Accuracy and speed in computing the Chebyshev collocation derivative

We studied several algorithms for computing the Chebyshev spectral derivative and compare their roundoff error. For a large number of collocation points, the elements of the Chebyshev differentiation matrix, if constructed in the usual way, are not computed accurately. A subtle cause is is found to account for the poor accuracy when computing the derivative by the matrix-vector multiplication method. Methods for accurately computing the elements of the matrix are presented, and we find that if the entities of the matrix are computed accurately, the roundoff error of the matrix-vector multiplication is as small as that of the transform-recursion algorithm. Results of CPU time usage are shown for several different algorithms for computing the derivative by the Chebyshev collocation method for a wide variety of two-dimensional grid sizes on both an IBM and a Cray 2 computer. We found that which algorithm is fastest on a particular machine depends not only on the grid size, but also on small details of the computer hardware as well. For most practical grid sizes used in computation, the even-odd decomposition algorithm is found to be faster than the transform-recursion method

Spectral simulation of unsteady compressible flow past a circular cylinder

An unsteady compressible viscous wake flow past a circular cylinder was successfully simulated using spectral methods. A new approach in using the Chebyshev collocation method for periodic problems is introduced. It was further proved that the eigenvalues associated with the differentiation matrix are purely imaginary, reflecting the periodicity of the problem. It was been shown that the solution of a model problem has exponential growth in time if improper boundary conditions are used. A characteristic boundary condition, which is based on the characteristics of the Euler equations of gas dynamics, was derived for the spectral code. The primary vortex shedding frequency computed agrees well with the results in the literature for Mach = 0.4, Re = 80. No secondary frequency is observed in the power spectrum analysis of the pressure data

High-resolution simulations and modeling of reshocked single-mode Richtmyer-Meshkov instability: Comparison to experimental data and to amplitude growth model predictions

The reshocked single-mode Richtmyer-Meshkov instability is simulated in two spatial dimensions using the fifth- and ninth-order weighted essentially nonoscillatory shock-capturing method with uniform spatial resolution of 256 points per initial perturbation wavelength. The initial conditions and computational domain are modeled after the single-mode, Mach 1.21 air(acetone)/SF6 shock tube experiment of Collins and Jacobs [J. Fluid Mech. 464, 113 (2002)]. The simulation densities are shown to be in very good agreement with the corrected experimental planar laser-induced fluorescence images at selected times before reshock of the evolving interface. Analytical, semianalytical, and phenomenological linear and nonlinear, impulsive, perturbation, and potential flow models for single-mode Richtmyer-Meshkov unstable perturbation growth are summarized. The simulation amplitudes are shown to be in very good agreement with the experimental data and with the predictions of linear amplitude growth models for small times, and with those of nonlinear amplitude growth models at later times up to the time at which the driver-based expansion in the experiment (but not present in the simulations or models) expands the layer before reshock. The qualitative and quantitative differences between the fifth- and ninth-order simulation results are discussed. Using a local and global quantitative metric, the prediction of the Zhang and Sohn [Phys. Fluids 9, 1106 (1997)] nonlinear Padé model is shown to be in best overall agreement with the simulation amplitudes before reshock. The sensitivity of the amplitude growth model predictions to the initial growth rate from linear instability theory, the post-shock Atwood number and amplitude, and the velocity jump due to the passage of the shock through the interface is also investigated numerically

Physics of reshock and mixing in single-mode Richtmyer-Meshkov instability

The ninth-order weighted essentially nonoscillatory (WENO) shock-capturing method is used to investigate the physics of reshock and mixing in two-dimensional single-mode Richtmyer-Meshkov instability to late times. The initial conditions and computational domain were adapted from the Mach 1.21 air (acetone)/SF6 shock tube experiment of Collins and Jacobs [J. Fluid Mech. 464, 113 (2002)]: the growth of the bubble and spike amplitudes from fifth- and ninth-order WENO simulations of this experiment were compared to the predictions of linear and nonlinear amplitude growth models, and were shown to be in very good agreement with the experimental data prior to reshock by Latini, Schilling, and Don [Phys. Fluids 19, 024104 (2007)]. In the present investigation, the density, vorticity, baroclinic vorticity production, and simulated density Schlieren fields are first presented to qualitatively describe the reshock process. The baroclinic circulation deposition on the interface is shown to agree with the predictions of the Samtaney-Zabusky model and with linear instability theory. The time evolution of the positive and negative circulation on the interface is considered before and after reshock: it is shown that the magnitudes of the circulations are equal before as well as after reshock, until the interaction of the reflected rarefaction with the layer induces flow symmetry breaking and different evolutions of the magnitude of the positive and negative circulation. The post-reshock mixing layer growth is shown to be in generally good agreement with three models predicting linear growth for a short time following reshock. Next, a comprehensive investigation of local and global mixing properties as a function of time is performed. The distribution and amount of mixed fluid along the shock propagation direction is characterized using averaged mole fraction profiles, a fast kinetic reaction model, and mixing fractions. The modal distribution of energy in the mixing layer is quantified using the spectra of the fluctuating kinetic energy, fluctuating enstrophy, pressure variance, density variance, and baroclinic vorticity production variance. It is shown that a broad range of scales already exists prior to reshock, indicating that the single-mode Richtmyer-Meshkov instability develops nontrivial spectral content from its inception. The comparison of the spectra to the predictions of classical inertial subrange scalings in two-dimensional turbulence shows that the post-reshock spectra may be consistent with many of these scalings over wave number ranges less than a decade. At reshock, fluctuations in all fields (except for the density) are amplified across all scales. Reshock strongly amplifies the circulation, profiles, and mixing fractions, as well as the energy spectra and statistics, leading to enhanced mixing followed by a decay. The mole and mixing fraction profiles become nearly self-similar at late times following reshock; the mixing fraction exhibits an approach toward unity across the layer at the latest time, signifying nearly complete mixing of the gases. To directly quantify the amplification of fluctuations by reshock, the previously considered quantities are compared immediately after and before reshock. Finally, to investigate the decay of fluctuations in the absence of additional waves interacting with the mixing layer following reshock, the boundary condition at the end of the computational domain is changed from reflecting to outflow to allow the reflected rarefaction wave to exit the domain. It is demonstrated that the reflected rarefaction has an important role in breaking symmetry and achieving late-time statistical isotropy of the velocity field

The Chebyshev-Legendre method: Implementing Legendre methods on Chebyshev points

We present a new collocation method for the numerical solution of partial differential equations. This method uses the Chebyshev collocation points, but because of the way the boundary conditions are implemented, it has all the advantages of the Legendre methods. In particular, L2 estimates can be obtained easily for hyperbolic and parabolic problems

Secondary frequencies in the wake of a circular cylinder with vortex shedding

A detailed numerical study of two-dimensional flow past a circular cylinder at moderately low Reynolds numbers was conducted using three different numerical algorithms for solving the time-dependent compressible Navier-Stokes equations. It was found that if the algorithm and associated boundary conditions were consistent and stable, then the major features of the unsteady wake were well-predicted. However, it was also found that even stable and consistent boundary conditions could introduce additional periodic phenomena reminiscent of the type seen in previous wind-tunnel experiments. However, these additional frequencies were eliminated by formulating the boundary conditions in terms of the characteristic variables. An analysis based on a simplified model provides an explanation for this behavior

The theoretical accuracy of Runge-Kutta time discretizations for the initial boundary value problem: A careful study of the boundary error

The conventional method of imposing time dependent boundary conditions for Runge-Kutta (RK) time advancement reduces the formal accuracy of the space-time method to first order locally, and second order globally, independently of the spatial operator. This counter intuitive result is analyzed in this paper. Two methods of eliminating this problem are proposed for the linear constant coefficient case: (1) impose the exact boundary condition only at the end of the complete RK cycle, (2) impose consistent intermediate boundary conditions derived from the physical boundary condition and its derivatives. The first method, while retaining the RK accuracy in all cases, results in a scheme with much reduced CFL condition, rendering the RK scheme less attractive. The second method retains the same allowable time step as the periodic problem. However it is a general remedy only for the linear case. For non-linear hyperbolic equations the second method is effective only for for RK schemes of third order accuracy or less. Numerical studies are presented to verify the efficacy of each approach

High Order Numerical Methods for the Investigation of the Two Dimensional Richtmyer-Meshkov Instability

For flows that contain significant structure, high order schemes offer large advantages over low order schemes. Fundamentally, the reason comes from the truncation error of the differencing operators. If one examines carefully the expression for the truncation error, one will see that for a fixed computational cost that the error can be made much smaller by increasing the numerical order than by increasing the number of grid points. One can readily derive the following expression which holds for systems dominated by hyperbolic effects and advanced explicitly in time: flops = const * p{sup 2} * k{sup (d+1)(p+1)/p}/E{sup (d+1)/p} where flops denotes floating point operations, p denotes numerical order, d denotes spatial dimension, where E denotes the truncation error of the difference operator, and where k denotes the Fourier wavenumber. For flows that contain structure, such as turbulent flows or any calculation where, say, vortices are present, there will be significant energy in the high values of k. Thus, one can see that the rate of growth of the flops is very different for different values of p. Further, the constant in front of the expression is also very different. With a low order scheme, one quickly reaches the limit of the computer. With the high order scheme, one can obtain far more modes before the limit of the computer is reached. Here we examine the application of spectral methods and the Weighted Essentially Non-Oscillatory (WENO) scheme to the Richtmyer-Meshkov Instability. We show the intricate structure that these high order schemes can calculate and we show that the two methods, though very different, converge to the same numerical solution indicating that the numerical solution is very likely physically correct

Single-cell profiling reveals distinct immune response landscapes in tuberculous pleural effusion and non-TPE

BackgroundTuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb) and remains a major health threat worldwide. However, a detailed understanding of the immune cells and inflammatory mediators in Mtb-infected tissues is still lacking. Tuberculous pleural effusion (TPE), which is characterized by an influx of immune cells to the pleural space, is thus a suitable platform for dissecting complex tissue responses to Mtb infection.MethodsWe employed singe-cell RNA sequencing to 10 pleural fluid (PF) samples from 6 patients with TPE and 4 non-TPEs including 2 samples from patients with TSPE (transudative pleural effusion) and 2 samples with MPE (malignant pleural effusion).ResultCompared to TSPE and MPE, TPE displayed obvious difference in the abundance of major cell types (e.g., NK, CD4+T, Macrophages), which showed notable associations with disease type. Further analyses revealed that the CD4 lymphocyte population in TPE favored a Th1 and Th17 response. Tumor necrosis factors (TNF)-, and XIAP related factor 1 (XAF1)-pathways induced T cell apoptosis in patients with TPE. Immune exhaustion in NK cells was an important feature in TPE. Myeloid cells in TPE displayed stronger functional capacity for phagocytosis, antigen presentation and IFN-γ response, than TSPE and MPE. Systemic elevation of inflammatory response genes and pro-inflammatory cytokines were mainly driven by macrophages in patients with TPE.ConclusionWe provide a tissue immune landscape of PF immune cells, and revealed a distinct local immune response in TPE and non-TPE (TSPE and MPE). These findings will improve our understanding of local TB immunopathogenesis and provide potential targets for TB therapy