arXiv subjects

Lin Lin

Publications and source records attributed to Lin Lin.

At least 307 records · Page 17Linked to original sources

arXiv2015

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

We describe an efficient parallel implementation of the selected inversion algorithm for distributed memory computer systems, which we call \texttt{PSelInv}. The \texttt{PSelInv} method computes selected elements of a general sparse matrix $A$ that can be decomposed as $A = LU$, where $L$ is lower triangular and $U$ is upper triangular. The implementation described in this paper focuses on the case of sparse symmetric matrices. It contains an interface that is compatible with the distributed memory parallel sparse direct factorization \texttt{SuperLU\_DIST}. However, the underlying data structure and design of \texttt{PSelInv} allows it to be easily combined with other factorization routines such as \texttt{PARDISO}. We discuss general parallelization strategies such as data and task distribution schemes. In particular, we describe how to exploit the concurrency exposed by the elimination tree associated with the $LU$ factorization of $A$. We demonstrate the efficiency and accuracy of \texttt{PSelInv} by presenting a number of numerical experiments. In particular, we show that \texttt{PSelInv} can run efficiently on more than $4,000$ cores for a modestly sized matrix. We also demonstrate how \texttt{PSelInv} can be used to accelerate large-scale electronic structure calculations.

math.NA↗

arXiv2015

X-ray Perspective of the Twisted Magnetospheres of Magnetars

Anomalous X-ray pulsars (AXPs) and soft gamma-ray repeaters (SGRs) are recognized as the most promising magnetar candidates, as indicated by their energetic bursts and rapid spin-downs. It is expected that the strong magnetic field leaves distinctive imprints on the emergent radiation both by affecting the radiative processes in atmospheres of magnetars and by scattering in the upper magnetospheres. We construct a self-consistent physical model that incorporates emission from the magnetar surface and its reprocessing in the three-dimensional (3D) twisted magnetosphere using a Monte Carlo technique. The synthetic spectra are characterized by four parameters: surface temperature kT, surface magnetic field strength $B$, magnetospheric twist angle $Δϕ$, and the normalized electron velocity $β$. We also create a tabular model (STEMS3D) and apply it to a large sample of XMM-Newton spectra of magnetars. The model successfully fits nearly all spectra, and the obtained magnetic field for 7 out of the 11 sources are consistent with the values inferred from the spin-down rates. We conclude that the continuum-fitting by our model is a robust method to measure the magnetic field strength and magnetospheric configuration of AXPs and SGRs. Investigating the multiple observations of variable sources, we also study the mechanism of their spectral evolution. Our results suggest that the magnetospheres in these sources are highly twisted ($Δϕ> 1$), and the behavior of magnetospheric twisting and untwisting is revealed in the 2002 outburst of 1E 2259+586.

astro-ph.HE↗

arXiv2015

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.

cs.DC↗

arXiv2015

Large-scale ab initio simulations based on systematically improvable atomic basis

We present a first-principles computer code package (ABACUS) that is based on density functional theory and numerical atomic basis sets. Theoretical foundations and numerical techniques used in the code are described, with focus on the accuracy and transferability of the hierarchical atomic basis sets as generated using a scheme proposed by Chen, Guo and He [J. Phys.:Condens. Matter \textbf{22}, 445501 (2010)]. Benchmark results are presented for a variety of systems include molecules, solids, surfaces, and defects. All results show that the ABACUS package with its associated atomic basis sets is an efficient and reliable tool for simulating both small and large-scale materials.

cond-mat.mtrl-sci↗

arXiv2015

P-MaNGA: Gradients in Recent Star Formation Histories as Diagnostics for Galaxy Growth and Death

We present an analysis of the data produced by the MaNGA prototype run (P-MaNGA), aiming to test how the radial gradients in recent star formation histories, as indicated by the 4000AA-break (D4000), Hdelta absorption (EW(Hd_A)) and Halpha emission (EW(Ha)) indices, can be useful for understanding disk growth and star formation cessation in local galaxies. We classify 12 galaxies observed on two P-MaNGA plates as either centrally quiescent (CQ) or centrally star-forming (CSF), according to whether D4000 measured in the central spaxel of each datacube exceeds 1.6. For each galaxy we generate both 2D maps and radial profiles of D4000, EW(Hd_A) and EW(Ha). We find that CSF galaxies generally show very weak or no radial variation in these diagnostics. In contrast, CQ galaxies present significant radial gradients, in the sense that D4000 decreases, while both EW(Hd_A) and EW(Ha) increase from the galactic center outward. The outer regions of the galaxies show greater scatter on diagrams relating the three parameters than their central parts. In particular, the clear separation between centrally-measured quiescent and star-forming galaxies in these diagnostic planes is largely filled in by the outer parts of galaxies whose global colors place them in the green valley, supporting the idea that the green valley represents a transition between blue-cloud and red-sequence phases, at least in our small sample. These results are consistent with a picture in which the cessation of star formation propagates from the center of a galaxy outwards as it moves to the red sequence.

astro-ph.GA↗

arXiv2015

Drive laser system for the DC-SRF photoinjector at Peking University

Photoinjectors are widely used for linear accelerators as electron sources to generate high-brightness electron beam. Drive laser, which determines the timing structure and quality of the electron beam, is a crucial device of photoinjector. A new drive laser system has been designed and constructed for the upgraded 3.5-cell DC-SRF photoinjector at Peking University. The drive laser system consists of a 1064 nm laser oscillator, a four- stage amplifier, the second and fourth harmonic generators, the optical system to transfer the UV pulses to the photocathode, and the synchronization system. The drive laser system has been successfully applied in the stable operation of DC-SRF photoinjector and its performance meets the requirements. 266 nm laser with an average power close to 1W can be delivered to illuminate the Cs2Te photocathode and the instability is less than 5% for long time operation. The design consideration for improving the UV laser quality, a detailed description of laser system, and its performance are presented in this paper.

physics.acc-ph↗

arXiv2015

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.

cond-mat.mtrl-sci↗

arXiv2014

Compressed representation of Kohn-Sham orbitals via selected columns of the density matrix

Given a set of Kohn-Sham orbitals from an insulating system, we present a simple, robust, efficient and highly parallelizable method to construct a set of, optionally orthogonal, localized basis functions for the associated subspace. Our method explicitly uses the fact that density matrices associated with insulating systems decay exponentially along the off-diagonal direction in the real space representation. Our method avoids the usage of an optimization procedure, and the localized basis functions are constructed directly from a set of selected columns of the density matrix (SCDM). Consequently, the only adjustable parameter in our method is the truncation threshold of the localized basis functions. Our method can be used in any electronic structure software package with an arbitrary basis set. We demonstrate the numerical accuracy and parallel scalability of the SCDM procedure using orbitals generated by the Quantum ESPRESSO software package. We also demonstrate a procedure for combining SCDM with Hockney's algorithm to efficiently perform Hartree-Fock exchange energy calculations with near linear scaling.

physics.comp-ph↗

arXiv2014

Approximating spectral densities of large matrices

In physics, it is sometimes desirable to compute the so-called \emph{Density Of States} (DOS), also known as the \emph{spectral density}, of a real symmetric matrix $A$. The spectral density can be viewed as a probability density distribution that measures the likelihood of finding eigenvalues near some point on the real line. The most straightforward way to obtain this density is to compute all eigenvalues of $A$. But this approach is generally costly and wasteful, especially for matrices of large dimension. There exists alternative methods that allow us to estimate the spectral density function at much lower cost. The major computational cost of these methods is in multiplying $A$ with a number of vectors, which makes them appealing for large-scale problems where products of the matrix $A$ with arbitrary vectors are relatively inexpensive. This paper defines the problem of estimating the spectral density carefully, and discusses how to measure the accuracy of an approximate spectral density. It then surveys a few known methods for estimating the spectral density, and proposes some new variations of existing methods. All methods are discussed from a numerical linear algebra point of view.

math.NA↗

arXiv2014

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.

cond-mat.mtrl-sci↗

arXiv2014

Characterizing Ultraviolet and Infrared Observational Properties for Galaxies. II. Features of Attenuation Law

Variations in the attenuation law have a significant impact on observed spectral energy distributions for galaxies. As one important observational property for galaxies at ultraviolet and infrared wavelength bands, the correlation between infrared-to-ultraviolet luminosity ratio and ultraviolet color index (or ultraviolet spectral slope), i.e., the IRX-UV relation (or IRX-beta relation), offered a widely used recipe for correcting dust attenuation in galaxies, but the usability appears to be in doubt now because of considerable dispersion in this relation found by many studies. In this paper, on the basis of spectral synthesis modeling and spatially resolved measurements of four nearby spiral galaxies, we provide an interpretation of the deviation in the IRX-UV relation with variations in the attenuation law. From both theoretical and observational viewpoints, two components in the attenuation curve, the linear background and the 2175 Angstrom bump, are suggested to be the parameters in addition to the stellar population age (addressed in the first paper of this series) in the IRX-UV function; different features in the attenuation curve are diagnosed for the galaxies in our sample. Nevertheless, it is often difficult to ascertain the attenuation law for galaxies in actual observations. Possible reasons for preventing the successful detection of the parameters in the attenuation curve are also discussed in this paper, including the degeneracy of the linear background and the 2175 Angstrom bump in observational channels, the requirement for young and dust-rich systems to study, and the difficulty in accurate estimates of dust attenuations at different wavelength bands.

astro-ph.GA↗

arXiv2014

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.

math.NA↗

arXiv2014

SIESTA-PEXSI: Massively parallel method for efficient and accurate \textit{ab initio} materials simulation without matrix diagonalization

We describe a scheme for efficient large-scale electronic-structure calculations based on the combination of the pole expansion and selected inversion (PEXSI) technique with the SIESTA method, which uses numerical atomic orbitals within the Kohn-Sham density functional theory (KSDFT) framework. The PEXSI technique can efficiently utilize the sparsity pattern of the Hamiltonian and overlap matrices generated in SIESTA, and for large systems has a much lower computational complexity than that associated with the matrix diagonalization procedure. The PEXSI technique can be used to evaluate the electron density, free energy, atomic forces, density of states and local density of states without computing any eigenvalue or eigenvector of the Kohn-Sham Hamiltonian. It can achieve accuracy fully comparable to that obtained from a matrix diagonalization procedure for general systems, including metallic systems at low temperature. The PEXSI method is also highly scalable. With the recently developed massively parallel PEXSI technique, we can make efficient use of more than $10,000$ processors on high performance machines. We demonstrate the performance and accuracy of the SIESTA-PEXSI method using several examples of large scale electronic structure calculations, including 1D, 2D and bulk problems with insulating, semi-metallic, and metallic character.

physics.comp-ph↗

arXiv2014

Pole expansion for solving a type of parametrized linear systems in electronic structure calculations

We present a new method for solving parametrized linear systems. Under certain assumptions on the parametrization, solutions to the linear systems for all parameters can be accurately approximated by linear combinations of solutions to linear systems for a small set of fixed parameters. Combined with either direct solvers or preconditioned iterative solvers for each linear system with a fixed parameter, the method is particularly suitable for situations when solutions to a large number of distinct parameters or a large number of right hand sides are required. The method is also simple to parallelize. We demonstrate the applicability of the method to the calculation of the response functions in electronic structure theory. We demonstrate the numerical performance of the method using a benzene molecule and a DNA molecule.

math.NA↗

arXiv2014

The low level radio frequency control system for DC-SRF photo-injector at Peking University

A low level radio frequency (LLRF) control system is designed and constructed at Peking University, which is for the DC-SRF photo injector operating at 2K. Besides with continuous wave (CW), the system is also reliable with pulsed RF and pulsed beam, the stability of amplitude and phase can achieve 0.13% and 0.1°respectively. It is worth noting that the system works perfectly when the cavity is driven at both generator driven resonator (GDR) and self-excited loop (SEL), the latter is useful in measuring the performance of the cavity.

physics.acc-ph↗

arXiv2014

Quasi-Periodic Oscillations in Short Recurring Bursts of the Soft-Gamma Repeater J1550-5418

The discovery of quasi-periodic oscillations (QPOs) in magnetar giant flares has opened up prospects for neutron star asteroseismology. The scarcity of giant flares makes a search for QPOs in the shorter, far more numerous bursts from Soft Gamma Repeaters (SGRs) desirable. In Huppenkothen et al (2013), we developed a Bayesian method for searching for QPOs in short magnetar bursts, taking into account the effects of the complicated burst structure, and have shown its feasibility on a small sample of bursts. Here, we apply the same method to a much larger sample from a burst storm of 286 bursts from SGR J1550-5418. We report a candidate signal at 260 Hz in a search of the individual bursts, which is fairly broad. We also find two QPOs at 93 Hz and one at 127 Hz, when averaging periodograms from a number of bursts in individual triggers, at frequencies close to QPOs previously observed in magnetar giant flares. Finally, for the first time, we explore the overall burst variability in the sample, and report a weak anti-correlation between the power-law index of the broadband model characterising aperiodic burst variability, and the burst duration: shorter bursts have steeper power law indices than longer bursts. This indicates that longer bursts vary over a broader range of time scales, and are not simply longer versions of the short bursts.

astro-ph.HE↗

arXiv2014

Numerical integration for ab initio many-electron self energy calculations within the GW approximation

We present a numerical integration scheme for evaluating the convolution of a Green's function with a screened Coulomb potential on the real axis in the GW approximation of the self energy. Our scheme takes the zero broadening limit in Green's function first, replaces the numerator of the integrand with a piecewise polynomial approximation, and performs principal value integration on subintervals analytically. We give the error bound of our numerical integration scheme and show by numerical examples that it is more reliable and accurate than the standard quadrature rules such as the composite trapezoidal rule. We also discuss the benefit of using different self energy expressions to perform the numerical convolution at different frequencies.

physics.comp-ph↗

arXiv2014

The Fermi GBM Gamma-Ray Burst Spectral Catalog: Four Years Of Data

In this catalog we present the updated set of spectral analyses of GRBs detected by the Fermi Gamma-Ray Burst Monitor (GBM) during its first four years of operation. It contains two types of spectra, time-integrated spectral fits and spectral fits at the brightest time bin, from 943 triggered GRBs. Four different spectral models were fitted to the data, resulting in a compendium of more than 7500 spectra. The analysis was performed similarly, but not identically to Goldstein et al. 2012. All 487 GRBs from the first two years have been re-fitted using the same methodology as that of the 456 GRBs in years three and four. We describe, in detail, our procedure and criteria for the analysis, and present the results in the form of parameter distributions both for the observer-frame and rest-frame quantities. The data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center (HEASARC).

astro-ph.HE↗