September 20, 2023 Journal of Hydraulic Research output

To appear in the Journal of Hydraulic Research

Vol. 00, No. 00, Month 20XX, 1–16

Research Paper

Simulations of Scalar Transport in Oscillatory Flow over a Wavy Wall

EDWIN R. APONTE-CRUZ, MS Student, Department of Mechanical Engineering, University of Puerto
Rico at Mayagüez, Mayagüez, USA
Email: edwin.aponte1@upr.edu

SYLVIA RODRÍGUEZ-ABUDO, Associate Professor, Department of Engineering Sciences and Materials,

University of Puerto Rico at Mayagüez, Mayagüez, USA
Email: rodriguez.abudo@upr.edu

Scalar Transport in Oscillatory Flow

v1.0 released Month YEAR

September 20, 2023 Journal of Hydraulic Research output

Simulations of Scalar Transport in Oscillatory Flow over a Wavy Wall

ABSTRACT
A three-dimensional model that couples Reynolds–Averaged Navier–Stokes equations with an advection–diffusion
solver for flow and concentration fields over a fixed, non-permeable boundary is presented. The model simulates
oscillatory flow over a wavy wall with a constant scalar source to assess the effects of a boundary-induced pressure
gradient on passive scalar mixing. Results were compared to experimental data collected in an oscillating tray
facility. Hydrodynamic quantities are in favourable agreement with observations. The model captured vortex dynamics
correctly, and turbulence statistics were modeled reasonably well. Comparisons of time-resolved and bulk scalar
quantities for crest and trough sources were in favourable agreement with observations. Results indicate that the
model can be utilized to study processes with highly intermittent phenomena, such as the transport of wastes and
dissolved nutrients in the coastal bottom.

Keywords: 3D model, RANS, fixed bed, wavy walls, scalar transport, wave-induced flows.

1 Introduction

The sediment–water interface (SWI) of the coastal ocean is a highly dynamic zone where many
physical, chemical, and biological processes take place. It is dominated by wave bottom boundary
layer (WBBL) hydrodynamics which in turn dictates transport processes in the zone (Huettel et
al., 2007; Warhaft, 2000). This WBBL is defined as the layer close to the coastal bottom, where
the wave-induced water motion is noticeably affected by the bottom boundary (Nielsen, 1992). In
this region, the flow induces shear stresses and turbulence, which are key parameters for sediment
and scalar transport as they induce drag, velocity gradients and turbulent mixing.
The bottom boundary can take many forms, with the simplest type being a flat sediment bed.
For flat beds, turbulent effects are caused by stresses due to the bed roughness associated with
the sediment characteristics. Bottom boundaries in nearshore regions are not necessarily flat, as
coastal flows may generate distinct morphological features (bedforms) on the seabed, such as ripples
and sand dunes. These bedforms are often described through their steepness, the ratio between
their height and wavelength. In addition to their steepness, ripples are also classified based on
relationships between their height and wavelength with flow and sediment characteristics. A com-
prehensive review of the relationships between ripple geometry and sediment transport in various
flow conditions can be found in publications such as Wiberg & Harris (1994). The occurrence of
these bedforms introduces elements that significantly affect the temporal and spatial distribution
of momentum fluxes and the transport of sediment and other substances in the SWI, as they in-
duce additional pressure gradients into the flow field that often result in coherent motions near
the boundary (Davies & Thorne, 2005; Rodrı́guez-Abudo et al., 2013). It has been found that os-
cillatory flows over bedforms with a steepness beyond 0.1 lead to the generation of these coherent
motions, with these bedforms being known as vortex ripples (Sleath, 1984).
The small-scale flow structures formed by vortex-generated turbulence serve a critical role in
mixing processes, as they can accelerate scalar diffusion in the nearbed flow (Ouro et al., 2018).
These scalars can be considered passive if they are non-reactive. Processes such as the transport of
pollutants including dredged material, liquid wastes and chemicals, as well as dissolved nutrients,
are often analyzed using the passive scalar assumption (Bomminayuni et al., 2014; McCave, 1976).
The transport and mixing of these scalars within a flow is governed by advective and diffusive
processes, which for SWI applications include a number of effects stemming from flow turbulence
and sediment roughness.
The numeric modeling of flows over ripples can be traced to the discrete vortex methods (DVM),
such as those developed by Longuet-Higgins (1981). The DVM was able to describe the vortex
formation–ejection process around a ripple, but it struggled to represent highly turbulent cases.
To that end, efforts such as those of Sato et al. (1984) used finite difference models to solve the
flow over ripples. Later, Blondeaux & Vittori (1991) implemented a numerical approach utilizing

2
September 20, 2023 Journal of Hydraulic Research output

the vorticity and Poisson equations that enabled the detailed analysis of the vorticity dynamics
of an oscillatory flow over a rippled bed. Later, Scandura et al. (2000) presented a study of the
three-dimensional dynamics of oscillatory flow over vortex ripples using direct numerical simulation
(DNS), which allowed for the characterization of vorticity dynamics and the study of destabilizing
effects in the third dimension. Numerical studies of sediment transport in oscillatory flows over
rippled beds include those of Barr et al. (2004), Penko et al. (2013) and Salimi-Tarazouj et al.
(2021). However, very few efforts have been able to numerically resolve passive scalar transport on
a rippled bed under oscillating flows. Key studies that quantify scalar concentration and transport
in turbulent flows include those of Crimaldi et al. (2002) and Wagner et al. (2007), yet they are
limited to steady-unidirectional flows. This distinction is significant, since oscillating flows have
very small boundary layer thicknesses compared to steady-unidirectional flows commonly found on
rivers or tidal-dominated environments.
The objective of this effort is to quantify the effects of an oscillatory fluid forcing on the fate and
transport of scalars near a bedform. In order to isolate the effect of bedforms from the small–scale
roughness and permeability problems associated with the flow over a sediment bed, the sediment-
laden coastal bottom is modeled as a non-permeable, fixed, wavy wall. The results are then com-
pared with experimental data obtained in an oscillating boundary layer facility.

2 Model description

2.1 Governing equations

The hydrodynamic model used in this effort is based on the solver pimpleFOAM, included in
the open-source CFD software OpenFOAM v7. The basis for this solver is the PIMPLE al-
gorithm, a combination of the PISO (Pressure Implicit with Splitting of Operator) and SIM-
PLE (Semi-Implicit Method for Pressure-Linked Equations) used to solve the Reynolds-Averaged
Navier–Stokes (RANS) equations for a three-dimensional, unsteady flow of an incompressible and
homogeneous fluid. The RANS equations are derived by decomposing the velocity (u) and pressure
(p) fields into ensemble-averaged (denoted with overbars) and fluctuating (denoted with primes)
terms, such that

u = u + u′ (1)

and

p = p + p′ (2)

The resulting continuity and momentum equations are as follows:

∇ · u = 0, ∇ · u′ = 0 (3)

and
∂u 1
+ ∇ · (uu) = g + ∇ · τ − ∇ · R + f (4)
∂t ρ

where ρ is the fluid density, g is the gravitational term and f contains external forces. The fluid
(τ ) and Reynolds (R) stress tensors are defined as follows:
 
2  
τ = − p + µ∇ · u I + µ ∇u + (∇u)T (5)
3

3
September 20, 2023 Journal of Hydraulic Research output

R = u′ u′ (6)

where I is the identity matrix and µ is the dynamic viscosity of the fluid. The k-epsilon closure
model was used to model the turbulent energy transfer that occurs at subgrid levels, where the
turbulent kinetic energy (κ) and turbulent kinetic energy dissipation rate (ε) are given by:

D
(κ) = ∇ · (Dκ ∇κ) + KP − ε (7)
Dt

D C1 ε ε2
(ε) = ∇ · (Dε ∇ε) + (KP ) − C2 (8)
Dt κ κ
where Dκ and Dε are the effective diffusivities for κ and ε, respectively, KP is the turbulent
kinetic energy production rate, and C1 and C2 are calibration coefficients. Respectively, the values
of these coefficients are 1.44 and 1.92. Additionally, the eddy viscosity νt = Cµ κ2 ε−1 is calculated
to quantify the effects of turbulence on the transport of momentum, where Cµ is a coefficient with
a value of 0.09.

In order to simulate scalar transport in the wave bottom boundary layer, the advection–diffusion
equation was introduced into the numerical solver:

∂C
= (D + Dt )∇2 C − u · ∇C + Ω, (9)
∂t
where C is the scalar concentration, D is the molecular diffusion coefficient, Ω represents scalar
sources or sinks, and Dt = νt Sct −1 is the turbulent diffusion coefficient, where Sct is the turbulent
Schmidt number. Rhodamine 6G fluorescent dye (D = 3 × 10−10 m2 s−1 ) was used as the scalar
substance.

2.2 Initial conditions

The flow is driven by an oscillating pressure gradient, such that

∂p ∂p
= + ρf (10)
∂x ∂x
where the first and second terms on the right-hand side represent the mean and oscillating pressure
gradients, respectively. The external forcing f is defined as:

∂U0
f= (11)
∂t
and U0 is defined as follows:

U0 = U1 sin (ωt + σ0 ) (12)

where U1 is the velocity amplitude, ω = 2πT −1 is the radian frequency of a wave with period T,
and σ0 is the phase shift. For the case presented in the current work, the corresponding values for
U1 and σ0 are 0.31 m s−1 and 0, respectively. The initial values of the closure model variables are

4
September 20, 2023 Journal of Hydraulic Research output

estimated as follows:
3
κ = (I|uref |)2 (13)
2

Cµ 0.75 κ1.5
ε= (14)
L
where I is the turbulence intensity defined as a percentage of the characteristic velocity uref and
L is the characteristic length scale. A value of I = 0.1 was chosen to obtain an initial value for κ.
The domain height was established to be at least five times the wall height (η) to ensure free-
stream conditions at the top, as suggested by Chen & Yu (2015). The domain length was chosen to
be twice the wave excursion amplitude, defined as A = U1 T (2π)−1 , in order to capture the entire
path of a scalar source located near the centerline (y = 0) of the domain. The computational domain
(Fig. 1) is composed of a hexahedral grid with varying size. Near the area of interest (0 < x < 15
cm, 0 < z < 7 cm, −2.5 < y < 2.5 cm), the grid size is ∆x = ∆z = 0.5 mm and ∆y = 2.5 mm,
increasing linearly in the vertical direction to ∆z = 2.0 mm at the top of the domain. ∆x values
also increase linearly away from the area of interest to further preserve computational time. The
total number of gridpoints in each direction is 999 in x, 107 in z and 25 in y. The data presented
in this effort correspond to a single x–z slice located at y = 0 cm, as seen in Fig.1. The simulation
was carried out using the second-order numerical scheme Crank–Nicolson 0.9. In order to optimize
computational time, the solution time-step ∆t is varied within a range ∆tmin = 1 × 10−6 s and
∆tmax = 2 × 10−4 s, as limited by the maximum allowable Courant number (Comax = 0.1). This
value of Comax was chosen to ensure solution stability at the initial stages of the simulation.

2.3 Boundary conditions

The boundary conditions for the hydrodynamic model (Fig. 1) consist of a fixed rigid wall with a
no-slip condition at the bottom. The bottom geometry is identical to the experimental wall profile
used to validate and compare results. The profile of the experimental wavy wall was obtained from
image processing techniques, and a 2D profile of the wall geometry was mapped into OpenFOAM.
This profile served as the no-slip, fixed bottom boundary for the simulations. A slip boundary
condition is used at the top. Additionally, a cyclic (or periodic) condition is applied at the inlet
and outlet boundaries. A zero gradient boundary condition was applied at the top and bottom for
the scalar transport model to ensure mass conservation at the boundaries and a cyclic condition
on the sides. The implementation of these boundary conditions means that no scalar quantity can
escape the domain. The injection of a scalar into the domain was implemented by introducing a
scalar point source at the wall surface at point x = 7.50, z = 1.60 and y = 0 cm for the crest case
and at x = 10.94, z = 0.55 and y = 0 cm for the trough case. This point source was forced to
remain at a normalized constant concentration value of 1.

2.4 Grid Independence Analysis

A grid independence analysis is a crucial step in computational simulations, particularly in numer-
ical methods such as finite element analysis, computational fluid dynamics and other related fields.
The analysis helps to determine the effect of the grid size on the simulation results and ensures
that the simulation outputs are not dependent on the size of the computational grid used. This
process is important for achieving accurate and reliable results in the simulation and for validating
the computational model used for the analysis. For the present work, a grid independence analysis

5
September 20, 2023 Journal of Hydraulic Research output

was carried out for several variables of interest, mainly flow velocity, turbulent kinetic energy, eddy
viscosity and passive scalar concentration (Table 1).
The comparison mesh was generated by increasing the grid sizes by a factor of 1.5 in each
direction, resulting in a coarser mesh with 666, 71 and 17 gridpoints in x, z and y, respectively.
The absolute error was computed from the absolute difference between the present values and
those interpolated from the coarser grid. Upon analyzing the results, it was found that both the
hydrodynamic quantities (u and w) and turbulent quantities (κ and νt ) had maximum absolute
errors that were approximately one order of magnitude smaller than their absolute quantities. The
passive scalar concentrations showed slightly higher absolute errors in regions with large spatial
gradients, yet these errors were localized and did not represent the behavior of the entire field. This
was demonstrated by the low mean absolute errors of all variables. Overall, the analysis implies
that the grid size had a relatively minor effect on the accuracy of the results, indicating that they
are grid-independent. These findings confirm the accuracy and reliability of the computational
model used in this study and validate its use for further analysis and simulations.

3 Experimental setup

Experiments were performed at a 2-m-long tray suspended from a cart oscillating horizontally atop
a 8 x 0.7 x 0.7 m acrylic tank, with a plastic undulating boundary with a wall height of η =1.6
cm and length of λ = 7.5 cm attached to the cart tray (Fig. 2). It is important to note that these
dimensions correspond to a steepness of 0.21, which is above the steepness of realistic ripples formed
by the flow conditions of this experiment. Furthermore, η and λ are much smaller than the predicted
values of ∼ 5 and 32.5 cm, respectively, for the given flow conditions according to Wiberg & Harris
(1994). The tray mechanism allows control of the oscillation frequency and velocity amplitude to
replicate a range of wave conditions. For the case presented here, a symmetric sinusoidal wave with
U1 = 0.31 m s−1 and wave period T = 5 s was used. Experimental velocity measurements of a
236×137-mm field-of-view were obtained from Particle Image Velocimetry (PIV) that aquired at a
frequency of 15 Hz with 1 ms between pulses. This permitted 50 s of acquisition times, or 10 flow
cycles. Concentration measurements were obtained in a similar way using Planar Laser-Induced
Fluorescence (PLIF). With the aid of an image-splitting device (Dantec Dynamics DualScope), the
system was able to capture both PIV and PLIF images simultaneously using a single camera. An
injection system capable of pumping rhodamine dye from different locations along the fixed bed
was used to study the different scalar transport dynamics associated with sources either at the
trough or crest locations along the bedforms.

4 Model data comparison

4.1 Hydrodynamics
Bulk quantities related to the velocity field show fairly good agreement between the model and
the observations (Fig. 3). The time-averaged velocity fields (Fig. 3a) are very close to zero in the
free–stream, as expected for purely oscillating flows, while inside the boundary layer, coherent
structures and non-zero velocities are present. This phenomenon is visible in the numerical data as
well, although the experimental data show higher time-averaged velocities. As a consequence, the
coherent structures also appear larger in the experimental case. RMS velocities show favourable
agreement over the entire field, with slightly higher velocities near the crests and a considerable
reduction in magnitude above the troughs (Fig. 3b).
Oscillating flows commonly present a phase shift between the nearbed and free-stream velocities
due to the shear stresses inside the boundary layer (Nielsen, 1992). Analytically, Stokes (1851)

6
September 20, 2023 Journal of Hydraulic Research output

found that, for a laminar flat bed, the boundary layer leads the free-stream by 45◦ . Further studies
on turbulent flows over rough beds found that the phase lead diminishes due to friction-induced
turbulence, such that the maximum phase lead is between 10◦ –30◦ (Jonsson & Carlsen, 1976;
Hurther & Thorne, 2011). A cross-correlation analysis between u(x, z, t) and u(x, z = 13 cm, t)
was performed for both the simulated and the observed data (Fig. 3c). The phase differences show
similarities in magnitudes and locations. Both cases show phase differences up to ∼ 3 cm from the
trough, which corresponds to the start of the free-stream region (see Fig. 4). A phase lag of ∼ 30◦
appears near the left trough in both cases. The extent of the phase lag region is different for both
troughs, likely due to the different wall steepness and resulting vortex formation. This is consistent
with results from previous efforts. For example, van der Werf et al. (2007) found that the phase
lead of nearbed flows over rippled beds is highly affected by vortex formation. However, these phase
leads were in the range of 30-90◦ , which is representative of phase leads over realistic vortex ripples
(η = 6.5 cm; λ = 29 cm). Ripples with deeper troughs (and, in turn, larger steepness) represent
a larger space for flow circulation to occur, which foments the formation of larger vortices (Lin &
Yuan, 2005). A high phase lead is observed just above the phase lag region. It gradually diminishes
in value in the vertical direction until the phase difference becomes zero outside the boundary
layer, which is consistent with the studies of Malarkey & Davies (2004) and Rodrı́guez-Abudo et
al. (2013), who found that phase leads are present over rippled beds until elevations close to η
above the crest.
The swirling strength parameter, described by Eq. 15, was used to isolate coherent structures
from shear stresses in the boundary layer.
 
  λr  −1
D ≡ ν r ν cr ν ci  λcr λci  ν r ν cr ν ci (15)
−λci λcr

where D is the velocity gradient tensor, λr is the real eigenvalue with eigenvector ν r , and λcr ± λci
are the complex eigenvalues with complex eigenvectors ν cr ± ν ci .
Zhou et al. (1999) suggested the usage of the imaginary part of the complex eigenvalue pair
(λci ) to represent the local swirling strength of vortices. The procedure was carried out in previous
efforts (Penko et al., 2013; Rodrı́guez-Abudo et al., 2013). This evaluation allows for a qualitative
comparison of the local vortex structures between observations and simulations. Overall, good
agreement was found between the two cases in terms of time-resolved velocity fields and λci (Fig.
4). During positive flow acceleration (Fig. 4b), there were no vortices present, and a pressure-
gradient-induced acceleration was observed near the crest and deceleration near the troughs. Near
the maximum positive velocity (Fig. 4c), large pressure gradients caused flow separation and the
generation of a vortex above the left trough. During the first half-period (Figs. 4b–c), there was a
process of vortex trapping and development on the crests, characterized by a high λci , in agreement
with previous studies by Penko et al. (2013) and Chen & Yu (2015). Near flow reversal (Fig.
4d), the vortices were ejected upwards up to a height of ∼ 2 cm from the trough in both cases.
During flow deceleration (Fig. 4f), vortices were formed above the troughs, although the simulation
underestimated the vortex size over the trough and overestimated it over the crest. Near the second
flow reversal (Fig. 4g), the vortices were ejected in a manner similar to that seen in the flow reversal
at the half cycle, and good agreement was observed between the observed and the simulated λci .
It is important to note that there is a difference in both size and strength between the coherent
structure on the left trough and those on the right. As discussed in regards to the phase lags
(Fig. 3c), it has been found that deeper troughs lend themselves to the formation of larger and
stronger vortices. Ejected vortices were observed to travel a maximum vertical distance of 2η from
the crest, which is in good agreement with the behavior observed in Fig. 4b (Grigoriadis et al.,
2012; Malarkey & Davies, 2004).
Observed and simulated Reynolds stresses (u′ w′ ) and Reynolds stress tensor components (u′ u′ ,

7
September 20, 2023 Journal of Hydraulic Research output

w′ w′ ) are depicted in Fig. 5. In general, the Reynolds stresses compare favourably, with the highest
stresses of 0.0005 m2 s−2 and positive values occurring over the left flanks, while negative values
are on the right flanks. Uncharacteristic values of 0.0001 m2 s−2 outside the boundary layer may be
attributed to experimental errors associated with vibrations or secondary flows. Magnitudes inside
the boundary layer are in good agreement, and the locations of positive and negative stresses also
compare favorably. The observed u′ u′ (Fig. 5c), whose values extend up to ∼ 3 cm from the trough,
is in relatively good agreement with the simulated values (Fig. 5d). The simulation shows a sharp
gradient that increases from zero at the wall surface to a maximum of 0.0025 m2 s−2 at z = η and
decreases again until it reaches zero outside of the boundary layer. These magnitudes are relatively
similar to the ones observed experimentally, with the distinction that the simulated values are
uniform along x, while the experimental values have a greater local variation. The simulated values
of w′ w′ hold much more closely to u′ u′ , displaying isotropic behavior inherent in the numerical
model assumptions. However, the experimental values of w′ w′ are in a lower order of magnitude
with respect to the simulation, which suggest an anisotropic behavior that is not being captured
by the RANS model.

4.2 Scalar transport

Two comparisons were performed between the observed and the simulated concentration fields, one
with a constant concentration point source located at the crest and another at the trough (Figs.
6–8). All comparisons show good agreement in terms of maximum concentration magnitudes, as
both cases show that most of the magnitudes inside the scalar plume are in the 0.05-0.2 range
(Fig. 7), and this range is also similar to other instantaneous concentration magnitudes observed
in studies of flows over wavy walls, such as Wagner et al. (2007), even though the flow in this study
is steady. For the crest case, there is good agreement in the behavior of the scalar plumes during
the initial flow acceleration phases (Fig. 6b-c), as the scalar plumes propagate to the right at a very
similar rate. In the spatially averaged sense (Fig. 7b-c), it can be seen that during these phases
both curves display a gradual increase in concentration from z = 0.5 cm up to the injection point at
z = 1.6 cm, but simulated values overestimate the concentration magnitudes at those elevations.
Around flow reversal (Fig. 6d-e) the model concentration plume dissipates more slowly than in
the experimental case, leading to a large presence of dye to the right of the central bedform. The
spatially-averaged plot shows lower concentration magnitudes below the injection point (z = 1.6
cm) during flow reversal (Fig. 7d-e). Experiments higher magnitudes above the injection point
(Fig. 7d), indicating that the dye plume extends vertically as the flow starts to change direction.
This is not replicated by the simulations.
Interestingly, exactly at flow reversal (Fig. 7e) there is better agreement between experimental
and simulated values. Vortex ejection occurs between these phases (Fig. 4d-e). Poor agreement at
phase (d) suggests that the numerical model struggles during the beginning of the vortex ejection
process, yet improves once the vortices have completely detached. Qualitatively, there seems to
be poor agreement during the two deceleration phases (Fig. 6f–g), as the model overpredicts the
size of the scalar plume that propagates towards the left-hand side of the crest. The same is
evidenced by the spatially-averaged concentration profiles (Fig. 7f), where a clear discrepancy
is observed from z = 0.5 to z = 1.6 cm. Experimentally this region appears to have negligible
concentration magnitudes, in contrast to the acceleration phases in the first half-cycle, while the
simulated curves reflect a closer behavior to the ones in the first half-cycle. However, the spatially-
averaged concentration profiles near flow reversal (Fig. 7g) are in better agreement. As with phase
(e), it can be seen that at phase (g) the vortices are already detached (Fig. 4g) reinforcing the idea
that the model represents these phases well.
For the trough case, there is generally good agreement in the acceleration phases (Fig. 7b–c). In
these phases concentration magnitudes reduce sharply above the injection point. There is better

8
September 20, 2023 Journal of Hydraulic Research output

agreement around flow reversal than for the crest case, where both curves show similar concentra-
tion magnitudes that decrease gradually from the injection point until z = 2 cm (Fig. 7d–e). This
is likely due to shedding vortices that transport dye upwards during these phases. There is good
agreement during the deceleration phase (Fig. 7f). There is not such good agreement at the end of
the second half-cycle (Fig. 7g), as the model underpredicts vertical scalar dispersion. The relatively
large experimental magnitudes above the injection point (z = 0.5 cm) at this phase suggest that
dye is being carried upward by ejected vortices, something that is not reflected in the simulated
case. The poor agreement for the trough case may occur because the vortices are located directly
above the trough source (Fig. 4g) and, as such, the effects of the vortices is greater.
Comparisons between observed and numerical bulk scalar quantities (Fig. 8) show that time-
averaged concentration fields are in good agreement in terms of magnitudes (Fig. 8a). Experiments
with crest injection show more dye than the simulations for elevations between z = 0.5 and z = 1.6
cm, which would correspond to elevations below the injection point. The trough case shows much
better agreement, indicating that the model is able to capture the physical mechanism that overall
cause vertical transport from the troughs.
A comparison between observed and simulated concentration intermittency was also carried out
(Fig. 8b). Intermittency quantifies the percentage of time that the concentration at a point is
nonzero or above a certain threshold value, and is defined by Chatwin & Sullivan (1993) as follows:

d
γ= [prob{C/C0 } ≥ θ] (16)
dθ
where θ is a concentration threshold value, which was chosen as 0.01 for the present study. This
statistical quantity is well suited for studies involving intermittent scalar processes such as the pol-
lutant transport of sediment-associated contaminants (Förstner, 1987) or the transport of marine
microorganisms (Seuront et al., 2001), and has been used by studies such as Crimaldi et al. (2002)
to study the mean structure of scalar concentrations in steady flows. For the crest case, the model
overpredicts the intermittency values below the crest. This is indicative of dye plumes lingering for
longer and occupying a larger area, which is consistent with the concentration fields shown in Fig.
6. The trough case is in better agreement, suggesting that simulated and experimental dye plumes
in this case usually occupy similar areas.
These results seem to indicate that the model underpredicts the amount of turbulent diffusion
that is present experimentally. A possible explanation is that there are likely more diffusive mech-
anisms in the experimental case that cannot be replicated numerically, such as high mechanical
vibrations occurring as the tray decelerates and changes direction. These vibrations can improve
mixing close to the wall boundary and aid in dissipation.
Using the half-width spread method presented by Wagner et al.(2007), the extent of the dye
plumes was quantified at various flow phases (Fig. 9). As opposed to Wagner et al. (2007), who
used the 50 percent level of concentration, this analysis was performed using the 5 percent level, in
order to illustrate a greater extent of the concentration field. For the crest case (Fig. 9 left column),
the scalar plumes remain confined to the crest and flanks of the central bedform, with the longest
distance traveled occurring during flow acceleration (60◦ and 240◦ phases). As flow decelerates, the
scalar plumes retreat towards the crest and reduce in size (120◦ and 300◦ phases), finalizing with
small spreads at the instances of flow reversal (180◦ and 360◦ phases). For the trough case (Fig. 9
right column), dye remains localized in a smaller region of the domain. This may be attributed to
the large coherent structures present over the troughs that entrap the scalar plume and inhibit dye
spread much more than in the crest case. This is supported by the λci fields (Fig. 4), which show
that large values of λci are present very close to the trough and flanks for the majority of the flow
cycle. These high λci areas only disappear during flow reversal, as the vortices are ejected upwards
and away from the bed.

9
September 20, 2023 Journal of Hydraulic Research output

5 Conclusions

In this effort, a three-dimensional RANS model with a κ − ε closure scheme was coupled to an
advection-diffusion model for scalars, to simulate dye transport under oscillatory flow conditions.
A comparison between observed and simulated velocity fields compares favourably, with time-
averaged results showing locations of flow circulation accurately, albeit with smaller magnitudes in
the simulated case. The RMS velocity magnitudes comparison shows greater similarity. Simulated
time-resolved velocity fields were able to capture the flow separation caused by bedform-induced
pressure gradients, yet some differences were observed in locations with high velocity gradients, such
as the wall crests. These differences may be attributed to the spatial resolution of the numerical
model, as well as the particular turbulence closure scheme used. The model was also able to
successfully resolve boundary layer phase shifts. As suggested by previous efforts, deeper troughs
lead to greater phase lags and to the formation of stronger vortices, as evidenced by our λci results.
The λci comparison showed good agreement in the size and strength of vortices for most flow
phases, although the values during the flow reversal stage were slightly inconsistent.
Turbulent quantities are consistent in terms of maximum values, which were also in agreement
with other experimental efforts (Barr et al., 2004). However, simulated results show greater ho-
mogeneity than observed values. On one hand, the κ − ε turbulence model has been found to
show inaccuracies near walls and in the presence of adverse pressure gradients due to the way
the dissipation rate (ε) is estimated. Previous studies have found that this limitation causes an
overprediction in TKE values (Driver & Seegmiller, 1985). In addition to mechanical vibrations
and roughness elements present in the experimental facility, this can also be a contributing factor
for these discrepancies.
Simulations with scalar sources located at the crest and trough were performed and compared
to experimental results. Time-resolved scalar fields compare favourably in terms of magnitudes,
although the model seems to overestimate dye propagation into the flow. This is especially evi-
denced during flow reversal, where a large plume of low concentration dye is still present in the
model results. This may indicate that the model underpredicts the amount of turbulence. A pos-
sible explanation is that there are likely more diffusive mechanisms present in the experimental
case that cannot be replicated numerically, as well as turbulence dynamics at scales much smaller
than those resolvable by the present model. Comparisons between concentration statistics are gen-
erally in good agreement, even though there are some discrepancies in the time-resolved results.
The intermittency results are of particular interest, showing a significant overprediction in the
model that is consistent with the lower dye dissipation rate, particularly for the crest case. The
trough case shows better agreement. Nonetheless, the locations of significant intermittency values
show qualitatively favourable agreement in both cases. This suggests that using different concen-
tration thresholds depending on the location of the scalar source could improve the intermittency
magnitude predictions. This is highly relevant, as it indicates that the present three-dimensional
model shows promise and may be useful in the study of scalar transport in turbulent oscillatory
flows, which have been shown to be regulated by highly intermittent phenomena. Results suggest
that the numerical model struggles during the phases around the beginning of the vortex ejection
process, yet improves once the vortices have completely detached for the crest case. In contrast,
the modeled trough case behaves better during these phases as dye remains localized in a smaller
region of the domain. This behavior is reflected in the concentration statistics, where the model
predicts a slightly lower peak concentration for the crest case near the injection point. However, the
agreement between the model and the experiments improves significantly as the vortices detach.
Overall, the results demonstrate the importance of considering the specific flow and scalar source
configuration when evaluating the performance of numerical models for turbulent scalar transport
over wavy walls.

10
September 20, 2023 Journal of Hydraulic Research output

Acknowledgments

The authors are grateful to the Coastal Boundary Layers Lab research group at the University of
Puerto Rico Mayagüez Campus for their help in providing the experimental results used in this
study. Special thanks to Dr. Umberto Ciri, for sharing his insight and access to the University of
Texas TACC clusters, which were crucial to this work. The authors also kindly acknowledge Juan
Vargas–Martı́nez and Dr. Gustavo Gutierrez for their help and insights.

Disclosure

The authors report there are no competing interests to declare.

Funding

This work was supported by the NSF under OCE-1753158.

Supplemental data

The model setup and data presented in this paper may be obtained free of charge upon request.

11
September 20, 2023 Journal of Hydraulic Research output

Notation

A = wave excursion amplitude (m)

C = scalar concentration (–)
C0 = source concentration (–)
CRM S t = Root-mean-squared scalar concentration (–)
C1 = calibration coefficient (–)
C2 = calibration coefficient (–)
Cµ = calibration coefficient (–)
Comax = maximum allowable Courant number (–)
D = molecular diffusion coefficient (m2 s−1 )
D = velocity gradient tensor (s−1 )
Dε = effective diffusivity for ε (m2 s−1 )
Dκ = effective diffusivity for κ (m2 s−1 )
Dt = turbulent diffusion coefficient (m2 s−1 )
f = external forces per unit mass (m s−2 )
g = gravitational acceleration (m s−2 )
I = identity matrix (–)
I = turbulence intensity (–)
KP = turbulent kinetic energy production rate (m2 s−3 )
L = characteristic length scale (m)
lk = Kolmogorov length scale (m)
p = pressure (Pa)
p = time-averaged pressure (Pa)
p′ = fluctuating pressure (Pa)
R = Reynolds stress tensor (m2 s−2 )
Sct = turbulent Schmidt number (–)
T = wave period (s)
tk = Kolmogorov time scale (s)
U0 = time-varying free-stream velocity (m s−1 )
U1 = velocity amplitude (m s−1 )
U2 = velocity amplitude (m s−1 )
u = velocity vector (m s−1 )
u = time-averaged velocity (m s−1 )
u′ = fluctuating horizontal velocity (m s−1 )
u′ u′ = horizontal component of the Reynolds stress tensor (m2 s−2 )
u′ w′ = Reynolds stress (m2 s−2 )
uk = Kolmogorov velocity scale (m s−1 )
uref = characteristic velocity scale (m s−1 )

12
September 20, 2023 Journal of Hydraulic Research output

uRM S t = Root-mean-squared horizontal velocity (m s−1 )

w′ = fluctuating vertical velocity (m s−1 )
w′ w′ = vertical component of the Reynolds stress tensor (m2 s−2 )
wRM S t = Root-mean-squared vertical velocity (m s−1 )
x = horizontal coordinate (cm)
y = spanwise coordinate (cm)
z = vertical coordinate (cm)
∆t = solution time step (s)
∆tmax = maximum allowable solution time step (s)
∆tmin = minimum allowable solution time step (s)
∆x = horizontal grid size (mm)
∆z = vertical grid size (mm)
γ = concentration intermittency (–)
ϵ = absolute error
ε = turbulent kinetic energy dissipation rate (m2 s−3 )
η = bedform height (cm)
θ = concentration threshold (–)
ν ci = imaginary component of eigenvector (s−1 )
ν cr = real component of eigenvector (s−1 )
νr = real eigenvector (s−1 )
κ = turbulent kinetic energy (m2 s−2 )
κRM S t = Root-mean-squared turbulent kinetic energy (m2 s−2 )
λ = bedform length (cm)
λci = local swirling strength (s−1 )
λcr = real part of complex eigenvalue (s−1 )
λr = real eigenvalue (s−1 )
µ = dynamic viscosity (kg m−1 s−1 )
νt = turbulent eddy viscosity (m2 s−1 )
νtRM S t = Root-mean-squared turbulent eddy viscosity (m2 s−1 )
ρ = fluid density (kg m−3 )
σ0 = wave phase shift (–)
τ = ensemble-averaged fluid stress tensor (Pa)
Ω = scalar source or sink (–)
ω = wave radian frequency (s−1 )

References

Barr, B. C., Slinn, D. N., Pierro, T., & Winters, K. B. (2004). Numerical simulation of turbulent,
oscillatory flow over sand ripples. Journal of Geophysical Research: Oceans, 109 (C9).
Blondeaux, P., & Vittori, G. (1991). Vorticity dynamics in an oscillatory flow over a rippled bed.
Journal of Fluid Mechanics, 226, 257–289.
Bomminayuni, S., Stoesser, T., & Rüther, N. (2014). Dispersion of a passive scalar in turbulent
open channel flow. Proceedings of the International Conference on Fluvial Hydraulics, RIVER
FLOW 2014.
Chatwin, P. C., & Sullivan, P. J. (1993). The structure and magnitude of concentration fluctuations.
Boundary-Layer Meteorology, 62, 269-280.
Chen, X., & Yu, X. (2015). A numerical study on oscillatory flow-induced sediment motion over
vortex ripples. Journal of Physical Oceanography.
Crimaldi, J. P., Wiley, M. B., & Koseff, J. R. (2002). The relationship between mean and instan-

13
September 20, 2023 Journal of Hydraulic Research output

taneous structure in turbulent passive scalar plumes. Journal of Turbulence, 3, N14.

Davies, A., & Thorne, P (2005). Modeling and measurement of sediment transport by waves in the
vortex ripple regime. Journal of Geophysical Research, 110.
Driver, D. M., & Seegmiller, H. L. (1985). Features of a reattaching turbulent shear layer in
divergent channel flow. AIAA Journal, 23 (2), 163-171.
Förstner, U. (1987). Sediment-associated contaminants - an overview of scientific bases for devel-
oping remedial options. Hydrobiologia, 149 (1), 221–246.
Grigoriadis, D. G., Dimas, A. A., & Balaras, E. (2012). Large-eddy simulation of wave turbulent
boundary layer over rippled bed. Coastal Engineering, 60, 174-189.
Huettel, M., Cook, P., Janssen, F., Lavik, G., & Middelburg, J. (2007). Transport and degradation
of a dinoflagellate bloom in permeable sublittoral sediment. Marine Ecology-progress Series -
MAR ECOL-PROGR SER, 340, 139-153.
Hurther, D., & Thorne, P. D. (2011). Suspension and near-bed load sediment transport processes
above a migrating, sand-rippled bed under shoaling waves. Journal of Geophysical Research:
Oceans, 116 (C7).
Jonsson, I., & Carlsen, N. (1976). Experimental and theoretical investigations in an oscillatory
turbulent boundary layer. Journal of Hydraulic Research, 14 (1), 45-60.
Lin, M., & Yuan, Z. (2005). An experimental study of the flow field over wavy beds under oscillatory
flow. Chinese Journal of Geophysics, 48 (6), 1526-1535.
Longuet-Higgins, M. S. (1981). Oscillating flow over steep sand ripples. Journal of Fluid Mechanics,
107 , 1–35.
Malarkey, J., & Davies, A. G. (2004). An eddy viscosity formulation for oscillatory flow over vortex
ripples. Journal of Geophysical Research: Oceans, 109 (C12).
McCave, I. (1976). The benthic boundary layer. Springer New York, NY.
Nielsen, P. (1992). Coastal bottom boundary layers and sediment transport. World Scientific.
Ouro, P., Fraga, B., Viti, N., Angeloudis, A., Stoesser, T., & Gualtieri, C. (2018). Instantaneous
transport of a passive scalar in a turbulent separated flow. Environmental Fluid Mechanics, 18,
487-513.
Penko, A., Calantoni, J., Rodrı́guez-Abudo, S., Foster, D., & Slinn, D. (2013). Three-dimensional
mixture simulations of flow over dynamic rippled beds. Journal of Geophysical Research: Oceans,
118 (3), 1543-1555.
Rodrı́guez-Abudo, S., Foster, D. L., & Henriquez, M. (2013). Spatial variability of the wave bottom
boundary layer over movable rippled beds. Journal of Geophysical Research: Oceans, 118 (7),
3490-3506.
Salimi-Tarazouj, A., Hsu, T.-J., Traykovski, P., Cheng, Z., & Chauchat, J. (2021). A numerical
study of onshore ripple migration using a eulerian two-phase model. Journal of Geophysical
Research: Oceans, 126 (2).
Sato, S., Mimura, N., & Watanabe, A. (1984). Oscillatory boundary layer flow over rippled beds.
Coastal Engineering Proceedings, 1 (19), 154.
Scandura, P., Vittori, G., & Blondeaux, P. (2000). Three-dimensional oscillatory flow over steep
ripples. Journal of Fluid Mechanics, 412, 355–378.
Seuront, L., Schmitt, F., & Lagadeuc, Y. (2001). Turbulence intermittency, small-scale phyto-
plankton patchiness and encounter rates in plankton: Where do we go from here? Deep-sea
Research Part I-Oceanographic Research Papers - DEEP-SEA RES PT I-OCEANOG RES, 48,
1199-1215.
Sleath, J. (1984). Sea bed mechanics. Wiley.
Stokes, G. G. (1851). On the effect of the internal friction of fluids on the motion of pendulums.
In Mathematical and physical papers, 3, 1–10. Cambridge University Press.
Ting, D. (2016). Basics of engineering turbulence. Elsevier.
van der Werf, J. J., Doucette, J. S., O’Donoghue, T., & Ribberink, J. S. (2007). Detailed measure-
ments of velocities and suspended sand concentrations over full-scale ripples in regular oscillatory

14
September 20, 2023 Journal of Hydraulic Research output

flow. Journal of Geophysical Research: Earth Surface, 112 (F2).

Wagner, C., Kuhn, S., & Rudolf von Rohr, P. (2007). Scalar transport from a point source in flows
over wavy walls. Experiments in Fluids, 43, 261-271.
Warhaft, Z. (2000). Passive scalars in turbulent flows. Annu. Rev. Fluid Mech, 32, 203-240.
Wiberg, P. L., & Harris, C. K. (1994). Ripple geometry in wave-dominated environments. Journal
of Geophysical Research, 99 (C1), 775-789.
Zhou, J., Adrian, R. J., Balachandar, S., & Kendall, T. M. (1999). Mechanisms for generating
coherent packets of hairpin vortices in channel flow. Journal of Fluid Mechanics, 387, 353-396.

List of Tables

1 Mean and maximum absolute errors of selected variables at 4 locations along the
ripple profile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

List of Figures

1 (Top) Full computational domain with boundary conditions (grid sizes not to scale).
(Bottom) Three-dimensional area of interest in the computational domain with the
locations of point sources. The x–z slice located at y = 0 indicates the area of
interest further presented in the results section. . . . . . . . . . . . . . . . . . . . . 16
2 Front view of the Oscillating Boundary Layer Apparatus. . . . . . . . . . . . . . . 17
3 (a) Observed (left column) and simulated (right column) time-averaged velocity
fields over their corresponding time-averaged concentration fields. (b) Observed and
simulated root-mean-squared velocity fields over their corresponding root-mean-
squared concentration fields. (c) Observed and simulated phase difference between
the horizontal velocity field and the free-stream horizontal velocity. Scale vectors in
m s−1 are shown at the bottom of each panel. . . . . . . . . . . . . . . . . . . . . . 17
4 (a) Free-stream horizontal velocity. (b–g) Observed (left column) and simulated
(right column) phase-averaged velocity fields (m s−1 ) over swirling strength fields,
λci (s−1 ), labeled according to the time instances in (a). Scale vectors of 0.3 m s−1
are shown at the bottom left of each panel. . . . . . . . . . . . . . . . . . . . . . . 18
5 Time-averaged (a) observed and (b) simulated Reynolds stress (u′ w′ ). Observed (c)
and simulated (d) horizontal component of Reynolds stress tensor (u′ u′ ). Observed
(e) and simulated (f) vertical component of Reynolds stress tensor (w′ w′ ). . . . . . 19
6 (a) Free-stream horizontal velocity. (b–g) Observed (left column) and simulated
(right column) concentration fields, C /C0 , for a crest point source, labeled according
to the time instances in (a). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
7 (a) Free-stream horizontal velocity. (b–g) Observed (dots) and simulated (solid lines)
spatially-averaged concentration profiles at phases labeled according to the time
instances in (a). Black values indicate a crest source, while red values correspond to
trough. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
8 (a) Observed (dots) and simulated (solid lines) spatially-averaged mean concentra-
tion profiles. (b) Observed (dots) and simulated (solid lines) spatially-averaged inter-
mittency profiles. Black values indicate a crest source, while red values correspond
to trough. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
9 (Top) Free-stream horizontal velocity. (a) Extent and (b) centroid location of simu-
lated dye plumes for a point source located at the ripple crest (left column) and at
the ripple trough (right column). Phases are color-coded as in the top panel. . . . 22

15
September 20, 2023 Journal of Hydraulic Research output

5.1 Tables

Table 1: Mean and maximum absolute errors of selected variables at 4 locations along the ripple
profile.
Position
Variables Trough Left Flank Crest Right Flank
|ϵ| |ϵ|max |ϵ| |ϵ|max |ϵ| |ϵ|max |ϵ| |ϵ|max
uRM S t
0.76E-02 1.91E-02 0.53E-02 2.92E-02 0.58E-02 2.66E-02 0.49E-02 2.16E-02
(m s−1 )
wRM S t
0.17E-02 0.49E-02 0.25E-02 0.14E-02 0.23E-02 1.04E-02 0.13E-02 0.65E-02
(m s−1 )
νtRM S t
1.79E-06 8.99E-06 0.79E-06 5.14E-06 0.84E-06 5.81E-06 1.24E-06 4.94E-06
(m2 s−1 )
κRM S t
1.36E-04 7.55E-04 1.12E-04 7.29E-04 1.19E-04 7.88E-04 0.99E-04 6.54E-04
(m2 s−2 )
CRM S t
0.12E-02 0.97E-02 0.29E-02 7.48E-02 0.07E-02 5.81E-02 0.23E-02 5.93E-02
(–)

5.2 Illustrations (figures)

Figure 1: (Top) Full computational domain with boundary conditions (grid sizes not to scale).
(Bottom) Three-dimensional area of interest in the computational domain with the locations of
point sources. The x–z slice located at y = 0 indicates the area of interest further presented in the
results section.
.

16
September 20, 2023 Journal of Hydraulic Research output

Figure 2: Front view of the Oscillating Boundary Layer Apparatus.

.

Figure 3: (a) Observed (left column) and simulated (right column) time-averaged velocity fields
over their corresponding time-averaged concentration fields. (b) Observed and simulated root-
mean-squared velocity fields over their corresponding root-mean-squared concentration fields. (c)
Observed and simulated phase difference between the horizontal velocity field and the free-stream
horizontal velocity. Scale vectors in m s−1 are shown at the bottom of each panel.
.

17
September 20, 2023 Journal of Hydraulic Research output

Figure 4: (a) Free-stream horizontal velocity. (b–g) Observed (left column) and simulated (right
column) phase-averaged velocity fields (m s−1 ) over swirling strength fields, λci (s−1 ), labeled
according to the time instances in (a). Scale vectors of 0.3 m s−1 are shown at the bottom left of
each panel.
.

18
September 20, 2023 Journal of Hydraulic Research output

Figure 5: Time-averaged (a) observed and (b) simulated Reynolds stress (u′ w′ ). Observed (c) and
simulated (d) horizontal component of Reynolds stress tensor (u′ u′ ). Observed (e) and simulated
(f) vertical component of Reynolds stress tensor (w′ w′ ).
.

19
September 20, 2023 Journal of Hydraulic Research output

Figure 6: (a) Free-stream horizontal velocity. (b–g) Observed (left column) and simulated (right
column) concentration fields, C /C0 , for a crest point source, labeled according to the time instances
in (a).
.

20
September 20, 2023 Journal of Hydraulic Research output

Figure 7: (a) Free-stream horizontal velocity. (b–g) Observed (dots) and simulated (solid lines)
spatially-averaged concentration profiles at phases labeled according to the time instances in (a).
Black values indicate a crest source, while red values correspond to trough.

Figure 8: (a) Observed (dots) and simulated (solid lines) spatially-averaged mean concentration
profiles. (b) Observed (dots) and simulated (solid lines) spatially-averaged intermittency profiles.
Black values indicate a crest source, while red values correspond to trough.

21
September 20, 2023 Journal of Hydraulic Research output

Figure 9: (Top) Free-stream horizontal velocity. (a) Extent and (b) centroid location of simulated
dye plumes for a point source located at the ripple crest (left column) and at the ripple trough
(right column). Phases are color-coded as in the top panel.

22