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

Parallel energy-stable phase field crystal simulations based on domain decomposition methods

In this paper, we present a parallel numerical algorithm for solving the phase field crystal equation. In the algorithm, a semi-implicit finite difference scheme is derived based on the discrete variational derivative method. Theoretical analysis is provided to show that the scheme is unconditionally energy stable and can achieve second-order accuracy in both space and time. An adaptive time step strategy is adopted such that the time step size can be flexibly controlled based on the dynamical evolution of the problem. At each time step, a nonlinear algebraic system is constructed from the discretization of the phase field crystal equation and solved by a domain decomposition based, parallel Newton--Krylov--Schwarz method with improved boundary conditions for subdomain problems. Numerical experiments with several two and three dimensional test cases show that the proposed algorithm is second-order accurate in both space and time, energy stable with large time steps, and highly scalable to over ten thousands processor cores on the Sunway TaihuLight supercomputer

Electronic Structure of Large-Scale Graphene Nanoflakes

With the help of the recently developed SIESTA-PEXSI method [J. Phys.: Condens. Matter \textbf{26}, 305503 (2014)], we perform Kohn-Sham density functional theory (DFT) calculations to study the stability and electronic structure of hexagonal graphene nanoflakes (GNFs) with up to 11,700 atoms. We find the electronic properties of GNFs, including their cohesive energy, HOMO-LUMO energy gap, edge states and aromaticity, depend sensitively on the type of edges (ACGNFs and ZZGNFs), size and the number of electrons. We observe that, due to the edge-induced strain effect in ACGNFs, large-scale ACGNFs' cohesive energy decreases as their size increases. This trend does not hold for ZZGNFs due to the presence of many edge states in ZZGNFs. We find that the energy gaps $E_g$ of GNFs all decay with respect to $1/L$, where $L$ is the size of the GNF, in a linear fashion. But as their size increases, ZZGNFs exhibit more localized edge states. We believe the presence of these states makes their gap decrease more rapidly. In particular, when $L$ is larger than 6.40 $nm$, we find that ZZGNFs exhibit metallic characteristics. Furthermore, we find that the aromatic structures of GNFs appear to depend only on whether the system has $4N$ or $4N+2$ electrons, where $N$ is an integer.Comment: 11 pages, 9 figure

Ricci-flat graphs with girth four

Lin-Lu-Yau introduced an interesting notion of Ricci curvature for graphs and obtained a complete characterization for all Ricci-flat graphs with girth at least five [1]. In this paper, we propose a concrete approach to construct an infinite family of distinct Ricci-flat graphs of girth four with edge-disjoint 4-cycles and completely characterize all Ricci-flat graphs of girth four with vertex-disjoint 4-cycles

GCP Code Applied in J/ψJ/\psi Production and Absorption

Using the General Cascade Program(GCP), the production and absorption of $J/\psi$ in p-A and A-A collisions have been studied. Nucleon absorption mechanism and comover absorption mechanism are considered to investigate the $J/\psi$ suppression. The results agree well with experimental data of $J/\psi$ production, except for the data in Pb-Pb collision.Comment: 17 pages, revtex, 6 figure

Quantum Discrete Cosine Transform for Image Compression

Discrete Cosine Transform (DCT) is very important in image compression. Classical 1-D DCT and 2-D DCT has time complexity O(NlogN) and O(N²logN) respectively. This paper presents a quantum DCT iteration, and constructs a quantum 1-D and 2-D DCT algorithm for image compression by using the iteration. The presented 1-D and 2-D DCT has time complexity O(sqrt(N)) and O(N) respectively. In addition, the method presented in this paper generalizes the famous Grover's algorithm to solve complex unstructured search problem.Comment: Modify on Jan. 22, 2006. Only Add ref. 1

Testing the Einstein's equivalence principle with polarized gamma-ray bursts

The Einstein's equivalence principle can be tested by using parameterized post-Newtonian parameters, of which the parameter $\gamma$ has been constrained by comparing the arrival times of photons with different energies. It has been constrained by a variety of astronomical transient events, such as gamma-ray bursts (GRBs), fast radio bursts as well as pulses of pulsars, with the most stringent constraint of $\Delta \gamma \lesssim 10^{-15}$. In this letter, we consider the arrival times of lights with different circular polarization. For a linearly polarized light, it is the combination of two circularly polarized lights. If the arrival time difference between the two circularly polarized lights is too large, their combination may lose the linear polarization. We constrain the value of $\Delta \gamma_{\rm p} < 1.6 \times 10^{-27}$ by the measurement of the polarization of GRB 110721A, which is the most stringent constraint ever achieved

Wetting and Diffusion of Water on Pristine and Strained Phosphorene

Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, have exhibited promising application prospect in biology. Nonetheless, the wetting and diffusive properties of bio-fluids on phosphorene are still elusive. In this study, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on pristine and strained phosphorene. The MD simulations illustrated that the diffusion of water molecules on the phosphorene surface is anisotropic, while strain-enhanced diffusion is clearly present which arises from strain-induced smooth of the energy landscape. The contact angle of water droplet on phosphorene exhibited a nonmonotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene was demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, we discovered that the contact angle of water on strained phosphorene is proportional to the quotient of longitudinal and transverse diffusion coefficients of interfacial water. These findings would offer helpful insights in potential ways of manipulating the wetting and transport of water at nanoscale, and in future bio-applications of phosphorene.Comment: 8 pages, 6 figure