Journal Pre-proof

Scour modeling based on immersed boundary method: A pathway to

practical use of three-dimensional scour models

Yalan Song, Yuncheng Xu, Hassan Ismail, Xiaofeng Liu

PII: S0378-3839(21)00180-0
DOI: https://doi.org/10.1016/j.coastaleng.2021.104037
Reference: CENG 104037

To appear in: Coastal Engineering

Received date : 18 May 2021

Revised date : 3 October 2021
Accepted date : 19 October 2021

Please cite this article as: Y. Song, Y. Xu, H. Ismail et al., Scour modeling based on immersed
boundary method: A pathway to practical use of three-dimensional scour models. Coastal
Engineering (2021), doi: https://doi.org/10.1016/j.coastaleng.2021.104037.

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Scour modeling based on immersed boundary method:

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a pathway to practical use of three-dimensional scour
models
Yalan Songa , Yuncheng Xub , Hassan Ismailc , Xiaofeng Liud
a
Department of Civil and Environmental Engineering, Pennsylvania State University, 406 Sackett
Building, University Park, State College, 16802, PA, United States
b
College of Water Resources and Civil Engineering, China Agricultural
University, Beijing, 100083, China
c
d
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Seamon Whiteside and Associates, 508 Rhett Street, Greenville, 29601, United States
Department of Civil and Environmental Engineering, Institute of Computational and Data
Science, Pennsylvania State University, 223B Sackett Building, University Park, State
College, 16802, PA, United States

Abstract
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Local scour around structures is an important hydraulic phenomenon that in-
volves multiple coupled physical processes, including turbulent flow, sediment
transport, and the evolution of erodible bed. This paper presents a new three-
dimensional (3D) scour model, ibScourFoam, which is based on an immersed
boundary method. This model is capable of dealing with scour around complex
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structures and thus it paves the way for practical use of 3D scour models. A spe-
cial wall function has been developed to overcome the non-smoothness problem
of wall shear stress in previous immersed boundary methods. Smooth and accu-
rate wall shear is of critical importance for successful simulation of scour. The
model was validated against cases reported in the literature and one flume ex-
periment conducted in this work. The validation case of flow and scour around
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a vertical pile was reproduced well by our model. The flume experiment is for
scour around a partially-buried, horizontal cylinder placed on a foundation. The

Preprint submitted to Coastal Engineering October 3, 2021

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horizontal cylinder is of finite length and the scour is initiated by flow contraction.

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The model revealed the distinct stages of scour in the experiment. The complex
process of undermining and exposure of initially buried cylinder and foundation
was captured well by the model.
Keywords:
Hydrodynamics, wall shear stress, sediment transport, scour, complex structures

1. Introduction
1

3
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Local scour, induced by accelerated flow field and sediment transport around
coastal and riverine structures, is a common phenomenon with great importance
4 for engineering practice. For example, surveys after major Tsunami and Hur-
5 ricanes have revealed that a major cause of structural failure is foundation scour
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6 (FEMA, 2011; Bricker et al., 2012; Tonkin et al., 2013). In 2014, U.S. National In-
7 stitute of Standard and Technology (NIST) identified the erosion and scour around
8 foundations as a key factor for infrastructure resilience against extreme coastal in-
9 undation events (Coulbourne et al., 2014). The severity and extent of scour are
usually estimated with formulas in design guidelines such as U.S. Federal High-
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11 way Administration’s Hydraulic Engineering Circular-18 (Arneson et al., 2012).

12 Most local scour formulas are of empirical nature. The research and practice
13 communities have long desired to have more reliable and deterministic means to
14 predict the hydrodynamics and morphodynamics that govern the scour process.
15 High-fidelity computational modeling is one of the increasingly popular means
16 thanks to the advancements in computing techniques and power. This paper de-
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17 scribes and demonstrates one such model which has the potential to handle scour
18 around complex structures, a difficult task for many existing models.

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19 Since the 1970s, many numerical scour and sediment transport models have

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20 been developed. They can be classified into one-dimensional (1D) models, two-
21 dimensional (2D) models, and three-dimensional (3D) models. One-dimensional
22 models are not adequate for the simulation of local scour. Some 2D scour models
23 solve 2D Reynolds-Averaged Navier-Stokes equations (RANS) for 2D scour prob-
24 lems, such as scour under pipelines or scour due to submerged wall jets (Liang
25 et al., 2005; Fuhrman et al., 2014; Larsen et al., 2016; Yan et al., 2020). The other
26

27

28
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2D scour models solve the depth-averaged shallow water equations (Liu et al.,
2008, 2016). However, vertical fluid motion is very prominent in the vicinity of
structures and is a primary contributor to local scour. Thus, depth-averaged mod-
29 els should theoretically not be used for local scour modeling. In practice, they
30 are often used anyway to obtain flow information, such as velocity magnitude and
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31 water depth, to be plugged into empirical formulas to estimate scour depth.
32 Due to the three-dimensional nature of local scour, both hydrodynamically and
33 morphodynamically (Fredsoe and Sumer, 2002), 3D models are naturally needed.
34 A typical 3D scour model consists of at least three parts, namely a hydrodynamic
35 solver to obtain the turbulent flow field of waves and currents, a sediment trans-
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36 port solver to calculate sediment fluxes, and a bed evolution solver to update the
37 bed position due to sediment motion (Figure 1). For practical purposes, the hy-
38 drodynamic solver usually uses the Reynolds-Averaged Navier-Stokes equations
39 (RANS) approach to model turbulent flow, although some models also adopt com-
40 putationally more expensive approaches such as Large Eddy Simulation (LES).
41 The sediment transport solver calculates the bed-load transport rate with empir-
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42 ical formulas and the suspended load transport rate with an advection-diffusion
43 equation. The bed evolution part solves the bed sediment mass balance equation,

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44 i.e., the Exner equation, usually in conjunction with a sand slide treatment to en-

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45 sure the resulted bed slope does not exceed the angle of repose (Roulund et al.,
46 2005; Liang et al., 2005; Khosronejad et al., 2011; Jacobsen, 2015; Song et al.,
47 2020b).

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Figure 1: Scheme diagram of a scour model: qb is the bed-load transport rate, D
is the deposition rate, and E is the entrainment rate.

48 Computationally, one key difficulty in all 3D scour models is how to track

49 the interface between fluid and sediment. Several approaches have been pro-
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50 posed in the literature. One approach is the Arbitrary Lagrangian-Eulerian (ALE)

51 method (Chen, 2006; Liu and Garcı́a, 2008; Liu et al., 2016; Song et al., 2020b).
52 In this approach, the bed surface is a boundary of the computational domain for
53 the flow field. As the bed evolves, the boundary and computational mesh deform
54 accordingly. Though simple, this approach is very limited for practical use. The
55 deformation of mesh may cause excessive stretching and compression such that
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56 mesh quality deteriorates and simulation fails. In addition, the ALE approach can
57 only be used for very simple geometry, such as a vertical pile (Figure 2a) (Roulund
58 et al., 2005; Liu and Garcı́a, 2008; Zhao et al., 2010; Baykal et al., 2017). Fig-

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59 ure 2b shows the difficulty of the ALE approach for simulating a typical pier

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60 foundation with a cap and sub-piles. During a storm event, the foundation may
61 be exposed or re-buried due to scour and sedimentation. Complicated geometric
62 operations have to be performed as the bed boundary sweeps through the foun-
63 dation. It is computationally challenging to use this approach to track the eroded
64 bed and its interaction with the structure.

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(a) cylindrical pier (b) Complex pier with a foundation
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Figure 2: Schematic diagram of the ALE approach for local scour: (a) simple
vertical pier, (b) complex pier with a cap and sub-piles.

65 The second approach to bed tracking is the two-phase Eulerian-Eulerian model (Link
66 et al., 2012; Nagel et al., 2020). Both water and sediment are modeled as con-
67 tinuous phases, whose interactions can be added into their respective governing
equations. One example is the sedFoam model (Cheng et al., 2017). It is built
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69 with the open-source computational physics platform OpenFOAM (OpenFOAM

70 Foundation, 2018). With this approach, the bed interface is implicitly modeled

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71 and its interaction with structures can be captured without complicated geomet-

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72 ric operations. This method has shown good performance in simulating scour
73 processes (Cheng et al., 2017; Chauchat et al., 2017; Nagel et al., 2020). How-
74 ever, this approach heavily relies on the parameterization of non-Newtonian fluid
75 behavior of sediment-water mixture, a field still in need of more research.
76 The third approach to bed tracking is the immersed boundary (IB) method,
77 which is used in this work. The IB method was first proposed in Peskin (1973)
78

79

80
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to simulate blood flow in hearts and has flourished since then in many fields of
fluid dynamics. The basic idea of the IB method is to use a fixed background
mesh which does not conform to a solid boundary. Instead, the boundary is “im-
81 mersed” within the simulation domain and its effect on the flow is enforced im-
82 plicitly (Tamaki et al., 2017; Capizzano, 2011; Zhou, 2017; Song et al., 2020a;
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83 Xu and Liu, 2021). In the context of scour modeling, the bed is treated as an
84 immersed boundary and can move as scour hole develops. The bed surface is in-
85 dependent of the background mesh and thus the moving bed does not cause any
86 geometric change.
87 The 3D scour model presented in this paper adopts a sharp-interface immersed
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88 boundary method. The bed is represented by an unstructured triangular surface

89 mesh embedded in the background mesh (Afzal et al., 2015, 2020; Ahmad et al.,
90 2020; Khosronejad et al., 2011; Song et al., 2020a). Sediment fluxes are calcu-
91 lated on the immersed bed surface based on simulated wall shear stress. Thus,
92 it is critical to obtain accurate and smooth wall shear from the IB method. Non-
93 smoothness is often observed in simulated wall shear due to the arbitrary wall dis-
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94 tance caused by the moving boundary and the different behaviors of wall functions
95 in different sublayers of the near-wall region. Recently, two improved methods for

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96 smooth wall shear were developed in Song et al. (2020a) and Xu and Liu (2021)

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97 for k −  turbulence model. A similar method of Song et al. (2020a) was used in
98 the current 3D scour model under the framework of k − ω model. Additionally,
99 a physically-based slope-limited diffusive sand slide model is used to correct the
100 bed in areas where the slope is larger than the angle of repose (Song et al., 2020b).
101 In this paper, we firstly validated our model by simulating the flow and scour
102 around a vertical pile mounted on the bed. Then, we simulated the scour around
103

104

105
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a horizontal cylinder with a complex foundation. In the real world, the complex
foundations are very common, for example large wood debris, complex bridge
piers, and jacket structures in coastal areas. We show the model results match
106 well with experiments. In the second case, we analyzed the undermining process
107 around the foundation and how the exposure of foundation, in turns, impacts the
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108 scour process.
109 The organization of this paper is as follows. First we describe the numerical
110 methods of the 3D scour model, including the k − ω SST-SAS turbulence model,
111 the immersed boundary method, the bed morphodynamic solver, and the coupling
112 between the hydrodynamic solver and morphodynamic solver. Then, the scour
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113 model is validated against experimental data, followed by an application to scour

114 around a relatively complex structure. This paper concludes with a discussion of
115 the results and future work.

116 2. Numerical Model

The scour model, ibScourFoam, proposed in this work is implemented in

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117

118 OpenFOAM version 5.x (OpenFOAM Foundation, 2018). The immersed bound-
119 ary method part is based on the algorithm in Xu and Liu (2021), which utilizes

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120 some data structures and code functionalities in the original immersed boundary

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121 method in the foam-extend project, a branch of OpenFOAM development (Jasak
122 et al., 2014). The source code and the simulation cases used in this paper are
123 publicly available on GitHub (https://github.com/psu-efd/ibScourFoam).

124 2.1. Hydrodynamic model

125 This section first describes the 3D RANS equations and the k − ω SST-SAS
126 model for turbulence. Then, the immersed boundary method and the near-wall
127

128
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treatment are introduced.

2.1.1. Governing equations

129 The 3D incompressible Reynolds-Averaged Navier-Stokes equations can be
130 written as:
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∇·u=0 (1)

131

∂u ∇p
+ ∇ · (uu) = − + ∇ · [(ν + νt ) ∇u] (2)
∂t ρ
132 where u is the Reynolds-averaged flow velocity, p is the mean pressure, ρ is water
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133 density, ν is kinematic viscosity, and νt denotes the eddy viscosity.

134 The k − ω model has been proven to have better performance in the near-wall
135 region and numerical stability (Wilcox, 2006). In this work, the k − ω SST-SAS
136 model (Egorov and Menter, 2008) is adopted and its governing equations are:
∂k
+ ∇ · (uk) = ∇ · [(ν + αk νt ) ∇k] + Pk − Cµ kω (3)
∂t
137
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∂ω ω
+ ∇ · (uω) =∇ · [(ν + αω νt ) ∇ω] + α Pk − βω2
∂t k (4)
2 1
+ (1 − F1 ) ∇k∇ω + QS AS
αω2 ω

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138 where k denotes the turbulence kinetic energy, ω denotes the specific dissipation
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139 rate. Pk = νt S2 is the production term, S = 2Si j Si j is a scalar invariant of the
140 strain rate tensor Sij = 0.5[(∇u)i j + (∇u)i j ]. To reduce the length of the main text,
141 additional terms and coefficients in the model can be found in Appendix A.

142 2.1.2. Immersed boundary method with smooth wall shear

143 The hydrodynamic solver utilizes a background mesh that conforms to the
simulation domain including in-stream structures. However, the mobile sediment
144

145

146

147
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bed is modeled as an immersed boundary in the format of an STL (STereoLithog-
raphy) surface (Figure 3). The size of the background mesh needs to be larger than
the physical domain, especially in the vertical direction. This is to leave enough
148 room for the bed to evolve.
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Figure 3: Schematic view of a 3D background mesh and an embedded immersed

boundary for a mobile sediment bed.
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149 In the adopted IB method, three different types of cell types can be identified
150 depending on their relative position to the immersed bed surface (see Figure 4): 1)
151 the cells that intersect with the immersed boundary and have their centers located

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152 on the fluid side are identified as IB cells; 2) the cells fully on the fluid side are

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153 identified as fluid cells; and 3) the cells centered on the solid (sediment) side are
154 called solid cells. In the hydrodynamic solver, only the flow variables of fluid
155 cells are solved. Flow variables of solid cells are set to zero. For the IB cells in
156 between, the flow variables are set according to a wall model.
157 In the wall model, three different point types are specified in the near-wall
158 region as shown in Figure 4. The first point is the IB cell center; the second is the
159

160

161
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image point (IP) on the normal line to the immersed boundary that passes through
the IB cell center; the third is the hit point (HP), which is the intersection of the
normal line and the immersed boundary. The flow values at IPs are interpolated
162 from their neighboring cells.
163 The distance between an IP and the immersed boundary is set to dIP = 3 l∗ ,
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164 where l∗ is the minimum dimension of the IB cell. Through extensive experimen-
165 tation, this distance gives the most reasonable result for all test cases. Near the
166 bed, if the cells have comparable size, this distance is almost uniform. In many
167 existing methods, dIP is set to be proportional to yIB , which is the distance be-
168 tween an IB cell and the immersed boundary. However, since IB cells can have
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169 arbitrary distances to the immersed boundary and the distances change when the
170 bed is evolving, dIP in many existing methods can have arbitrary and non-uniform
171 values. One consequence is spiky wall shear stress. As will be shown next, dIP is
172 a key variable in the wall function which controls the accuracy and smoothness of
173 wall shear.
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174
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Figure 4: Schematic of cell classification in the IB method.

The wall function in the IB method is as follows. It is assumed that an IP and

175 its corresponding IB cell’s center are on the same log-law velocity profile, which
can be written as:
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176

1
u+ = ln(E 0 y+ ) (5)
κ
177 where u+ = u/uτ and y+ = yuτ /ν are the dimensionless velocity and wall distance,
178 respectively. The shear velocity is denoted as uτ and the wall shear is τ = ρu2τ . E 0
179 is a wall roughness parameter related to the roughness of the boundary.
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180 With the interpolated velocity at an IP, uIP and the distance dIP , the log-law
181 can be written as:
uIP uIP 1

= + = ln E 0 y+IP (6)
uτ yIP ν/y κ
182 From this equation, the Newton-Raphson method can be used to solve for y+IP
183 iteratively using the following formula (OpenFOAM Foundation, 2018):
y+IP,i + κyuIP /ν
y+IP,i+1 =   (7)
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1 + ln E 0 y+IP,i
184 Here i is the iteration number. Then, the shear velocity, uτ , can be calculated based
185 on the definition of y+IP .

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186 Another issue in the IB method is the velocity profile between an IB cell center

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187 and the immersed bed boundary. If the distance yIB is too small, it may create
188 numerical instability if a log-law profile is used (even if the IB cell is indeed in
189 the log-law layer). To address this, a linear velocity distribution between the IP
190 and HP is assumed for the purpose of assessing the velocity at IB (see Figure 5).
191 We found this is a good and reasonable approximation to the log-law when yIB is
192 not large (which is the case for immersed boundary methods). The slope of the
193

194

195
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linear profile is equal to the slope of the log-law profile at the IP. In essence, it
is a linear extension of the log-law velocity profile to the wall. To maintain the
same value of the shear stress on the immersed boundary (u2τ = (ν + νt )∂u /∂y),
196 the eddy viscosity is held constant between IP and HP. This approach has been
197 previously used in Tamaki et al. (2017) and Song et al. (2020a). It has shown good
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198 performance in velocity and wall shear stress predictions. Another advantage of
199 this method is that it avoids the discontinuous behavior of different wall functions
200 used in the laminar sublayer and the log-law layer.
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Figure 5: Velocity profile in the boundary layer. The dash line is the original
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profile. The solid line is the modified profile.

201 Based on the method described above, the tangential velocity, uIB,tan , at the IB
202 cell center is calculated as:
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!
∂u+
uIB,tan = uIP,tan − (yIP − yIB )uτ (8)
∂y+ IP,tan

203 where ∂u+ /∂y+ = 1/(κy+ ). The normal velocity, uIB,norm , satisfies the non-penetration
204 condition and is given as:

dIP
uIB,norm = uIP,norm (9)
dIB
p
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205 The turbulence kinetic energy, k = u2τ / Cµ , is approximately constant in the

206 near-wall region (Kalitzin et al. (2005)). Here, Cµ = 0.09. Since the eddy viscosity
207 νt = k/ω is also approximately constant between an IP and an IB cell center to

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208 maintain a constant shear stress (Tamaki et al., 2017), ωIB is also a constant in this

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209 region such that ωIB at the IB cell center can be calculated as:

v
t  2
q !2
6.0ν  k1/2 
ωIB = ωIP = ω2vis + ω2log = +   (10)
0.075y2IP Cµ1/4 κyIP
210 As a proof of the efficacy of the modified wall function described above, a 2D
211 benchmark case for the turbulence flow over a flat plate is presented in Appendix
B. The simulated wall shear and friction coefficient match well with experimental
212

213

214
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2.2. Bed morphodynamic model

215 Currently, the morphodynamic model can only simulate the bed-load. In all
216 cases shown in this paper, suspended sediment transport is insignificant. The
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217 morphodynamics is solved on a unstructured triangular mesh, which is used as
218 the immersed boundary for the flow solver. The bed-load transport rate for a flat,
219 horizontal bed is calculated by the empirical formula proposed in Engelund and
220 Fredsøe (1976),

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

 1/2 1/2
q0 18.74(θ − θc )(θ − 0.7θc ),

 if θ > θc
p =
 (11)
Rgdd 


0, if θ < θc

221 where R is the submerged specific gravity (1.65 for quartz), d is the sediment grain
222 size, θ = |τ|/(ρgRd) is the Shields number, and θc is the critical Shields number,
223 which can be calculated from the modified fit to the Shields diagram (Parker et al.,
2003)
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224

−0.6
θc0 = 0.5 × (0.22Re−0.6
p + 0.06 × 10−7.7Re p ) (12)

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225 To include the effect of local bed slope and local flow direction, the critical

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226 Shields number is adjusted by
 s 
 sin 2
φ tan2β cos φ sin β 
θc = θc0 cos β 1 − − 
 (13)
µ2s µs

227 where β is the angle of local bed slope, φ is the angle between the velocity and
228 bed slop, and µ s is the static friction coefficient.
229 The evolution of the bed elevation is then solved from the Exner equation,

230
re- (1 − n)
∂zb
∂t
= −∇ · q0
τ
|τ|
!
(14)

where zb is the bed elevation, and n is the porosity of the bed. The Exner equation
231 only considers the conservation of mass for bed sediment. It does not consider
other factors such as the stability of the granular bed if the angle exceeds the angle
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232

233 of repose. To correct that, a sand slide model must be applied. In this work, the
234 sand slide model based on slope-limited diffusion is adopted (Song et al., 2020b).

235 2.3. Hydrodynamics and morphodynamics coupling

The flow, sediment transport, and bed evolution are interdependent. Thus, a
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236

237 monolithic (fully-coupled) approach in which all of the governing equations are
238 solved simultaneously would be computationally expensive. Similar to most pre-
239 vious scour modeling work, a sequential coupling method is used (see Figure 6).
240 A fully-developed flow field is pre-simulated with an rigid bed as the initial condi-
241 tion. Then, flow and sediment transport are solved sequentially during each time
step. The wall shear stresses at HPs on the immersed boundary are calculated
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242

243 with the wall model. The HPs are not necessary at the centers of triangles of the
244 immersed bed surface mesh. Thus, an interpolation is used to get the wall shear

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245 at the triangle centers of the bed surface. From there, the sediment transport rate

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246 is calculated, and the Exner equation is solved to get the new bed elevation. Once
247 the bed surface is moved, the whole coupling loop starts again.

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Figure 6: Flow chart of the scour model

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248 For practical purpose, this sequential coupling approach is valid because sed-
249 iment transport is a very slow process, i.e., the morphodynamic time scale (tm )
250 is much larger than that of hydrodynamics (th ) (Liu and Garcı́a, 2008; Termini,
251 2011; Afzal et al., 2015). In fact, most scour models take advantage of this to
252 accelerate the simulation by using a morphological factor α:

α = th /tm , α << 1 (15)

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253 During each time step, the change of bed elevation is amplified by 1/α. The exact
254 value of α to be used may vary from case to case. A balance between computing

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255 speed and accuracy should be sought. Different values have been used previously.

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256 For example, Ponce et al. (1979) suggested the range of 0.01 ≤ α ≤ 0.05. In
257 the context of immersed boundary method, the numerical stability must also be
258 considered. In one time step, the bed elevation change at any location should not
259 exceed the size of an IB cell. This is to avoid spurious oscillations caused by the
260 direct change of a computational cell from solid to fluid (or vice versa) without
261 first transitioning to an intermediate IB cell (Kim et al., 2001; Lee et al., 2011).

262

263

264
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2.4. Code implementation

The scour model was implemented in the OpenFOAM version 5.x (Open-
FOAM Foundation, 2018) based on the algorithm of the pisoFoam solver. The
265 scour model contains three parts: the pre-processing of IB information required
by the IB method, the flow solver of pisoFoam with a new wall model described
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266

267 in the previous section, and the morphodynamic calculation. The finite volume
268 method (FVM) was used to solve the governing equations of hydrodynamics and
269 morphodynamics on unstructured meshes. The discretization schemes used for
270 simulations are listed in Table 1.
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271 3. Validation and Demonstration Cases

272 3.1. Validation case

273 This section shows a 3D validation case of flow and scour around a vertical
274 circular pile reported in Roulund et al. (2005). The flow and scour parts are val-
275 idated separately in the following. The cases shown in this paper are small-scale
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276 problems. Due to the parallel computing capability, large scale applications are
277 feasible given sufficient computing power.

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Table 1: Summary of discretisation schemes used for simulations (see Open-

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FOAM user manual for more details).

Discretisation scheme

Time scheme backward

Gradient scheme Gauss linear
U: Gauss linearUpwind grad(U)

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Divergence schemes

Laplacian scheme
k: Gauss upwind
ω: Gauss upwind
Gauss linear corrected
Interpolation scheme linear
Surface normal gradient scheme corrected
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278 3.1.1. Flow around a vertical pile mounted on a rigid bed
279 A vertical circular pile is placed on a rigid and flat bed in steady flow as shown
280 in Figure 7. The bed is modeled as an immersed boundary. The validation is
281 mainly focused on whether the model can capture the main flow features which
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282 are responsible for scour. The main features are the horseshoe vortex upstream of
283 the pile and the lee-wake vortex downstream. Two cases were validated. The first
284 is with a smooth bed and the second is with a rough bed. Experimental conditions
285 are listed in Table 2.
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Figure 7: Schematic view of flow around a vertical circular pile.

Table 2: Simulation conditions for flow around a vertical circular pile on a rigid
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bed reported in Roulund et al. (2005).

Parameters Values

Water depth H (cm) 54

Mean flow velocity U (cm/s) 32.6
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Pile diameter D (cm) 53.6

Roughness height k s (cm) 0, 1.0
Hydrodynamic time step ∆th (s) 0.005

286 Figure 8 shows the mesh used. The mesh conforms to the pile, i.e., the pile is
part of the background mesh boundary. On the other hand, the bed is modeled as
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287

288 an immersed boundary. This arrangement is optimal because the pile is stationary
289 thus not necessary to be modeled as an immersed boundary which is computa-

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290 tionally more expensive. The length, width, and height of the domain are 9D, 5D,

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291 and 1D, respectively. Here, D is the pile diameter. The mesh has about 7 million
292 cells and is refined near the cylinder, bed, and in the downstream region to better
293 capture the flow structure. The smallest cell size is approximately 1 mm near the
294 cylinder and bed. The largest cell is approximately 50 mm in size near the inlet
295 and outlet. The maximum dimensionless wall distance for the IB cells, y+IBmax , is
296 approximately 13 and 30 for the smooth and rough bed cases, respectively.

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Figure 8: Schematic view of mesh used for flow around a vertical circular pile on
a rigid bed.
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297 In addition to the immersed bed, the boundary conditions are as follows for
298 the rest of the domain, which include inlet, outlet, two sides of the channel, top
299 surface, and the pile surface:

300 1. At the inlet, profiles for velocity, k, and ω were mapped from a pre-simulated
301 channel flow with no pile.
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302 2. At the outlet, the Neumann boundary conditions were used for all flow vari-
303 ables except the pressure, which was set to zero.
304 3. The two sides were treated as symmetry boundaries.

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305 4. The shear-free rigid-lid approximation was used for the free surface.

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306 5. The pile surface was modeled as a smooth, rigid wall.

307 Figures 9 and 10 show the streamwise velocity at different elevations in the
308 plane of symmetry. The red dots and green dashed lines in the figures represent
309 the experimental measurements and numerical results, respectively, from Roulund
310 et al. (2005). The blue lines represent the results of this work. All the simulations
311 ran for at least 300 s. This is equivalent to approximately 20 flow through time
312

313

314
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which is defined as the domain length divided by the average velocity. This en-
sured the simulations reached steady state. Then, the simulations were ran for
more than 100 s (about 7 flow through time) to calculate the mean flow variables.
315 The horseshoe vortex manifests itself as the negative value of the streamwise ve-
locity (pointed to the upstream direction) near the bed (see Figures 9 and 10). The
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316

317 comparison is satisfactory and the immersed boundary method captures main flow
318 dynamics well.
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Figure 9: Streamwise veloicty, u x , in the plane of symmetry at different elevations

for the smooth, rigid bed case.
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Figure 10: Streamwise veloicty, u x , in the plane of symmetry at different eleva-

tions for the rough, rigid bed case.
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319 On the downstream side of the pile, the experimental measurement in Roulund

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320 et al. (2005) showed an anticlockwise circulation in the smooth bed case, and a
321 clockwise circulation in the rough bed case. These circulations are relatively weak
322 and are difficult to capture by numerical models. For example, the simulated cir-
323 culation in Roulund et al. (2005) was clockwise for the smooth bed case. In our
324 work, the immersed boundary method correctly captured the circulation directions
325 for both smooth and rough bed cases as shown in Figure 11. In addition, the pre-
326

327

328
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diction of the downstream velocity was improved in this work (see Figure 9). One
possible reason is that a more refined mesh was used in this work, in comparison
with only 0.2 million cells used in Roulund et al. (2005).
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(b)
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Figure 11: Velocity field in the plane of symmetry: (a) Smooth bed (b) Rough
bed.

329 Figure 12 shows the comparison of the bed shear stress amplification τ/τo
330 along the x-axis in front of the pile between simulations and the experiment for the
331 smooth bed case. The negative value is due to the horseshoe vortex which makes
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332 the shear pointing upstream. In general, the comparison is acceptable given the
333 dynamic nature of the horseshoe vortex and uncertainties in measurement data.

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334 Both simulations in this work and Roulund et al. (2005) under-predicted the mag-

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335 nitude of the bed shear stress by about 30%. The discrepancy may result from the
336 implementation of two-equation turbulence model in RANS equations that under-
337 estimates the effect of horseshoe vortex system (Khosronejad et al., 2012). It also
338 may be caused by a relatively low order numerical scheme used for the advection
339 terms.

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Figure 12: Bed shear stress amplification along the symmetry line upstream of the
pile
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340 3.1.2. Scour around a vertical circular pile

341 In this section, the scour model was validated with the experimental case
342 where a pile is mounted on erodible sediment bed (Roulund et al., 2005). The
343 flow resistance estimator in Chen et al. (2019) was used to estimate the roughness
344 height based on the shear velocity measured in the experiment. The diffusivity
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345 for the sand slide model used the same value as in Song et al. (2020b). The mor-
346 phological factor α was adjusted during the simulation because the scour process
347 happens much faster during the early stage than the later stage. Thus, α had a

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348 value 0.2 at the beginning and then was reduced to 0.05 to accelerate the simula-

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349 tion. The simulation ran for 45 mins of real time and took approximately 330 h
350 (14 days) on 80 processors Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz. The
351 flow condition and sediment properties are shown in Table 3.

Table 3: Parameters for the scour around a vertical circular pile case.

Parameters Values

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Water depth H (cm)
Mean flow velocity U (cm/s)
Pile diameter D (cm)
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46
10
Shear velocity uτ (cm/s) 2.8
Roughness height k s (cm) 0.5
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Grain size d50 (mm) 0.26
Critical Shields number for flat bed 0.022
Static friction coefficient µ s 0.63
2
Diffusivity for sand slide (m /s) 0.0005
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Hydrodynamic time step ∆th (s) 0.002

Time scale factor α 0.05 ∼ 0.2

352 Figure 13 shows the domain and mesh used for the scour simulation. The
353 domain’s length, width, and height are 16D, 10D, and 3.3D, respectively. The
354 upper part with a height of 2D is the initial fluid domain, and the lower part with
a height of 1.3D is the initial sediment domain. The mesh has about 10 million
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355

356 cells and is refined near the cylinder, bed, and the downstream part. The smallest
357 cell size is approximately 1 mm in the vicinity of the cylinder and the sediment

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358 bed. The largest cell is approximately 50 mm in size near the inlet and outlet.

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359 The maximum dimensionless wall distance for IB cells, y+IBmax , is approximately
360 130. The immersed bed surface mesh has about 60,000 triangles. The boundary
361 conditions are similar to the flow validation case.

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Figure 13: Mesh used for scour around a vertical circular pile.

362 Figure 14 shows the contours of bed elevation at four representative times
during the scour process (t = 10 s, 60 s, 150 s, and 600 s). Animations of the
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363

364 scour process can be viewed in the Supplementary Materials. The elevation is
365 made dimensionless with the pile diameter, D. The arrows show the direction of
366 the wall shear stress, as well as the direction of the bed-load flux. The reference
367 value of the arrow is the wall shear stress at the inlet, |τ0 |(= ρu2τ ).
368 The four representative scour stages revealed by our model are as follows.
369 First, the scour occurs on the two sides of the pile due to flow contraction and the
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370 horseshoe vortex. Second, the scour hole starts to expand in the upstream direc-
371 tion where the horseshoe vortex strengthens because water flows into the scour

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372 hole (Ettema et al., 2011) . During this stage, eroded sediment accumulates at the

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373 immediate downstream side of the pile. Third, the scour expands to downstream to
374 form a complete hole around the pile. The sediment accumulation downstream of
375 the pile is further washed away due to vortex shedding in the wake. And lastly, the
376 erosion gradually slows down to equilibrium as the scour hole enlarges. Within
377 the scour hole, sediment still moves. However, sediment cannot escape the hole
378 due to sand slide (Song et al., 2020b).

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(a) t = 10 s (b) t = 60 s
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(c) t = 150 s (d) t = 600 s

Figure 14: Four representative stages of simulated scour hole development. It

shows the bed elevation made dimensionless with the pile diameter D at (a) 10 s,
(b) 60 s, (c) 150 s, and (d) 600 s. The arrows show the direction of wall shear
stress and the bed-load flux.
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379 Figures 15a and 15b show the time evolution of the scour depth at the upstream
380 and downstream side of the pile, respectively. For comparison, the experimental

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381 and numerical results from Roulund et al. (2005), as well as the simulation results

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382 by sedFoam in Nagel et al. (2020) are also plotted. All the numerical models per-
383 form well at the initial scour stage up to 5 mins. The erosion rate of the two-phase
384 flow simulation is smaller than the other simulations and the experiment from 5 to
385 10 mins. All simulations reach equilibrium at around 10 mins. On the upstream
386 side, the two-phase flow simulation gives the maximum zb = 0.63D, whereas
387 the predicted maximum scour depths in Roulund et al. (2005) and ibS courFoam
388

389

390
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are 0.91D and 1.06D, respectively. The measured maximum scour depth from
the experiment is 1.25D. On the downstream side, the two-phase flow shows the
maximum zb = 0.18D. Simulations in Roulund et al. (2005) and ibS courFoam
391 both give the maximum zb = 0.6D. The measured maximum scour depth from
392 the experiment is 0.89D. As a result, even though all the numerical models un-
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393 derestimate the maximum scour depths at both upstream and downstream sides,
394 the results in Roulund et al. (2005) and ibS courFoam are similar and close to
395 the measured scour depth. One explanation of the underestimation is that two-
396 equation isotropic eddy viscosity turbulence models used to close RANS equa-
397 tions underpredict the effect of the horseshoe vortex system, the main factor of
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398 scour around a vertical pile (Khosronejad et al., 2012). The other reason is that
399 the contribution of suspended load to the equilibrium scour depth is not included
400 in these two models (?). In addition, a perturbation was added in the simulation of
401 Roulund et al. (2005) to trigger the development of ripples. However, the impact
402 of ripples was not included in our simulation. This could be another reason that
403 the predicted scour depth in ibS courFoam is slightly less than that in Roulund
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404 et al. (2005). In general, our model captures the scour depth time history rela-
405 tively well.

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(a) Upstream

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(b) Downstream
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Figure 15: Time history of scour depth at (a) the upstream and (b) the downstream
side of pile.

406 3.2. Demonstration case

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407 To demonstrate the capabilities of the model in dealing with scour around
408 complex structures, a flume experiment was carried out to obtain detailed flow and
409 scour information for comparison purpose. In the experiment, flow and scour were
410 measured around a horizontal cylinder with finite length placed on a foundation
411 (cradle) as shown in Figure 16a. The foundation was fully buried in the sand
412 initially. The cylinder, measuring 0.514 m long and 0.089 m in diameter, was
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413 placed onto the foundation. The position of the cylinder is fixed by the two crosses
414 of the cradle. To prevent excessive undercutting of the cylinder and to ensure it

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415 engages with the cradle, the cylinder was partially buried initially to a depth of

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416 14.5 mm. It was oriented such that the long axis of the cylinder was perpendicular
417 to the primary flow direction. With the development of scour, the bed gradually
418 lowered. As a result, the scour exposed the initially buried part of the cylinder
419 and the cradle. Figure 16b shows the computational mesh. It also shows that as
420 the scour hole develops, the simulated bed (shown as red solid lines) evolves and
421 interacts with the solid boundaries at x = 0 m, where x is the streamwise position
422

423

424
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with x = 0 at the center of the cylinder (shown as red dash lines in Figure 16a).
The mesh marked with blue is the initial fluid and the mesh marked with yellow
is the initial sediment.
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(a)

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(b)

Figure 16: Demonstration case setup: (a) schematic view of the domain for scour
around a horizontal cylinder placed on a foundation. (b) interaction of the bed
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with solid boundaries in the background mesh. The red lines are the simulated
bed at different times on the vertical slice of the domain at x = 0 m.

425 Laboratory experiments were conducted in a re-circulating, tilting flume mea-

426 suring 15.24 m in length, 1.52 m in width, and 0.91 m in depth. The test reach
of the flume, extending from 3.048 m to 7.621 m from the inlet, was covered to a
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427

428 depth of 0.12 m with sand having a median grain size of 0.67 mm. Water circu-
429 lated through the system via a horizontal pump capable of delivering a maximum

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430 flow rate of 240 l/s. Before the test, the sand bed was planed using a scraper

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431 attached to an instrument carriage. Once the bed was prepared, the initial bed sur-
432 face including the cylinder and cradle was measured using a handheld 3D scanner
433 (Artec EVA). The same scanner was used to measure the final, eroded bed surface.
434 The flume was slowly filled to a depth of 0.40 m above the sand bed surface,
435 and the pump was turned on. The targeted flow rate was selected by limiting the
436 flow conditions to remain within the clear water scour regime. This meant that the
437

438

439
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free-stream flow conditions did not significantly transport bed sediment, and any
erosion was caused by local accelerations. This threshold was first determined
using an estimated Chezy coefficient, then confirmed through preliminary testing.
440 A description of the methodology can be found in Ismail et al. (2021). The flow
441 condition and sediment properties are summarized in Table 4.
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442 Once the flow began, the sand bed started to be eroded near the cylinder and
443 cradle and formed a deposit downstream. The flow continued until the bed reached
444 equilibrium at which time there was no noticeable change in the bed surface.
445 Then, measurements of the velocity field were obtained. These include two sets
446 of velocity data: 1) the free-stream inlet velocity far upstream from the structure,
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447 and 2) the velocity field in a streamwise, vertical transect extending from x = [-
448 1.03, 1.03]. The streamwise transect measurements were spaced 0.04 m in the
449 streamwise direction and at five elevations from the initial plane bed (15, 30, 45,
450 60, and 75 mm). Note that the streamwise transect did not include data collection
451 immediately above the cylinder.
452 In our experiment, the upstream of the flume was a transitional section filled
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453 with large cobblestones to ensure a gradual flow adjustment from the lower rigid
454 bed to the higher sand bed. The existing of the cobblestones increases the flow

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Table 4: Test conditions for scour around a horizontal cylinder placed on a cradle
foundation.

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Parameters

Water depth H (cm)

Mean flow velocity U (cm/s)
Values

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Cylinder diameter D (cm) 8.9
Cylinder length L (cm) 51.4
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Shear velocity uτ (cm/s) 1.5
Roughness height k s (cm) 1
Grain size d50 (mm) 0.67
Critical Shields number for flat bed 0.016
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Static friction coefficient µ s 0.63

2
Diffusivity for sand slide (m /s) 0.0005
Hydrodynamic time step ∆th (s) 0.005
Time scale factor α 0.002 ∼ 0.02
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455 resistance of the bed, as well as the Nikuradse equivalent roughness at the up-

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456 stream region of the sand bed. Thus, the hydraulic roughness is related to not only
457 sediment sizes, but also incoming flow state. In this work, we adapted the value
458 of roughness k s by fitting the inlet velocity profile measured from the experiment,
459 instead of only using the sediment size d50 . Figure 17 shows the mean velocity
460 profiles upstream of the test section. The red dots are the measured velocity. The
461 blue dots are the pre-simulated profile in the channel with no object. The black
462

u+ =
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line is the velocity profile fitted with the general log-law

1
κ
u
ln(y+ ) + B − ∆B(k+s ), u+ = + , y+ =
u
uτ y
ν
(16)

463 where B is 5.2. The roughness function ∆B depends on k+s = k s uτ /ν and represents
464 the downward shift of the logarithmic velocity profile due to roughness. The
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465 functional form of ∆B in Cebeci and Bradshaw (1977) was used:






0 if k+s < 2.25




∆B = 
[B − 8.5 + 1κ ln k+s ] sin[0.4258(ln k+s − 0.811)] if 2.25 ≤ k+s < 90 (17)







 B − 8.5 + 1 ln k+s if k+s ≥ 90
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466 The fitted shear velocity uτ is 0.015 m/s and the Nikuradse equivalent sand rough-
467 ness k s is 0.01 m.
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Figure 17: Mean velocity profile measured at the undisturbed inlet of flume
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468 In the model, the inlet condition mapped from the uniform-channel flow cal-
469 culation with the fitted roughness k s is a standard logarithmic profile. Even though
470 the measured velocity profile deviates from the log law in the upper region, the
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471 effect of different inlet conditions used in the model and the experiment is not
472 significant since the scour is induced by flow contraction near the object.
473 The simulation domain has a length, width, and height of 2.2 m, 1.2 m, and
474 5.2 m, respectively. The mesh has approximately 8 million cells and the smallest
475 cell is approximately 1.6 mm in size. The maximum dimensionless wall distance
476 for IB cells, y+IBmax , is approximately 40. The immersed bed surface has 60,000
triangles. The simulation ran for 17 hours of real time and took approximately
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478 170 h (about 7 days) on 200 processors (Intel(R) Xeon(R) CPU E5-2680 v3 @
479 2.50GHz).

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480 Figure 18 shows four stages of scour from the initial to equilibrium in four

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481 rows. The columns, in their order, show the following: slices of bed at x = 0 m
482 (column a), scour depth patterns (column b), streamlines (column c), wall shear
483 stress amplification factors (column d), dimensionless sediment flux (column e),
484 and photos from experiment (column f). Arrows in column d show the direction
485 of wall shear stress. The reference value of the arrow is the wall shear stress at the
486 inlet |τ0 |(= ρu2τ )
487

488

489
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With the details revealed by the computational model, the four stages of ero-
sion observed in the laboratory experiment and laid out in Figure 18 can be further
examined:

490 1. Wake flow stage (Figure 18, row 1): water flows over the cylinder and con-
tracts when passing around the two ends of the cylinder. The approaching
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491

492 flow decelerates in front of the cylinder. Most of the incoming water flows
493 up and over the cylinder. A small portion of incoming water flow down and
494 forms a weak vortex that erodes the sand at the upstream side the cylinder.
495 In this stage, most sediment movement and erosion happen at the two ends
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496 of the cylinder where flow contracts. As sediment moves away, the two ends
497 are undermined and the underside of the cylinder starts to be exposed.
498 2. First jet flow stage (Figure 18, row 2): In this stage, the dominant flow is the
499 two jet flows under the two ends of the cylinder. Once the scour holes there
500 are developed, the incoming flow is split when it encounters the cylinder.
501 The downward flow into the scour holes contracts and accelerates to form
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502 two jet flows under the cylinder. The sediment in the scour holes is pushed
503 out and deposited in the adjacent downstream side. It is also observed that
504 some sediment near the two ends of the cylinder slides down to the deep

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505 part of scour hole and then is washed away by the jet flow. Gradually, the

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506 scour holes on the two ends expand toward the center.
507 3. Second jet flow stage (Figure 18, row 3): The two scour holes merge at
508 the center and expose the two crosses of the cradle. More incoming flow
509 goes under the cylinder and contacts at the center due to the existence of
510 two crosses. At this stage, the dominant flow is the one single jet under the
511 whole cylinder. The sediment flux is maximum and thus the scour rate is
512

513

514
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the largest under the center of the cylinder because of the cradle’s blocking
effect. As a result, more sediment is being moved out from the center and
then deposited downstream. The newly deposited sediment merges with
515 the sediment from previous two stages and form a ridge downstream. With
516 time, the bed under the cylinder slightly flattens.
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517 4. Pier-like flow stage (Figure 18, row 4): In this stage, undermining under
518 the cylinder continues but mainly happens around the two crosses of the
519 supporting cradle. The two crosses act like bridge piers and two local scour
520 holes around them start to form. The scour pattern around the two crosses
bears some resemblance to the vertical pile scour shown in Figure 14. Scour
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521

522 continues near the cradle until equilibrium and the deepest part of the scour
523 hole is around the two crosses. During the process, the sediment that moved
524 out of the center region deposited in the bar downstream and forms the
525 highest point in the middle.
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 a b c d e f
Stage 1
t = 0.4 hr
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Stage 2
t = 1.4 hr
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Stage 3
t = 3.6 hr
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Stage 4
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Figure 18: Different stages of the simulated scour process around a horizontal cylinder supported by a cradle
foundation. Rows corresponds to different stages. Columns a, b, c, d, e, and f are bed profile, scour depth contour,
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526 It should be noted that the wall shear stress distribution in Figure 18 (column

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527 d) is smooth, which enables a successful scour simulation. This demonstrates
528 the capability of the immersed boundary method and the associated wall model
529 proposed in this work.
530 Figure 19 shows a good comparison of the scour profile on the vertical slice
531 at x = 0 m. The maximum scour depth is well captured near the crosses of the
532 cradle. Bed slope of the scour hole is also consistent with the experimental data.
533

534

535
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The main discrepancy is that the scour hole on the right side is slightly deeper
than that on left side in the experiment. It may result from the slight asymmetry of
experimental setup. For comparison, the simulated result is symmetric along the
536 symmetry plane of the flume. In this case, the driving flow of scour is dominated
537 by flow contraction, rather than the horseshoe vortex that is underestimated by the
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538 RANS model. Thus, a better agreement between the simulation and experiment
539 is produced by our model than that of the previous scour case.
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Figure 19: Equilibrium scour profile on the vertical slice at x = 0 m.

540 We made more comparisons between simulations and experiments. To reduce

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541 the length, they can be found in Appendix C.

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542 4. Limitations

543 Despite the success shown in this paper, the current model still has limitations.
544 The major one is it is computationally more demanding than previous methods,
545 such as the ALE method. In the current model, the simulation domain has to be
546 larger to include the sediment part. In addition, the mesh in the sediment part has
547

548

549
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to be refined to have accurate results of flow and wall shear stress. As the Reynolds
number increases, the required mesh resolution of the immersed boundary method
increases much faster than the ALE method (Mittal and Iaccarino, 2005). The
550 other limitation is the numerical instability caused by the switch among the IB,
551 fluid, and solid cells when the boundary moves. Our background mesh is very
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552 stretched in the vertical direction to increase the mesh resolution and decrease
553 the total mesh size, which also increases the instability of our model. There-
554 fore, we used a relatively low order numerical scheme for the advection terms
555 in Table 1. This scheme adds more numerical diffusion into the model and de-
creases its capability to capture finer flow features downstream. In addition, scour
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556

557 models solving RANS equations with two-equation turbulence models underesti-
558 mate the wall shear, as well as the scour depth induced by the horseshoe vortex
559 system (Khosronejad et al., 2012). To alleviate this problem, a conservative mod-
560 ification of Brownlie’s (?) curve from Parker et al. (2003) was used to calculate
561 the critical shields number, which amplifies the bed-load transport rate and in-
creases the estimated maximum scour depth. The current model also lacks the
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562

563 suspended sediment component. Suspended sediment transport within the frame-
564 work of immersed boundary method, especially how entrainment and deposition

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565 can be modeled, is currently under development.

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566 5. Conclusions

567 A 3D scour model, ibScourFoam, has been developed based on a sharp-interface

568 immersed boundary method. It can simulate the scour process around complex
569 structures, a difficult task for many previous scour models. This paper describes
570 the details of the model and its implementation. In particular, the wall model
571

572

573
scour simulations.
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proposed here produces accurate and smooth wall shear stress, a prerequisite for

The model was validated by simulating the flow and scour cases in Roulund
574 et al. (2005). The flow structures and the temporal evolution of scour depth were
575 well predicted. The model was further validated with a more complicated flume
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576 experiment case where a short cylinder sits on a cradle. The cylinder is initially
577 partially buried and the cradle is fully buried. The model successfully simulated
578 the undermining process starting at the two ends of the cylinder, the progressive
579 enlargement of the scour holes, the merging of the two scour holes, and the sub-
sequent scour around the fully exposed crosses of the cradle. With the 3D scour
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580

581 simulation results, it is now possible to analyze the details of the process and
582 different stages of the scour development.
583 The 3D scour model developed in this work provides a viable path for scour
584 modeling to be used in engineering practice. It helps us go beyond the “scour
585 around simple geometry” phase in this field. With ever increasing computing
power, the relatively high computational cost required by the immersed boundary
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586

587 method will soon become more affordable.

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588 Appendix A. Terms and coefficients in the turbulence model

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589 Additional terms and coefficients in the k − ω SST-SAS model are described
590 below. The blending function, F1 , is calculated as:
   √   
4




   k 500ν  4αω2 k 
 

F1 = tanh 

 min max  ∗ , 2  ,   (A.1)

 β ωy y ω 2αω2 ω ∇k∇ωy  
−1 2  


591 QS AS is the additional SAS source term which has the form of
 !2 ! 

592
√
where L = k/(c0.25
re- 
QS AS = max ζ2 κS2
L
LνK
−
2Ck
σΦ
max
|∇ω|2 |∇k|2
ω2
,
k 2

, 0 (A.2)

µ ω) is the modeled length scale. LνK is a three-dimensional

593 generalization of the classic one-dimensional boundary layer definition and is cal-
594 culated as:
p
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LνK = max(κS/|∇2 ū|, CS δ ζ2 κ/(β/β∗ − γ)) (A.3)

595 where δ is the cubic root of computational cell volume.

596 The eddy viscosity, νt , is then calculated as:

a1 k
νt = (A.4)
max(a1 ω, b1 SF2 )
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597 where the second blending function, F2 , is calculated as:

  √ 2 


  2 k 500ν  


F2 = tanh 
 max  ∗ , 2   (A.5)
 β ωy y ω  

598 The coefficients used in the turbulence formulas are listed as follows: αk = F1 (αk1 −
599 αk2 ) + αk2 , αk1 = 0.85, αk2 = 1.0, Cµ = 0.09, αω = F1 (αω1 − αω2 ) + αω2 , αω1 =
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600 0.5, αω2 = 0.856, α = 0.8, β = F1 (β1 − β2 ) + β2 , β1 = 0.075, β2 = 0.0828, β∗ =

601 0.09, ζ2 = 3.51, κ = 0.41, C = 2, σΦ = 2/3, CS = 0.11, γ = F1 (γ1 − γ2 ) +
602 γ2 , γ1 = 5/9, γ2 = 0.44, a1 = 0.31, and b1 = 1.0.

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603 Appendix B. Validation of wall function

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604 The turbulent flow over a flat plate is a widely used 2D case to validate the wall
605 shear prediction of hydrodynamic solvers. A 2D boundary layer without pressure
606 gradient was tested at ReL = 5 × 106 . The length, L, of the plate is 2 m. A slip
607 surface with a length of 0.1L is added in front of the flat plate to generate a free
608 stream. The upper boundary is 0.4L away from the flat plate. We refined the
609 mesh near the leading edge of the flat plate and the boundary layer region (0.2L).
610

611

612
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A schematic view of the simulation mesh is shown in Fig. B.20. The mesh is
aligned with the flat plate. N is the number of cells and R is the cell expansion
ratio (R is the ratio of the size of the end cell ∆N to the size of the start cell ∆1
613 along the edge direction). Five different cell expansion ratios were tested in the
614 y-direction of the boundary layer region to change the size of the first wall cell.
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Figure B.20: Schematic view of mesh for flow over a flat plate

615 In the simulation, the slip surface uses symmetric boundary condition and the
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616 flat plate is set as an immersed boundary. The proposed wall model is applied
617 on the flat plate. Figure B.21 shows the predicted skin friction coefficient, C f ,
618 compared with the experimental data from Wieghardt and Tillmann (1951). As

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619 the y+IB decreases due to the progressive refinement of the mesh, the simulation

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620 results match closely to the experimental data. When the averaged y+IB is located
621 in the laminar layer, the prediction of the shear velocity is still good, especially at
622 the leading edge where the flow is dominantly laminar.

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Figure B.21: Skin friction coefficient (C f = τw /(1/2ρU 2 )) along the flat plate.
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623 Appendix C. More comparison for the cylinder on a cradle case

624 The flow field at scour equilibrium was also measured in the experiment. It is
used here to compare with the simulation results. The velocity under the cylinder
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625

626 is unable to be measured by the Nortec Vectrino Plus Acoustic Doppler Velocime-
627 ter (ADV). Figure C.22 shows the streamwise velocity contour on the center slice
628 (y = 0 m) at equilibrium. The tail of the jet flow at the downstream of the cylinder
629 is in relatively good agreement with the experiment. The back flow circulation
630 behind the cylinder is not as strong as that in the experiment. This may be due
to the use of RANS model and the mesh behind the cylinder is not fine enough.
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631

632 Nonetheless, the bed profiles (black lines in Figure C.22) compare well.

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(a)

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(b)

Figure C.22: Contour of streamwise velocity, u x , on the center slice at equilibrium:

(a) Simulation, (b) Experiment. The black lines are the bed profiles.
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633 Figure C.23 shows the comparison of the bed contours at equilibrium from the
634 simulation and the experiment. Though not an exact match, it can be observed that
635 the features of the scour hole and deposition bar are well captured by the model.
636 Even the details of the scour holes around the crosses of the cradle are captured.
637 In both the experiment and the simulation, a large deposition bar appears in the
downstream, and the peak bed elevation is at the center. The simulated deposition
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638

639 height behind the cylinder is lower than the experimental value. This could be due
640 to the coarse mesh used in the downstream side of the domain.

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(a) (b)

Figure C.23: Bed contours at scour equilibrium: (a) Simulation (b) Experiment.

641 Acknowledgements

This work is supported by the Strategic Environmental Research and Devel-

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642

643 opment Program (SERDP, Award Number W74RDV70063408).

644 Supplementary Materials

645 Supplementary materials (animation videos) associated with this article can
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646 be found in the online version. Source code and cases can be found on GitHub
647 (https://github.com/psu-efd/ibScourFoam).

648 References

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Highlights
Scour modeling based on immersed boundary method: a pathway to practical use of three-
dimensional scour models

Yalan Song, Yuncheng Xu, Hassan Ismail, Xiaofeng Liu

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 An open-source three-dimensional (3D) scour model based on an immersed boundary
method has been developed.
 The model utilizes a new algorithm to produce smooth and accurate wall shear, which is
key for sediment transport.
 The model can simulate scour around structures with complex geometries under waves
and currents, paving the way for practical use of 3D scour modeling.

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Yalan Song: Software, Investigation, Visualization, Writing
Yuncheng Xu: Software, Writing
Hassan Ismail: Experiment, Writing
Xiaofeng Liu: Conceptualization, Methodology, Supervision

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Declaration of interests

☒ The authors declare that they have no known competing financial interests or
personal relationships that could have appeared to influence the work reported in
this paper.

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☐The authors declare the following financial interests/personal relationships which
may be considered as potential competing interests:

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