A dynamic equation for the potential energy anomaly for

analysing mixing and stratication in estuaries and coastal seas

Hans Burchard
*
, Richard Hofmeister
Baltic Sea Research Institute Warnemu nde, Seestrasse 15, D-18119 Rostock, Germany
Received 16 July 2007; accepted 31 October 2007
Available online 6 November 2007
Abstract
In this paper, a time-dependent dynamic equation for the potential energy anomaly, f, is rigorously derived from dynamic equations for po-
tential temperature and salinity, the continuity equation and the equation of state for sea water. The terms locally changing f are (A) the f-
advection, (B) the depth-mean straining, (C) the non-mean straining, (D) the vertical advection, (E) the vertical mixing, (F) surface and bottom
density uxes, (G) inner sources of density e.g. due to absorption of solar radiation and the non-linearity of the equation of state, and (H) hor-
izontal divergence of horizontal turbulent density uxes. In order to derive the equation in concise form, a vertical velocity (linearly varying with
depth) with respect to depth-proportional vertical coordinates had to be dened. The evaluation of the terms in the f-equation is then carried out
for a one-dimensional tidal straining study and a two-dimensional estuarine circulation study. Comparisons to empirical estimates for these terms
are made for the one-dimensional study. It is concluded that the f-equation provides a general reference for empirical bulk parameterisations of
stratication and mixing processes in estuaries and coastal seas and that it is a tool for complete analysis of the relevant terms from numerical
models.
2007 Elsevier Ltd. All rights reserved.
Keywords: mixing; stratication; estuaries; potential energy anomaly; tidal straining; differential advection
1. Introduction
Processes of stratication and destratication play a major
role in the physics of shallow coastal seas. It is therefore es-
sential to dene a suitable measure for the stability of the wa-
ter column, which can be easily quantied from eld
observations as well as from numerical models. As a conve-
nient measure, the potential energy anomaly f has been de-
ned by Simpson (1981) as the amount of mechanical
energy (per m
3
) required to instantaneously homogenise the
water column with a given density stratication:
f
1
D
_
h
H
gzr r dz
1
D
_
h
H
gz~r dz 1
with the depth-mean density
r
1
D
_
h
H
r dz; 2
the deviation from the depth-mean density, ~r r r, the
mean water depth H, the sea surface elevation h, the actual
water depth D h H, and the gravitational acceleration g.
Due to its tremendous relevance to the marine ecosystem,
the understanding of stratication and de-stratication pro-
cesses in shelf seas has been intensively studied during the
last decades. In their key paper on fronts in the Irish Sea,
Simpson and Hunter (1974) made an important step towards
quantifying processes determining stratication in shelf seas.
Simpson et al. (1977) rst suggested to use the potential den-
sity of the water column derived from continuous density pro-
les as a measure for stratication, and Simpson (1981) nally
dened the potential energy anomaly as shown in eq. (1).
Several authors have derived dynamic equations for f un-
der idealised conditions. Simpson (1981) assumed vanishing
horizontal density gradients and divergence-free depth-mean
* Corresponding author.
E-mail address: hans.burchard@io-warnemuende.de (H. Burchard).
0272-7714/$ - see front matter 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.ecss.2007.10.025
Available online at www.sciencedirect.com
Estuarine, Coastal and Shelf Science 77 (2008) 679e687
www.elsevier.com/locate/ecss
horizontal currents and considered surface heat uxes as the
only source of stratication, and from these assumptions de-
rived a f-equation including f-advection, surface heat ux
and vertical mixing. The f-advection term has been neglected
by van Aken (1986), but he added the effects of horizontal
density gradients (constant over the vertical). This process
was denoted as differential advection and includes effects of
tidal straining and estuarine circulation. Recently, in order to
investigate the processes of stratication and mixing in an
idealised Rhine outow model, de Boer et al. (submitted for
publication) derived a dynamic equation for f under the as-
sumptions of constant water depth and zero surface and bot-
tom density uxes, as well as vanishing horizontal turbulent
transport and sea surface elevation and water depth gradients.
There have been many suggestions made for parameterisa-
tions of the source and sink terms in the f-equation. Based on
constant bulk mixing efciencies and drag coefcients, Simp-
son (1981) and Simpson and Bowers (1981) derived expres-
sions for wind and tidal mixing. Since indeed the mixing
efciency is highly variable (zero for vanishing stratication),
Simpson and Bowers (1981) suggested mixing efciencies de-
pending on f itself. Nunes Vaz et al. (1989) parameterised the
mixing effect of convective surface cooling by means of a con-
stant mixing efciency for this process. As further mixing pro-
cess, Wiles et al. (2006) parameterised the effect of surface
wave breaking as function of signicant wave height and
wave period. Straining of vertically constant horizontal den-
sity gradients by tides and estuarine circulation has been para-
meterised by Simpson et al. (1990) on the basis of velocity
proles from analytical theory for tidal ow and for estuarine
circulation. Wiles et al. (2006) furthermore suggested an
empirical expression for the effect of absorption of short-
wave radiation in the water column and (for shallow water)
at the sea bed.
The potential energy anomaly has been used in numerous
studies for quantifying the relative contributions of different
processes of stratication and de-stratication in coastal seas
and estuaries. Early studies concentrated on the positions
and movements of fronts in shelf seas, see e.g. Simpson
et al. (1977), Simpson (1981) and Simpson and Bowers
(1981) who analysed eld data from the Irish Sea and the Brit-
ish Channel, and van Aken (1986) who studied frontal dynam-
ics in the Southern North Sea. Mixing by surface cooling and
re-stratication by dense water overows have been studied by
Rippeth and Simpson (1996) for the Clyde Sea. The competi-
tion between tidal straining and vertical mixing has been
intensively investigated for the Liverpool Bay by Simpson
et al. (1990), Sharples and Simpson (1995), Rippeth et al.
(2001), and Scott (2004). For the shallow Limfjord in Den-
mark in which competition between the straticational effects
of estuarine circulation and surface heating and the mixing due
to wind, waves and surface cooling leads to episodic stratica-
tion in summer with potentially hazardous consequences for
benthic lter feeder populations, Wiles et al. (2006) studied
the balance of empirical source terms in the f-equation. The
dynamics of Intermittently Closed and Open Lakes and
Lagoons (ICOLLs) has been intensively studied by means of
analysing the empirical f-equation terms by Ranasinghe and
Pattiaratchi (1999) and Gale et al. (2006)
No study however has so far rigorously derived the f-
equation. Effects of sloping sea beds, surface slopes, vertical
variations of horizontal density gradients, vertical advection,
internal heating due to absorption of short-wave radiation,
non-linear effects of the equation of state for sea water and
the divergence of horizontal turbulent density uxes have
not yet been considered.
It is therefore the aim of this study to rigorously derive
a time-dependent dynamic equation for f, based on the
dynamic equations for potential temperature and salinity, the
continuity equation and an equation of state for the potential
density. With these equations given, no further approximations
will be made. A f-equation which is fully consistent with the
dynamic equations discretised in numerical models will pro-
vide a tool for numerically quantifying all terms relevant for
generation and destruction of stratication. It will further
help to improve parameterisations for empirical f-equations
as they have been extensively used for studying the dynamics
of estuaries and coastal seas.
This paper is organised as follows. First, the time-dependent
dynamic equation for f is derived in Section 2 and the result-
ing terms in the f-equation are discussed. Afterwards, the dy-
namics of f is evaluated for idealised vertically-resolving
model studies (Section 3). The models applied for this purpose
are briey introduced in Section 3.1. In Section 3.2, a one-
dimensional study of tidal straining and wind mixing is de-
scribed, and the resulting source terms in the f-equation are
compared to empirical estimates in Section 3.3. In Section
3.4, a two-dimensional estuarine study is presented, with the
evaluation of f-terms at two locations, in the periodically strat-
ied area of the outer estuary and further upstream in the per-
manently stratied salt wedge area. Some conclusions about
implications of the f-equation will be given in Section 4.
2. Dynamic equation for f
The dynamic equation for f will be obtained by combining
the denition of f from eq. (1) with a dynamic equation for the
potential density r, see van Aken (1986). In oceanography, this
may be derived from the dynamic equations for potential tem-
perature q and salinity S:
v
t
qu$V
h
qwv
z
qv
z
K
v
v
z
q V
h
K
h
V
h
q
1
r
0
C
p
v
z
I; 3
v
t
S u$V
h
S wv
z
S v
z
K
v
v
z
S V
h
K
h
V
h
S 0; 4
with the horizontal velocity vector u and the vertical velocity
w, jointly fullling the continuity equation
V
h
u v
z
w 0: 5
Here, V
h
denotes the horizontal gradient operator, such that
V
h
$ u is the horizontal ow divergence. In eqs. (3) and (4),
K
v
and K
h
denote the vertical eddy diffusivity and the horizon-
tal eddy diffusivity, respectively, resulting from down-gradient
680 H. Burchard, R. Hofmeister / Estuarine, Coastal and Shelf Science 77 (2008) 679e687
parameterisations of vertical and horizontal turbulent uxes.
For simplicity, higher order turbulence closure approaches par-
tially resulting in counter-gradient parameterisations are not
considered here, but may be included in this approach in
a straight-forward way. The term on the right-hand side of
the temperature equation is the heating due to absorption of
solar radiation, with the constant reference density r
0
, the
heat capacity C
p
(here assumed to be constant) and the short
wave radiation I, the gradient of which strongly depends on
the light attenuation properties of the water, see Paulson and
Simpson (1977).
For the derivation of a dynamic equation for potential den-
sity based on the temperature and salinity equation, it is essen-
tial to consider the non-linear equation of state for sea water
(see e.g. Jackett et al., 2006):
r rq; S; p
0
0
V
h
r raV
h
q rbV
h
S;
v
z
r rav
z
q rbv
z
S;
v
t
r rav
t
q rbv
t
S;
_

_
6
with the constant reference pressure p
0
, the thermal expansion
coefcient a (1/r)v
qr
and the haline contraction coef-
cient b (1/r)v
S
r.
By combining eqs. (3) and (4) under consideration of eq.
(6), we obtain
v
t
r u$V
h
r wv
z
r v
z
K
v
v
z
r V
h
K
h
V
h
r Q 7
with the source term for density,
Q
ra
r
0
C
p
v
z
I K
v
v
z
q v
z
ra K
v
v
z
S v
z
rb
K
h
V
h
q$V
h
ra K
h
V
h
S$V
h
rb:
8
For the derivation of a dynamic f-equation, we furthermore
need to dene the depth mean horizontal velocity vector
u
1
D
_
h
H
u dz: 9
It is furthermore convenient to dene a vertical velocity w,
which together with u fulls a continuity equation:
V
h
$u v
z
w 0: 10
From eq. (10), it is clear that w is linear and integration of eq.
(10) gives
w u$V
h
H
h z
D
v
t
h u$V
h
h
z H
D
: 11
Here, we have used the vertically integrated incompressibility
equation,
v
t
h V
h
$Du; 12
and we have applied a kinematic boundary condition for w at
the bottom,
wH u$V
h
H: 13
With this, w is the vertical velocity which would result from
kinematic boundary conditions (alignment of the ow velocity
vector with bottom and surface) and the incompressibility con-
dition for the case of vertically homogeneous horizontal ow
velocity. For this case, the ow would be parallel to depth-pro-
portional coordinates (so-called s coordinates, see e.g. Blum-
berg and Mellor (1987)). With this denition of the linearly
varying vertical velocity w, a dynamic equation for f can be
derived in a concise form (see below).
The deviation from the depth-mean horizontal velocity vec-
tor is dened as ~ u u u and the deviation from the linear
vertical velocity as ~ w w w. Surface volume uxes due
to precipitation and evaporation are neglected here for simplic-
ity, but may be included in a straight-forward way.
Combining eqs. (1), (2), (7), (9) and (11), we obtain a time-
dependent dynamic equation for f:
v
t
fV
h
uf
..
A

g
D
V
h
r$
_
h
H
z ~ udz
..
B

g
D
_
h
H
_
h
D
2
z
_
~ u V
h
~rdz
..
C

g
D
_
h
H
_
h
D
2
z
_
~ wv
z
~rdz
..
D

r
0
D
_
h
H
P
b
dz
..
E

r
0
2
_
P
s
b
P
b
b
_
..
F

g
D
_
h
H
_
h
D
2
z
_
Qdz
..
G

g
D
_
h
H
_
h
D
2
z
_
V
h
K
h
V
h
rdz
..
H
; 14
with the vertical buoyancy ux
P
b

g
r
0
K
v
v
z
r; 15
and the surface buoyancy ux P
s
b
and the bottom buoyancy
ux P
b
b
. For the derivation of eq. (14), we have applied the ki-
nematic boundary conditions
wh v
t
h uh$V
h
h; wH uH$V
h
H 16
as well as the Leibniz rule for derivatives of integrals with
moving limits,
v
s
_
bs
as
f s; xdx
_
bs
as
v
s
f s; xdx v
s
bsf s; bs
v
s
asf s; as:
17
681 H. Burchard, R. Hofmeister / Estuarine, Coastal and Shelf Science 77 (2008) 679e687
In eq. (14) the terms on the right-hand side have the following
meaning:
A: f-advection due to the vertical mean horizontal velocity
vector, u, including also density advection with the linearly
varying vertical velocity w as dened in eq. (11)dthe con-
sideration of f-advection has already been suggested by
Simpson (1981), who however assumed a non-divergent
depth-mean ow (V
h
$u 0) for better estimating the
movements of fronts in shelf seas;
B: depth-mean straining, based on the vertical mean hori-
zontal density gradient strained by the deviation from the
depth-mean velocity vector, ~ u; this term has rst been de-
rived by Bowden (1981) and has been denoted as the differ-
ential advection term by van Aken (1986);
C: non-mean straining, based on straining of the devia-
tion from the vertical mean horizontal density gradient;
for the case of no mean horizontal density gradient
(V
h
r 0), the non-mean straining term may still change
the stratication. If in the lower half of the water column
(h D/2 z > 0) the velocity anomaly is in the direc-
tion of decreasing density (~ u$V
h
~r < 0), then the water
column is stabilised (v
t
f > 0), and vice versa, see Fig. 1;
D: vertical advection, based on the deviation from the linear
vertical velocity, ~ w; for a stably stratied two-layer ow the
value of f is largest when the interface between the two
layers is at mid-depth. Therefore, for stable stratication
(v
z
~r < 0), an upward displacement of isopycnals (~ w > 0)
in the lower half of the water column (h D/2 z > 0) in-
creases f and vice versa, see Fig. 1;
E: vertical mixing of density expressed as the integrated
vertical buoyancy ux. By using the dynamic equation
for the turbulent kinetic energy, this term may be expressed
by means of the vertically integrated shear production and
dissipation, see e.g. van Aken (1986);
F: surface and bottom buoyancy uxes, with negative
(downward, e.g. surface warming) buoyancy uxes both in-
creasing f;
G: inner sinks or sources of potential density, with a density
decrease (Q < 0, e.g. solar radiation) in the upper half of
the water column (h D/2 z < 0) increasing f and
vice versa;
H: divergence of horizontal turbulent transport. The struc-
ture of this term is in analogy to term G, i.e. horizontal den-
sity ux divergence (V
h
K
h
V
h
r < 0) in the upper half of
the water column has a stabilising effect.
A
B
C
D
Fig. 1. Sketch explaining the principle of how the kinematic terms AeD in equation eq. (14) change the potential energy anomaly f. (A) Horizontal advection of f
for at (upper left) or sloping (upper right) sea bed. (B) Depth-mean straining. (C) Non-mean straining. (D) Vertical advection.
682 H. Burchard, R. Hofmeister / Estuarine, Coastal and Shelf Science 77 (2008) 679e687
The kinematic terms AeD are graphically sketched in
Fig. 1.
3. Applications to estuarine ow
3.1. Model description
The turbulence closure model which is applied for the verti-
cally resolving simulations of the present study is the k-3 model
with transport equations for the turbulent kinetic energy (TKE),
k, and the turbulence dissipation rate, 3. As second-moment clo-
sure, the model suggested by Cheng et al. (2002) is used.
In several applications, this model has proven to agree
quantitatively well with turbulence observations in coastal
and shelf sea waters, see e.g. the investigations by Burchard
et al. (2002), Simpson et al. (2002), and Arneborg et al.
(2007).
The turbulence closure schemes described above have been
implemented into the Public Domain water column model
GOTM (General Ocean Turbulence Model, see http://
www.gotm.net and Umlauf et al., 2005), which is used here
for the one-dimensional studies described in Section 3.2.
The three-dimensional General Estuarine Transport Model
(GETM, see Burchard and Bolding, 2002; Burchard et al.,
2004) which is used for the two-dimensional estuarine study
in Section 3.4 combines the advantages of bottom-following
coordinates with the turbulence module of GOTM.
3.2. One-dimensional strain-induced periodic
stratication
Here, the dynamics of strain-induced periodic stratication
(SIPS, see Simpson et al., 1990) is studied with the one-di-
mensional model by prescribing a rectilinear tide interacting
with a constant wind stress and a constant density gradient,
both acting in the direction of the ow. For simplicity, Earth
rotation is neglected. With this, the dynamic momentum equa-
tion reads as
v
t
u v
z
A
v
v
z
u z
g
r
0
v
x
r gp
g
t; 18
where the rst term on the right-hand side represents the effect
of the internal pressure gradient and p
g
is the surface slope os-
cillating with period T chosen in such a way that the depth-
averaged transport is sinosodial:
ut u
max
cos
_
2p
t
T
_
; 19
with the vertical mean velocity amplitude u
max
(see Burchard,
1999 for details). In eq. (18), A
v
denotes the vertical eddy
viscosity.
In this one-dimensional case, the transport equation for
density is given as
v
t
r uv
x
r v
z
K
v
v
z
r 0; 20
with zero density uxes through surface and bottom.
For the simulation discussed here, the following parameters
are used: constant water depth D H 10 m; tidal period
T 44,714 s (same as for M
2
tide); tidal velocity amplitude
u
max
0.5 m s
1
, constant horizontal density gradient v
x
r
5 10
4
kg m
4
; surface wind stress t
s
0.1 N m
2
(equivalent to a 10 m wind speed of the order of 5 m s
1
).
Fig. 2 shows the resulting density structure, potential en-
ergy anomaly f and the balance of the f-equation after 30
tidal periods. After ood (t/T 0 and t/T 1), the water col-
umn is vertically fully homogenised, resulting in vanishing f.
With the onset of the ebb current (0 t/T 0.5), less dense
water is sheared over denser water, with an increasingly pos-
itive straining term, not fully balanced by vertical mixing,
such that f is growing. At the end of the ebb tide (t/
T 0.4), the vertical mixing is ceasing, leading to a maximum
increase of f. After the onset of ood (t/T > 0.5), straining is
reversed with the effect of decreasing f. With full ood (t/
T 0.75) vertical mixing is supporting the erosion of strati-
cation, resulting in a maximum decrease of f at t/T 0.8, and
slightly unstable stratication (f < 0). With unstable
1.0
10
8
6
4
2
0
0.0 0.2 0.4 0.6 0.8
Density , contour interval: 0.5 kg m
3
z

/

m
5
0
5
10
15
20
25
0 0.2 0.4 0.6 0.8 1

/

J
m

3
5
4
3
2
1
0
1
2
0 0.2 0.4 0.6 0.8 1
t / T
t

/

(
1
0
-
3
W

m
-
3
)
Tendency (
t
)
Vertical mixing (E)
Depth-mean Straining (B)
Fig. 2. Idealised one-dimensional simulation of tidal straining during one tidal
cycle. Upper panel: time series of density proles; middle panel: time series of
potential energy anomaly f; lower panel: time series of the tendency (v
t
f),
vertical mixing (E) and depth-mean straining (B) terms in the f-equation.
There is ebb tide for t/T < 0.5 and ood tide for t/T > 0.5.
683 H. Burchard, R. Hofmeister / Estuarine, Coastal and Shelf Science 77 (2008) 679e687
stratication, however, mixing is increasing f, such that for
the last phase of the ood tide (0.8 < t/T < 1) destabilising
straining and stabilising mixing are in balance.
3.3. Comparison to empirical estimates
Simpson et al. (1990) suggested an empirical model for es-
timating some of the forcing terms in the f-equation. Their
model is valid for scenarios with ow and gradients only in
one horizontal direction (which is here aligned with the x-di-
rection, with the x-component of the ow velocity denoted
as u). For the depth-mean straining term (B) they overlaid
an empirical prole for unstratied tidal ow (see Bowden
and Fairbairn, 1952) with a prole for estuarine circulation
derived from analytical theory (see Ofcer, 1976) as estimate
for ~u. With these assumptions, the empirical depth-mean
straining term is of the following form:
v
t
f
B

_
au b
gD
3
A
v
r
0
v
x
r
_
gDv
x
r 21
with the empirical parameters a 0.031 and b 0.0031, and
the depth mean eddy diffusivity
A
v
gjujD; 22
see Simpson et al. (1990). In eq. (22), g is an empirical param-
eter which is estimated here as g 0.00333 (see also Nunes
Vaz et al. (1989)) by taking the depth average of the parabolic
empirical eddy viscosity formulation for channel ow (see e.g.
Fischer et al. (1979)):
A
v
ku

z
_
1
z
D
_
kc
1=2
d
juj z
_
1
z
D
_
23
with the bed friction coefcient c
d
2.5 $ 10
3
, the von Kar-
man number k 0.4 and the bed friction velocity, u
*
. In order
to prevent the estuarine circulation part of eq. (21) from in-
creasing towards innity for slack tides, a lower background
limit for A
v
has been prescribed as one tenth of the maximum
value.
The mixing term has been estimated by Simpson et al.
(1990) as
v
t
f
E
c
d
Gr
0
ju
3
j
D
24
with the bulk mixing efciency G. Here we use G 0.04,
which means that 4% of the turbulent kinetic energy produced
in the entire water column is used for vertical mixing (increas-
ing the potential energy) and 96% are dissipated into heat.
Given that a typical local mixing efciency is 20% for strati-
ed ow (Osborn, 1980) and that unstably or neutrally strati-
ed situations (with negative or zero mixing efciencies) are
present at times, a bulk mixing efciency of 4% seems reason-
able. This is by a factor of 10 larger than the value chosen by
Simpson et al. (1990) who used estimates from mixing in shelf
seas which are substantially deeper than the 10 m deep test
case considered here and where mixing is probably is much
less efcient due to the typically well-mixed bottom boundary
layer. Thus, the bulk mixing efciency may be considered as
an adjustable parameter which may be estimated by means
of comparing v
t
f
E
from eq. (24) and the mixing term E in
eq. (14).
Wind mixing, although included in our simulations dis-
cussed in Section 3.2, is not considered for this comparison,
since it is here hardly contributing to changes in f. Nonethe-
less, in order to roughly separate mixing in the surface (SBL)
and in the bottom boundary layer (BBL), we have estimated
the height of the SBL by nding at each time the highest local
minimum of the turbulent kinetic energy (TKE) and dening
this location as the lower bound of the SBL. The tidal mixing
part of term B in the f-equation has then been dened as the
integral of the buoyancy ux G from the bottom to the lower
bound of the SBL, thus excluding wind mixing.
Fig. 3 shows a comparison between the straining and mix-
ing terms of the f-equation computed from the one-dimen-
sional model in Section 3.2 and as estimated from the
empirical model given in the equations (21) and (24). It can
be seen that there is good agreement for the straining term be-
tween the empirical and the resolved model only during late
ood when stratication is weak. During full ebb (t/
T 0.25) and full ood (t/T 0.75) straining is underesti-
mated by the empirical model, because the modication of
the velocity proles due the tidal mixing asymmetry (en-
hanced mixing during ood and suppressed mixing during
ebb due to tidal straining, see Jay and Musiak, 1994), is not
considered. The mixing terms of the resolved and the empiri-
cal model are in quite good agreement for ebb (0 < t/T < 0.5).
However for ood, the agreement is poor, in the rst half of
the ood (0.5 < t/T < 0.75) due to a time lag between mixing
and ow velocity represented only in the resolved model, and
around the end of the ood (0.8 < t/T < 0.95) due to the fact
that most of the mixing acts on unstable stratication in the re-
solved model, such that the effective bulk mixing efciency
becomes negative. The mixing term may be parameterised in
a more realistic way by using a formulation with the mixing
efciency varying with the value of f (see Simpson and
Bowers, 1981).
3
2
1
0
1
2
0 0.2 0.4 0.6 0.8 1
t/T
Vertical mixing (1D)
Vertical mixing (emp)
Depth-mean Straining (1D)
Depth-mean Straining (emp)
t

/

(
1
0
-
3
W

m
-
3
)
Fig. 3. Comparison between forcing terms in the f-equation as calculated from
the one-dimensional model discussed in Section 3.2 (full lines) and as esti-
mated from the empirical model suggested by Simpson et al. (1990) (dashed
lines). The bold lines show the vertical mixing term (E) and the thin lines
show the depth-mean straining term (B).
684 H. Burchard, R. Hofmeister / Estuarine, Coastal and Shelf Science 77 (2008) 679e687
3.4. Two-dimensional estuarine dynamics
For studying the impact of f-advection (term A in eq. (14)),
the non-mean straining (term C in eq. (14)) and vertical
advection (term D in eq. (14)), which are all not included in
the one-dimensional simulations of Section 3.2, we carry out
a two-dimensional simulation along an idealised estuary.
This scenario is a slight modication of the idealised estuarine
used by Warner et al. (2005) for comparing various turbulence
closure schemes. The length of the estuary is 100 km, the
depth is linearly decreasing from the open boundary at the
river mouth at x 0 km (depth: 15 m) to the riverine boundary
at x 100 km (depth: 10 m). Earth rotation is neglected. The
horizontal resolution is Dx 500 m, and 20 equidistant s
layers are used in the vertical. The timestep is dt 20 s for
the barotropic mode (explicitly calculated free surface) as
well as for the baroclinic mode, including the rate of change
of potential energy and its contributions. As initial conditions,
we chose the same setup as Warner et al. (2005), with a verti-
cally homogeneous salt distribution, with a salinity of 30 for
x 30 km, a salinity of 0 for x 80 km and decreasing line-
arly from 30 to 0 in between. As boundary conditions, we pre-
scribe a salinity of 30 at x 0 and a freshwater runoff at the
river boundary with a velocity of 0.01 m s
1
. At the open
boundary, we further prescribe a sinosodial semi-diurnal tide
with a sea surface elevation amplitude of 1 m, resulting into
a horizontal velocity amplitude of about 1 m s
1
near the
open boundary. Meteorological forcing is not considered. In
order to allow for complete destabilisation of the water column
due to tidal straining at the end of the ood in parts of the es-
tuary, the present scenario deviates from the Warner et al.
(2005) idealised estuary by increased the tidal forcing and
depth and decreased freshwater inow.
The simulation was carried out for 8 days. After about
5 days, a periodic steady state is reached, with a salt wedge
moving up and down the estuary with the tide, see the snap-
shot at the end of ebb in Fig. 4.
The dynamics of the potential energy anomaly is examined
at two locations with different characteristics: at x 38 km
(position A), where the SIPS mechanism fully destabilises
the water column during ood and at x 80 km (position
B), where the water column is strongly stratied during the
whole tidal period.
At position A, the dynamics is comparable to the situation
simulated with the one-dimensional model in Section 3.2. The
only terms playing a signicant role are the depth-mean strain-
ing and the vertical mixing, see Fig. 5. After the end of ebb, f
has a maximum, which is then steeply eroded by both, depth-
mean straining and mixing, such that at full ood the water
column becomes unstably stratied. Here, in contrast to the
one-dimensional study, a local maximum of f is visible
around the slack water after ood, showing that here estuarine
circulation is more effective than in the one-dimensional
model. A similar intensication of the stratication maximum
after slack tide ood has been observed by Burchard et al. (in
press) for a three-dimensional model simulation in the Wadden
Sea if horizontal density gradients are considered. A small
contribution of f-advection is also visible for location A.
At location B, the balance of the terms in the f-equation is
completely different. Here, the major balance is between the
f-advection, the vertical advection and the depth-mean strain-
ing. Smaller contributions come from vertical mixing and
non-mean straining. After ebb, f has a minimum value, since
the salt wedge, the maximum extent of which is always up-
stream of location B, has a minimum thickness at minimum
density. After the onset of ood, f-advection strongly forces
stabilisation of stratication, however, depth-mean straining is
opposing to it, similarly to the situation at location A. With in-
creasing ood current, the vertical advection is stabilising the
ow as well, due to a rise of the main halocline. At slack tide
after ood, f has a maximum value, which is then mainly re-
duced by f-advection, again opposed by depth-mean straining.
The signicant role of the non-mean straining is explained here
by the fact that the horizontal density gradient is substantial in-
side the salt wedge, but negligible in the near-surface waters.
4. Conclusions
With the time-dependent dynamic equation for the potential
energy anomaly, f, which has been rigorously derived here
from the dynamic equations for potential temperature and sa-
linity, the continuity equation and the equation of state for sea
water, we have now provided a complete reference solution for
all empirical model parameterisations. The physical basis
which has been used here is sufciently general for including
most of the processes relevant for estuaries and coastal seas.
0 10 20 30 40 50 60 70 80 90 100
15
10
5
0
2
4
6
8
10 12
14 16 18
20 22 24 26 28
A B
x / km
z

/

m
Fig. 4. Salinity distribution in the idealised estuary near the end of ebb. The sections A and B indicate the two positions at which time series of f and the terms in
the f-equation have been extracted, see Fig. 5.
685 H. Burchard, R. Hofmeister / Estuarine, Coastal and Shelf Science 77 (2008) 679e687
The major approximation on which the dynamic equations for
potential temperature and salinity are based on is the Reynolds
averaging of state variables leading to the denition of turbu-
lent uxes. The down-gradient approximation for these turbu-
lent uxes applied here has been included for convenience
since it is used in most coastal models, but a general formula-
tion of the turbulent salt and heat uxes could be considered in
a straight-forward way. A number of thermodynamic approx-
imations has been made as well, commonly summarised as the
Boussinesq approximation. Some of these idealisations could
also be relaxed and included into the f-equation. With the
f-equation, we have now a tool for completely quantifying
the processes of mixing and stratication from numerical
model simulations.
In realistic estuarine and coastal scenarios, all terms in the
f-equation will be present, but typically the major local bal-
ance will be based on a few terms only. It is however clear
from the two-dimensional estuarine scenario discussed in Sec-
tion 3.4 that completely different regimes may be spatially lo-
cated close to each other, each with a different balance of
terms. Regimes may also change in time (e.g. seasonal cycle,
spring-neap cycle) and with this also the balance of terms in
the f-equation.
Great effort has been made by many studies to nd empir-
ical estimates for various processes leading to depth-mean
straining (term B) and vertical mixing (term E), for which
the f-equation provides only one term each. Depth-mean
straining is divided into estuarine circulation (asymmetric)
and tidal straining (symmetric for ebb and ood), see equa-
tion eq. (21). It should in principle be possible in numerical
model studies to separate tidal ow velocity proles into
symmetric and asymmetric parts in order improve the empir-
ical estimates for depth-mean straining, but wind, Earth
rotation and non-rectilinear tides would complicate this. Al-
though rotational effects are not directly included in the f-
equation, they have an indirect impact on the stability of
the water column through the advection and straining terms.
This has been demonstrated by Rippeth et al. (2001) in their
eld observations of transverse straining in Liverpool Bay
due to Coriolis acceleration; see also the numerical simula-
tions by Simpson et al. (2002).
Due to non-linear interactions, similar problems would
arise for numerically separating inuences of wind, tides, sur-
face cooling and waves on vertical mixing. An attempt to do
so has been demonstrated in Section 3.3 where wind mixing
was assumed to be the part of mixing which takes place in
the surface mixing layer, dened by the depth range above
the highest TKE minimum in the water column. This worked
ne for constant wind stress, but for highly varying wind stress
and simultaneous impact of surface waves and surface cooling,
these impacts can practically not be separated. This means that
for realistic ow situations empirical estimates of mixing will
be inaccurate and that the model-based mixing impact on strat-
ication as given by the potential energy anomaly has to be
limited to term E, the vertically integrated vertical buoyancy
ux.
Acknowledgements
The authors are grateful to John Simpson (Bangor, Wales),
Charita Pattiaratchi (Crawley, Australia), Rainer Feistel (War-
nemunde, Germany), Julie Pietrzak and Gerben de Boer
(Delft, The Netherlands) for their valuable comments on the
manuscript. We are further indebted to Karsten Bolding (Bar-
ing, Denmark) for keeping GOTM and GETM up and running
1T 2T 3T
0
5
10

/

J
m
-
3
A
3
2
1
0
1
2
x 10
3
t
t

/

W
m
-
3
t / T
1T 2T 3T
45
50
55
60
B
1
0.5
0
0.5
1
1.5
x 10
3
t / T

3
depthmean straining mixing advection vertical advection nonmean straining :
Fig. 5. Time series of f (upper panels) and the terms in the f-equation (lower panels) for the locations indicated in Fig. 4. The terms shown in the lower panel are
the depth-mean straining (term B in eq. (14)), vertical mixing (term E in eq. (14)), f-advection (term A in eq. (14)), vertical advection (term D in eq. (14)), and
non-mean straining (term C in eq. (14)). The vertical dotted lines roughly indicate the end of the ebb ow.
686 H. Burchard, R. Hofmeister / Estuarine, Coastal and Shelf Science 77 (2008) 679e687
and to Anja Bachmann (Warnemunde, Germany) for her sup-
port in setting up the two-dimensional idealised estuary.
References
Arneborg, L., Fiekas, V., Umlauf, L., Burchard, H., 2007. Gravity current dy-
namics and entrainmentda process study based on observations in the Ar-
kona Basin. Journal of Physical Oceanograhy 37, 2094e2113.
Blumberg, A.F., Mellor, G.L., 1987. A description of a coastal ocean circula-
tion model. In: Heaps, N.S. (Ed.), Three Dimensional Ocean Models.
American Geophysical Union, Washington, DC, pp. 1e16.
de Boer, G.J., Pietrzak, J.D., Winterwerp, J.C. Using the potential energy
anomaly equation to investigate the roles of tidal straining and advection
in river plumes. Ocean Modelling, submitted for publication.
Bowden, K.F., 1981. Turbulent mixing in estuaries. Ocean Management 6,
117e135.
Bowden, K.F., Fairbairn, L.A., 1952. A determination of the frictional forces
in a tidal current. Proceedings of the Royal Society London Series A 214,
371e392.
Burchard, H., 1999. Recalculation of surface slopes as forcing for numerical
water column models of tidal ow. Applied Mathematical Modelling 23,
737e755.
Burchard, H., Bolding, K., 2002. GETMda general estuarine transport model.
Scientic documentation. Technical Report EUR 20253 EN, European
Commission.
Burchard, H., Bolding, K., Rippeth, T.P., Stips, A., Simpson, J.H.,
Sundermann, J., 2002. Microstructure of turbulence in the Northern North
Sea: A comparative study of observations and model simulations. Journal
of Sea Research 47, 223e238.
Burchard, H., Bolding, K., Villarreal, M.R., 2004. Three-dimensional model-
ling of estuarine turbidity maxima in a tidal estuary. Ocean Dynamics 54,
250e265.
Burchard, H., Floser, G., Staneva, J.V., Riethmuller, R., Badewien, T. Impact
of density gradients on net sediment transport into the Wadden Sea. Jour-
nal of Physical Oceanography, in press.
Cheng, Y., Canuto, V.M., Howard, A.M., 2002. An improved model for
the turbulent PBL. Journal of the Atmospheric Sciences 59, 1550e
1565.
Fischer, H.B., List, E.J., Koh, R.C.Y., Imberger, J., Brooks, N.H., 1979. Mix-
ing in Inland and Coastal Waters. Academic Press, New York.
Gale, E., Pattiaratchi, C., Ranasinghe, R., 2006. Vertical mixing processes in
intermittently closed and open lakes and lagoons, and the dissolved oxygen
response. Estuarine, Coastal and Shelf Science 69, 205e216.
Jackett, D.R., McDougall, T.J., Feistel, R., Wright, D.G., Grifes, S.M., 2006.
Algorithms for density, potential temperature, conservative temperature
and the freezing temperature of seawater. Journal of Atmospheric and Oce-
anic Technology 23, 1709e1728.
Jay, D.A., Musiak, J.D., 1994. Particle trapping in estuarine tidal ows. Journal
of Geophysical Research 99, 445e461.
Nunes Vaz, R.A., Lennon, G.W., de Silva Samarasinghe, J.R., 1989. The neg-
ative role of turbulence in estuarine mass transport. Estuarine, Coastal and
Shelf Science 28, 361e377.
Ofcer, C.B., 1976. Physical Oceanography of Estuaries. Wiley, New York.
Osborn, T.R., 1980. Estimates of the local rate of vertical diffusion from dis-
sipation measurements. Journal of Physical Oceanography 10, 83e89.
Paulson, C.A., Simpson, J.J., 1977. Irradiance measurements in the upper
ocean. Journal of Physical Oceanography 7, 952e956.
Ranasinghe, R., Pattiaratchi, C., 1999. Circulation and mixing characteristics
of a seasonally open tidal inlet: a eld study. Marine and Freshwater
Research 50, 281e290.
Rippeth, T.P., Simpson, J.H., 1996. The frequency and duration of episodes of
complete vertical mixing in the Clyde Sea. Continental Shelf Research 16,
933e947.
Rippeth, T.P., Fisher, N., Simpson, J.H., 2001. The semi-diurnal cycle of tur-
bulent dissipation in the presence of tidal straining. Journal of Physical
Oceanography 31, 2458e2471.
Scott, C.F., 2004. A prescriptive bulk model of periodic estuarine stratication
driven by density currents and tidal straining. Environmental Modeling and
Assessment 9, 13e22.
Sharples, J., Simpson, J.H., 1995. Semi-diurnal and longer period stability cy-
cles in the Liverpool Bay region of freshwater inuence. Continental Shelf
Research 15, 295e313.
Simpson, J.H., 1981. The shelf-sea fronts: implications of their existence and
behaviour. Philosophical Transactions of the Royal Society London Series
A 302, 531e546.
Simpson, J.H., Bowers, D., 1981. Models of stratication and frontal move-
ment in shelf seas. Deep-Sea Research 28, 727e738.
Simpson, J.H., Hunter, J.R., 1974. Fronts in the Irish Sea. Nature 250,
404e406.
Simpson, J.H., Brown, J., Matthews, J., Allen, G., 1990. Tidal straining, den-
sity currents, and stirring in the control of estuarine stratication. Estuaries
26, 1579e1590.
Simpson, J.H., Hughes, D.G., Morris, N.C.G., 1977. The relation of seasonal
stratication to tidal mixing on the continental shelf. In: Angel, M. (Ed.),
A Voyage of Discovery. Deep-Sea Research (suppl.), pp. 327e340.
Simpson, J.H., Burchard, H., Fisher, N.R., Rippeth, T.P., 2002. The semi-diur-
nal cycle of dissipation in a ROFI: model-measurement comparisons. Con-
tinental Shelf Research 22, 1615e1628.
Umlauf, L., Burchard, H., Bolding, K., 2005. General Ocean Turbulence
Model. Source code documentation. Technical Report 63. Baltic Sea Re-
search Institute Warnemunde, Warnemunde, Germany.
van Aken, H.M., 1986. The onset of stratication in shelf seas due to differen-
tial advection in the presence of a salinity gradient. Continental Shelf Re-
search 5, 475e485.
Warner, J.C., Sherwood, C.R., Arango, H.G., Signell, R.P., 2005. Performance
of four turbulence closure models implemented using a generic length
scale method. Ocean Modelling 8, 81e113.
Wiles, P.J., van Duren, L.A., Hase, C., Larsen, J., Simpson, J.H., 2006. Strat-
ication and mixing in the Limfjorden in relation to mussel culture. Jour-
nal of Marine Systems 60, 129e143.
687 H. Burchard, R. Hofmeister / Estuarine, Coastal and Shelf Science 77 (2008) 679e687