Elliptic preconditioner for accelerating the self consistent field iteration in Kohn-Sham density functional theory

We discuss techniques for accelerating the self consistent field (SCF) iteration for solving the Kohn-Sham equations. These techniques are all based on constructing approximations to the inverse of the Jacobian associated with a fixed point map satisfied by the total potential. They can be viewed as preconditioners for a fixed point iteration. We point out different requirements for constructing preconditioners for insulating and metallic systems respectively, and discuss how to construct preconditioners to keep the convergence rate of the fixed point iteration independent of the size of the atomistic system. We propose a new preconditioner that can treat insulating and metallic system in a unified way. The new preconditioner, which we call an elliptic preconditioner, is constructed by solving an elliptic partial differential equation. The elliptic preconditioner is shown to be more effective in accelerating the convergence of a fixed point iteration than the existing approaches for large inhomogeneous systems at low temperature

Flexible Computing Services for Comparisons and Analyses of Classical Chinese Poetry

We collect nine corpora of representative Chinese poetry for the time span of 1046 BCE and 1644 CE for studying the history of Chinese words, collocations, and patterns. By flexibly integrating our own tools, we are able to provide new perspectives for approaching our goals. We illustrate the ideas with two examples. The first example show a new way to compare word preferences of poets, and the second example demonstrates how we can utilize our corpora in historical studies of the Chinese words. We show the viability of the tools for academic research, and we wish to make it helpful for enriching existing Chinese dictionary as well.Comment: 6 pages, 2 tables, 1 figure, 2017 International Conference on Digital Humanitie

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

A posteriori error estimator for adaptive local basis functions to solve Kohn-Sham density functional theory

Kohn-Sham density functional theory is one of the most widely used electronic structure theories. The recently developed adaptive local basis functions form an accurate and systematically improvable basis set for solving Kohn-Sham density functional theory using discontinuous Galerkin methods, requiring a small number of basis functions per atom. In this paper we develop residual-based a posteriori error estimates for the adaptive local basis approach, which can be used to guide non-uniform basis refinement for highly inhomogeneous systems such as surfaces and large molecules. The adaptive local basis functions are non-polynomial basis functions, and standard a posteriori error estimates for $hp$-refinement using polynomial basis functions do not directly apply. We generalize the error estimates for $hp$-refinement to non-polynomial basis functions. We demonstrate the practical use of the a posteriori error estimator in performing three-dimensional Kohn-Sham density functional theory calculations for quasi-2D aluminum surfaces and a single-layer graphene oxide system in water.Comment: 34 pages, 12 figure

The combination of context information to enhance simple question answering

With the rapid development of knowledge base,question answering based on knowledge base has been a hot research issue. In this paper, we focus on answering singlerelation factoid questions based on knowledge base. We build a question answering system and study the effect of context information on fact selection, such as entity's notable type,outdegree. Experimental results show that context information can improve the result of simple question answering

Possible Supersymmetric Kinematics

The contraction method in different limits to obtain 22 different realizations of kinematical algebras is applied to study the supersymmetric extension of \AdS\ algebra and its contractions. It is shown that $\frak{p}_2$ $\frak{h}_-$, $\frak{p}'$, $\frak{c}_2$ and $\frak{g}'$ algebras, in addition to $\frak{d}_-$, $\frak{p}$, $\frak{n}_-$, $\frak{g}$ and $\frak{c}$ algebras, have supersymmetric extension, while $\frak{n}_{-2}$, $\frak{g}_2$ and $\frak{g}'_2$ algebras have no supersymmetric extension. The connections among the superalgebras are established

Matrix and Graph Operations for Relationship Inference: An Illustration with the Kinship Inference in the China Biographical Database

Biographical databases contain diverse information about individuals. Person names, birth information, career, friends, family and special achievements are some possible items in the record for an individual. The relationships between individuals, such as kinship and friendship, provide invaluable insights about hidden communities which are not directly recorded in databases. We show that some simple matrix and graph-based operations are effective for inferring relationships among individuals, and illustrate the main ideas with the China Biographical Database (CBDB).Comment: 3 pages, 3 figures, 2017 Annual Meeting of the Japanese Association for Digital Humanitie

Enhancing the scalability and load balancing of the parallel selected inversion algorithm via tree-based asynchronous communication

We develop a method for improving the parallel scalability of the recently developed parallel selected inversion algorithm [Jacquelin, Lin and Yang 2014], named PSelInv, on massively parallel distributed memory machines. In the PSelInv method, we compute selected elements of the inverse of a sparse matrix A that can be decomposed as A = LU, where L is lower triangular and U is upper triangular. Updating these selected elements of A-1 requires restricted collective communications among a subset of processors within each column or row communication group created by a block cyclic distribution of L and U. We describe how this type of restricted collective communication can be implemented by using asynchronous point-to-point MPI communication functions combined with a binary tree based data propagation scheme. Because multiple restricted collective communications may take place at the same time in the parallel selected inversion algorithm, we need to use a heuristic to prevent processors participating in multiple collective communications from receiving too many messages. This heuristic allows us to reduce communication load imbalance and improve the overall scalability of the selected inversion algorithm. For instance, when 6,400 processors are used, we observe over 5x speedup for test matrices. It also mitigates the performance variability introduced by an inhomogeneous network topology

Broadcasting Correlated Vector Gaussians

The problem of sending two correlated vector Gaussian sources over a bandwidth-matched two-user scalar Gaussian broadcast channel is studied in this work, where each receiver wishes to reconstruct its target source under a covariance distortion constraint. We derive a lower bound on the optimal tradeoff between the transmit power and the achievable reconstruction distortion pair. Our derivation is based on a new bounding technique which involves the introduction of appropriate remote sources. Furthermore, it is shown that this lower bound is achievable by a class of hybrid schemes for the special case where the weak receiver wishes to reconstruct a scalar source under the mean squared error distortion constraint.Comment: 13 page