2.

Governing Equations
2.1 3D governing Equations in Cartesian Co-ordinates
2.1.1 Shallow water equations
The model is based on the solution of the three-dimensional
incompressible Reynolds averaged navier-stokes equations, subject to the
assumptions of boussinesq and of hydrostatic pressure.
The local continuity equation is written as

u
x

v
w
+
y
z

=S

And the two horizontal momentum equations for the x- and y- component,
respectively

u
t

dz

v
t

dz

u 2
x

1
0 h

1
0 h

vu
y

( sxxx + sxyy )
v2
x

vu
y

wu
z

( sxxx + sxyy )

= fv g

+ Fu +

wv
z

n
x

+ Fv +

( v uz )
n
x

= fv g

1 0
0 x

( v vz )

g
0

g
0

x
s

+ uS

1 0
0 x

x
s

+ vS

Where t is the time; x, y, and z are the Cartesian co-ordinates; is the surface
elevation; d is the still water depth; h = + d is the total water depth; u, v, and
w are the velocity components in the x,y and z direction; f = 2 sin is the
Coriolis parameter ( is the angular rate of revolution and the geographic
latitude); g is the gravitational acceleration; is the density of water; s xx, sxy, syx
dan syy arecomponents of the radiation stress tensor; Vt is the vertical turbulent
(or eddy) viscosity; Pa is the atmospheric preassure; o is the reference density
of water. S is the magnitude of the discharge due to point sources and (Us, Vs) is
the velocity by which the water is discharged into the ambient water. The
horizontal stress terms are described using a gradient- stress relation, which is
simplified to

Fu =

(2 A ux )

((
A

u v
+
y x

))

((

Fv =

u v
+
y x

))

(2 A vx )

Where A is the horizontal eddy viscosity.

The surface and bottom boundary condition for u, v and w are
At z = :

n
t

n
n
u v
1
+v
w=0,
,
=
( xx , xy )
x
y
z z
0 Vt

At z = - d :

d
d
u v
1
+v
w=0,
,
=
( dx , dy )
x
y
z z
0 Vt

( xx , xy )

Where

and

( dx , dy )

are the x and y components of the surface

wind and bottom stresses.

h h u h v
^ ^
+
+
=hS+ P
E
t x
y
^
P

Where
and

^
E

and

are precipitation and evaporation rates, respectively, and

are the depth-averaged velocities.

h u= udz ,h v= vdz
d

the fluid assumed to be incompressible. Hence, the density, , does not depend
on the pressure, but only on the temperature, T, and the salinity, s, via the
equation of state.

= (T , s )
2. 13 Transport equation for a scalar quantity
The conservation equation for a scalar quantity is given by

C uC vC wC

C
+
+
+
=Fc +
Dv
kpC+Cs S
t
x
y
z
z
z

Where C is the concentration of the scalar quantity, kp is the linear decay rate of
the scalar quantity, Cs is the concentration of the scalar quantity at the source
and Dv is the vertical diffusion coefficient. Fc is the horizontal diffusion term
defined by

Fc=

[ (

)]

Dh
+
Dh
C
x
x y
y

) (

Where Dh is the horizontal diffusion coefficient.

2.1.4 Turbulence model
Vertical eddy viscosity
The eddy viscosity derived from the log-law is calculsted by

Vt = Uh

z +d
h

z+d
c1
+c 2( 2)
h

Where U = max (Us,Ub) and c1 and c2 are two constants. Us and Ub are
the friction velocities associated with the surface and bottom stresses, c1 = 0.41
and c2 = -0.41 give the standard parabolic profile.
Vt = Vta (1 +aRi)- b
Where Vt* is the undamped eddy viscosity and Ri is the local gradient Richardson
number

Ri =-

g
0 z

(( ) ( ) )
u
v
+
z
z

-1

.a = 10 and b=0.5 are empirical constants.

Vt = c

k2

Where k is the turbulent kinetic energy per unit mass (TKE), is the dissipation
of TKE and c is an empirical constant.

k uk vk w k
+
+
+
t x y
z

= Fk +

vt K
+ P+B
z k x

 u v w
+
+
+
t x y z

=F

c 1 P +c 3 Bc 2
vt
+ )
z x K

Where the shear production, P, and the buoyancy production, B, are given as
2

(( ) ( ) )

xz u yz v
u
v
+
Vt
+
0 z 0 z
z
z

P=

B=

Vt
N
t

With the Brunt-Visl frequency, N, defined by

N 2=

g
0 z

.t is the turbulent prandtl number and k, , c1, c2 and c3 are empirical

constants. F are the horizontal diffusion terms defined by

[ (

Dh
+
( Dh
) (k , )
x
x y
y

(Fk, F ) =

The horizontal diffusion coefficients are given by Dh = A/k and Dh = A/,

respectively.
At z = n

k=

1
U2
c

U3
k zb

k
=0
z

tz

for U > 0

( k c )
akh

3 /2

for U = 0

Where k=0.4 is the von Karman constant, =0.07 is and empirical constant and
zs is the distance from the surface where the boundary condition is imposed. At
the seabed the boundary conditions are
At z = - d :

k=

1
U2
c

U
k zb

Where zb is the distance from the bottom where the boundary condition is
imposed
Horizontal eddy viscosity

A=c 2 s l 2 2 SijSij
Where cs is a constant, l is a characteristic length and the deformation rate is
given by
Sy =

1 u i u j
+
2 x j xi

(i, j = 1, 2)

2. 1. 5 Governing equations in cartesian and sigma-co-ordinates

zz b '
, x =x y ' = y
h

Where varies between 0 at the bottom and 1 at the surface. The co-ordinate
transformation implies relations such as

1
=
z h

( x , y )( x 1h ( dx + hx ) y 1h ( yd + hy ) )
'

'

'

In the new co-ordinate system the governing equations are given as

h hu hv h
+
+
+
=hS
t x' y '
n

hu hu2 hv h
n
h po hg
1 sxx sxy
v u
+
+
+
=fvhgh

dz
+
+hF+
+ huS
t x' y '
x ' 0 x ' o z x
o x
y
h

hv hv 2 huv hv
n
h po hg
1 sxx sxy
v v
+
+
+
=fuhgh

dz
+
+ hF+
+
t x ' y'

y ' 0 x ' o z x
o x
y
h
hT huT hvT hT
D T
+
+
+
=hFt +
+ hs S
t
x'
y'

hs hus hvs hs
D s
+
+
+
=hFs+
+hs S
t x' y'

hk huk hvk hk
1 v k
+
+
+
=hFk +
+ h( P+ Bs)
t
x ' y'

h h u h v h
1 D
s
+
+
+
=h F +
+h (c 1 xP+c 3 xBc 2 xs )
t
x'
y'

h h
k

hC huC hvC hC
D C
+
+
+
=hFc+
+ hkp C+hC
t
x'
y'

The modified vertical velocity is defined by

1
d
d
h
h
h
w+u
+v

+u
+v
h
x '
y'
t
x'
y'

)]

The modified vertical velocity is the velocity across a level of constant . The
horizontal diffusion terms are defined as

hFu

hFv

u v
2hA
+
hA
+
x
x y
y x

) ( (

))

) ( (

u v
2 hA
+
hA
+
y
y y
y x

h(FT, FS, FK, FE, Fc)

[ ( ) (

))

)]

hD
+
hD
(T , s , k , ,C)
x
x y
y

the boundary condition at the free surface and at the bottom are given as follows
At

=0,

At

=0,

=1:

( u , v )= 0hVt ( xx , xy)
=0

( u , v )= 0hVt ( bx , by)

2.3.1 shallow water equations

Integration of the horizontal momentum equations and the continuity
equation over depth h=+d the following two-dimentional shallow water
equations are obtained

h h u h v
+
+
=hS
t x
y
The overbar indicates a depth average value. For example,

and

v are the

depth-averaged velocities defined by

n

hu

udz , h v= vdz
d

the lateral stresses Tij include viscous friction, turbulent friction and differential
advection. They are estimated using an eddy viscosity formulation based on of
the depth average velocity gradients

Txx=2 A

u
u v
v
, Txy= A
+
,Tyy=2 A
x
y x
y

2. 3. 2 transport equations for salt and temperature

Integrating the transport equations for salt and temperature over depth
the following two-dimentional transport equations are obtained

h T h u T v T
+
+
=hF +hH +hTS
t
x
y
h s hu s v s
+
+
=hFs+hsS
t
x
y
Where

and

is the depth average temperature and salinity.

2.3.3 transport equations for a scalar

Integrating the transport equations for a scalar quantity over depth the
following two-dimentional transport equations are obtained

h C h u C v C
+
+
=hFc+ hk C+hCS
t
x
x
Where

is the depth average scalar quantity.

2.4 2D governing equations

u=R cos

d
dt

v =R

2.5 bottom

=cf ub|ub|
o
Ub= cf |ub|
cf =

cf =

cf =

g
2
C
g

( Mh 1/ 6 )

1
l
b
ln
K
z0

( ( ))

Zo = mks

M=

25.4
1 /6
k

2.6 wind stress

s=o c d|u w|u w

Un=

o c d|u w|
0

2.7 ice coverange

s
=c u |u |
0 f s s
Us= cf |us|

d
dt

cf =

M=

cf =

( Mh 1/ 6 )

25.4
k 1 /6
1
l
b
ln
K
z0

( ( ))

z 0=m k s
2.8 tidal potential