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On Simplified Numerical Turbulence Models in Test-particle Simulations

Using the conventional approach of superposing plane waves, it is not possible to create a strictly isotropic turbulent magnetic field structure that obeys all physical constraints, which are (i) equal mean of all magnetic field components; (ii) isotropy of the wave vectors; and (iii) vanishing divergence of the magnetic field. Such magnetic fields are widely implemented in test-particle Monte-Carlo simulations, which are used to obtain (i) scattering mean free paths of charged particles; (ii) field line diffusion coefficients. It is shown that, while the turbulent magnetic field strength plays an important role for the results, such does not seem to be the case for a non-zero magnetic field divergence and/or the isotropy of the wave vectors.

physics.comp-ph↗

A coarse-grid projection method for accelerating incompressible flow computations

We present a coarse-grid projection (CGP) method for accelerating incompressible flow computations, which is applicable to methods involving Poisson equations as incompressibility constraints. The CGP methodology is a modular approach that facilitates data transfer with simple interpolations and uses black-box solvers for the Poisson and advection-diffusion equations in the flow solver. After solving the Poisson equation on a coarsened grid, an interpolation scheme is used to obtain the fine data for subsequent time stepping on the full grid. A particular version of the method is applied here to the vorticity-stream function, primitive variable, and vorticity-velocity formulations of incompressible Navier-Stokes equations. We compute several benchmark flow problems on two-dimensional Cartesian and non-Cartesian grids, as well as a three-dimensional flow problem. The method is found to accelerate these computations while retaining a level of accuracy close to that of the fine resolution field, which is significantly better than the accuracy obtained for a similar computation performed solely using a coarse grid. A linear acceleration rate is obtained for all the cases we consider due to the linear-cost elliptic Poisson solver used, with reduction factors in computational time between 2 and 42. The computational savings are larger when a suboptimal Poisson solver is used. We also find that the computational savings increase with increasing distortion ratio on non-Cartesian grids, making the CGP method a useful tool for accelerating generalized curvilinear incompressible flow solvers.

physics.flu-dyn↗

Computation of frequency responses for linear time-invariant PDEs on a compact interval

We develop mathematical framework and computational tools for calculating frequency responses of linear time-invariant PDEs in which an independent spatial variable belongs to a compact interval. In conventional studies this computation is done numerically using spatial discretization of differential operators in the evolution equation. In this paper, we introduce an alternative method that avoids the need for finite-dimensional approximation of the underlying operators in the evolution model. This method recasts the frequency response operator as a two point boundary value problem and uses state-of-the-art automatic spectral collocation techniques for solving integral representations of the resulting boundary value problems with accuracy comparable to machine precision. Our approach has two advantages over currently available schemes: first, it avoids numerical instabilities encountered in systems with differential operators of high order and, second, it alleviates difficulty in implementing boundary conditions. We provide examples from Newtonian and viscoelastic fluid dynamics to illustrate utility of the proposed method.

physics.comp-ph↗

Stochastic superparameterization in quasigeostrophic turbulence

In this article we expand and develop the authors' recent proposed methodology for efficient stochastic superparameterization (SP) algorithms for geophysical turbulence. Geophysical turbulence is characterized by significant intermittent cascades of energy from the unresolved to the resolved scales resulting in complex patterns of waves, jets, and vortices. Conventional SP simulates large scale dynamics on a coarse grid in a physical domain, and couples these dynamics to high-resolution simulations on periodic domains embedded in the coarse grid. Stochastic SP replaces the nonlinear, deterministic eddy equations on periodic embedded domains by quasilinear stochastic approximations on formally infinite embedded domains. The result is a seamless algorithm which never uses a small scale grid and is far cheaper than conventional SP, but with significant success in difficult test problems. Various design choices in the algorithm are investigated in detail here, including decoupling the timescale of evolution on the embedded domains from the length of the time step used on the coarse grid, and sensitivity to certain assumed properties of the eddies (e.g. the shape of the assumed eddy energy spectrum). The different design choices are compared and contrasted on a stringent test suite for quasigeostrophic turbulence involving two-layer dynamics on a beta-plane forced by an imposed background shear. The algorithms developed are expected to be particularly useful in providing accurate and efficient stochastic parameterizations for use in ensemble-based state estimation and prediction.

physics.comp-ph↗

Hydrodynamic Shock Wave Studies within a Kinetic Monte Carlo Approach

Kinetic approaches are routinely employed to simulate the dynamics of systems that are too rarified to be described by the Navier-Stokes equations. However, generally they are far too computationally expensive to be applied for systems that are governed by continuum hydrodynamics. In this paper, we introduce a massively parallelized test-particle based kinetic Monte Carlo code that is capable of modeling the phase space evolution of an arbitrarily sized system that is free to move in and out of the continuum limit. Using particle mean free paths which are small with respect to the characteristic length scale of the simulated system, we retrieve continuum behavior, while non-equilibrium effects are observed when the mean free path is increased. To demonstrate the ability of our code to reproduce hydrodynamic solutions, we apply a test-suite of classic hydrodynamic shock problems. Simulations using tens of millions of test-particles are found to reproduce the analytical solutions well.

physics.flu-dyn↗

Jacobian-free Newton-Krylov methods with GPU acceleration for computing nonlinear ship wave patterns

The nonlinear problem of steady free-surface flow past a submerged source is considered as a case study for three-dimensional ship wave problems. Of particular interest is the distinctive wedge-shaped wave pattern that forms on the surface of the fluid. By reformulating the governing equations with a standard boundary-integral method, we derive a system of nonlinear algebraic equations that enforce a singular integro-differential equation at each midpoint on a two-dimensional mesh. Our contribution is to solve the system of equations with a Jacobian-free Newton-Krylov method together with a banded preconditioner that is carefully constructed with entries taken from the Jacobian of the linearised problem. Further, we are able to utilise graphics processing unit acceleration to significantly increase the grid refinement and decrease the run-time of our solutions in comparison to schemes that are presently employed in the literature. Our approach provides opportunities to explore the nonlinear features of three-dimensional ship wave patterns, such as the shape of steep waves close to their limiting configuration, in a manner that has been possible in the two-dimensional analogue for some time.

physics.flu-dyn↗

CRKSPH - A Conservative Reproducing Kernel Smoothed Particle Hydrodynamics Scheme

We present a formulation of smoothed particle hydrodynamics (SPH) that utilizes a first-order consistent reproducing kernel, a smoothing function that exactly interpolates linear fields with particle tracers. Previous formulations using reproducing kernel (RK) interpolation have had difficulties maintaining conservation of momentum due to the fact the RK kernels are not, in general, spatially symmetric. Here, we utilize a reformulation of the fluid equations such that mass, linear momentum, and energy are all rigorously conserved without any assumption about kernel symmetries, while additionally maintaining approximate angular momentum conservation. Our approach starts from a rigorously consistent interpolation theory, where we derive the evolution equations to enforce the appropriate conservation properties, at the sacrifice of full consistency in the momentum equation. Additionally, by exploiting the increased accuracy of the RK method's gradient, we formulate a simple limiter for the artificial viscosity that reduces the excess diffusion normally incurred by the ordinary SPH artificial viscosity. Collectively, we call our suite of modifications to the traditional SPH scheme Conservative Reproducing Kernel SPH, or CRKSPH. CRKSPH retains many benefits of traditional SPH methods (such as preserving Galilean invariance and manifest conservation of mass, momentum, and energy) while improving on many of the shortcomings of SPH, particularly the overly aggressive artificial viscosity and zeroth-order inaccuracy. We compare CRKSPH to two different modern SPH formulations (pressure based SPH and compatibly differenced SPH), demonstrating the advantages of our new formulation when modeling fluid mixing, strong shock, and adiabatic phenomena.

physics.comp-ph↗

A positivity preserving and conservative variational scheme for phase-field modeling of two-phase flows

We present a positivity preserving variational scheme for the phase-field modeling of incompressible two-phase flows with high density ratio and using meshes of arbitrary topology. The variational finite element technique relies on the Allen-Cahn phase-field equation for capturing the phase interface on a fixed mesh with a mass conservative and energy-stable discretization. Mass is conserved by enforcing a Lagrange multiplier which has both temporal and spatial dependence on the solution of the phase-field equation. The spatial part of the Lagrange multiplier is written as a mid-point approximation to make the scheme energy-stable. This enables us to form a conservative, energy-stable and positivity preserving scheme. The proposed variational technique reduces spurious and unphysical oscillations in the solution while maintaining second-order spatial accuracy. To model a generic two-phase free-surface flow, we couple the Allen-Cahn phase-field equation with the Navier-Stokes equations. Comparison of results between standard linear stabilized finite element method and the present variational formulation shows a remarkable reduction of oscillations in the solution while retaining the boundedness of the phase-indicator field. We perform a standalone test to verify the accuracy and stability of the Allen-Cahn two-phase solver. Standard two-phase flow benchmarks such as Laplace-Young law and sloshing tank problem are carried out to assess the convergence and accuracy of the coupled Navier-Stokes and Allen-Cahn solver. Two- and three-dimensional dam break problem are then solved to assess the scheme for the problem with topological changes of the air-water interface on unstructured meshes. Finally, we demonstrate the phase-field solver for a practical problem of wave-structure interaction in offshore engineering using general three-dimensional unstructured meshes.

physics.flu-dyn↗

A unified Quasi-Spectral Viscosity (QSV) approach to shock capturing and large-eddy simulation

The Quasi-Spectral Viscosity (QSV) method is a novel closure for a high-order finite-difference discretization of the filtered compressible Navier-Stokes equations capable of unifying dynamic sub-filter scale (SFS) modeling and shock capturing under a single mathematical framework. Its innovation lies in the introduction of a physical-space implementation of a spectral-like SFS dissipation term by leveraging residuals of filter operations, achieving two goals: (1) estimating the energy of the resolved solution near the grid cutoff; (2) imposing a plateau-cusp shape to the spectral distribution of the added dissipation. The QSV approach has been tested in a variety of flows to showcase its capability to act interchangeably as: a shock capturing method, in the Shu-Osher, shock/vortex or shock/wall interactions problems; or as a SFS closure, in subsonic Taylor Green Vortex (TGV), and supersonic/hypersonic turbulent channel flows. QSV performs well compared to previous eddy-viscosity closures and shock capturing methods in such test cases. In a supersonic TGV flow, a case which exhibits shock/turbulence interactions, QSV alone outperforms the simple superposition of separate numerical treatments for SFS turbulence and shocks. QSV's combined capability of simulating shocks and turbulence independently, as well as simultaneously, effectively achieves the unification of shock capturing and Large-Eddy Simulation.

physics.flu-dyn↗

Multi-scale approach to invasion percolation of rock fracture networks

A multi-scale scheme for the invasion percolation of rock fracture networks with heterogeneous fracture aperture fields is proposed. Inside fractures, fluid transport is calculated on the finest scale and found to be localized in channels as a consequence of the aperture field. The channel network is characterized and reduced to a vectorized artificial channel network (ACN). Different realizations of ACNs are used to systematically calculate efficient apertures for fluid transport inside differently sized fractures as well as fracture intersection and entry properties. Typical situations in fracture networks are parameterized by fracture inclination, flow path length along the fracture and intersection lengths in the entrance and outlet zones of fractures. Using these scaling relations obtained from the finer scales, we simulate the invasion process of immiscible fluids into saturated discrete fracture networks, which were studied in previous works.

physics.geo-ph↗

The influence of winter convection on primary production: a parameterisation using a hydrostatic three-dimensional biogeochemical model

In the recent past observational and modelling studies have shown that the vertical displacement of water parcels, and therefore, phytoplankton particles in regions of deep-reaching convection plays a key role in late winter/early spring primary production. The underlying mechanism describes how convection cells capture living phytoplankton cells and recurrently expose them to sunlight. This study presents a parameterisation called `phytoconvection' which focuses on the influence of convection on primary production. This parameterisation was implemented into a three-dimensional physical-biogeochemical model and applied to the Northwestern European Continental Shelf and areas of the adjacent Northeast Atlantic. The simulation was compared to a `conventional' parameterisation with respect to its influence on phytoplankton concentrations during the annual cycle and its effect on the carbon cycle. The simulation using the new parameterisation showed good agreement with observation data recorded during winter, whereas the reference simulation did not capture the observed phytoplankton concentrations. The new parameterisation had a strong influence on the carbon export through the sinking of particulate organic carbon. The carbon export during late winter/early spring significantly exceeded the export of the reference run. Furthermore, a non-hydrostatic convection model was used to evaluate the major assumption of the presented parameterisation which implies the matching of the mixed layer depth with the convective mixing depth. The applied mixed layer depth criterion principally overestimates the actual convective mixing depth. However, the results showed that this assumption is reasonable during late winter, while indicating a mismatch during spring.

physics.ao-ph↗

Self-organizing magnetic beads for biomedical applications

In the field of biomedicine magnetic beads are used for drug delivery and to treat hyperthermia. Here we propose to use self-organized bead structures to isolate circulating tumor cells using lab-on-chip technologies. Typically blood flows past microposts functionalized with antibodies for circulating tumor cells. Creating these microposts with interacting magnetic beads makes it possible to tune the geometry in size, position and shape. We developed a simulation tool that combines micromagnetics and discrete particle dynamics, in order to design micropost arrays made of interacting beads. The simulation takes into account the viscous drag of the blood flow, magnetostatic interactions between the magnetic beads and gradient forces from external aligned magnets. We developed a particle-particle particle-mesh method for effective computation of the magnetic force and torque acting on the particles.

physics.bio-ph↗

Analyzing and Modeling the Performance of the HemeLB Lattice-Boltzmann Simulation Environment

We investigate the performance of the HemeLB lattice-Boltzmann simulator for cerebrovascular blood flow, aimed at providing timely and clinically relevant assistance to neurosurgeons. HemeLB is optimised for sparse geometries, supports interactive use, and scales well to 32,768 cores for problems with ~81 million lattice sites. We obtain a maximum performance of 29.5 billion site updates per second, with only an 11% slowdown for highly sparse problems (5% fluid fraction). We present steering and visualisation performance measurements and provide a model which allows users to predict the performance, thereby determining how to run simulations with maximum accuracy within time constraints.

physics.comp-ph↗

On a difficulty in the formulation of initial and boundary conditions for eigenfunction expansion solutions for the start-up of fluid flow

Most mathematics and engineering textbooks describe the process of "subtracting off" the steady state of a linear parabolic partial differential equation as a technique for obtaining a boundary-value problem with homogeneous boundary conditions that can be solved by separation of variables (i.e., eigenfunction expansions). While this method produces the correct solution for the start-up of the flow of, e.g., a Newtonian fluid between parallel plates, it can lead to erroneous solutions to the corresponding problem for a class of non-Newtonian fluids. We show that the reason for this is the non-rigorous enforcement of the start-up condition in the textbook approach, which leads to a violation of the principle of causality. Nevertheless, these boundary-value problems can be solved correctly using eigenfunction expansions, and we present the formulation that makes this possible (in essence, an application of Duhamel's principle). The solutions obtained by this new approach are shown to agree identically with those obtained by using the Laplace transform in time only, a technique that enforces the proper start-up condition implicitly (hence, the same error cannot be committed).

physics.flu-dyn↗

Large-eddy simulations of turbulent flow for grid-to-rod fretting in nuclear reactors

The grid-to-rod fretting (GTRF) problem in pressurized water reactors is a flow-induced vibration problem that results in wear and failure of the fuel rods in nuclear assemblies. In order to understand the fluid dynamics of GTRF and to build an archival database of turbulence statistics for various configurations, implicit large-eddy simulations of time-dependent single-phase turbulent flow have been performed in 3x3 and 5x5 rod bundles with a single grid spacer. To assess the computational mesh and resolution requirements, a method for quantitative assessment of unstructured meshes with no-slip walls is described. The calculations have been carried out using Hydra-TH, a thermal-hydraulics code developed at Los Alamos for the Consortium for Advanced Simulation of Light water reactors, a United States Department of Energy Innovation Hub. Hydra-TH uses a second-order implicit incremental projection method to solve the single-phase incompressible Navier-Stokes equations. The simulations explicitly resolve the large scale motions of the turbulent flow field using first principles and rely on a monotonicity-preserving numerical technique to represent the unresolved scales. Each series of simulations for the 3x3 and 5x5 rod-bundle geometries is an analysis of the flow field statistics combined with a mesh-refinement study and validation with available experimental data. Our primary focus is the time history and statistics of the forces loading the fuel rods. These hydrodynamic forces are believed to be the key player resulting in rod vibration and GTRF wear, one of the leading causes for leaking nuclear fuel which costs power utilities millions of dollars in preventive measures. We demonstrate that implicit large-eddy simulation of rod-bundle flows is a viable way to calculate the excitation forces for the GTRF problem.

physics.flu-dyn↗

Approximate deconvolution large eddy simulation of a stratified two-layer quasigeostrophic ocean model

We present an approximate deconvolution (AD) large eddy simulation (LES) model for the two-layer quasigeostrophic equations. We applied the AD-LES model to mid-latitude two-layer square oceanic basins, which are standard prototypes of more realistic stratified ocean dynamics models. Two spatial filters were investigated in the AD-LES model: a tridiagonal filter and an elliptic differential filter. A sensitivity analysis of the AD-LES results with respect to changes in modeling parameters was performed. The results demonstrate that the AD-LES model used in conjunction with the tridiagonal or differential filters provides additional dissipation to the system, allowing the use of a smaller eddy viscosity coefficient. Changing the spatial filter makes a significant difference in characterizing the effective dissipation in the model. It was found that the tridiagonal filter introduces the least amount of numerical dissipation into the AD-LES model. The differential filter, however, added a significant amount of numerical dissipation to the AD-LES model for large values of the filter width. All AD-LES models reproduced the DNS results at a fraction of the cost within a reasonable level of accuracy.

physics.ao-ph↗

Seeding optimization for instantaneous volumetric velocimetry. Application to a jet in crossflow

Every volumetric velocimetry measurements based on tracer (particles, bubbles, etc.) detection can be strongly influenced by the optical screening phenomenon. It has to be taken into account when the the statistical properties associated to the performances of the particle detection and tracking algorithms are significantly affected. It leads to a maximum concentration of particles in the images thus limiting the final spatial resolution of the instantaneous three-dimensional three-components (3D3C) velocity fields. A volumetric velocimetry system based on Defocused Digital Particle Image Velocimetry is used to show that above a critical visual concentration of particles in the images, the concentration and accuracy of the final instantaneous raw velocity vector field drop. The critical concentration depends on physical parameters as well as on the processing algorithms. Three distinct regimes are identified. In the first regime, the concentration is well adapted to volumetric velocimetry, the largest concentration being optimal to maximize the number of valid velocity vectors. In the second regime, the performances of the detection and tracking algorithms are no longer optimal. Finally, the third regime is strongly influenced by optical screening. A rigorous methodology is proposed to optimize volumetric measurements taking into account the system specifications (pixel size, focal length, system magnification, etc.). An optimal particle concentration of 0.045 particles/pixel (ppp) is found. A relationship between the imaged concentration and the optimal final spatial resolution for fully interpolated instantaneous velocity field is obtained. The present study can be used as a guideline to achieve the measurement of instantaneous three-dimensional velocity fields with a good spatial resolution. It is finally successfully applied to a complex 3D flow test case: a jet in crossflow.

physics.flu-dyn↗

A stability condition for turbulence model: From EMMS model to EMMS-based turbulence model

The closure problem of turbulence is still a challenging issue in turbulence modeling. In this work, a stability condition is used to close turbulence. Specifically, we regard single-phase flow as a mixture of turbulent and non-turbulent fluids, separating the structure of turbulence. Subsequently, according to the picture of the turbulent eddy cascade, the energy contained in turbulent flow is decomposed into different parts and then quantified. A turbulence stability condition, similar to the principle of the energy-minimization multi-scale (EMMS) model for gas-solid systems, is formulated to close the dynamic constraint equations of turbulence, allowing the heterogeneous structural parameters of turbulence to be optimized. We call this model the `EMMS-based turbulence model', and use it to construct the corresponding turbulent viscosity coefficient. To validate the EMMS-based turbulence model, it is used to simulate two classical benchmark problems, lid-driven cavity flow and turbulent flow with forced convection in an empty room. The numerical results show that the EMMS-based turbulence model improves the accuracy of turbulence modeling due to it considers the principle of compromise in competition between viscosity and inertia.

physics.flu-dyn↗