Numerical oscillation of the total energy can be observed when the Kohn- Sham equation is solved by real-space methods to simulate the translational move of an electronic system. Effectively remove or reduce the unphysical oscillation is crucial not only for the optimization of the geometry of the electronic structure, but also for the study of molecular dynamics. In this paper, we study such unphysical oscillation based on the numerical framework in [G. Bao, G. H. Hu, and D. Liu, An h-adaptive finite element solver for the calculations of the electronic structures, Journal of Computational Physics, Volume 231, Issue 14, Pages 4967–4979, 2012], and deliver some numerical methods to constrain such unphysical effect for both pseudopotential and all-electron calculations, including a stabilized cubature strategy for Hamiltonian operator, and an a posteriori error estimator of the finite element methods for Kohn-Sham equation. The numerical results demonstrate the effectiveness of our method on restraining unphysical oscillation of the total energies.

In this paper, we introduce a high-order accurate constrained transport type finite volume method to solve ideal magnetohydrodynamic equations on two-dimensional triangular meshes. A new divergence-free WENO-based reconstruction method is developed to maintain exactly divergence-free evolution of the numerical magnetic field. In this formulation, the normal component of the magnetic field at each face of a triangle is reconstructed uniquely and with the desired order of accuracy. Additionally, a new weighted flux interpolation approach is also developed to compute the z-component of the electric field at vertices of grid cells. We also present numerical examples to demonstrate the accuracy and robustness of the proposed scheme.

Simulation of turbulent flows with shocks employing subgrid-scale (SGS) filtering may encounter a loss of accuracy in the vicinity of a shock. This paper addresses the accuracy improvement of LES of turbulent flows in two ways: (a) from the SGS model standpoint and (b) from the numerical method improvement standpoint. In an internal report, Kotov et al. ( “High Order Numerical Methods for large eddy simulation (LES) of Turbulent Flows with Shocks”, CTR Tech Brief, Oct. 2014, Stanford University), we performed a preliminary comparative study of different approaches to reduce the loss of accuracy within the framework of the dynamic Germano SGS model. The high order low dissipative method of Yee & Sjögreen (2009) using local flow sensors to control the amount of numerical dissipation where needed is used for the LES simulation. The considered improved dynamics model approaches include applying the one-sided SGS test filter of Sagaut & Germano (2005) and/or disabling the SGS terms at the shock location. For Mach 1.5 and 3 canonical shock-turbulence interaction problems, both of these approaches show a similar accuracy improvement to that of the full use of the SGS terms. The present study focuses on a five levels of grid refinement study to obtain the reference direct numerical simulation (DNS) solution for additional LES SGS comparison and approaches. One of the numerical accuracy improvements included here applies Harten's subcell resolution procedure to locate and sharpen the shock, and uses a one-sided test filter at the grid points adjacent to the exact shock location.

In this article, we discuss the stability of soft quasicrystalline phases in a coupled-mode Swift-Hohenberg model for three-component systems, where the characteristic length scales are governed by the positive-definite gradient terms. Classic two-mode approximation method and direct numerical minimization are applied to the model. In the latter approach, we apply the projection method to deal with the potentially quasiperiodic ground states. A variable cell method of optimizing the shape and size of higher-dimensional periodic cell is developed to minimize the free energy with respect to the order parameters. Based on the developed numerical methods, we rediscover decagonal and dodecagonal quasicrystalline phases, and find diverse periodic phases and complex modulated phases. Furthermore, phase diagrams are obtained in various phase spaces by comparing the free energies of different candidate structures. It does show not only the important roles of system parameters, but also the effect of optimizing computational domain. In particular, the optimization of computational cell allows us to capture the ground states and phase behavior with higher fidelity. We also make some discussions on our results and show the potential of applying our numerical methods to a larger class of mean-field free energy functionals.

In this paper, we study the Camassa-Holm equation and the Degasperis-Procesi equation. The two equations are in the family of integrable peakon equations, and both have very rich geometric properties. Based on these geometric structures, we construct the geometric numerical integrators for simulating their soliton solutions. The Camassa-Holm equation and the Degasperis-Procesi equation have many common properties, however they also have the significant difference, for example there exist the shock wave solutions for the Degasperis-Procesi equation. By using the symplectic Fourier pseudo-spectral integrator, we simulate the peakon solutions of the two equations. To illustrate the smooth solitons and shock wave solutions of the DP equation, we use the splitting technique and combine the composition methods. In the numerical experiments, comparisons of these two kinds of methods are presented in terms of accuracy, computational cost and invariants preservation.

Mesh generation is a bottleneck for finite element simulations of biomolecules. A robust and efficient approach, based on the immersed boundary method proposed in [8], has been developed and implemented to generate large-scale mesh body-fitted to molecular shape for general parallel finite element simulations. The molecular Gaussian surface is adopted to represent the molecular surface, and is finally approximated by piecewise planes via the tool phgSurfaceCut in PHG [43], which is improved and can reliably handle complicated molecular surfaces, through mesh refinement steps. A coarse background mesh is imported first and then is distributed into each process using a mesh partitioning algorithm such as space filling curve [5] or METIS [22]. A bisection method is used for the mesh refinements according to the molecular PDB or PQR file which describes the biomolecular region. After mesh refinements, the mesh is optionally repartitioned and redistributed for load balancing. For finite element simulations, the modification of region mark and boundary types is done in parallel. Our parallel mesh generation method has been successfully applied to a sphere cavity model, a DNA fragment, a gramicidin A channel and a huge Dengue virus system. The results of numerical experiments show good parallel efficiency. Computations of electrostatic potential and solvation energy also validate the method. Moreover, the meshing process and adaptive finite element computation can be integrated as one PHG project to avoid the mesh importing and exporting costs, and improve the convenience of application as well.

This work deals with the numerical resolution of the M1-Maxwell system in the quasi-neutral regime. In this regime the stiffness of the stability constraints of classical schemes causes huge calculation times. That is why we introduce a new stable numerical scheme consistent with the transitional and limit models. Such schemes are called Asymptotic-Preserving (AP) schemes in literature. This new scheme is able to handle the quasi-neutrality limit regime without any restrictions on time and space steps. This approach can be easily applied to angular moment models by using a moments extraction. Finally, two physically relevant numerical test cases are presented for the Asymptotic-Preserving scheme in different regimes. The first one corresponds to a regime where electromagnetic effects are predominant. The second one on the contrary shows the efficiency of the Asymptotic-Preserving scheme in the quasi-neutral regime. In the latter case the illustrative simulations are compared with kinetic and hydrodynamic numerical results.

This paper concerns the computation of nonlinear crest distributions for irregular Stokes waves, and a numerical algorithm based on the Fast Fourier Transform (FFT) technique has been developed for carrying out the nonlinear computations. In order to further improve the computational efficiency, a new Transformed Rayleigh procedure is first proposed as another alternative for computing the nonlinear wave crest height distributions, and the corresponding computer code has also been developed. In the proposed Transformed Rayleigh procedure, the transformation model is chosen to be a monotonic exponential function, calibrated such that the first three moments of the transformed model match the moments of the true process. The numerical algorithm based on the FFT technique and the proposed Transformed Rayleigh procedure have been applied for calculating the wave crest distributions of a sea state with a Bretschneider spectrum and a sea statewith the surface elevation datameasured at the Poseidon platform. It is demonstrated in these two cases that the numerical algorithm based on the FFT technique and the proposed Transformed Rayleigh procedure can offer better predictions than those from using the empirical wave crest distribution models. Meanwhile, it is found that our proposed Transformed Rayleigh procedure can compute nonlinear crest distributions more than 25 times faster than the numerical algorithm based on the FFT technique.

We propose an entropy stable high-resolution finite volume scheme to approximate systems of two-dimensional symmetrizable conservation laws on unstructured grids. In particular we consider Euler equations governing compressible flows. The scheme is constructed using a combination of entropy conservative fluxes and entropy-stable numerical dissipation operators. High resolution is achieved based on a linear reconstruction procedure satisfying a suitable sign property that helps to maintain entropy stability. The proposed scheme is demonstrated to robustly approximate complex flow features by a series of benchmark numerical experiments.

This paper introduces a two-stage model for multi-channel image segmentation, which is motivated by minimal surface theory. Indeed, in the first stage, we acquire a smooth solution u from a convex variational model related to minimal surface property and different data fidelity terms are considered. This minimization problem is solved efficiently by the classical primal-dual approach. In the second stage, we adopt thresholding to segment the smoothed image u. Here, instead of using K-means to determine the thresholds, we propose a more stable hill-climbing procedure to locate the peaks on the 3D histogram of u as thresholds, in the meantime, this algorithm can also detect the number of segments. Finally, numerical results demonstrate that the proposed method is very robust against noise and superior to other image segmentation approaches.

Transient diffusion equations arise in many branches of engineering and applied sciences (e.g., heat transfer and mass transfer), and are parabolic partial differential equations. It is well-known that these equations satisfy important mathematical properties like maximum principles and the non-negative constraint, which have implications in mathematical modeling. However, existing numerical formulations for these types of equations do not, in general, satisfy maximum principles and the non-negative constraint. In this paper, we present a methodology for enforcing maximum principles and the non-negative constraint for transient anisotropic diffusion equation. The proposed methodology is based on the method of horizontal lines in which the time is discretized first. This results in solving steady anisotropic diffusion equation with decay equation at every discrete time-level. We also present other plausible temporal discretizations, and illustrate their shortcomings in meeting maximum principles and the non-negative constraint. The proposed methodology can handle general computational grids with no additional restrictions on the time-step. We illustrate the performance and accuracy of the proposed methodology using representative numerical examples. We also perform a numerical convergence analysis of the proposed methodology. For comparison, we also present the results from the standard single-field semi-discrete formulation and the results from a popular software package, which all will violate maximum principles and the non-negative constraint.

We propose efficient and accurate numerical methods for computing the ground state and dynamics of the dipolar Bose-Einstein condensates utilising a newly developed dipole-dipole interaction (DDI) solver that is implemented with the non-uniform fast Fourier transform (NUFFT) algorithm. We begin with the three-dimensional (3D) Gross-Pitaevskii equation (GPE) with a DDI term and present the corresponding two-dimensional (2D) model under a strongly anisotropic confining potential. Different from existing methods, the NUFFT based DDI solver removes the singularity by adopting the spherical/polar coordinates in the Fourier space in 3D/2D, respectively, thus it can achieve spectral accuracy in space and simultaneously maintain high efficiency by making full use of FFT and NUFFT whenever it is necessary and/or needed. Then, we incorporate this solver into existing successful methods for computing the ground state and dynamics of GPE with a DDI for dipolar BEC. Extensive numerical comparisons with existing methods are carried out for computing the DDI, ground states and dynamics of the dipolar BEC. Numerical results show that our new methods outperform existing methods in terms of both accuracy and efficiency.

In two-phase flow simulations, a difficult issue is usually the treatment of surface tension effects. These cause a pressure jump that is proportional to the curvature of the interface separating the two fluids. Since the evaluation of the curvature incorporates second derivatives, it is prone to numerical instabilities. Within this work, the interface is described by a level-set method based on a discontinuous Galerkin discretization. In order to stabilize the evaluation of the curvature, a patch-recovery operation is employed. There are numerous ways in which this filtering operation can be applied in the whole process of curvature computation. Therefore, an extensive numerical study is performed to identify optimal settings for the patch-recovery operations with respect to computational cost and accuracy.

In this paper a three-step scheme is applied to solve the Camassa-Holm (CH) shallow water equation. The differential order of the CH equation has been reduced in order to facilitate development of numerical scheme in a comparatively smaller grid stencil. Here a three-point seventh-order spatially accurate upwinding combined compact difference (CCD) scheme is proposed to approximate the firstorder derivative term. We conduct modified equation analysis on the CCD scheme and eliminate the leading discretization error terms for accurately predicting unidirectional wave propagation. The Fourier analysis is carried out as well on the proposed numerical scheme to minimize the dispersive error. For preserving Hamiltonians in Camassa- Holm equation, a symplecticity conserving time integrator has been employed. The other main emphasis of the present study is the use of u–P–α formulation to get nondissipative CH solution for peakon-antipeakon and soliton-anticuspon head-on wave collision problems.

In this paper, we study the selectivity of the potassium channel KcsA by a recently developed image-charge solvation method (ICSM) combined with molecular dynamics simulations. The hybrid solvation model in the ICSM is able to demonstrate atomistically the function of the selectivity filter of the KcsA channel when potassium and sodium ions are considered and their distributions inside the filter are simulated. Our study also shows that the reaction field effect, explicitly accounted for through image charge approximation in the ICSM model, is necessary in reproducing the correct selectivity property of the potassium channels.

Defects in liquid crystals are of great practical importance and theoretical interest. Despite tremendous efforts, predicting the location and transition of defects under various topological constraint and external field remains to be a challenge. We investigate defect patterns of nematic liquid crystals confined in three-dimensional spherical droplet and two-dimensional disk under different boundary conditions, within the Landau-de Gennes model. We implement a spectral method that numerically solves the Landau-de Gennes model with high accuracy, which allows us to study the detailed static structure of defects. We observe five types of defect structures. Among them the 1/2-disclination lines are the most stable structure at low temperature. Inspired by numerical results, we obtain the profile of disclination lines analytically. Moreover, the connection and difference between defect patterns under the Landau-de Gennes model and the Oseen-Frank model are discussed. Finally, three conjectures are made to summarize some important characteristics of defects in the Landau-de Gennes theory. This work is a continuing effort to deepen our understanding on defect patterns in nematic liquid crystals.

An efficient and accurate numerical scheme is proposed for solving the transverse electric (TE) mode electromagnetic (EM) propagation problem in two-dimensional earth. The scheme is based on the alternating direction finite-difference time-domain (ADI-FDTD) method. Unlike the conventional upward continuation approach for the earth-air interface, an integral formulation for the interface boundary is developed and it is effectively incorporated to the ADI solver. Stability and convergence analysis together with an error estimate are presented. Numerical simulations are carried out to validate the proposed method, and the advantage of the present method over the popular Du-Fort-Frankel scheme is clearly demonstrated. Examples of the electromagnetic field propagation in the ground with anomaly further verify the effectiveness of the proposed scheme.

In order to solve the partial differential equations that arise in the Hartree- Fock theory for diatomicmolecules and inmolecular theories that include electron correlation, one needs efficient methods for solving partial differential equations. In this article, we present numerical results for a two-variablemodel problem of the kind that arises when one solves the Hartree-Fock equations for a diatomic molecule. We compare results obtained using the spline collocation and domain decomposition methods with third-order Hermite splines to results obtained using the more-established finite difference approximation and the successive over-relaxation method. The theory of domain decomposition presented earlier is extended to treat regions that are divided into an arbitrary number of subregions by families of lines parallel to the two coordinate axes. While the domain decomposition method and the finite difference approach both yield results at the micro-Hartree level, the finite difference approach with a 9- point difference formula produces the same level of accuracy with fewer points. The domain decompositionmethod has the strength that it can be applied to problemswith a large number of grid points. The time required to solve a partial differential equation for a fine grid with a large number of points goes down as the number of partitions increases. The reason for this is that the length of time necessary for solving a set of linear equations in each subregion is very much dependent upon the number of equations. Even though a finer partition of the region has more subregions, the time for solving the set of linear equations in each subregion is very much smaller. This feature of the theory may well prove to be a decisive factor for solving the two-electron pair equation, which – for a diatomic molecule – involves solving partial differential equations with five independent variables. The domain decomposition theory also makes it possible to study complex molecules by dividing them into smaller fragments that are calculated independently. Since the domain decomposition approachmakes it possible to decompose the variable space into separate regions in which the equations are solved independently, this approach is well-suited to parallel computing.

Arterial diseases such as aneurysm and stenosis may result from the mechanical and/or morphological change of an arterial wall structure and correspondingly altered hemodynamics. The development of a 3D computational model of blood flow can be useful to study the hemodynamics in major blood vessels and may provide an insight into the noninvasive technique to detect arterial diseases in early stage. In this paper, we present a three-dimensional model of blood flow in the aorta, which is based on the immersed boundary method to describe the interaction of blood flow with the aortic wall. Our simulation results show that the hysteresis loop is evident in the pressure-diameter relationship of the normal aorta when the arterial wall is considered to be viscoelastic. In addition, it is shown that flow patterns and pressure distributions are altered in response to the change of aortic morphology.