_0$-group. More complicated estimates are given in the presence of non-trivial $K_1$-information.Comment: 64 pages, JFA to appea

On the Cauchy problem for two dimensional incompressible viscoelastic flows

We study the large-data Cauchy problem for two dimensional Oldroyd model of incompressible viscoelastic fluids. We prove the global-in-time existence of the Leray-Hopf type weak solutions in the physical energy space. Our method relies on a new $\textit{a priori}$ estimate on the space-time norm in L^{\f32}_{loc} of the Cauchy-Green strain tensor \tau=\F\F^\top, or equivalently the $L^3_{loc}$ norm of the Jacobian of the flow map \F. It allows us to rule out possible concentrations of the energy due to deformations associated with the flow maps. Following the general compactness arguments due to DiPerna and Lions (\cite{DL}, \cite{FNP}, \cite{PL}), and using the so-called \textit{effective viscous flux}, $\mathcal{G}$, which was introduced in our previous work \cite{HL}, we are able to control the possible oscillations of deformation gradients as well

In-plane dissipation as a possible synchronization mechanism for terahertz radiation from intrinsic Josephson junctions of layered superconductors

Strong terahertz radiation from mesa structure of $\rm{Bi_2Sr_2CaCu_2O_{8+\delta}}$ single crystal has been observed recently, where the mesa intrinsically forms a cavity. For a thick mesa of large number of junctions, there are many cavity modes with different wave vectors along the c-axis corresponding to almost degenerate bias voltages. The mechanism responsible for exciting the uniform mode which radiates coherent terahertz waves in experiments is unknown. In this work, we show that the in-plane dissipation selects the uniform mode. For perturbations with non-zero wave numbers along the c-axis, the in-plane dissipations are significantly enhanced, which prevent the excitation of corresponding cavity modes. Our analytical results are confirmed by numerical simulations.Comment: 7 pages, 5 figure

The Convergence Rate and Necessary-and-Sufficient Condition for the Consistency of Isogeometric Collocation Method

Although the isogeometric collocation (IGA-C) method has been successfully utilized in practical applications due to its simplicity and efficiency, only a little theoretical results have been established on the numerical analysis of the IGA-C method. In this paper, we deduce the convergence rate of the consistency of the IGA-C method. Moreover, based on the formula of the convergence rate, the necessary and sufficient condition for the consistency of the IGA-C method is developed. These results advance the numerical analysis of the IGA-C method.Comment: 19 pages, 3 figure

The natural measure of a symbolic dynamical system

This study investigates the natural or intrinsic measure of a symbolic dynamical system $\Sigma$. The measure $\mu([i_{1},i_{2},...,i_{n}])$ of a pattern $[i_{1},i_{2},...,i_{n}]$ in $\Sigma$ is an asymptotic ratio of $[i_{1},i_{2},...,i_{n}]$, which arises in all patterns of length $n$ within very long patterns, such that in a typical long pattern, the pattern $[i_{1},i_{2},...,i_{n}]$ appears with frequency $\mu([i_{1},i_{2},...,i_{n}])$. When $\Sigma=\Sigma(A)$ is a shift of finite type and $A$ is an irreducible $N\times N$ non-negative matrix, the measure $\mu$ is the Parry measure. $\mu$ is ergodic with maximum entropy. The result holds for sofic shift $\mathcal{G}=(G,\mathcal{L})$, which is irreducible. The result can be extended to $\Sigma(A)$, where $A$ is a countably infinite matrix that is irreducible, aperiodic and positive recurrent. By using the Krieger cover, the natural measure of a general shift space is studied in the way of a countably infinite state of sofic shift, including context free shift. The Perron-Frobenius Theorem for non-negative matrices plays an essential role in this study