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Published work

105 published item(s)

preprint2026arXiv

One for All: A Non-Linear Transformer can Enable Cross-Domain Generalization for In-Context Reinforcement Learning

A central challenge in reinforcement learning (RL) is to learn models that generalize beyond the tasks on which they are trained, a goal traditionally pursued through multi-task and meta RL. Recently, transformer architectures have emerged as a promising approach, enabling adaptation to new tasks via in-context learning without explicit parameter updates. From a functional perspective, a transformer can be viewed as a functional operator that maps a context to a task-specific function. It is thus fundamental to understand and design this operator to support stronger generalization in RL. In this work, we address this resulting question of generalization from a kernel-based perspective by establishing a connection between non-linear transformers and kernel-based temporal difference learning. By interpreting the transformer as performing regression in a Reproducing Kernel Hilbert Space (RKHS), we show that value functions from different domains can be represented using a shared set of weights, provided they lie within the same RKHS. Experiments on multiple MetaWorld domains support this interpretation, demonstrating convergence of the temporal-difference objective.

preprint2022arXiv

A Search for Millilensing Gamma-Ray Bursts in the Observations of Fermi GBM

Millilensing of Gamma-Ray Bursts (GRBs) is expected to manifest as multiple emission episodes in a single triggered GRB with similar light-curve patterns and similar spectrum properties. Identifying such lensed GRBs could help improve constraints on the abundance of compact dark matter. Here we present a systemic search for millilensing among 3000 GRBs observed by the \textit{Fermi} GBM up to 2021 April. Eventually we find 4 interesting candidates by performing auto-correlation test, hardness test, and time-integrated/resolved spectrum test to the whole sample. GRB 081126A and GRB 090717A are ranked as the first class candidate based on their excellent performance both in temporal and spectrum analysis. GRB 081122A and GRB 110517B are ranked as the second class candidates (suspected candidates), mainly because their two emission episodes show clear deviations in part of the time-resolved spectrum or in the time-integrated spectrum. Considering a point mass model for the gravitational lens, our results suggest that the density parameter of lens objects with mass $M_{\rm L}\sim10^{6} M_{\odot}$ is larger than $1.5\times10^{-3}$.

preprint2022arXiv

Automatic Depression Detection: An Emotional Audio-Textual Corpus and a GRU/BiLSTM-based Model

Depression is a global mental health problem, the worst case of which can lead to suicide. An automatic depression detection system provides great help in facilitating depression self-assessment and improving diagnostic accuracy. In this work, we propose a novel depression detection approach utilizing speech characteristics and linguistic contents from participants' interviews. In addition, we establish an Emotional Audio-Textual Depression Corpus (EATD-Corpus) which contains audios and extracted transcripts of responses from depressed and non-depressed volunteers. To the best of our knowledge, EATD-Corpus is the first and only public depression dataset that contains audio and text data in Chinese. Evaluated on two depression datasets, the proposed method achieves the state-of-the-art performances. The outperforming results demonstrate the effectiveness and generalization ability of the proposed method. The source code and EATD-Corpus are available at https://github.com/speechandlanguageprocessing/ICASSP2022-Depression.

preprint2022arXiv

Ferroelectric superdomain controlled graphene plasmon for tunable mid-infrared photodetector with dual-band spectral selectivity

Dual-band infrared photodetectors (DBIPs) can discriminate desired signals from complex scenes and thus are highly expected for threat-warning, remote sensing, and astronomy applications. Conventional DBIPs with high-performances are, however, typically based on semiconductor thin films, but remain the challenges of complex spatial align, expensive growth and cooling requirement. Here, we report a tunable graphene plasmonic photodetector with dual-band infrared spectral selectivity driven by ferroelectric superdomain. The periodic ferroelectric polarization array with nanoscale ring shapes provides ultrahigh electrostatic field for spatially doping of monolayer graphene to desired patterns, and is further used to excite and confine intrinsic graphene plasmons. Our devices exhibit tunable resonance photoresponse in both two bands of 3.7-16.3 um and 15.1-52.1 um. The numerical calculations show that our devices own ultrahigh responsivities of 667-1080 A W-1 at room temperature in range of 5-50 um. Our devices make possible the applications of infrared imaging system and both stationary and motion state of objects detection. These investigations provide a novel approach for advanced infrared system construction by employing simple, low-cost, uncooling multispectral detectors array.

preprint2022arXiv

Filters for ISI Suppression in Molecular Communication via Diffusion

Molecular communication via diffusion (MCvD) is considered as one of the most feasible communication paradigms for nanonetworks, especially for bio-nanonetworks which are usually in water-rich biological environments. Two effects that deteriorates the signal in MCvD are noise and inter-symbol interference (ISI). The expected channel impulse response of MCvD has a long and slow attenuating tail due to molecular diffusion which causes ISI and further limits the slow data rate of MCvD. The extent that ISI and noise are suppressed in an MCvD system determines its effectiveness, especially at a high data rate. Although ISI-suppression approaches have been investigated, most of them are addressed as non-essential parts in other topics, such as signal detection or modulation. Furthermore, most of the state-of-the-art ISI-suppression approaches are performed by subtracting the estimated ISI from the total signal. In this work, we investigate ISI-suppression from a new perspective of filters to filter ISI out without any ISI estimation. The principles for a good design of ISI-suppression filters in MCvD are investigated. Based on the principles, an ISI-suppression filter with good anti-noise capability and an associated signal detection scheme is proposed for MCvD scenarios with both ISI and noise. We compare the proposed scheme with the state-of-the-art ISI-suppression approaches. The result manifests that the proposed ISI-suppression scheme could recover signals deteriorated severely by both ISI and noise, which could not be effectively detected by the state-of-the-art ISI-suppression approaches.

preprint2022arXiv

Heisenberg-limited ground state energy estimation for early fault-tolerant quantum computers

Under suitable assumptions, the quantum phase estimation (QPE) algorithm is able to achieve Heisenberg-limited precision scaling in estimating the ground state energy. However, QPE requires a large number of ancilla qubits and large circuit depth, as well as the ability to perform inverse quantum Fourier transform, making it expensive to implement on an early fault-tolerant quantum computer. We propose an alternative method to estimate the ground state energy of a Hamiltonian with Heisenberg-limited precision scaling, which employs a simple quantum circuit with one ancilla qubit, and a classical post-processing procedure. Besides the ground state energy, our algorithm also produces an approximate cumulative distribution function of the spectral measure, which can be used to compute other spectral properties of the Hamiltonian.

preprint2022arXiv

Insight-HXMT dedicated 33-day observation of SGR J1935+2154 I. Burst Catalog

Magnetars are neutron stars with extreme magnetic field and sometimes manifest as soft gamma-ray repeaters (SGRs). SGR J1935+2154 is one of the most prolific bursters and the first confirmed source of fast radio burst (i.e. FRB 200428). Encouraged by the discovery of the first X-ray counterpart of FRB, Insight-Hard X-ray Modulation Telescope (Insight-HXMT) implemented a dedicated 33-day long ToO observation of SGR J1935+2154 since April 28, 2020. With the HE, ME, and LE telescopes, Insight-HXMT provides a thorough monitoring of burst activity evolution of SGR J1935+2154, in a very broad energy range (1-250 keV) with high temporal resolution and high sensitivity, resulting in a unique valuable data set for detailed studies of SGR J1935+2154. In this work, we conduct a comprehensive analysis of this observation including detailed burst search, identification and temporal analyses. After carefully removing false triggers, we find a total of 75 bursts from SGR J1935+2154, out of which 70 are single-pulsed. The maximum burst rate is about 56 bursts/day. Both the burst duration and the waiting time between two successive bursts follow log-normal distributions, consistent with previous studies. We also find that bursts with longer duration (some are multi-pulsed) tend to occur during the period with relatively high burst rate. There is no correlation between the waiting time and the fluence or duration of either the former or latter burst. It also seems that there is no correlation between burst duration and hardness ratio, in contrast to some previous reports. In addition, we do not find any X-ray burst associated with any reported radio bursts except for FRB 200428.

preprint2022arXiv

Insight-HXMT dedicated 33-day observation of SGR J1935+2154 II. Burst Spectral Catalog

Since April 28, 2020, Insight-HXMT has implemented a dedicated observation on the magnetar SGR J1935+2154. Thanks to the wide energy band (1-250 keV) and high sensitivity of Insight-HXMT, we obtained 75 bursts from SGR J1935+2154 during a month-long activity episode after the emission of FRB 200428. Here, we report the detailed time-integrated spectral analysis of these bursts and the statistical distribution of the spectral parameters. We find that for 15%(11/75) of SGR J1935+2154 bursts, the CPL model is preferred, and most of them occurred in the latter part of this active epoch. In the cumulative fluence distribution, we find that the fluence of bursts in our sample is about an order of magnitude weaker than that of Fermi/GBM, but follows the same power law distribution. Finally, we find a burst with similar peak energy to the time-integrated spectrum of the X-ray burst associated with FRB 200428 (FRB 200428-Associated Burst), but the low energy index is harder.

preprint2022arXiv

KSSOLV 2.0: An efficient MATLAB toolbox for solving the Kohn-Sham equations with plane-wave basis set

KSSOLV (Kohn-Sham Solver) is a MATLAB toolbox for performing Kohn-Sham density functional theory (DFT) calculations with a plane-wave basis set. KSSOLV 2.0 preserves the design features of the original KSSOLV software to allow users and developers to easily set up a problem and perform ground-state calculations as well as to prototype and test new algorithms. Furthermore, it includes new functionalities such as new iterative diagonalization algorithms, k-point sampling for electron band structures, geometry optimization and advanced algorithms for performing DFT calculations with local, semi-local, and hybrid exchange-correlation functionals. It can be used to study the electronic structures of both molecules and solids. We describe these new capabilities in this work through a few use cases. We also demonstrate the numerical accuracy and computational efficiency of KSSOLV on a variety of examples.

preprint2022arXiv

Lecture Notes on Quantum Algorithms for Scientific Computation

This is a set of lecture notes used in a graduate topic class in applied mathematics called ``Quantum Algorithms for Scientific Computation'' at the Department of Mathematics, UC Berkeley during the fall semester of 2021. These lecture notes focus only on quantum algorithms closely related to scientific computation, and in particular, matrix computation. The main purpose of the lecture notes is to introduce quantum phase estimation (QPE) and ``post-QPE'' methods such as block encoding, quantum signal processing, and quantum singular value transformation, and to demonstrate their applications in solving eigenvalue problems, linear systems of equations, and differential equations. The intended audience is the broad computational science and engineering (CSE) community interested in using fault-tolerant quantum computers to solve challenging scientific computing problems.

preprint2022arXiv

On the pure state $v$-representability of density matrix embedding theory

Density matrix embedding theory (DMET) formally requires the matching of density matrix blocks obtained from high-level and low-level theories, but this is sometimes not achievable in practical calculations. In such a case, the global band gap of the low-level theory vanishes, and this can require additional numerical considerations. We find that both the violation of the exact matching condition and the vanishing low-level gap are related to the assumption that the high-level density matrix blocks are non-interacting pure-state $v$-representable (NI-PS-V), which assumes that the low-level density matrix is constructed following the Aufbau principle. In order to relax the NI-PS-V condition, we develop an augmented Lagrangian method to match the density matrix blocks without referring to the Aufbau principle. Numerical results for 2D Hubbard and hydrogen model systems indicate that in some challenging scenarios, the relaxation of the Aufbau principle directly leads to exact matching of the density matrix blocks, which also yields improved accuracy.

preprint2022arXiv

Quantum linear system solver based on time-optimal adiabatic quantum computing and quantum approximate optimization algorithm

We demonstrate that with an optimally tuned scheduling function, adiabatic quantum computing (AQC) can readily solve a quantum linear system problem (QLSP) with $\mathcal{O}(κ~\text{poly}(\log(κ/ε)))$ runtime, where $κ$ is the condition number, and $ε$ is the target accuracy. This is near optimal with respect to both $κ$ and $ε$. Our method is applicable to general non-Hermitian matrices, and the cost as well as the number of qubits can be reduced when restricted to Hermitian matrices, and further to Hermitian positive definite matrices. The success of the time-optimal AQC implies that the quantum approximate optimization algorithm (QAOA) with an optimal control protocol can also achieve the same complexity in terms of the runtime. Numerical results indicate that QAOA can yield the lowest runtime compared to the time-optimal AQC, vanilla AQC, and the recently proposed randomization method.

preprint2022arXiv

Quasi-periodic oscillations of the X-ray burst from the magnetar SGR J1935+2154 and associated with the fast radio burst FRB 200428

The origin(s) and mechanism(s) of fast radio bursts (FRBs), which are short radio pulses from cosmological distances, have remained a major puzzle since their discovery. We report a strong Quasi-Periodic Oscillation(QPO) of 40 Hz in the X-ray burst from the magnetar SGR J1935+2154 and associated with FRB 200428, significantly detected with the Hard X-ray Modulation Telescope (Insight-HXMT) and also hinted by the Konus-Wind data. QPOs from magnetar bursts have only been rarely detected; our 3.4 sigma (p-value is 2.9e-4) detection of the QPO reported here reveals the strongest QPO signal observed from magnetars (except in some very rare giant flares), making this X-ray burst unique among magnetar bursts. The two X-ray spikes coinciding with the two FRB pulses are also among the peaks of the QPO. Our results suggest that at least some FRBs are related to strong oscillation processes of neutron stars. We also show that we may overestimate the significance of the QPO signal and underestimate the errors of QPO parameters if QPO exists only in a fraction of the time series of a X-ray burst which we use to calculate the Leahy-normalized periodogram.

preprint2022arXiv

Time-dependent Hamiltonian Simulation of Highly Oscillatory Dynamics and Superconvergence for Schrödinger Equation

We propose a simple quantum algorithm for simulating highly oscillatory quantum dynamics, which does not require complicated quantum control logic for handling time-ordering operators. To our knowledge, this is the first quantum algorithm that is both insensitive to the rapid changes of the time-dependent Hamiltonian and exhibits commutator scaling. Our method can be used for efficient Hamiltonian simulation in the interaction picture. In particular, we demonstrate that for the simulation of the Schrödinger equation, our method exhibits superconvergence and achieves a surprising second order convergence rate, of which the proof rests on a careful application of pseudo-differential calculus. Numerical results verify the effectiveness and the superconvergence property of our method.

preprint2022arXiv

Universal approximation of symmetric and anti-symmetric functions

We consider universal approximations of symmetric and anti-symmetric functions, which are important for applications in quantum physics, as well as other scientific and engineering computations. We give constructive approximations with explicit bounds on the number of parameters with respect to the dimension and the target accuracy $ε$. While the approximation still suffers from the curse of dimensionality, to the best of our knowledge, these are the first results in the literature with explicit error bounds for functions with symmetry or anti-symmetry constraints.

preprint2021arXiv

Bursts before Burst: A Comparative Study on FRB 200428-associated and FRB-absent X-ray Bursts from SGR J1935+2154

Accompanied by an X-ray burst, the fast radio burst (FRB) FRB 200428 was recently confirmed as originating from the Galactic magnetar soft gamma repeater (SGR) SGR J1935+2154. Just before and after FRB 200428 was detected, the Five-hundred-meter Aperture Spherical radio Telescope (FAST) had been monitoring SGR J1935+2154 for eight hours. From UTC 2020 April 27 23:55:00 to 2020 April 28 00:50:37, FAST detected no pulsed radio emission from SGR J1935+2154, while Fermi/Gamma-ray Burst Monitor registered 34 bursts in the X/soft $γ$-ray band, forming a unique sample of X-ray bursts in the absence of FRBs. After a comprehensive analysis on light curves, time-integrated, and time-resolved spectral properties of these FRB-absent X-ray bursts, we compare this sample with the FRB-associated X-ray burst detected by Insight-HXMT, INTEGRAL, and Konus-Wind. The FRB-associated burst distinguishes itself from other X-ray bursts by its nonthermal spectrum and a higher spectral peak energy, but otherwise is not atypical. We also compare the cumulative energy distribution of our X-ray burst sample with that of first repeating FRB source, FRB 121102, with the calibration of FRB 200428-X-ray burst association. We find a similarity between the two, offering indirect support of the magnetar origin of cosmological FRBs. The event rate density of magnetar bursts is about $\sim 150$ times higher than the FRB event rate density at the energy of FRB 200428. This again suggests that, if all FRBs originate from magnetars, only a small fraction of X-ray bursts are associated with FRBs.

preprint2021arXiv

NeurT-FDR: Controlling FDR by Incorporating Feature Hierarchy

Controlling false discovery rate (FDR) while leveraging the side information of multiple hypothesis testing is an emerging research topic in modern data science. Existing methods rely on the test-level covariates while ignoring possible hierarchy among the covariates. This strategy may not be optimal for complex large-scale problems, where hierarchical information often exists among those test-level covariates. We propose NeurT-FDR which boosts statistical power and controls FDR for multiple hypothesis testing while leveraging the hierarchy among test-level covariates. Our method parametrizes the test-level covariates as a neural network and adjusts the feature hierarchy through a regression framework, which enables flexible handling of high-dimensional features as well as efficient end-to-end optimization. We show that NeurT-FDR has strong FDR guarantees and makes substantially more discoveries in synthetic and real datasets compared to competitive baselines.

preprint2020arXiv

Burst properties of the most recurring transient magnetar SGR J1935+2154

We present timing and time-integrated spectral analysis of 127 bursts from SGR J1935+2154. These bursts were observed with the Gamma-ray Burst Monitor on the Fermi Gamma-ray Space Telescope and the Burst Alert Telescope on the Neil Gehrels Swift Observatory during the source's four active episodes from 2014 to 2016. This activation frequency makes SGR J1935+2154 the most burst prolific transient magnetar. We find the average duration of all the detected bursts to be much shorter than the typical, anticipated value. We fit the burst time-integrated spectra with two black-body functions, a Comptonized model and three other simpler models. Bursts from SGR J1935+2154 exhibit similar spectral properties to other magnetars, with the exception of the power law index from the Comptonized model, which correlates with burst fluence. We find that the durations and both black-body temperatures of the bursts have significantly evolved across the four active episodes. We also find that the burst time history exhibits two trends, which are strongly correlated with the decay of the persistent emission in each outburst.

preprint2020arXiv

Convergence of Stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation

Extended Lagrangian molecular dynamics (XLMD) is a general method for performing molecular dynamics simulations using quantum and classical many-body potentials. Recently several new XLMD schemes have been proposed and tested on several classes of many-body polarization models such as induced dipoles or Drude charges, by creating an auxiliary set of these same degrees of freedom that are reversibly integrated through time. This gives rise to a singularly perturbed Hamiltonian system that provides a good approximation to the time evolution of the real mutual polarization field. To further improve upon the accuracy of the XLMD dynamics, and to potentially extend it to other many-body potentials, we introduce a stochastic modification which leads to a set of singularly perturbed Langevin equations with degenerate noise. We prove that the resulting Stochastic-XLMD converges to the accurate dynamics, and the convergence rate is both optimal and is independent of the accuracy of the initial polarization field. We carefully study the scaling of the damping factor and numerical noise for efficient numerical simulation for Stochastic-XLMD, and we demonstrate the effectiveness of the method for model polarizable force field systems.

preprint2020arXiv

Efficient hybridization fitting for dynamical mean-field theory via semi-definite relaxation

We introduce a nested optimization procedure using semi-definite relaxation for the fitting step in Hamiltonian-based cluster dynamical mean-field theory (DMFT) methodologies. We show that the proposed method is more efficient and flexible than state-of-the-art fitting schemes, which allows us to treat as large a number of bath sites as the impurity solver at hand allows. We characterize its robustness to initial conditions and symmetry constraints, thus providing conclusive evidence that in the presence of a large bath, our semi-definite relaxation approach can find the correct set of bath parameters without needing to include \emph{a priori} knowledge of the properties that are to be described. We believe this method will be of great use for Hamiltonian-based calculations, simplifying and improving one of the key steps in cluster dynamical mean-field theory calculations.

preprint2020arXiv

ELSI -- An Open Infrastructure for Electronic Structure Solvers

Routine applications of electronic structure theory to molecules and periodic systems need to compute the electron density from given Hamiltonian and, in case of non-orthogonal basis sets, overlap matrices. System sizes can range from few to thousands or, in some examples, millions of atoms. Different discretization schemes (basis sets) and different system geometries (finite non-periodic vs. infinite periodic boundary conditions) yield matrices with different structures. The ELectronic Structure Infrastructure (ELSI) project provides an open-source software interface to facilitate the implementation and optimal use of high-performance solver libraries covering cubic scaling eigensolvers, linear scaling density-matrix-based algorithms, and other reduced scaling methods in between. In this paper, we present recent improvements and developments inside ELSI, mainly covering (1) new solvers connected to the interface, (2) matrix layout and communication adapted for parallel calculations of periodic and/or spin-polarized systems, (3) routines for density matrix extrapolation in geometry optimization and molecular dynamics calculations, and (4) general utilities such as parallel matrix I/O and JSON output. The ELSI interface has been integrated into four electronic structure code projects (DFTB+, DGDFT, FHI-aims, SIESTA), allowing us to rigorously benchmark the performance of the solvers on an equal footing. Based on results of a systematic set of large-scale benchmarks performed with Kohn-Sham density-functional theory and density-functional tight-binding theory, we identify factors that strongly affect the efficiency of the solvers, and propose a decision layer that assists with the solver selection process. Finally, we describe a reverse communication interface encoding matrix-free iterative solver strategies that are amenable, e.g., for use with planewave basis sets.

preprint2020arXiv

Enhancing robustness and efficiency of density matrix embedding theory via semidefinite programming and local correlation potential fitting

Density matrix embedding theory (DMET) is a powerful quantum embedding method for solving strongly correlated quantum systems. Theoretically, the performance of a quantum embedding method should be limited by the computational cost of the impurity solver. However, the practical performance of DMET is often hindered by the numerical stability and the computational time of the correlation potential fitting procedure, which is defined on a single-particle level. Of particular difficulty are cases in which the effective single-particle system is gapless or nearly gapless. To alleviate these issues, we develop a semidefinite programming (SDP) based approach that can significantly enhance the robustness of the correlation potential fitting procedure compared to the traditional least squares fitting approach. We also develop a local correlation potential fitting approach, which allows one to identify the correlation potential from each fragment independently in each self-consistent field iteration, avoiding any optimization at the global level. We prove that the self-consistent solutions of DMET using this local correlation potential fitting procedure are equivalent to those of the original DMET with global fitting. We find that our combined approach, called L-DMET, in which we solve local fitting problems via semidefinite programming, can significantly improve both the robustness and the efficiency of DMET calculations. We demonstrate the performance of L-DMET on the 2D Hubbard model and the hydrogen chain. We also demonstrate with theoretical and numerical evidence that the use of a large fragment size can be a fundamental source of numerical instability in the DMET procedure.

preprint2020arXiv

Learning the mapping $\mathbf{x}\mapsto \sum_{i=1}^d x_i^2$: the cost of finding the needle in a haystack

The task of using machine learning to approximate the mapping $\mathbf{x}\mapsto\sum_{i=1}^d x_i^2$ with $x_i\in[-1,1]$ seems to be a trivial one. Given the knowledge of the separable structure of the function, one can design a sparse network to represent the function very accurately, or even exactly. When such structural information is not available, and we may only use a dense neural network, the optimization procedure to find the sparse network embedded in the dense network is similar to finding the needle in a haystack, using a given number of samples of the function. We demonstrate that the cost (measured by sample complexity) of finding the needle is directly related to the Barron norm of the function. While only a small number of samples is needed to train a sparse network, the dense network trained with the same number of samples exhibits large test loss and a large generalization gap. In order to control the size of the generalization gap, we find that the use of explicit regularization becomes increasingly more important as $d$ increases. The numerically observed sample complexity with explicit regularization scales as $\mathcal{O}(d^{2.5})$, which is in fact better than the theoretically predicted sample complexity that scales as $\mathcal{O}(d^{4})$. Without explicit regularization (also called implicit regularization), the numerically observed sample complexity is significantly higher and is close to $\mathcal{O}(d^{4.5})$.

preprint2020arXiv

Noise-Robust End-to-End Quantum Control using Deep Autoregressive Policy Networks

Variational quantum eigensolvers have recently received increased attention, as they enable the use of quantum computing devices to find solutions to complex problems, such as the ground energy and ground state of strongly-correlated quantum many-body systems. In many applications, it is the optimization of both continuous and discrete parameters that poses a formidable challenge. Using reinforcement learning (RL), we present a hybrid policy gradient algorithm capable of simultaneously optimizing continuous and discrete degrees of freedom in an uncertainty-resilient way. The hybrid policy is modeled by a deep autoregressive neural network to capture causality. We employ the algorithm to prepare the ground state of the nonintegrable quantum Ising model in a unitary process, parametrized by a generalized quantum approximate optimization ansatz: the RL agent solves the discrete combinatorial problem of constructing the optimal sequences of unitaries out of a predefined set and, at the same time, it optimizes the continuous durations for which these unitaries are applied. We demonstrate the noise-robust features of the agent by considering three sources of uncertainty: classical and quantum measurement noise, and errors in the control unitary durations. Our work exhibits the beneficial synergy between reinforcement learning and quantum control.

preprint2020arXiv

Persistent Emission Properties of SGR J1935+2154 During Its 2020 Active Episode

We present detailed spectral and temporal characteristics of the persistent X-ray emission of SGR J1935+2154 based on our XMM-Newton and Chandra observations taken in the aftermath of its April 2020 burst storm, during which hundreds of energetic X-ray bursts were emitted, including one associated with an extraordinary fast radio burst. We clearly detect the pulsed X-ray emission in the XMM-Newton data. An average spin-down rate of 1.6$\times$10$^{-11}$ s s$^{-1}$ is obtained using our spin period measurement combined with three earlier values reported from the same active episode. Our investigations of the XMM-Newton and Chandra spectra with a variety of phenomenological and physically-motivated models, concluded that the magnetic field topology of SGR J1935+2154 is most likely highly non-dipolar. The spectral models indicate that surface field strengths in somewhat localized regions substantially exceed the polar value of 4.4$\times$10$^{14}$ G inferred from a spin-down torque associated with a rotating magnetic dipole.

preprint2020arXiv

Physical Properties of H II Regions in M51 from Spectroscopic Observations

M51 and NGC 5195 is an interacting system that can be explored in great details with ground-based telescopes. The H II regions in M51 were observed using the 2.16 m telescope of the National Astronomical Observatories of the Chinese Academy of Sciences and the 6.5 m Multiple Mirror Telescope with spatial resolution of less than $\sim100$ pc. We obtain a total of 113 spectra across the galaxy and combine the literature data of Croxall et al. to derive a series of physical properties, including the gas-phase extinction, stellar population age, star formation rate (SFR) surface density, and oxygen abundance. The spatial distributions and radial profiles of these properties are investigated in order to study the characteristics of M51 and the clues to the formation and evolution of this galaxy. M51 presents a mild radial extinction gradient. The lower gas-phase extinction in the north spiral arms compared to the south arms are possibly caused by the past encounters with the companion galaxy of NGC 5195. A number of H II regions have the stellar age between 50 and 500 Myr, consistent with the recent interaction history by simulations in the literatures. The SFR surface density presents a mild radial gradient, which is ubiquitous in spiral galaxies. There is a negative metallicity gradient of $-0.08$ dex $R_{e}^{-1}$ in the disk region, which is also commonly found in many spiral galaxies. It is supported by the "inside-out" scenario of galaxy formation. We find a positive abundance gradient of 0.26 dex $R_{e}^{-1}$ in the inner region. There are possible reasons causing the positive gradient, including the freezing of the chemical enrichment due to the star-forming quenching in the bulge and the gas infall and dilution due to the pseudobulge growth and/or galactic interaction.

preprint2020arXiv

Policy Gradient based Quantum Approximate Optimization Algorithm

The quantum approximate optimization algorithm (QAOA), as a hybrid quantum/classical algorithm, has received much interest recently. QAOA can also be viewed as a variational ansatz for quantum control. However, its direct application to emergent quantum technology encounters additional physical constraints: (i) the states of the quantum system are not observable; (ii) obtaining the derivatives of the objective function can be computationally expensive or even inaccessible in experiments, and (iii) the values of the objective function may be sensitive to various sources of uncertainty, as is the case for noisy intermediate-scale quantum (NISQ) devices. Taking such constraints into account, we show that policy-gradient-based reinforcement learning (RL) algorithms are well suited for optimizing the variational parameters of QAOA in a noise-robust fashion, opening up the way for developing RL techniques for continuous quantum control. This is advantageous to help mitigate and monitor the potentially unknown sources of errors in modern quantum simulators. We analyze the performance of the algorithm for quantum state transfer problems in single- and multi-qubit systems, subject to various sources of noise such as error terms in the Hamiltonian, or quantum uncertainty in the measurement process. We show that, in noisy setups, it is capable of outperforming state-of-the-art existing optimization algorithms.

preprint2020arXiv

Pushing the limit of molecular dynamics with ab initio accuracy to 100 million atoms with machine learning

For 35 years, {\it ab initio} molecular dynamics (AIMD) has been the method of choice for modeling complex atomistic phenomena from first principles. However, most AIMD applications are limited by computational cost to systems with thousands of atoms at most. We report that a machine learning-based simulation protocol (Deep Potential Molecular Dynamics), while retaining {\it ab initio} accuracy, can simulate more than 1 nanosecond-long trajectory of over 100 million atoms per day, using a highly optimized code (GPU DeePMD-kit) on the Summit supercomputer. Our code can efficiently scale up to the entire Summit supercomputer, attaining $91$ PFLOPS in double precision ($45.5\%$ of the peak) and {$162$/$275$ PFLOPS in mixed-single/half precision}. The great accomplishment of this work is that it opens the door to simulating unprecedented size and time scales with {\it ab initio} accuracy. It also poses new challenges to the next-generation supercomputer for a better integration of machine learning and physical modeling.

preprint2020arXiv

Quantum Dynamics with the Parallel Transport Gauge

The dynamics of a closed quantum system is often studied with the direct evolution of the Schrodinger equation. In this paper, we propose that the gauge choice (i.e. degrees of freedom irrelevant to physical observables) of the Schrodinger equation can be generally non-optimal for numerical simulation. This can limit, and in some cases severely limit the time step size. We find that the optimal gauge choice is given by a parallel transport formulation. This parallel transport dynamics can be simply interpreted as the dynamics driven by the residual vectors, analogous to those defined in eigenvalue problems in the time-independent setup. The parallel transport dynamics can be derived from a Hamiltonian structure, thus suitable to be solved using a symplectic and implicit time discretization scheme, such as the implicit midpoint rule, which allows the usage of a large time step and ensures the long time numerical stability. We analyze the parallel transport dynamics in the context of the singularly perturbed linear Schrodinger equation, and demonstrate its superior performance in the near adiabatic regime. We demonstrate the effectiveness of our method using numerical results for linear and nonlinear Schrodinger equations, as well as the time-dependent density functional theory (TDDFT) calculations for electrons in a benzene molecule driven by an ultrashort laser pulse.

preprint2020arXiv

Quenching as a Contest between Galaxy Halos and their Central Black Holes

Existing models of galaxy formation have not yet explained striking correlations between structure and star-formation activity in galaxies, notably the sloped and moving boundaries that divide star-forming from quenched galaxies in key structural diagrams. This paper uses these and other relations to ``reverse-engineer'' the quenching process for central galaxies. The basic idea is that star-forming galaxies with larger radii (at a given stellar mass) have lower black-hole masses due to lower central densities. Galaxies cross into the green valley when the cumulative effective energy radiated by their black hole equals $\sim4\times$ their halo-gas binding energy. Since larger-radii galaxies have smaller black holes, one finds they must evolve to higher stellar masses in order to meet this halo-energy criterion, which explains the sloping boundaries. A possible cause of radii differences among star-forming galaxies is halo concentration. The evolutionary tracks of star-forming galaxies are nearly parallel to the green-valley boundaries, and it is mainly the sideways motions of these boundaries with cosmic time that cause galaxies to quench. BH-scaling laws for star-forming, quenched, and green-valley galaxies are different, and most BH mass growth takes place in the green valley. Implications include: the radii of star-forming galaxies are an important second parameter in shaping their black holes; black holes are connected to their halos but in different ways for star-forming, quenched, and green-valley galaxies; and the same BH-halo quenching mechanism has been in place since $z \sim 3$. We conclude with a discussion of black hole-galaxy co-evolution, the origin and interpretation of BH scaling laws.

preprint2020arXiv

Semidefinite relaxation of multi-marginal optimal transport for strictly correlated electrons in second quantization

We consider the strictly correlated electron (SCE) limit of the fermionic quantum many-body problem in the second-quantized formalism. This limit gives rise to a multi-marginal optimal transport (MMOT) problem. Here the marginal state space for our MMOT problem is the binary set $\{0,1\}$, and the number of marginals is the number $L$ of sites in the model. The costs of storing and computing the exact solution of the MMOT problem both scale exponentially with respect to $L$. We propose an efficient convex relaxation which can be solved by semidefinite programming (SDP). In particular, the semidefinite constraint is only of size $2L\times 2L$. Moreover, the SDP-based method yields an approximation of the dual potential needed to the perform self-consistent field iteration in the so-called Kohn-Sham SCE framework, which, once converged, yields a lower bound for the total energy of the system. We demonstrate the effectiveness of our methods on spinless and spinful Hubbard-type models. Numerical results indicate that our relaxation methods yield tight lower bounds for the optimal cost, in the sense that the error due to the semidefinite relaxation is much smaller than the intrinsic modeling error of the Kohn-Sham SCE method. We also describe how our relaxation methods generalize to arbitrary MMOT problems with pairwise cost functions.

preprint2020arXiv

SIESTA: recent developments and applications

A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-nineties, SIESTA's flexibility, efficiency and free distribution has given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here we describe the more recent implementations on top of that core scheme, which include: full spin-orbit interaction, non-repeated and multiple-contact ballistic electron transport, DFT+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient Van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as Wannier90 and the second-principles modelling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various postprocessing utilities. SIESTA has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low level libraries, as well as data standards and support for them, in particular the PSML definition and library for transferable pseudopotentials, and the interface to the ELSI library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments.

preprint2020arXiv

Sparsity pattern of the self-energy for classical and quantum impurity problems

We prove that for various impurity models, in both classical and quantum settings, the self-energy matrix is a sparse matrix with a sparsity pattern determined by the impurity sites. In the quantum setting, such a sparsity pattern has been known since Feynman. Indeed, it underlies several numerical methods for solving impurity problems, as well as many approaches to more general quantum many-body problems, such as the dynamical mean field theory. The sparsity pattern is easily motivated by a formal perturbative expansion using Feynman diagrams. However, to the extent of our knowledge, a rigorous proof has not appeared in the literature. In the classical setting, analogous considerations lead to a perhaps less-known result, i.e., that the precision matrix of a Gibbs measure of a certain kind differs only by a sparse matrix from the precision matrix of a corresponding Gaussian measure. Our argument for this result mainly involves elementary algebraic manipulations and is in particular non-perturbative. Nonetheless, the proof can be robustly adapted to various settings of interest in physics, including quantum systems (both fermionic and bosonic) at zero and finite temperature, non-equilibrium systems, and superconducting systems.

preprint2020arXiv

Spatially-resolved Stellar Population Properties of the M 51-NGC 5195 System from Multi-wavelength Photometric Data

Using multi-band photometric images of M 51 and its companion NGC 5195 from ultraviolet to optical and infrared, we investigate spatially resolved stellar population properties of this interacting system with stellar population synthesis models. The observed IRX is used to constrain dust extinction. Stellar mass is also inferred from the model fitting. By fitting observed spectral energy distributions (SEDs) with synthetical ones, we derive two-dimensional distributions of stellar age, metallicity, dust extinction, and stellar mass. In M 51, two grand-designed spiral arms extending from the bulge show young age, rich metallicity, and abundant dust. The inter-arm regions are filled with older, metal-poorer, and less dusty stellar populations. Except for the spiral arm extending from M 51 into NGC 5195, the stellar population properties of NGC 5195 are quite featureless. NGC 5195 is much older than M 51, and its core is very dusty with $A_V$ up to 1.67 mag and dense in stellar mass surface density. The close encounters might drive the dust in the spiral arm of M51 into the center of NGC 5195.

preprint2020arXiv

Split representation of adaptively compressed polarizability operator

The polarizability operator plays a central role in density functional perturbation theory and other perturbative treatment of first principle electronic structure theories. The cost of computing the polarizability operator generally scales as $\mathcal{O}(N_{e}^4)$ where $N_e$ is the number of electrons in the system. The recently developed adaptively compressed polarizability operator (ACP) formulation [L. Lin, Z. Xu and L. Ying, Multiscale Model. Simul. 2017] reduces such complexity to $\mathcal{O}(N_{e}^3)$ in the context of phonon calculations with a large basis set for the first time, and demonstrates its effectiveness for model problems. In this paper, we improve the performance of the ACP formulation by splitting the polarizability into a near singular component that is statically compressed, and a smooth component that is adaptively compressed. The new split representation maintains the $\mathcal{O}(N_e^3)$ complexity, and accelerates nearly all components of the ACP formulation, including Chebyshev interpolation of energy levels, iterative solution of Sternheimer equations, and convergence of the Dyson equations. For simulation of real materials, we discuss how to incorporate nonlocal pseudopotentials and finite temperature effects. We demonstrate the effectiveness of our method using one-dimensional model problem in insulating and metallic regimes, as well as its accuracy for real molecules and solids.

preprint2020arXiv

Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models

We present a new stochastic extended Lagrangian solution to charge equilibration that eliminates self-consistent field (SCF) calculations, eliminating the computational bottleneck in solving the many-body solution with standard SCF solvers. By formulating both charges and chemical potential as latent variables, and introducing a holonomic constraint that satisfies charge conservation, the SC-XLMD method accurately reproduces structural, thermodynamic, and dynamics properties using ReaxFF, and shows excellent weak- and strong-scaling performance in the LAMMPS molecular simulation package.

preprint2020arXiv

Structural and Stellar Population Properties vs. Bulge Types in Sloan Digital Sky Survey Central Galaxies

This paper studies pseudo-bulges (P-bulges) and classical bulges (C-bulges) in Sloan Digital Sky Survey central galaxies using the new bulge indicator $ΔΣ_1$, which measures relative central stellar-mass surface density within 1 kpc. We compare $ΔΣ_1$ to the established bulge-type indicator $Δ\langleμ_e\rangle$ from Gadotti (2009) and show that classifying by $ΔΣ_1$ agrees well with $Δ\langleμ_e\rangle$. $ΔΣ_1$ requires no bulge-disk decomposition and can be measured on SDSS images out to $z = 0.07$. Bulge types using it are mapped onto twenty different structural and stellar-population properties for 12,000 SDSS central galaxies with masses 10.0 < log $M_*$/$M_{\odot}$ < 10.4. New trends emerge from this large sample. Structural parameters show fairly linear log-log relations vs. $ΔΣ_1$ and $Δ\langleμ_e\rangle$ with only moderate scatter, while stellar-population parameters show a highly non-linear "elbow" in which specific star-formation rate remains roughly flat with increasing central density and then falls rapidly at the elbow, where galaxies begin to quench. P-bulges occupy the low-density end of the horizontal arm of the elbow and are universally star-forming, while C-bulges occupy the elbow and the vertical branch and exhibit a wide range of star-formation rates at fixed density. The non-linear relation between central density and star-formation rate has been seen before, but this mapping onto bulge class is new. The wide range of star-formation rates in C-bulges helps to explain why bulge classifications using different parameters have sometimes disagreed in the past. The elbow-shaped relation between density and stellar indices suggests that central structure and stellar-populations evolve at different rates as galaxies begin to quench.

preprint2020arXiv

The SFR-radius connection: data and implications for wind strength and halo concentration

This paper is one in a series that explores the importance of radius as a second parameter in galaxy evolution. The topic investigated here is the relationship between star formation rate (SFR) and galaxy radius ($R_{\rm e}$) for main-sequence star-forming galaxies. The key observational result is that, over a wide range of stellar mass and redshift in both CANDELS and SDSS, there is little trend between SFR and $R_{\rm e}$ at fixed stellar mass. The Kennicutt-Schmidt law, or any similar density-related star formation law, then implies that smaller galaxies must have lower gas fractions than larger galaxies (at fixed $M_{\ast}$), and this is supported by observations of local star-forming galaxies. We investigate the implication by adopting the equilibrium "bathtub" model: the ISM gas mass is assumed to be constant over time and the net star formation rate is the difference between the accretion rate of gas onto the galaxy from the halo and the outflow rate due to winds. To match the observed null correlation between SFR and radius, the bathtub model requires that smaller galaxies at fixed mass have weaker galactic winds. Our hypothesis is that galaxies are a 2-dimensional family whose properties are set mainly by halo mass and concentration. Galaxy radius and accretion rate plausibly both depend on halo concentration, which predicts how wind strength should vary with $R_{\rm e}$ and SFR.

preprint2020arXiv

Variational embedding for quantum many-body problems

Quantum embedding theories are powerful tools for approximately solving large-scale strongly correlated quantum many-body problems. The main idea of quantum embedding is to glue together a highly accurate quantum theory at the local scale and a less accurate quantum theory at the global scale. We introduce the first quantum embedding theory that is also variational, in that it is guaranteed to provide a one-sided bound for the exact ground-state energy. Our method, which we call the variational embedding method, provides a lower bound for this quantity. The method relaxes the representability conditions for quantum marginals to a set of linear and semidefinite constraints that operate at both local and global scales, resulting in a semidefinite program (SDP) to be solved numerically. The accuracy of the method can be systematically improved. The method is versatile and can be applied, in particular, to quantum many-body problems for both quantum spin systems and fermionic systems, such as those arising from electronic structure calculations. We describe how the proper notion of quantum marginal, sufficiently general to accommodate both of these settings, should be phrased in terms of certain algebras of operators. We also investigate the duality theory for our SDPs, which offers valuable perspective on our method as an embedding theory. As a byproduct of this investigation, we describe a formulation for efficiently implementing the variational embedding method via a partial dualization procedure and the solution of quantum analogs of the Kantorovich problem from optimal transport theory.

preprint2019arXiv

Estimating the molecular gas mass of low-redshift galaxies from a combination of mid-infrared luminosity and optical properties

We present CO(J=1-0) and/or CO(J=2-1) spectroscopy for 31 galaxies selected from the ongoing MaNGA survey, obtained with multiple telescopes. This sample is combined with CO observations from the literature to study the correlation of the CO luminosities ($L_{\rm CO(1-0)}$) with the mid-infrared luminosities at 12 ($L_{12 μm}$) and 22 $μ$m ($L_{\rm 22 μm}$), as well as the dependence of the residuals on a variety of galaxy properties. The correlation with $L_{\rm 12 μm}$ is tighter and more linear, but galaxies with relatively low stellar masses and blue colors fall significantly below the mean $L_{\rm CO(1-0)}-L_{\rm 12μm}$ relation. We propose a new estimator of the CO(1-0) luminosity (and thus the total molecular gas mass) that is a linear combination of three parameters: $L_{\rm 12 μm}$, $M_\ast$ and $g-r$. We show that, with a scatter of only 0.18 dex in log $(L_{\rm CO(1-0)})$, this estimator provides unbiased estimates for galaxies of different properties and types. An immediate application of this estimator to a compiled sample of galaxies with only CO(J=2-1) observations yields a distribution of the CO(J=2-1) to CO(J=1-0) luminosity ratios ($R21$) that agrees well with the distribution of real observations, in terms of both the median and the shape. Application of our estimator to the current MaNGA sample reveals a gas-poor population of galaxies that are predominantly early-type and show no correlation between molecular gas-to-stellar mass ratio and star formation rate, in contrast to gas-rich galaxies. We also provide alternative estimators with similar scatters, based on $r$ and/or $z$ band luminosities instead of $M_\ast$. These estimators serve as cheap and convenient $M_{\rm mol}$ proxies to be potentially applied to large samples of galaxies, thus allowing statistical studies of gas-related processes of galaxies.

preprint2019arXiv

Influence of point defects on the electronic and topological properties of monolayer WTe$_2$

In some topological insulators, such as graphene and WTe$_2$, band inversion originates from chemical bonding and space group symmetry, in contrast to materials such as Bi$_2$Se$_3$, where the band inversion derives from relativistic effects in the atoms. In the former, band inversion is susceptible to changes of the chemical environment, e.g. by defects, while the latter are less affected by defects due to the larger energy scale associated with atomic relativistic effects. Motivated by recent experiments, we study the effect of Te-vacancies and Te-adatoms on the electronic properties of WTe$_2$. We find that the Te-vacancies have a formation energy of $2.21$ eV, while the formation energy of the Te-adatoms is much lower with $0.72$ eV. The vacancies strongly influence the band structure and we present evidence that band inversion is already reversed at the nominal composition of WTe$_{1.97}$. In contrast, we show that the adatoms do not change the electronic structure in the vicinity of the Fermi level and thus the topological properties. Our findings indicate that Te-adatoms should be present in thin films that are grown in a Te-rich environment, and we suggest that they have been observed in scanning tunneling microscopy experiments.

preprint2019arXiv

Systematically Improvable Tensor Hypercontraction: Interpolative Separable Density-Fitting for Molecules Applied to Exact Exchange, Second- and Third-Order Møller-Plesset Perturbation Theory

We present a systematically improvable tensor hypercontraction (THC) factorization based on interpolative separable density fitting (ISDF). We illustrate algorithmic details to achieve this within the framework of Becke's atom-centered quadrature grid. A single ISDF parameter $c_\text{ISDF}$ controls the tradeoff between accuracy and cost. In particular, $c_\text{ISDF}$ sets the number of interpolation points used in THC, $N_\text{IP} = c_\text{ISDF}\times N_\text{X}$ with $N_\text{X}$ being the number of auxiliary basis functions. In conjunction with the resolution-of-the-identity (RI) technique, we develop and investigate the THC-RI algorithms for cubic-scaling exact exchange for Hartree-Fock and range-separated hybrids (e.g., $ω$B97X-V) and quartic-scaling second- and third-order Møller-Plesset theory (MP2 and MP3). These algorithms were evaluated over the W4-11 thermochemistry (atomization energy) set and A24 non-covalent interaction benchmark set with standard Dunning basis sets (cc-pVDZ, cc-pVTZ, aug-cc-pVDZ, and aug-cc-pVTZ). We demonstrate the convergence of THC-RI algorithms to numerically exact RI results using ISDF points. Based on these, we make recommendations on $c_\text{ISDF}$ for each basis set and method. We also demonstrate the utility of THC-RI exact exchange and MP2 for larger systems such as water clusters and $\text{C}_{20}$. We stress that more challenges await in obtaining accurate and numerically stable THC factorization for wavefunction amplitudes as well as the space spanned by virtual orbitals in large basis sets and implementing sparsity-aware THC-RI algorithms.

preprint2017arXiv

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.

preprint2017arXiv

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.

preprint2016arXiv

A Left-Looking Selected Inversion Algorithm and Task Parallelism on Shared Memory Systems

Given a sparse matrix $A$, the selected inversion algorithm is an efficient method for computing certain selected elements of $A^{-1}$. These selected elements correspond to all or some nonzero elements of the LU factors of $A$. In many ways, the type of matrix updates performed in the selected inversion algorithm is similar to that performed in the LU factorization, although the sequence of operation is different. In the context of LU factorization, it is known that the left-looking and right-looking algorithms exhibit different memory access and data communication patterns, and hence different behavior on shared memory and distributed memory parallel machines. Corresponding to right-looking and left-looking LU factorization, selected inversion algorithm can be organized as a left-looking and a right-looking algorithm. The parallel right-looking version of the algorithm has been developed in [1]. The sequence of operations performed in this version of the selected inversion algorithm is similar to those performed in a left-looking LU factorization algorithm. In this paper, we describe the left-looking variant of the selected inversion algorithm, and based on task parallel method, present an efficient implementation of the algorithm for shared memory machines. We demonstrate that with the task scheduling features provided by OpenMP 4.0, the left-looking selected inversion algorithm can scale well both on the Intel Haswell multicore architecture and on the Intel Knights Corner (KNC) manycore architecture. Compared to the right-looking selected inversion algorithm, the left-looking formulation facilitates pipelining of work along different branches of the elimination tree, and can be a promising candidate for future development of massively parallel selected inversion algorithms on heterogeneous architecture.

preprint2016arXiv

A posteriori error estimates for discontinuous Galerkin methods using non-polynomial basis functions. Part II: Eigenvalue problems

We present the first systematic work for deriving a posteriori error estimates for general non-polynomial basis functions in an interior penalty discontinuous Galerkin (DG) formulation for solving eigenvalue problems associated with second order linear operators. Eigenvalue problems of such types play important roles in scientific and engineering applications, particularly in theoretical chemistry, solid state physics and material science. Based on the framework developed in [{\it L. Lin, B. Stamm, http://dx.doi.org/10.1051/m2an/2015069}] for second order PDEs, we develop residual type upper and lower bound error estimates for measuring the a posteriori error for eigenvalue problems. The main merit of our method is that the method is parameter-free, in the sense that all but one solution-dependent constants appearing in the upper and lower bound estimates are explicitly computable by solving local and independent eigenvalue problems, and the only non-computable constant can be reasonably approximated by a computable one without affecting the overall effectiveness of the estimates in practice. Compared to the PDE case, we find that a posteriori error estimators for eigenvalue problems must neglect certain terms, which involves explicitly the exact eigenvalues or eigenfunctions that are not accessible in numerical simulations. We define such terms carefully, and justify numerically that the neglected terms are indeed numerically high order terms compared to the computable estimators. Numerical results for a variety of problems in 1D and 2D demonstrate that both the upper bound and lower bound are effective for measuring the error of eigenvalues and eigenfunctions.

preprint2016arXiv

Adaptively Compressed Exchange Operator

The Fock exchange operator plays a central role in modern quantum chemistry. The large computational cost associated with the Fock exchange operator hinders Hartree-Fock calculations and Kohn-Sham density functional theory calculations with hybrid exchange-correlation functionals, even for systems consisting of hundreds of atoms. We develop the adaptively compressed exchange operator (ACE) formulation, which greatly reduces the computational cost associated with the Fock exchange operator without loss of accuracy. The ACE formulation does not depend on the size of the band gap, and thus can be applied to insulating, semiconducting as well as metallic systems. In an iterative framework for solving Hartree-Fock-like systems, the ACE formulation only requires moderate modification of the code, and can be potentially beneficial for all electronic structure software packages involving exchange calculations. Numerical results indicate that the ACE formulation can become advantageous even for small systems with tens of atoms. In particular, the cost of each self-consistent field iteration for the electron density in the ACE formulation is only marginally larger than that of the generalized gradient approximation (GGA) calculation, and thus offers orders of magnitude speedup for Hartree-Fock-like calculations.

preprint2016arXiv

Adaptively compressed polarizability operator for accelerating large scale \textit{ab initio} phonon calculations

Phonon calculations based on first principle electronic structure theory, such as the Kohn-Sham density functional theory, have wide applications in physics, chemistry and material science. The computational cost of first principle phonon calculations typically scales steeply as $\mathcal{O}(N_e^4)$, where $N_e$ is the number of electrons in the system. In this work, we develop a new method to reduce the computational complexity of computing the full dynamical matrix, and hence the phonon spectrum, to $\mathcal{O}(N_e^3)$. The key concept for achieving this is to compress the polarizability operator adaptively with respect to the perturbation of the potential due to the change of the atomic configuration. Such adaptively compressed polarizability operator (ACP) allows accurate computation of the phonon spectrum. The reduction of complexity only weakly depends on the size of the band gap, and our method is applicable to insulators as well as semiconductors with small band gaps. We demonstrate the effectiveness of our method using one-dimensional and two-dimensional model problems.

preprint2016arXiv

Chebyshev polynomial filtered subspace iteration in the Discontinuous Galerkin method for large-scale electronic structure calculations

The Discontinuous Galerkin (DG) electronic structure method employs an adaptive local basis (ALB) set to solve the Kohn-Sham equations of density functional theory (DFT) in a discontinuous Galerkin framework. The adaptive local basis is generated on-the-fly to capture the local material physics, and can systematically attain chemical accuracy with only a few tens of degrees of freedom per atom. A central issue for large-scale calculations, however, is the computation of the electron density (and subsequently, ground state properties) from the discretized Hamiltonian in an efficient and scalable manner. We show in this work how Chebyshev polynomial filtered subspace iteration (CheFSI) can be used to address this issue and push the envelope in large-scale materials simulations in a discontinuous Galerkin framework. We describe how the subspace filtering steps can be performed in an efficient and scalable manner using a two-dimensional parallelization scheme, thanks to the orthogonality of the DG basis set and block-sparse structure of the DG Hamiltonian matrix. The on-the-fly nature of the ALBs requires additional care in carrying out the subspace iterations. We demonstrate the parallel scalability of the DG-CheFSI approach in calculations of large-scale two-dimensional graphene sheets and bulk three-dimensional lithium-ion electrolyte systems. Employing 55,296 computational cores, the time per self-consistent field iteration for a sample of the bulk 3D electrolyte containing 8,586 atoms is 90 seconds, and the time for a graphene sheet containing 11,520 atoms is 75 seconds.

preprint2016arXiv

Decay estimates of discretized Green's functions for Schrödinger type operators

For a sparse non-singular matrix $A$, generally $A^{-1}$ is a dense matrix. However, for a class of matrices, $A^{-1}$ can be a matrix with off-diagonal decay properties, i.e. $\lvert A^{-1}_{ij}\rvert$ decays fast to $0$ with respect to the increase of a properly defined distance between $i$ and $j$. Here we consider the off-diagonal decay properties of discretized Green's functions for Schrödinger type operators. We provide decay estimates for discretized Green's functions obtained from the finite difference discretization, and from a variant of the pseudo-spectral discretization. The asymptotic decay rate in our estimate is independent of the domain size and of the discretization parameter. We verify the decay estimate with numerical results for one-dimensional Schrödinger type operators.

preprint2016arXiv

Hidden Markov Models on Variable Blocks with a Modal Clustering Algorithm and Applications

Motivated by high-throughput single-cell cytometry data with applications to vaccine development and immunological research, we consider statistical clustering in large-scale data that contain multiple rare clusters. We propose a new hierarchical mixture model, namely Hidden Markov Model on Variable Blocks (HMM-VB), and a new mode search algorithm called Modal Baum-Welch (MBW) for efficient clustering. Exploiting the widely accepted chain-like dependence among groups of variables in the cytometry data, we propose to treat the hierarchy of variable groups as a figurative time line and employ a HMM-type model, namely HMM-VB. We also propose to use mode-based clustering, aka modal clustering, and overcome the exponential computational complexity by MBW. In a series of experiments on simulated data HMM-VB and MBW have better performance than existing methods. We also apply our method to identify rare cell subsets in cytometry data and examine its strengths and limitations.

preprint2016arXiv

PEXSI-$Σ$: A Green's function embedding method for Kohn-Sham density functional theory

In this paper, we propose a new Green's function embedding method called PEXSI-$Σ$ for describing complex systems within the Kohn-Sham density functional theory (KSDFT) framework, after revisiting the physics literature of Green's function embedding methods from a numerical linear algebra perspective. The PEXSI-$Σ$ method approximates the density matrix using a set of nearly optimally chosen Green's functions evaluated at complex frequencies. For each Green's function, the complex boundary conditions are described by a self energy matrix $Σ$ constructed from a physical reference Green's function, which can be computed relatively easily. In the linear regime, such treatment of the boundary condition can be numerically exact. The support of the $Σ$ matrix is restricted to degrees of freedom near the boundary of computational domain, and can be interpreted as a frequency dependent surface potential. This makes it possible to perform KSDFT calculations with $\mathcal{O}(N^2)$ computational complexity, where $N$ is the number of atoms within the computational domain. Green's function embedding methods are also naturally compatible with atomistic Green's function methods for relaxing the atomic configuration outside the computational domain. As a proof of concept, we demonstrate the accuracy of the PEXSI-$Σ$ method for graphene with divacancy and dislocation dipole type of defects using the DFTB+ software package.

preprint2016arXiv

SCDM-k: Localized orbitals for solids via selected columns of the density matrix

The recently developed selected columns of the density matrix (SCDM) method [J. Chem. Theory Comput. 11, 1463, 2015] is a simple, robust, efficient and highly parallelizable method for constructing localized orbitals from a set of delocalized Kohn-Sham orbitals for insulators and semiconductors with $Γ$ point sampling of the Brillouin zone. In this work we generalize the SCDM method to Kohn-Sham density functional theory calculations with k-point sampling of the Brillouin zone, which is needed for more general electronic structure calculations for solids. We demonstrate that our new method, called SCDM-k, is by construction gauge independent and is a natural way to describe localized orbitals. SCDM-k computes localized orbitals without the use of an optimization procedure, and thus does not suffer from the possibility of being trapped in a local minimum. Furthermore, the computational complexity of using SCDM-k to construct orthogonal and localized orbitals scales as O(N log N ) where N is the total number of k-points in the Brillouin zone. SCDM-k is therefore efficient even when a large number of k-points are used for Brillouin zone sampling. We demonstrate the numerical performance of SCDM-k using systems with model potentials in two and three dimensions.

preprint2016arXiv

Using Non-invertible Data Transformations to Build Adversarial-Robust Neural Networks

Deep neural networks have proven to be quite effective in a wide variety of machine learning tasks, ranging from improved speech recognition systems to advancing the development of autonomous vehicles. However, despite their superior performance in many applications, these models have been recently shown to be susceptible to a particular type of attack possible through the generation of particular synthetic examples referred to as adversarial samples. These samples are constructed by manipulating real examples from the training data distribution in order to "fool" the original neural model, resulting in misclassification (with high confidence) of previously correctly classified samples. Addressing this weakness is of utmost importance if deep neural architectures are to be applied to critical applications, such as those in the domain of cybersecurity. In this paper, we present an analysis of this fundamental flaw lurking in all neural architectures to uncover limitations of previously proposed defense mechanisms. More importantly, we present a unifying framework for protecting deep neural models using a non-invertible data transformation--developing two adversary-resilient architectures utilizing both linear and nonlinear dimensionality reduction. Empirical results indicate that our framework provides better robustness compared to state-of-art solutions while having negligible degradation in accuracy.

preprint2015arXiv

A posteriori error estimates for discontinuous Galerkin methods using non-polynomial basis functions. Part I: Second order linear PDE

We present the first systematic work for deriving a posteriori error estimates for general non-polynomial basis functions in an interior penalty discontinuous Galerkin (DG) formulation for solving second order linear PDEs. Our residual type upper and lower bound error estimates measure the error in the energy norm. The main merit of our method is that the method is parameter-free, in the sense that all but one solution-dependent constants appearing in the upper and lower bound estimates are explicitly computable by solving local eigenvalue problems, and the only non-computable constant can be reasonably approximated by a computable one without affecting the overall effectiveness of the estimates in practice. As a side product of our formulation, the penalty parameter in the interior penalty formulation can be automatically determined as well. We develop an efficient numerical procedure to compute the error estimators. Numerical results for a variety of problems in 1D and 2D demonstrate that both the upper bound and lower bound are effective.

preprint2015arXiv

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracy required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H$_2$ and liquid Al-Si alloy systems, where we find excellent agreement with independent benchmark results in literature.

preprint2015arXiv

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.

preprint2015arXiv

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.

preprint2015arXiv

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.

preprint2015arXiv

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.

preprint2015arXiv

Experimental observation of magnetoelectricity in spin ice Dy$_2$Ti$_2$O$_7$

The intrinsic noncollinear spin patterns in rare-earth pyrochlore are physically interesting, hosting many emergent properties, e.g. spin ice and monopole-type excitation. Recently, the magnetic monopole excitation of spin ice systems was predicted to be magnetoelectric active, while rare experimental works have directly confirmed this scenario. In this work, we performed systematic experimental investigation on the magnetoelectricity of Dy$_2$Ti$_2$O$_7$ by probing the ferroelectricity, spin dynamics, and dielectric behaviors. Two ferroelectric transitions at $T_{c1}$=25 K and $T_{c2}$=13 K have been observed. Remarkable magnetoelectric coupling is identified below the lower transition temperature, with a significant suppression of the electric polarization upon applied magnetic field. It is surprised that the lower ferroelectric transition temperature just coincides with the Ising-spin paramagnetic transition point, below which the quasi-particle-like monopoles are populated, indicating implicit correlation between electric dipoles and spin moments. The possible magnetoelectric mechanisms have also been discussed although a decent theory remains unavailable up to date. Our results will stimulate more investigations to explore multiferroicity in these spin ice systems and other frustrated magnets.

preprint2015arXiv

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.

preprint2015arXiv

Localized spectrum slicing

Given a sparse Hermitian matrix $A$ and a real number $μ$, we construct a set of sparse vectors, each approximately spanned only by eigenvectors of $A$ corresponding to eigenvalues near $μ$. This set of vectors spans the column space of a localized spectrum slicing (LSS) operator, and is called an LSS basis set. The sparsity of the LSS basis set is related to the decay properties of matrix Gaussian functions. We present a divide-and-conquer strategy with controllable error to construct the LSS basis set. This is a purely algebraic process using only submatrices of $A$, and can therefore be applied to general sparse Hermitian matrices. The LSS basis set leads to sparse projected matrices with reduced sizes, which allows the projected problems to be solved efficiently with techniques using sparse linear algebra. As an example, we demonstrate that the LSS basis set can be used to solve interior eigenvalue problems for a discretized second order partial differential operator in one-dimensional and two-dimensional domains, as well as for a matrix of general sparsity pattern.

preprint2015arXiv

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.

preprint2015arXiv

Plasma cleaning: A new possible treatment for niobium superconducting cavity after nitrogen doping

Nitrogen doping treatment with the subsequent electropolishing (EP) of the niobium superconducting cavity can significantly increase the cavity's quality factor up to a factor of 3. But the process of the EP removal may reintroduce hydrogen in the cavity surface, which may influence the cavity's radio frequency performance. Plasma cleaning study on niobium samples with gas mixtures of argon and oxgen intended to remove contaminations (hydrocarbons and micronicdust particles) from cavity surface to avoid field emission, was performed in Peking University. The niobium samples have been analyzed using the time of flight secondary ion mass spectrometry (TOF-SIMS) to measure the depth profiles of H, C, O, F, P and Nb. The measuring results show that the plasma cleaning with gas mixtures of argon and oxgen and conditions of about 20Pa and 100W can remarkably reduce the contents of impurity elements in the depth of about 30 nm without introducing hydrogen in the cavity surface. So plasma cleaning has been proposed to be a new possible treatment for niobium superconducting cavity after nitrogen doping.

preprint2015arXiv

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.

preprint2015arXiv

Randomized estimation of spectral densities of large matrices made accurate

For a large Hermitian matrix $A\in \mathbb{C}^{N\times N}$, it is often the case that the only affordable operation is matrix-vector multiplication. In such case, randomized method is a powerful way to estimate the spectral density (or density of states) of $A$. However, randomized methods developed so far for estimating spectral densities only extract information from different random vectors independently, and the accuracy is therefore inherently limited to $\mathcal{O}(1/\sqrt{N_{v}})$ where $N_{v}$ is the number of random vectors. In this paper we demonstrate that the "$\mathcal{O}(1/\sqrt{N_{v}})$ barrier" can be overcome by taking advantage of the correlated information of random vectors when properly filtered by polynomials of $A$. Our method uses the fact that the estimation of the spectral density essentially requires the computation of the trace of a series of matrix functions that are numerically low rank. By repeatedly applying $A$ to the same set of random vectors and taking different linear combination of the results, we can sweep through the entire spectrum of $A$ by building such low rank decomposition at different parts of the spectrum. Under some assumptions, we demonstrate that a robust and efficient implementation of such spectrum sweeping method can compute the spectral density accurately with $\mathcal{O}(N^2)$ computational cost and $\mathcal{O}(N)$ memory cost. Numerical results indicate that the new method can significantly outperform existing randomized methods in terms of accuracy. As an application, we demonstrate a way to accurately compute a trace of a smooth matrix function, by carefully balancing the smoothness of the integrand and the regularized density of states using a deconvolution procedure.

preprint2015arXiv

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.

preprint2014arXiv

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.

preprint2014arXiv

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.

preprint2014arXiv

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.

preprint2014arXiv

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.

preprint2014arXiv

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.

preprint2014arXiv

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.

preprint2014arXiv

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.

preprint2014arXiv

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.

preprint2014arXiv

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).

preprint2014arXiv

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.

preprint2013arXiv

Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion and Selected Inversion

We describe how to apply the recently developed pole expansion and selected inversion (PEXSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating the charge density, the total energy, the Helmholtz free energy and the atomic forces (including both the Hellman-Feynman force and the Pulay force) without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEXSI is that it has a much lower computational complexity than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEXSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEXSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundreds. Both the wall clock time and the memory requirement of PEXSI is modest. This makes it even possible to perform Kohn-Sham DFT calculations for 10,000-atom nanotubes with a sequential implementation of the selected inversion algorithm. We also perform an accurate geometry optimization calculation on a truncated (8,0) boron-nitride nanotube system containing 1024 atoms. Numerical results indicate that the use of PEXSI does not lead to loss of accuracy required in a practical DFT calculation.

preprint2013arXiv

Analysis of the Time Reversible Born-Oppenheimer Molecular Dynamics

We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD) scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition as well as the accuracy of TRBOMD for computing physical properties such as the phonon frequency obtained from the molecular dynamic simulation. We connect and compare TRBOMD with the Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one dimensional model for Kohn-Sham density functional theory.

preprint2013arXiv

Detailed Investigations of the Dimmest Bursts from Two Magnetars, SGR J0501+4516 and SGR J1550-5418

We applied the Bayesian blocks representation technique to search for the dimmest bursts from two magnetars: we identified 320 events from SGR J0501+4516 using a deep XMM-Newton observation and 404 bursts from SGR J1550-5418 using two Swift/XRT pointings. The fluence level of our sample for both sources are about 1-2 orders of magnitude lower than earlier studies. We systematically investigated morphological characteristics and duration distributions of these bursts, as these properties are directly obtained from their Bayesian blocks profiles. We also studied the spectral behavior of the dimmest bursts, which were grouped based on the morphological types and fluences. Our results helped us further differentiate the spectral nature of very dim bursts from that of the persistent emission, both fitted with physically motivated continuum emission models. Moreover, we generated the differential burst fluence distribution for these two magnetars in the lowest fluence regime.

preprint2013arXiv

Efficient iterative method for solving the Dirac-Kohn-Sham density functional theory

We present for the first time an efficient iterative method to directly solve the four-component Dirac-Kohn-Sham (DKS) density functional theory. Due to the existence of the negative energy continuum in the DKS operator, the existing iterative techniques for solving the Kohn-Sham systems cannot be efficiently applied to solve the DKS systems. The key component of our method is a novel filtering step (F) which acts as a preconditioner in the framework of the locally optimal block preconditioned conjugate gradient (LOBPCG) method. The resulting method, dubbed the LOBPCG-F method, is able to compute the desired eigenvalues and eigenvectors in the positive energy band without computing any state in the negative energy band. The LOBPCG-F method introduces mild extra cost compared to the standard LOBPCG method and can be easily implemented. We demonstrate our method in the pseudopotential framework with a planewave basis set which naturally satisfies the kinetic balance prescription. Numerical results for Pt$_{2}$, Au$_{2}$, TlF, and Bi$_{2}$Se$_{3}$ indicate that the LOBPCG-F method is a robust and efficient method for investigating the relativistic effect in systems containing heavy elements.

preprint2013arXiv

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.

preprint2013arXiv

Gradients of Stellar Population Properties and Evolution Clues in a Nearby Galaxy M 101

Multi-band photometric images from ultraviolet and optical to infrared are collected to derive spatially resolved properties of a nearby Scd type galaxy M 101. With evolutionary stellar population synthesis models, two-dimensional distributions and radial profiles of age, metallicity, dust attenuation, and star formation timescale in the form of the Sandage star formation history are obtained. When fitting with the models, we use the IRX-$A_\mathrm{FUV}$ relation, found to depend on a second parameter of birth rate b (ratio of present and past-averaged star formation rate), to constrain the dust attenuation. There are obvious parameter gradients in the disk of M101, which supports the theory of an "inside-out disk" growth scenario. Two distinct disc regions with different gradients of age and color are discovered, similar to another late-type galaxy NGC 628. The metallicity gradient of the stellar content is flatter than that of H {\sc ii} regions. The stellar disk is optically thicker inside than outside and the global dust attenuation of this galaxy is lower, compared with galaxies of similar and earlier morphological type. We highlight that a variational star formation timescale describes the real star formation history of a galaxy. The timescale increases steadily from the center to the outskirt. We also confirm that the bulge in this galaxy is a disk-like pseudobulge, whose evolution is likely to be induced by some secular processes of the small bar with relatively young age, rich metal, and much dust.

preprint2013arXiv

The structure of massive quiescent galaxies at z~3 in the CANDELS-COSMOS field

In this letter, we use a two-color (J-L) vs. (V-J) selection criteria to search massive, quiescent galaxy candidates at 2.5<z<4.0 in the CANDELS-COSMOS field. We construct a H-selected catalogue and complement it with public auxiliary data. We finally obtain 19 passive VJL-selected (hereafter pVJL) galaxies as the possible massive quiescent galaxy candidates at z~3 by several constrains. We find the sizes of our pVJL galaxies are on average 3-4 times smaller than those of local ETGs with analogous stellar mass. The compact size of these z~3 galaxies can be modelled by assuming their formation at z ~ 4-6 according to the dissipative collapse of baryons. Up to z<4, the mass-normalized size evolution can be described by $r_e\propto (1+z)^{-1.0}$. Low Sersic index and axis ratio, with median values n~1.5 and b/a~0.65 respectively, indicate most of pVJL galaxies are disk-dominated. Despite large uncertainty, the inner region of the median mass profile of our pVJL galaxies is similar to those of quiescent galaxies (QGs) at 0.5<z<2.5 and local Early-type galaxies (ETGs). It indicates local massive ETGs have been formed according to an inside-out scenario: the compact galaxies at high redshift make up the cores of local massive ETGs and then build up the outskirts according to dissipationless minor mergers.

preprint2013arXiv

Towards the Kantorovich dual solution for strictly correlated electrons in atoms and molecules

The many-body Coulomb repulsive energy of strictly correlated electrons provides direct information of the exact Hohenberg-Kohn exchange-correlation functional in the strong interaction limit. Until now the treatment of strictly correlated electrons is based on the calculation of co-motion functions with the help of semi-analytic formulations. This procedure is system specific and has been limited to spherically symmetric atoms and strictly 1D systems. We develop a nested optimization method which solves the Kantorovich dual problem directly, and thus facilitates a general treatment of strictly correlated electrons for systems including atoms and small molecules.

preprint2012arXiv

A Comprehensive Analysis of Fermi Gamma-ray Burst Data: III. Energy-Dependent T90 Distributions of GBM GRBs and Instrumental Selection Effect on Duration Classification

The durations (T90) of 315 GRBs detected with Fermi/GBM (8-1000 keV) by 2011 September are calculated using the Bayesian Block method. We compare the T90 distributions between this sample and those derived from previous/current GRB missions. We show that the T90 distribution of this GRB sample is bimodal, with a statistical significance level being comparable to those derived from the BeppoSAX/GRBM sample and the Swift/BAT sample, but lower than that derived from the CGRO/BATSE sample. The short-to-long GRB number ratio is also much lower than that derived from the BATSE sample, i.e., 1:6.5 vs 1:3. We measure T90 in several bands, i.e., 8-15, 15-25, 25-50, 50-100, 100-350, and 350-1000 keV, to investigate the energy-dependence effect of the bimodal T90 distribution. It is found that the bimodal feature is well observed in the 50-100 and 100-350 keV bands, but is only marginally acceptable in the 25-50 keV and 350-1000 keV bands. The hypothesis of the bimodality is confidently rejected in the 8-15 and 15-25 keV bands. The T90 distributions in these bands are roughly consistent with those observed by missions with similar energy bands. The parameter T90 as a function of energy follows \bar T90 \propto E^{-0.20\pm 0.02} for long GRBs. Considering the erratic X-ray and optical flares, the duration of a burst would be even much longer for most GRBs. Our results, together with the observed extended emission of some short GRBs, indicate that the central engine activity time scale would be much longer than T90} for both long and short GRBs and the observed bimodal T90 distribution may be due to an instrumental selection effect.

preprint2012arXiv

Broadband Spectral Investigations of SGR J1550-5418 Bursts

We present the results of our broadband spectral analysis of 42 SGR J1550-5418 bursts simultaneously detected with the Swift/X-ray Telescope (XRT) and the Fermi/Gamma-ray Burst Monitor (GBM), during the 2009 January active episode of the source. The unique spectral and temporal capabilities of the XRT Windowed Timing mode have allowed us to extend the GBM spectral coverage for these events down to the X-ray domain (0.5-10 keV). Our earlier analysis of the GBM data found that the SGR J1550-5418 burst spectra were described equally well with a Comptonized model or with two blackbody functions; the two models were statistically indistinguishable. Our new broadband (0.5 - 200 keV) spectral fits show that, on average, the burst spectra are better described with two blackbody functions than with the Comptonized model. Thus, our joint XRT/GBM analysis clearly shows for the first time that the SGR J1550-5418 burst spectra might naturally be expected to exhibit a more truly thermalized character, such as a two-blackbody or even a multi-blackbody signal. Using the Swift and RXTE timing ephemeris for SGR J1550-5418 we construct the distribution of the XRT burst counts with spin phase and find that it is not correlated with the persistent X-ray emission pulse phase from SGR J1550-5418. These results indicate that the burst emitting sites on the neutron star need not be co-located with hot spots emitting the bulk of the persistent X-ray emission. Finally, we show that there is a significant pulse phase dependence of the XRT burst counts, likely demonstrating that the surface magnetic field of SGR J1550-5418 is not uniform over the emission zone, since it is anticipated that regions with stronger surface magnetic field could trigger bursts more efficiently.

preprint2012arXiv

Detection of spectral evolution in the bursts emitted during the 2008-2009 active episode of SGR J1550 - 5418

In early October 2008, the Soft Gamma Repeater SGRJ1550 - 5418 (1E 1547.0 - 5408, AXJ155052 - 5418, PSR J1550 - 5418) became active, emitting a series of bursts which triggered the Fermi Gamma-ray Burst Monitor (GBM) after which a second especially intense activity period commenced in 2009 January and a third, less active period was detected in 2009 March-April. Here we analyze the GBM data all the bursts from the first and last active episodes. We performed temporal and spectral analysis for all events and found that their temporal characteristics are very similar to the ones of other SGR bursts, as well the ones reported for the bursts of the main episode (average burst durations \sim 170 ms). In addition, we used our sample of bursts to quantify the systematic uncertainties of the GBM location algorithm for soft gamma-ray transients to < 8 deg. Our spectral analysis indicates significant spectral evolution between the first and last set of events. Although the 2008 October events are best fit with a single blackbody function, for the 2009 bursts an Optically Thin Thermal Bremsstrahlung (OTTB) is clearly preferred. We attribute this evolution to changes in the magnetic field topology of the source, possibly due to effects following the very energetic main bursting episode.

preprint2012arXiv

Element orbitals for Kohn-Sham density functional theory

We present a method to discretize the Kohn-Sham Hamiltonian matrix in the pseudopotential framework by a small set of basis functions automatically contracted from a uniform basis set such as planewaves. Each basis function is localized around an element, which is a small part of the global domain containing multiple atoms. We demonstrate that the resulting basis set achieves meV accuracy for 3D densely packed systems with a small number of basis functions per atom. The procedure is applicable to insulating and metallic systems.

preprint2012arXiv

Large Size Scatter of Passively Evolving Lensed Galaxies at z~2 in CLASH

In a systematic search over 11 cluster fields from Cluster Lensing And Supernova survey with Hubble (CLASH) we identify ten passively evolving massive galaxies at redshift z~2.We derive the stellar properties of these galaxies using HST WFC3/ACS multiband data, together with Spitzer IRAC observations. We also deduce the optical rest-frame effective radius of these high redshift objects. The derived stellar masses and measured effective radii have been corrected by the lensing magnification factors, which are estimated by simply adopting the spherical NFW model for the foreground cluster lens. The observed near-IR images, obtained by HST WFC3 camera with high spatial resolution and lensed by the foreground clusters, enable us to study the structures of such systems. Nine out of ten galaxies have on average three times smaller effective radius than local ETGs of similar stellar masses, in agreement with previous works at redshift 1.5 < z < 2.5. Combined with literature data for z~2, we find that the mass-normalized effective radius scales with redshift as re/M^0.56 \propto (1 + z)^{-1.13}. We confirm that their size distribution shows a large scatter: from normal size to ~5 times smaller compared to local ETGs with similar stellar masses. The 1-σ scatter σ_{logre} of the size distribution is 0.22 and 0.34 at z~1.6 and z~2.1,respectively.The observed large size scatter has to be carefully taken into account in galaxy evolution model predictions.

preprint2012arXiv

On the X-ray emission mechanisms of the persistent source and very low-fluence bursts of SGR J0501+4516

We present here a detailed spectral study of the X-ray emission of the persistent source and the low-fluence bursts of SGR J0501+4516 observed during a deep XMM-Newton observation near the peak of its 2008 outburst. For the persistent emission we employ a physically motivated continuum emission model and spectroscopically determine important source properties; such as, the surface magnetic field strength and the magnetospheric scattering optical depth. We find that the magnetar surface temperature near the peak of its activity is 0.38 keV, corresponding to an emission area of 131 km^2 at a distance of 2 kpc. The surface magnetic field strength determined spectroscopically, B=2.2E14 G, is consistent with the dipole field strength inferred from the source spin and spin down rate. We fit the stacked spectra of 129 very faint bursts with a modified blackbody model and find a temperature of 1.16 keV, corresponding to an emission area of 93 km^2. We also find an evidence for cooling during the burst decay phase.

preprint2012arXiv

Radial Angular Momentum Transfer and Magnetic Barrier for Short-Type Gamma-Ray Burst Central Engine Activity

Soft extended emission (EE) following initial hard spikes up to 100 seconds was observed with {\em Swift}/BAT for about half of short-type gamma-ray bursts (SGRBs). This challenges the conversional central engine models of SGRBs, i.e., compact star merger models. In the framework of the black hole-neutron star merger models, we study the roles of the radial angular momentum transfer in the disk and the magnetic barrier around the black hole for the activity of SGRB central engines. We show that the radial angular momentum transfer may significantly prolong the lifetime of the accretion process and multiple episodes may be switched by the magnetic barrier. Our numerical calculations based on the models of the neutrino-dominated accretion flows suggest that the disk mass is critical for producing the observed EE. In case of the mass being $\sim 0.8M_{\odot}$, our model can reproduce the observed timescale and luminosity of both the main and EE episodes in a reasonable parameter set. The predicted luminosity of the EE component is lower than the observed EE with about one order of magnitude and the timescale is shorter than 20 seconds if the disk mass being $\sim 0.2M_{\odot}$. {\em Swift}/BAT-like instruments may be not sensitive enough to detect the EE component in this case. We argue that the EE component would be a probe for merger process and disk formation for compact star mergers.

preprint2012arXiv

The Fermi GBM Gamma-Ray Burst Catalog: The First Two Years

The Fermi Gamma-ray Burst Monitor (GBM) is designed to enhance the scientific return from Fermi in studying gamma-ray bursts (GRBs). In its first two years of operation GBM triggered on 491 GRBs. We summarize the criteria used for triggering and quantify the general characteristics of the triggered GRBs, including their locations, durations, peak flux, and fluence. This catalog is an official product of the Fermi GBM science team, and the data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center (HEASARC).

preprint2012arXiv

X-ray Observations of a New Unusual Magnetar Swift J1834.9-0846

We present X-ray observations of the new transient magnetar Swift J1834.9-0846, discovered with Swift BAT on 2011 August 7. The data were obtained with Swift, RXTE, CXO, and XMM-Newton both before and after the outburst. Timing analysis reveals singe peak pulsations with a period of 2.4823 s and an unusually high pulsed fraction, 85+/-10%. Using the RXTE and CXO data, we estimated the period derivative, dot{P}=8\times 10^{-12} s/s, and confirmed the high magnetic field of the source, B=1.4\times 10^{14} G. The decay of the persistent X-ray flux, spanning 48 days, is consistent with a power law, t^{-0.5}. In the CXO/ACIS image, we find that the highly absorbed point source is surrounded by extended emission, which most likely is a dust scattering halo. Swift J1834.9-0846 is located near the center of the radio supernova remnant W41 and TeV source HESS J1834-087. An association with W41 would imply a source distance of about 4 kpc; however, any relation to the HESS source remains unclear, given the presence of several other candidate counterparts for the latter source in the field. Our search for an IR counterpart of Swift J1834.9-0846 revealed no source down to K_s=19.5 within the 0.6' CXO error circle.

preprint2011arXiv

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework I: Total energy calculation

Kohn-Sham density functional theory is one of the most widely used electronic structure theories. In the pseudopotential framework, uniform discretization of the Kohn-Sham Hamiltonian generally results in a large number of basis functions per atom in order to resolve the rapid oscillations of the Kohn-Sham orbitals around the nuclei. Previous attempts to reduce the number of basis functions per atom include the usage of atomic orbitals and similar objects, but the atomic orbitals generally require fine tuning in order to reach high accuracy. We present a novel discretization scheme that adaptively and systematically builds the rapid oscillations of the Kohn-Sham orbitals around the nuclei as well as environmental effects into the basis functions. The resulting basis functions are localized in the real space, and are discontinuous in the global domain. The continuous Kohn-Sham orbitals and the electron density are evaluated from the discontinuous basis functions using the discontinuous Galerkin (DG) framework. Our method is implemented in parallel and the current implementation is able to handle systems with at least thousands of atoms. Numerical examples indicate that our method can reach very high accuracy (less than 1meV) with a very small number ($4\sim 40$) of basis functions per atom.

preprint2011arXiv

Burst and Persistent Emission Properties during the Recent Active Episode of the Anomalous X-ray Pulsar 1E 1841-045

Swift/BAT detected the first burst from 1E 1841-045 in May 2010 with intermittent burst activity recorded through at least July 2011. Here we present Swift and Fermi/GBM observations of this burst activity and search for correlated changes to the persistent X-ray emission of the source. The T90 durations of the bursts range between 18-140 ms, comparable to other magnetar burst durations, while the energy released in each burst ranges between (0.8 - 25)E38 erg, which is in the low side of SGR bursts. We find that the bursting activity did not have a significant effect on the persistent flux level of the source. We argue that the mechanism leading to this sporadic burst activity in 1E 1841-045 might not involve large scale restructuring (either crustal or magnetospheric) as seen in other magnetar sources.

preprint2011arXiv

Fermi/GBM Observations of SGR J0501+4516 Bursts

We present our temporal and spectral analyses of 29 bursts from SGR J0501+4516, detected with the Gamma-ray Burst Monitor onboard the Fermi Gamma-ray Space Telescope during the 13 days of the source activation in 2008 (August 22 to September 3). We find that the T90 durations of the bursts can be fit with a log-normal distribution with a mean value of ~ 123 ms. We also estimate for the first time event durations of Soft Gamma Repeater (SGR) bursts in photon space (i.e., using their deconvolved spectra) and find that these are very similar to the T90s estimated in count space (following a log-normal distribution with a mean value of ~ 124 ms). We fit the time-integrated spectra for each burst and the time-resolved spectra of the five brightest bursts with several models. We find that a single power law with an exponential cutoff model fits all 29 bursts well, while 18 of the events can also be fit with two black body functions. We expand on the physical interpretation of these two models and we compare their parameters and discuss their evolution. We show that the time-integrated and time-resolved spectra reveal that Epeak decreases with energy flux (and fluence) to a minimum of ~30 keV at F=8.7e-6 erg/cm2/s, increasing steadily afterwards. Two more sources exhibit a similar trend: SGRs J1550-5418 and 1806-20. The isotropic luminosity corresponding to these flux values is roughly similar for all sources (0.4-1.5 e40 erg/s).

preprint2011arXiv

First-year Results of Broadband Spectroscopy of the Brightest Fermi-GBM Gamma-Ray Bursts

We present here our results of the temporal and spectral analysis of a sample of 52 bright and hard gamma-ray bursts (GRBs) observed with the Fermi Gamma-ray Burst Monitor (GBM) during its first year of operation (July 2008-July 2009). Our sample was selected from a total of 253 GBM GRBs based on each event peak count rate measured between 0.2 and 40MeV. The final sample comprised 34 long and 18 short GRBs. These numbers show that the GBM sample contains a much larger fraction of short GRBs, than the CGRO/BATSE data set, which we explain as the result of our (different) selection criteria and the improved GBM trigger algorithms, which favor collection of short, bright GRBs over BATSE. A first by-product of our selection methodology is the determination of a detection threshold from the GBM data alone, above which GRBs most likely will be detected in the MeV/GeV range with the Large Area Telescope (LAT) onboard Fermi. This predictor will be very useful for future multiwavelength GRB follow ups with ground and space based observatories. Further we have estimated the burst durations up to 10MeV and for the first time expanded the duration-energy relationship in the GRB light curves to high energies. We confirm that GRB durations decline with energy as a power law with index approximately -0.4, as was found earlier with the BATSE data and we also notice evidence of a possible cutoff or break at higher energies. Finally, we performed time-integrated spectral analysis of all 52 bursts and compared their spectral parameters with those obtained with the larger data sample of the BATSE data. We find that the two parameter data sets are similar and confirm that short GRBs are in general harder than longer ones.

preprint2011arXiv

Momentum distribution, vibrational dynamics and the potential of mean force in ice

By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasi-harmonic effective potential with three distinct principal frequencies that reflect molecular orientation. Due to the importance of anisotropy, anharmonic features of the environment cannot be extracted from existing experimental distributions that involve the spherical average. The full directional distribution is required, and we give a theoretical prediction for this quantity that could be verified in future experiments. Within the quasi-harmonic context, anharmonicity in the ground state dynamics of the proton is substantial and has quantal origin, a finding that impacts the interpretation of several spectroscopies.

preprint2011arXiv

Optimized local basis set for Kohn-Sham density functional theory

We develop a technique for generating a set of optimized local basis functions to solve models in the Kohn-Sham density functional theory for both insulating and metallic systems. The optimized local basis functions are obtained by solving a minimization problem in an admissible set determined by a large number of primitive basis functions. Using the optimized local basis set, the electron energy and the atomic force can be calculated accurately with a small number of basis functions. The Pulay force is systematically controlled and is not required to be calculated, which makes the optimized local basis set an ideal tool for ab initio molecular dynamics and structure optimization. We also propose a preconditioned Newton-GMRES method to obtain the optimized local basis functions in practice. The optimized local basis set is able to achieve high accuracy with a small number of basis functions per atom when applied to a one dimensional model problem.

preprint2010arXiv

Displaced path integral formulation for the momentum distribution of quantum particles

The proton momentum distribution, accessible by deep inelastic neutron scattering, is a very sensitive probe of the potential of mean force experienced by the protons in hydrogen-bonded systems. In this work we introduce a novel estimator for the end to end distribution of the Feynman paths, i.e. the Fourier transform of the momentum distribution. In this formulation, free particle and environmental contributions factorize. Moreover, the environmental contribution has a natural analogy to a free energy surface in statistical mechanics, facilitating the interpretation of experiments. The new formulation is not only conceptually but also computationally advantageous. We illustrate the method with applications to an empirical water model, ab-initio ice, and one dimensional model systems.

preprint2010arXiv

Fast construction of hierarchical matrix representation from matrix-vector multiplication

We develop a hierarchical matrix construction algorithm using matrix-vector multiplications, based on the randomized singular value decomposition of low-rank matrices. The algorithm uses $\mathcal{O}(\log n)$ applications of the matrix on structured random test vectors and $\mathcal{O}(n \log n)$ extra computational cost, where $n$ is the dimension of the unknown matrix. Numerical examples on constructing Green's functions for elliptic operators in two dimensions show efficiency and accuracy of the proposed algorithm.

preprint2009arXiv

Tunneling and delocalization in hydrogen bonded systems: a study in position and momentum space

Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.

preprint2008arXiv

Multipole Representation of the Fermi Operator with Application to the Electronic Structure Analysis of Metallic Systems

We propose a multipole representation of the Fermi-Dirac function and the Fermi operator, and use this representation to develop algorithms for electronic structure analysis of metallic systems. The new algorithm is quite simple and efficient. Its computational cost scales logarithmically with $βΔ\eps$ where $β$ is the inverse temperature, and $Δ\eps$ is the width of the spectrum of the discretized Hamiltonian matrix.