arXiv subjects

Xingyu Gao

Publications and source records attributed to Xingyu Gao.

83 records · Page 5Linked to original sources

arXiv2018

Mesoscopic magnetic resonance spectroscopy with a remote spin sensor

Quantum sensing based on nitrogen-vacancy (NV) centers in diamond has been developed as a powerful tool for microscopic magnetic resonance. However, the reported sensor-to-sample distance is limited within tens of nanometers because the signal of spin fluctuation decreases cubically with the increasing distance. Here we extend the sensing distance to tens of micrometers by detecting spin polarization rather than spin fluctuation. We detected the mesoscopic magnetic resonance spectra of polarized electrons of a pentacene-doped crystal, measured its two typical decay times and observed the optically enhanced spin polarization. This work paves the way for the NV-based mesoscopic magnetic resonance spectroscopy and imaging at ambient conditions.

quant-ph↗

arXiv2018

Applicability of Kerker preconditioning scheme to the self-consistent density functional theory calculations of inhomogeneous systems

Kerker preconditioner, based on the dielectric function of homogeneous electron gas, is designed to accelerate the self-consistent field (SCF) iteration in the density functional theory (DFT) calculations. However, question still remains regarding its applicability to the inhomogeneous systems. In this paper, we develop a modified Kerker preconditioning scheme which captures the long-range screening behavior of inhomogeneous systems thus improve the SCF convergence. The effectiveness and efficiency is shown by the tests on long-z slabs of metals, insulators and metal-insulator contacts. For situations without a priori knowledge of the system, we design the a posteriori indicator to monitor if the preconditioner has suppressed charge sloshing during the iterations. Based on the a posteriori indicator, we demonstrate two schemes of the self-adaptive configuration for the SCF iteration.

cond-mat.mtrl-sci↗

arXiv2017

The optimal particle-mesh interpolation basis

The fast Ewald methods are widely used to compute the point-charge electrostatic interactions in molecular simulations. The key step that introduces errors in the computation is the particle-mesh interpolation. In this work, the optimal interpolation basis is derived by minimizing the estimated error of the fast Ewald method. The basis can be either general or model specific, depending on whether or not the charge correlation has been taken into account. By using the TIP3P water as an example system, we demonstrate that the general optimal basis is always more accurate than the B-spline basis in the investigated parameter range, while the computational cost is at most 5\% more expensive. In some cases, the optimal basis is found to be two orders of magnitude more accurate. The model specific optimal basis further improves the accuracy of the general optimal basis, but requires more computational effort in the optimization, and may not be transferable to systems with different charge correlations. Therefore, the choice between the general and model specific optimal bases is a trade-off between the generality and the accuracy.

physics.chem-ph↗

arXiv2017

Kaiser-Bessel Basis for the Particle-Mesh Interpolation

In this work, we introduce the Kaiser-Bessel interpolation basis for the particle-mesh interpolation in the fast Ewald method. A reliable a priori error estimate is developed to measure the accuracy of the force computation in correlated charge systems, and is shown to be effective in optimizing the shape parameter of the Kaiser-Bessel basis in terms of accuracy. By comparing the optimized Kaiser-Bessel basis with the traditional B-spline basis, we demonstrate that the former is more accurate than the latter in part of the working parameter space, saying a relatively small real space cutoff, a relatively small reciprocal space mesh and a relatively large truncation of basis. In some cases, the Kaiser-Bessel basis is found to be more than one order of magnitude more accurate.

physics.chem-ph↗

arXiv2016

An efficient hybrid tridiagonal divide-and-conquer algorithm on distributed memory architectures

In this paper, an efficient divide-and-conquer (DC) algorithm is proposed for the symmetric tridiagonal matrices based on ScaLAPACK and the hierarchically semiseparable (HSS) matrices. HSS is an important type of rank-structured matrices.Most time of the DC algorithm is cost by computing the eigenvectors via the matrix-matrix multiplications (MMM). In our parallel hybrid DC (PHDC) algorithm, MMM is accelerated by using the HSS matrix techniques when the intermediate matrix is large. All the HSS algorithms are done via the package STRUMPACK. PHDC has been tested by using many different matrices. Compared with the DC implementation in MKL, PHDC can be faster for some matrices with few deflations when using hundreds of processes. However, the gains decrease as the number of processes increases. The comparisons of PHDC with ELPA (the Eigenvalue soLvers for Petascale Applications library) are similar. PHDC is usually slower than MKL and ELPA when using 300 or more processes on Tianhe-2 supercomputer.

cs.MS↗

arXiv2016

Multiple Staggered Mesh Ewald: Boosting the Accuracy of the Smooth Particle Mesh Ewald Method

The smooth particle mesh Ewald (SPME) method is the standard method for computing the electrostatic interactions in the molecular simulations. In this work, the multiple staggered mesh Ewald (MSME) method is proposed to boost the accuracy of the SPME method. Unlike the SPME that achieves higher accuracy by refining the mesh, the MSME improves the accuracy by averaging the standard SPME forces computed on, e.g. $M$, staggered meshes. We prove, from theoretical perspective, that the MSME is as accurate as the SPME, but uses $M^2$ times less mesh points in a certain parameter range. In the complementary parameter range, the MSME is as accurate as the SPME with twice of the interpolation order. The theoretical conclusions are numerically validated both by a uniform and uncorrelated charge system, and by a three-point-charge water system that is widely used as solvent for the bio-macromolecules.

physics.comp-ph↗

arXiv2016

Effect of vacancies on the mechanical properties of zirconium: An ab initio investigation

It is well known that the irradiation-induced defects strongly influence the mechanical properties of zirconium (Zr) or its alloys in nuclear reactors. However, how the point defect changes the mechanical properties has been rarely studied. Here, we systematically investigated the effect of vacancies on the mechanical properties of alpha-Zr based on density functional theory (DFT). Both uniformly distributed vacancies and vacancy clusters were considered. Our results reveal that the existence of vacancy will reduce the bulk modulus, while enhance the shear and Young's moduli. Based on these moduli, the ductility and hardness were further calculated. With the introduction of vacancy, the ductility decreases, but the hardness increases. However, when the vacancy concentration is larger than a critical value, a rise in the ductility and a reduction in the hardness occur, which indicates the degeneration of the material. Moreover, it was found that the vacancies lead to a more isotropic distribution of Young's modulus in 3D space. To further investigate how the clustering of vacancies influences the mechanical properties, the most stable configurations of di- and trivacancy clusters have been predicted, which correspond to the most compact distribution of vacancies. Compared with the uniform distribution of vacancies, clustering of vacancies will strengthen the above changes of elastic moduli, ductility and hardness. Our results indicate that the increase of the vacancy concentration may be the basic cause for the changes of the mechanical properties under irradiation, while the formation of vacancy clusters intensifies these changes.

cond-mat.mtrl-sci↗

arXiv2016

On the existence of the optimal order for wavefunction extrapolation in Born-Oppenheimer molecular dynamics

Wavefunction extrapolation greatly reduces the number of self-consistent field (SCF) iterations and thus the overall computational cost of Born-Oppenheimer molecular dynamics (BOMD) that is based on the Kohn-Sham density functional theory. Going against the intuition that the higher order of extrapolation possesses a better accuracy, we demonstrate, from both theoretical and numerical perspectives, that the extrapolation accuracy firstly increases and then decreases with respect to the order, and an optimal extrapolation order in terms of minimal number of SCF iterations always exists. We also prove that the optimal order tends to be larger when using larger MD time steps or more strict SCF convergence criteria. By example BOMD simulations of a solid copper system, we show that the optimal extrapolation order covers a broad range when varying the MD time step or the SCF convergence criterion. Therefore, we suggest the necessity for BOMD simulation packages to open the user interface and to provide more choices on the extrapolation order. Another factor that may influence the extrapolation accuracy is the alignment scheme that eliminates the discontinuity in the wavefunctions with respect to the atomic or cell variables. We prove the equivalence between the two existing schemes, thus the implementation of either of them does not lead to essential difference in the extrapolation accuracy.

physics.comp-ph↗

arXiv2016

Sampling the isothermal-isobaric ensemble by Langevin dynamics

We present a new method of conducting molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way, in the sense that the stationary configurational distribution is proved to be in consistent with that of the isothermal-isobaric ensemble. In order to apply the proposed method in computer simulations, a second order symmetric numerical integration scheme is developed by Trotter's splitting of the single-step propagator. Moreover, a practical guide of choosing working parameters is suggested for user specified thermo- and baro-coupling time-scales. The method and software implementation are carefully validated by a numerical example.

cond-mat.stat-mech↗

arXiv2016

Parallel 3-dim fast Fourier transforms with load balancing of the plane waves

The plane wave method is most widely used for solving the Kohn-Sham equations in first-principles materials science computations. In this procedure, the three-dimensional (3-dim) trial wave functions' fast Fourier transform (FFT) is a regular operation and one of the most demanding algorithms in terms of the scalability on a parallel machine. We propose a new partitioning algorithm for the 3-dim FFT grid to accomplish the trade-off between the communication overhead and load balancing of the plane waves. It is shown by qualitative analysis and numerical results that our approach could scale the plane wave first-principles calculations up to more nodes.

physics.comp-ph↗

arXiv2012

A Symmetry-based Decomposition Approach to Eigenvalue Problems: Formulation, Discretization, and Implementation

In this paper, we propose a decomposition approach for eigenvalue problems with spatial symmetries, including the formulation, discretization as well as implementation. This approach can handle eigenvalue problems with either Abelian or non-Abelian symmetries, and is friendly for grid-based discretizations such as finite difference, finite element or finite volume methods. With the formulation, we divide the original eigenvalue problem into a set of subproblems and require only a smaller number of eigenpairs for each subproblem. We implement the decomposition approach with finite elements and parallelize our code in two levels. We show that the decomposition approach can improve the efficiency and scalability of iterative diagonalization. In particular, we apply the approach to solving Kohn--Sham equations of symmetric molecules consisting of hundreds of atoms.

math.NA↗