arXiv subjects

Lin Lin

Publications and source records attributed to Lin Lin.

At least 271 records · Page 15Linked to original sources

arXiv2018

Accelerating Optical Absorption Spectra and Exciton Energy Computation for Nanosystems via Interpolative Separable Density Fitting

We present an efficient way to solve the Bethe-Salpeter equation (BSE), a model for the computation of absorption spectra in molecules and solids that includes electron-hole excitations. Standard approaches to construct and diagonalize the Bethe-Salpeter Hamiltonian require at least $Ø(N_e^5)$ operations, where $N_e$ is proportional to the number of electrons in the system, limiting its application to small systems. Our approach is based on the interpolative separable density fitting (ISDF) technique to construct low rank approximations to the bare and screened exchange operators associated with the BSE Hamiltonian. This approach reduces the complexity of the Hamiltonian construction to $Ø(N_e^3)$ with a much smaller pre-constant. Here, we implement the ISDF method for the BSE calculations within the Tamm-Dancoff approximation (TDA) in the BerkeleyGW software package. We show that ISDF-based BSE calculations in molecules and solids reproduce accurate exciton energies and optical absorption spectra with significantly reduced computational cost.

physics.comp-ph↗

arXiv2018

Internal Variations in Empirical Oxygen Abundances for Giant HII Regions in the Galaxy NGC 2403

This paper presents a spectroscopic investigation of 11 HII regions in the nearby galaxy NGC 2403. The HII regions are observed with a long-slit spectrograph mounted on the 2.16 m telescope at XingLong station of National Astronomical Observatories of China. For each of the HII regions, spectra are extracted at different nebular radii along the slit-coverage. Oxygen abundances are empirically estimated from the strong-line indices R23, N2O2, O3N2, and N2 for each spectrophotometric unit, with both observation- and model-based calibrations adopted into the derivation. Radial profiles of these diversely estimated abundances are drawn for each nebula. In the results, the oxygen abundances separately estimated with the prescriptions on the basis of observations and models, albeit from the same spectral index, systematically deviate from each other; at the same time, the spectral indices R23 and N2O2 are distributed with flat profiles, whereas N2 and O3N2 exhibit apparent gradients with the nebular radius. Because our study naturally samples various ionization levels which inherently decline at larger radii within individual HII regions, the radial distributions indicate not only the robustness of R23 and N2O2 against ionization variations but also the sensitivity of N2 and O3N2 to the ionization parameter. The results in this paper provide observational corroboration of the theoretical prediction about the deviation in the empirical abundance diagnostics. Our future work is planned to investigate metal-poor HII regions with measurable T_e, in an attempt to recalibrate the strong-line indices and consequently disclose the cause of the discrepancies between the empirical oxygen abundances.

astro-ph.GA↗

arXiv2018

Variational formulation for Wannier functions with entangled band structure

Wannier functions provide a localized representation of spectral subspaces of periodic Hamiltonians, and play an important role for interpreting and accelerating Hartree-Fock and Kohn-Sham density functional theory calculations in quantum physics and chemistry. For systems with isolated band structure, the existence of exponentially localized Wannier functions and numerical algorithms for finding them are well studied. In contrast, for systems with entangled band structure, Wannier functions must be generalized to span a subspace larger than the spectral subspace of interest to achieve favorable spatial locality. In this setting, little is known about the theoretical properties of these Wannier functions, and few algorithms can find them robustly. We develop a variational formulation to compute these generalized maximally localized Wannier functions. When paired with an initial guess based on the selected columns of the density matrix (SCDM) method, our method can robustly find Wannier functions for systems with entangled band structure. We formulate the problem as a constrained nonlinear optimization problem, and show how the widely used disentanglement procedure can be interpreted as a splitting method to approximately solve this problem. We demonstrate the performance of our method using real materials including silicon, copper, and aluminum. To examine more precisely the localization properties of Wannier functions, we study the free electron gas in one and two dimensions, where we show that the maximally-localized Wannier functions only decay algebraically. We also explain using a one dimensional example how to modify them to obtain super-algebraic decay.

physics.comp-ph↗

arXiv2017

A Stochastic Generalized Ginzburg-Landau Equation Driven by Jump Noise

This paper is concerned with the stochastic generalized Ginzburg-Landau equation driven by a multiplicative noise of jump type. By a prior estimate, weak convergence and monotonicity technique, we prove the existence and uniqueness of the solution of an initial-boundary value problem with homogeneous Dirichlet boundary condition. However, for the generalized Ginzburg-Landau equation, such a locally monotonic condition of the nonlinear term can not be satisfied in a straight way. For this, we utilize the characteristic structure of nonlinear term and refined analysis to overcome this gap.

math.AP↗

arXiv2017

Convergence of adaptive compression methods for Hartree-Fock-like equations

The adaptively compressed exchange (ACE) method provides an efficient way for solving Hartree-Fock-like equations in quantum physics, chemistry, and materials science. The key step of the ACE method is to adaptively compress an operator that is possibly dense and full-rank. In this paper, we present a detailed study of the adaptive compression operation and establish rigorous convergence properties of the adaptive compression method in the context of solving linear eigenvalue problems. Our analysis also elucidates the potential use of the adaptive compression method in a wide range of problems.

math.NA↗

arXiv2017

Variational structure of Luttinger-Ward formalism and bold diagrammatic expansion for Euclidean lattice field theory

The Luttinger-Ward functional was proposed more than five decades ago to provide a link between static and dynamic quantities in a quantum many-body system. Despite its widespread usage, the derivation of the Luttinger-Ward functional remains valid only in the formal sense, and even the very existence of this functional has been challenged by recent numerical evidence. In a simpler and yet highly relevant regime, namely the Euclidean lattice field theory, we rigorously prove that the Luttinger-Ward functional is a well-defined universal functional over all physical Green's functions. Using the Luttinger-Ward functional, the free energy can be variationally minimized with respect to Green's functions in its domain. We then derive the widely used bold diagrammatic expansion rigorously, without relying on formal arguments such as partial resummation of bare diagrams to infinite order.

math-ph↗

arXiv2017

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.

physics.comp-ph↗

arXiv2017

Strong Edge Magnetism and Tunable Energy Gaps in Zigzag Graphene Quantum Dots with High Stability

Graphene is a nonmagnetic semimetal and cannot be directly used as electronic or spintronic devices. We demonstrate that graphene quantum dots (GQDs) can exhibit strong edge magnetism and tunable energy gaps due to the presence of localized edge states. By using large-scale first principle density functional theory (DFT) calculations and detailed analysis based on model Hamiltonians, we can show that the zigzag edge states in GQDs become much stronger and more localized as the system size increases. The enhanced edge states induce strong electron-electron interactions along the edges of GQDs, ultimately resulting in a magnetic phase transition from nonmagnetic to intra-edge ferromagnetic and inter-edge antiferromagnetic, when the diameter is larger than 4.5 nm. Our analysis shows that the inter-edge superexchange interaction of antiferromagnetic states between two nearest-neighbor zigzag edges in GQDs is much stronger than that exists between two parallel zigzag edges in GQDs and graphene nanoribbons. Furthermore, such strong and localized edge states also induce GQDs semiconducting with tunable energy gaps, mainly controlled by adjusting the system size. Our results show that the quantum confinement effect, inter-edge superexchange (antiferromagnetic), and intra-edge direct exchange (ferromagnetic) interactions are crucial for the electronic and magnetic properties of zigzag GQDs at the nanoscale.

cond-mat.mtrl-sci↗

arXiv2017

A structure preserving Lanczos algorithm for computing the optical absorption spectrum

We present a new structure preserving Lanczos algorithm for approximating the optical absorption spectrum in the context of solving full Bethe--Salpeter equation without Tamm--Dancoff approximation. The new algorithm is based on a structure preserving Lanczos procedure, which exploits the special block structure of Bethe--Salpeter Hamiltonian matrices. A recently developed technique of generalized averaged Gauss quadrature is incorporated to accelerate the convergence. We also establish the connection between our structure preserving Lanczos procedure with several existing Lanczos procedures developed in different contexts. Numerical examples are presented to demonstrate the effectiveness of our Lanczos algorithm.

math.NA↗

arXiv2017

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.

physics.comp-ph↗

arXiv2017

Computing localized representations of the kohn-sham subspace via randomization and refinement

Localized representation of the Kohn-Sham subspace plays an important role in quantum chemistry and materials science. The recently developed selected columns of the density matrix (SCDM) method [J. Chem. Theory Comput. 11, 1463, 2015] is a simple and robust procedure for finding a localized representation of a set of Kohn-Sham orbitals from an insulating system. The SCDM method allows the direct construction of a well conditioned (or even orthonormal) and localized basis for the Kohn-Sham subspace. The SCDM algorithm avoids the use of an optimization procedure and does not depend on any adjustable parameters. The most computationally expensive step of the SCDM method is a column pivoted QR factorization that identifies the important columns for constructing the localized basis set. In this paper, we develop a two stage approximate column selection strategy to find the important columns at much lower computational cost. We demonstrate the effectiveness of this process using the dissociation process of a BH$_3$NH$_3$ molecule, an alkane chain and a supercell with 256 water molecules. Numerical results for the large collection of water molecules show that two stage localization procedure can be more than 30 times faster than the original SCDM algorithm and compares favorably with the popular Wannier90 package.

math.NA↗

arXiv2017

PSelInv - A Distributed Memory Parallel Algorithm for Selected Inversion: the non-symmetric Case

This paper generalizes the parallel selected inversion algorithm called PSelInv to sparse non- symmetric matrices. We assume a general sparse matrix A has been decomposed as PAQ = LU on a distributed memory parallel machine, where L, U are lower and upper triangular matrices, and P, Q are permutation matrices, respectively. The PSelInv method computes selected elements of A-1. The selection is confined by the sparsity pattern of the matrix AT . Our algorithm does not assume any symmetry properties of A, and our parallel implementation is memory efficient, in the sense that the computed elements of A-T overwrites the sparse matrix L+U in situ. PSelInv involves a large number of collective data communication activities within different processor groups of various sizes. In order to minimize idle time and improve load balancing, tree-based asynchronous communication is used to coordinate all such collective communication. Numerical results demonstrate that PSelInv can scale efficiently to 6,400 cores for a variety of matrices.

cs.MS↗

arXiv2017

Robust Determination of the Chemical Potential in the Pole Expansion and Selected Inversion Method for Solving Kohn-Sham density functional theory

Fermi operator expansion (FOE) methods are powerful alternatives to diagonalization type methods for solving Kohn-Sham density functional theory (KSDFT). One example is the pole expansion and selected inversion (PEXSI) method, which approximates the Fermi operator by rational matrix functions and reduces the computational complexity to at most quadratic scaling for solving KSDFT. Unlike diagonalization type methods, the chemical potential often cannot be directly read off from the result of a single step of evaluation of the Fermi operator. Hence multiple evaluations are needed to be sequentially performed to compute the chemical potential to ensure the correct number of electrons within a given tolerance. This hinders the performance of FOE methods in practice. In this paper we develop an efficient and robust strategy to determine the chemical potential in the context of the PEXSI method. The main idea of the new method is not to find the exact chemical potential at each self-consistent-field (SCF) iteration iteration, but to dynamically and rigorously update the upper and lower bounds for the true chemical potential, so that the chemical potential reaches its convergence along the SCF iteration. Instead of evaluating the Fermi operator for multiple times sequentially, our method uses a two-level strategy that evaluates the Fermi operators in parallel. In the regime of full parallelization, the wall clock time of each SCF iteration is always close to the time for one single evaluation of the Fermi operator, even when the initial guess is far away from the converged solution. We demonstrate the effectiveness of the new method using examples with metallic and insulating characters, as well as results from ab initio molecular dynamics.

physics.comp-ph↗

arXiv2017

Interpolative Separable Density Fitting Decomposition for Accelerating Hybrid Density Functional Calculations With Applications to Defects in Silicon

We present a new efficient way to perform hybrid density functional theory (DFT) based electronic structure calculation. The new method uses an interpolative separable density fitting (ISDF) procedure to construct a set of numerical auxiliary basis vectors and a compact approximation of the matrix consisting of products of occupied orbitals represented in a large basis set such as the planewave basis. Such an approximation allows us to reduce the number of Poisson solves from $\Or(N_{e}^2)$ to $\Or(N_{e})$ when we apply the exchange operator to occupied orbitals in an iterative method for solving the Kohn-Sham equations, where $N_{e}$ is the number of electrons in the system to be studied. We show that the ISDF procedure can be carried out in $\Or(N_{e}^3)$ operations, with a much smaller pre-constant compared to methods used in existing approaches. When combined with the recently developed adaptively compressed exchange (ACE) operator formalism, which reduces the number of times the exchange operator needs to be updated, the resulting ACE-ISDF method significantly reduces the computational cost \REV{associated with the exchange operator} by nearly two orders of magnitude compared to existing approaches for a large silicon system with $1000$ atoms. We demonstrate that the ACE-ISDF method can produce accurate energies and forces for insulating and metallic systems, and that it is possible to obtain converged hybrid functional calculation results for a 1000-atom bulk silicon within 10 minutes on 2000 computational cores. We also show that ACE-ISDF can scale to 8192 computational cores for a 4096-atom bulk silicon system. We use the ACE-ISDF method to geometrically optimize a 1000-atom silicon system with a vacancy defect using the HSE06 functional and computes its electronic structure.

physics.comp-ph↗

arXiv2017

The peculiar filamentary HI structure of NGC 6145

In this paper, we report the peculiar HI morphology of the cluster spiral galaxy NGC 6145, which has a 150 kpc HI filament on one side that is nearly parallel to its major axis. This filament is made up of several HI clouds and the diffuse HI gas between them, with no optical counterparts. We compare its HI distribution with other one-sided HI distributions in the literature, and find that the overall HI distribution is very different from the typical tidal and ram-pressure stripped HI shape, and its morphology is inconsistent with being a pure accretion event. Only about 30% of the total HI gas is anchored on the stellar disk, while most of HI gas forms the filament in the west. At a projected distance of 122 kpc, we find a massive elliptical companion (NGC 6146) with extended radio emission, whose axis points to an HI gap in NGC 6145. The velocity of the HI filament shows an overall light-of- sight motion of 80 to 180 km/s with respect to NGC 6145. Using the long-slit spectra of NGC 6145 along its major stellar axis, we find that some outer regions show enhanced star formation, while in contrast, almost no star formation activities are found in its center (less than 2 kpc). Pure accretion, tidal or ram-pressure stripping is not likely to produce the observed HI filament. An alternative explanation is the jet-stripping from NGC 6146, although direct evidence for a jet-cold gas interaction has not been found.

astro-ph.GA↗

arXiv2017

The Properties of Massive Star-forming galaxies with Outside-in Assembly Mode

Previous findings show that massive ($> 10^{10} M_{sun}$) star-forming (SF) galaxies usually have an inside-out stellar mass assembly mode. In this paper, we have for the first time selected a sample of 77 massive SF galaxies with an outside-in assembly mode (called targeted sample) from the Mapping Nearby Galaxies at the Apache Point Observatory (MaNGA) survey. For comparison, two control samples are constructed from MaNGA sample matched in stellar mass: a sample of 154 normal SF galaxies and a sample of 62 quiescent galaxies. In contrast to normal SF galaxies, the targeted galaxies appear to be more smooth-like and bulge-dominated, and have smaller size, higher concentration, higher star formation rate and higher gas-phase metallicity as a whole. However, they have larger size and lower concentration than quiescent galaxies. Unlike normal SF sample, the targeted sample exhibits a slightly positive gradient of 4000 Å break and a pronounced negative gradient of H$α$ equivalent width. Further more, their median surface mass density profile is between that of normal SF sample and quiescent sample, indicating that the gas accretion of quiescent galaxies is not likely to be the main approach for the outside-in assembly mode. Our results suggest that the targeted galaxies are likely in the transitional phase from normal SF galaxies to quiescent galaxies, with rapid on-going central stellar mass assembly (or bulge growth). We discuss several possible formation mechanisms for the outside-in mass assembly mode.

astro-ph.GA↗

arXiv2017

ELSI: A Unified Software Interface for Kohn-Sham Electronic Structure Solvers

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.

physics.comp-ph↗

arXiv2017

Towards Interrogating Discriminative Machine Learning Models

It is oftentimes impossible to understand how machine learning models reach a decision. While recent research has proposed various technical approaches to provide some clues as to how a learning model makes individual decisions, they cannot provide users with ability to inspect a learning model as a complete entity. In this work, we propose a new technical approach that augments a Bayesian regression mixture model with multiple elastic nets. Using the enhanced mixture model, we extract explanations for a target model through global approximation. To demonstrate the utility of our approach, we evaluate it on different learning models covering the tasks of text mining and image recognition. Our results indicate that the proposed approach not only outperforms the state-of-the-art technique in explaining individual decisions but also provides users with an ability to discover the vulnerabilities of a learning model.

cs.LG↗