MikeSHE Exercises Handouts 2015 2017

A.
Jonoski, PhD, MSc Hand-out

I.Popescu, PhD, MSc
Catchment Modelling
Setting up and running MIKE SHE
MIKE SHE: Step by Step Model building
ii
Table of Contents
OVERVIEW OF CATCHEMENT MODELLING WITH MIKESHE ................................... 1
EXERCISE 1. SATURATED ZONE............................................................................... 46
EXERCISE 2. OVERLAND FLOW AND RIVER NETWORK ........................................ 77
EXERCISE 3. SINGLE COLUMN UNSATURATED ZONE MODEL............................. 95
EXERCISE 4. SIMPLE INTEGRATED CATCHEMENT MODELLING........................ 117
GUIDES ....................................................................................................................... 141
GUIDE 1. DRAINS ...................................................................................................... 143
GUIDE 2. MIKESHE - MIKE 11 COUPLING ............................................................... 149
GUIDE 3. MIKESHE – AVAILABLE TYPES OF WATER BALANCES ...................... 159
ASSIGNMENT DESCRIPTION ................................................................................... 169
iii
Overview of Catchment Modelling with MikeSHE
A. Jonoski
I. Popescu
Department of Integrated Water Systems and Governance
Catchment modelling
 Catchment modelling is concerned with modelling
the hydrological and hydraulic processes in the
catchment
 Distinct from river-basin
ri er basin modelling where
here the foc
focus
s
is not on the hydrological processes, but more on
the functions and use of water resources in river
basins (RIBASIM)
 Catchment models serve as basis for developing
water quality and ecological models
 Detailed representation of physical processes
offers possibility for analysing and testing large
variety of alternatives and management options. 2
1
Types of catchment models
 Model seen as a system:

F
I O
P
O  F ( P, I )
I - set of inputs
P - set off parameters
O - set of outputs
F - transformation function
 Basic classification:
– Deterministic
 one set of inputs produces one unique
set of outputs
– Stochastic
 at least one input , or parameter has
random nature
 same inputs may produce different
outputs, uncertainties can be considered
2
 Classification on the basis of description of

processes in the model:
– Empirical (black box models)
– Lumped-conceptual models
– Physically-based models

 Empirical (or ‘black box’): fit between inputs and
outputs without detailed process descriptions (ex.
Linear regression, unit hydrograph)
 IImportant extension
i off the
h concept - Data-driven
D di
modelling
 In these models the parameters are not related to
field data or to catchment characteristics
Data
Model
3

 Lumped conceptual : Main physical compartments of the
hydrological cycle are represented by storage entities, without
looking at spatial variability of the parameters or inputs
 ((ex. NAM, HBV, XINANJIANG, Soil Moisture Accounting)
g)
 Parameters are related to field data and catchment
characteristics, but cannot be determined from them. They
need to be assessed through calibration
Surface water
Unsaturated
zone
Aquifers 7

 Physically-based : models based on numerical
solutions of partial differential equations which describe
physical processes, which satisfy physical laws such as
conservation of mass
mass, momentum and energy
– Examples: Saint Venant equations for 1-D river flow,
Darcy’s law and continuity for saturated zone .
   h
( K x h )  ( K y h )  ( K z h )  Ss  R
x x y y z z t
 Parameters of these models can in principle be
assessed from field data and measurable catchment
characteristics, although calibration is still necessary
 Examples (SWAT, MIKE SHE)
8
4
Use of different types of catchment models
 Empirical models : easy to calibrate, very fast, little

knowledge of the phenomena involved and of the
catchment is needed. Changes
g in the p physics
y of the basin
(new highway, urbanisation, change in land-use etc.)
cannot be modelled !
 Lumped, conceptual models : allow for more physical
insight into the processes involved over the modelled areas.
Very restricted capacity to model changes in the basin.
 Physically-based : More geometric and hydraulic data
needed. Changes in the physics of the basin can be
modelled. Possibility to deal with ungauged catchments!
 When the only objective is simulation of runoff

(especially for forecasting purposes) – the
simpler lumped
simpler, lumped-conceptual,
conceptual empirical or
data-driven models may be more appropriate.
 These models are frequently used in
operational management of water systems
 Theyy are simpler
p to be built, and much faster
to be run
10
5

 For design, planning and impact assessment applications,
physically-based models are needed
 Also, in analysing impacts of extreme events we have
scarcity of data, so we need to rely on physical
understanding of the processes
 Example application areas:
– Flood and drought risk assessment and management
– Simulation of spatial patterns (and their changes) within
the catchment (rainfall, slope, soil type, vegetation type,
underlying geology, etc)
– Surface-groundwater interactions, water allocation,
wetlands modelling, etc.
– Water pollution (including non-point)
– Soil erosion
– ….. 11
Spatially distributed catchment models
 Since physical processes are spatially distributed,

these models need also to be capable of spatially
distributed representation of input, parameters and
outputs
 Three approaches towards spatial representation:
– Lumped conceptual models for sub-catchments
linked with river system models (channel routing)
– Introducingg spatial
p elements with similar
hydrological behaviour (Hydrological Response
Units- HRUs)
– Grid-based spatial distribution
12
6
Combination of lumped conceptual models with

channel routing
 The whole catchment is divided in sub-catchments, and for
each sub-catchment a lumped conceptual model is
constructed.
 The sub-catchments outflows are introduced into a 1-D
representation of the river network
network, through which the total
runoff is routed to the main outlet of the catchment.
 Reservoirs can be included
 Examples:
– MIKE 11 (1-D channel routing) and NAM (rainfall-runoff
lumped conceptual model) for the sub-catchments
– HEC RAS (1-D channel routing) and HEC HMS (rainfall-
runoff) for the sub-catchments River
network
Sub-catchment Catchment
boundary outlet Q
13
t
Combination of lumped conceptual models with

channel routing
 Advantages:
– some level of spatial variability can be introduced through
the appropriate level of introduction of sub-catchments.
– The 1-D routing through the channel can be constructed
i quite
in it sophisticated
hi ti t d manner th thatt allows
ll ffor analyses
l off
spatial interventions along the river channels.
– Used in many engineering hydrology and hydraulics-
related studies (floods, spillway outflows analysis, river
works, etc.)
 Disadvantages:
– Cannot be used for land-use change related studies
(Detailed spatial representation of land-use, and soil
distribution is lacking)
– Cannot be used for groundwater-surface water
interactions (Poor representation of the sub-surface
systems) 14
7
Hydrological Response Units

 Hydrological Response Units (HRU) models:
– Based on GIS: by overlying different layers of spatial
information (soil, digital elevation, vegetation,
management practices)
practices), the units with similar
hydrological response are identified.
– They are embedded into sub-catchments, from where
the produced runoff is routed downstream through the
river network
– This is the approach
taken by the SWAT model
15
Hydrological Response Units
 Advantages:
– Detailed analyses of soil and land-use changes are
possible
– Hydrological
H drological processes can be combined with ith water
ater
quality (nutrients and pesticides), erosion and sediment
transport, and different agricultural management practices
– Particularly suitable for larger scale catchment modelling
 Disadvantages:
– The hydrodynamic processes in the river network are not
very well described (usually only hydrological routing
procedures are used)
– The groundwater system is not described with its physical
processes
– Surface-water groundwater interactions cannot be
simulated 16
8
Grid-based spatial distribution

 All spatial data are specified on a grid
 The same grid is also used as computational grid, for
obtaining numerical solutions of the partial differential
equations describing the included physical processes
 This approach is taken by MIKE SHE
Groundwater Table
Soil profiles
Rainfall stations etc. 17

Land Use/Vegetation
Integrated catchment modelling – MIKE SHE

Rain and snow
Canopy Evapotranspiration
interception
From intercepted From soil or
waters water surfaces From root zone
Net
precipitation
i it ti
Abstraction
Snow melt and recharge
model Surface runoff
Infiltration 2-D overland and

1-D channel flow model
Lake or reservoir
Water table Root Zone
rise and fall
1-D UZ
flow model
for each grid
element
3-D saturated flow Exchange across18

groundwater model boundaries
9
MIKE SHE
 Modules:
 Features
– Basic
– Integrated  PP Pre and Post processing
– Distributed  WM Water
ate Movement
o e e t
– Physically – Add-on
based  AD Advection-Dispersion
 PT Particle Tracking
 SD Sorption/Degradation
 MP Macro Pore Flow
 GM Geochemistry
 BM Biodegradation
 IR Irrigation and Crop Growth
 LR Linear Reservoir
 DAISY Crop Yield and Nitrogen
19
Consumption
MIKE SHE PP
The pre- and post-processing module has:
 Graphical editing functionalities

 Plotting facilities
 Various utility programs for data manipulation
 Water balance program
 Interpolation program
 Sub-model module
 Geological pre-processor
20
10
MIKE SHE WM
 3-D Boussinesq equation for saturated flow

 1-D Richards' equation for unsaturated flow
 2-D Saint Venant's equation (diffusive wave
approximation)
i ti ) ffor overland
l d fl
flow
 1-D river model: MIKE 11
 Evapotranspiration/Interception
 Snowmelt
 Sources/sinks, time variable head boundaries, and other
types of boundary conditions
 River/aquifer exchange
 Complete computational coupling between the individual
components
– Flexible automatic time step control which can vary
from seconds or minutes (river flow) to days
21
(groundwater flow)
MIKE SHE WM - Components

 ET Interception/Evapotranspiration
– Interception of rainfall by the canopy
– Drainage from the canopy
– Evaporation
p from the canopy py surface
– Evaporation from the soil surface
– Uptake of water by plant roots and its
transpiration
 OC Overland and Channel flow
– Surface runoff
– Routing in rivers
 UZ Unsaturated Zone flow
– Infiltration
– Moisture distribution
 SZ Saturated Zone flow
– 3D groundwater flow
– Exchange with boundaries
22
11
MIKE SHE applications and typical set-up
 Applications:
– Catchments with complex channel network,
varying spatial distribution of land use
use, soil
type and vegetation cover, with complex
aquifer system below the soil surface
– Small and medium-sized catchments (with
flexible set-up also for large catchments)
 Typical set-up:
– Typically 2000 grid points over the surface
surface, 30
points in vertical for the unsaturated zone and
2000 grid points for the 3-D or quasi 3-D
saturated zone
– Grid cell size from 25 – 2000m
23
MIKE SHE
 Advantages:
– Very flexible modelling system, which can be used for a
variety of applications:
 Impacts from land-use changes
 Surface water – groundwater interactions (quantity and
quality)
 Recharge dynamics (SZ and UZ interactions)
 Wetland and flood studies
 Groundwater vulnerability assessment and protection
 Well fields optimisation…
– Components can be flexibly connected according to the
type of application
– Full integration with data from GIS systems
– Easy use of new sources of grid-based data: radar, satellite,
airborne remote sensing, climate and meteorological 24
models
12
MIKE SHE
 Disadvantages:
– Constructing a MIKE SHE model is a very
complex tasks. The amount of data that
needs
d tto be
b supplied
li d iis very llarge, and
d
entails expensive data gathering
campaigns.
– Because of their cost, and data demands,
these models can be quite expensive.
– Because of the large number of
parameters, calibration may become a very
complex exercise, and clear calibration
strategy is needed.
25
MIKE SHE processes description
13
Integrated catchment modelling – MIKE SHE

Rain and snow
Canopy Evapotranspiration
interception
From intercepted From soil or
waters water surfaces From root zone
Net
precipitation
i it ti
Abstraction
Snow melt and recharge
model Surface runoff
Infiltration 2-D overland and

1-D channel flow model
Lake or reservoir
Water table Root Zone
rise and fall
1-D UZ
flow model
for each grid
element
3-D saturated flow Exchange across27

groundwater model boundaries
MIKE SHE
 Main physical processes included at

– Ground surface (hydrology and hydraulics)
– Unsaturated zone (infiltration and take up)
– Saturated zone (groundwater)
 Processes represented by one or more partial
differential equations
 Equations and parameters distributed in
space
28
14
MIKE SHE general data types
P Time series
(.dfs0)
Grid files:2-D maps 1D river

(.dfs2) networks
29
MIKE SHE - Precipitation

 Spatially distributed precipitation is main input to any MIKE
SHE model
30
15
MIKE SHE Frame component

RAINFALL
SNOW MELT
contribution
to net rainfall
net rainfall net rainfall
INTERCEPTION
potential
actual evapotranspiration
interception
soil moisture
EVAPOTRANSPIRATION in root zone
open water transpiration/
evaporation soil evaporation
OVERLAND AND infiltration UNSATURATED ZONE

CHANNEL FLOW
river base drain flow groundwater recharge / discharge

level flow table
groundwater table
EXCHANGE MODULE SATURATED ZONE
loss through riverbed
 Controls the sequence of computation of different

components and their data exchange 31
Saturated zone – Exercise 1
16
MIKE SHE Saturated zone component - Theory

 Solution of the general 3D groundwater flow equation:
   h
( K x h )  ( K y h )  ( K z h )  Ss  R
x x y y z z t
Kx, Ky, Kz – hydraulic conductivity
in three directions
h- groundwater head Similar to
Ss – specific storage MODFLOW
R - source / sink term
Full 3D, or
Quasi 3D
approach
Exchange
with other
components
33
Two approaches to
vertical discretisation
A) Computational layers
not coinciding with
geological layers
(used in 3D approach)
B) Computational layers
coinciding with
geological layers
(used in quasi 3D
approach): flow in aquifers
is only horizontal, and
in aquitards only vertical 34
17
 Exchange with other components:

– Well abstractions
– Recharge to and from UZ
– Transpiration from SZ (when root zone
extends into saturated zone)
– Infiltration from / to OL (when groundwater
table reaches soil surface)
– Flow exchange with rivers
– Drainage flow controlled by the
groundwater table elevation
35
MIKE SHE SZ – Data specification
 Data requirements for setting-up the SZ

component:
– Geological layers (geometry)
– Computational layers
– Hydrogeologic parameters (Kx, Ky, S, Sy)
– Boundary conditions
– Well abstractions
– Drainage network and exchange
parameters
36
18

 Saturated zone data input:
37

 Specifying geological layers:
– upper and lower level and hydrogeologic parameters
38
19

 Computational layers:
– Initial heads and boundary conditions
Boundaries
types:
-head
-flux
-mixed
Constant or
time
varying
39

 Pumping wells – through wells database:
40
20
MIKE SHE SZ – Drainage

 The drains option is useful for dealing with smaller drainage
patterns that cannot be included in MIKE 11 river network
 In regional models, the interflow component (medium fast
flow below the soil surface) of the runoff hydrograph can be
simulated conceptually by using the drains option
 The drain is conceptually assumed to be like a drain pipe in
each grid cell that can only receive water from the
groundwater system, if the groundwater level is above the
drain level. The so-produced drain flow is then routed by a
linear reservoir to the nearest river link, to a model boundary
or to a local depression
Drain flow: qdr  (h  z dr )Cdr
Cdr- time constant: a parameter which per grid cell
h
describes the actual density of the drains, the
zdr permeability conditions around the drains,
and the speed of routing of the drain flow
(T-1, usually 10-6 – 10-7) 41

 Drain flow is calculated within the SZ component, and the groundwater
level is adjusted
 The destination of the drain flow (where it will be routed) is determined
either by drain levels, or by integer grid codes (a map with codes)
A If the drain levels option is used the drain flow is routed
A.
downstream until the first river link or model boundary
B. If grid codes are used:
 grid cells with an Drain Code value of zero will not
produce or receive any drain flow
 grid cells with positive Drain Code values will drain to the
nearest river, boundary or local depression in the drain
level - in that priority - located next to a cell with the
same Drain Code value
 grid cells with negative Drain Code values will drain to
either a boundary or a local depression – in that priority
42
21

 Cells with Drain Code 3 drain to a
 Example local depression since no
boundary or river link is found
next to a cell with the same drain
code
 Cells with Drain Code 1 or 2
drain to nearest river link located
next to a cell with the same drain
code
 Cells with drain code 0 do not
contain drains and no drainage is
produced
 Cells with Drain Code -1 drain to
local depression since no
boundary is found next to a cell
with the same drain code
 Cells with Drain Code -2 drain to
nearest boundary cell with the
same drain code
43
MIKE SHE SZ – Drainage: Data specification

 Drain levels, drain time constants (uniform or spatially varying)
and drain codes are specified in the drainage sub-tree of the
SZ component
44
22
Overland and river flow – Exercise 2

- Flood Analysis Techniques applied
to the Var Catchment –
Simulation of the flood event of
4-6 November 1994
Geographic situation
VAR RIVER CATCHMENT
Location:
Location: southern part of
France
Area::
Area 2822 km² (70 x 75 km)
Tributaries:: 5
Tributaries
Length::
Length 125 km
Altitude::
Altitude 0 – 3000 m a.s.l.
46
23
Problems:
 How to explain the disaster caused by the flooding event of

the Var (5 November 1994) ?
 What kind of precautions have to be taken to avoid the
event ?
 Goals for the public authorities :
– Prevent flooding of the Nice airport
– Protect Napoleon bridge
– Real time warning system,
– Improved flood management by different structural
measures
47
Effects of human activities
Reduction of River width:

- capacity of the river
- water height
- sediment transport
Removal of gravel:
- groundwater levels
- consequences for the
farmers
Solution: construction of 9
weirs along the river 48
24
VAR Catchment
49
Hydrological data
Data from Météo France

 Hourly rainfall between
3rd November
o e be 199499 12:00
00
5 November 1994
th
24:00,
St Martin
on 6 stations of Var
Guillaumes
Vésubie
Catchments. Puget Théniers
Roquesteron Levens
 Mean dailyy rainfall in 1994 Carros
on 40 stations of Alpes-
Maritimes.
50
25
Modelling procedure
Mike She Hydrograph

Input data
Hydrological input for
model Mike11
Q
Critical points
– close to the
outlet: Airport
and Napoleon
Hydrodynamic
bridge modelling with Mike11
51
MIKE SHE Overland Flow Component (OL) - Theory
• Channel flow (MIKE11)

• Overland flow
OL: Saint Venant equations:

Momentum equation (diffusive Continuity equation:
wave approximation) in 2D: h  (uh)  (vh)
h h   q
 S ox  S fx  0  S oy  S fy  0 t x y
x y
With Strickler/Manning law for u,v – flow
fl velocities
l iti
friction slopes, using Kx and Ky in x- and y- directions
as friction coefficients : respectively
u2 v2
S fx  2 4 / 3 S fy 
Kx h K y2 h 4 / 3 52
26
MIKE SHE Overland Flow Component (OL) - Theory

 The two governing equations are solved numerically in 2D
 Terrain slopes are provided by a grid map of the topography
 The OL component needs two parameters to be specified:
– Strickler / Manning number: friction coefficient (ranges
between 10 and 100), uniform or spatially varying
– Detention storage depth (minimum depth in a given cell
before flow occurrence)
 The OL component time step is same as for UZ and ET
 At the
th beginning
b i i off each h time
ti step
t allll the
th exchanges
h with
ith
the other components are computed (evaporation, infiltration
or direct exchange with the saturated zone)
53
MIKE SHE OL – Data specifications

 Specification of data for OL component:
– Manning
number
– Detention
storage
– Initial
water
depth
54
27
MIKE SHE – MIKE 11 integration

 Mike 11 network is interpolated into a MIKE SHE
‘river’ links located in between computational cells
 From Mike 11 H-points

water levels are
interpolated to MIKE
SHE river links
 Exchange flows
between OL and SZ
component are
calculated on the basis of
the interpolated
p water
levels in MIKE SHE river
links
 These flows are
returned back to MIKE 11
as lateral inflows into
corresponding H-points55

 All branches, or a selected number of Mike 11 branches can be
linked to MIKE SHE. This information is specified in the MIKE
11 network file
56
28
Unsaturated zone and

Evapotranspiration – Exercise 3
MIKE SHE Unsaturated Zone - Theory
Water
content: V water
 
Unsaturated zone- (soil V total
pores partly
tl filled
fill d with
ith moisture)
water, partly with air:
3 phases: solid, air and
liquid
GW table
Saturated zone-
all pores filled with V pores
Porosity:
y n
water - no air: Vtotal
2 phases: solid and liquid
Saturated zone:  n
Unsaturated zone:   n 58
29

 In the unsaturated zone, the flow of water is dependent on
the available water content (soil moisture) (Θ )
 This parameters influences the pressure (hydraulic head)
in the UZ
UZ, and the hydraulic conductivity in the UZ
 We can define the hydraulic head in the UZ as:
h  z  Suction head
Elevation head ((negative)
ega e) due to o
( b
(above given
i d
datum)) capillary pressure
-gravity force - Surface tension forces
 The magnitude of  depends on Θ

59
Water Retention Curve

pF  log10  100 
 : meter
 As moisture content decreases
the pF value increases (the
pressure becomes more
negative)
 This relationshipp ((the shape
p of
the curve) is different for different
soil types
 Needs to be determined
experimentally
60
30
 The basic law the governs the flow through

the UZ is Darcy’s law:
h
q   K ( )
z
 where q is specific discharge (LT-1)

 Here the hydraulic
y conductivityy K is also
dependent on Θ
61

K(Θ) – relationship between
hydraulic conductivity and
water content
 K-value increases with Θ
 Can be determined
experimentally, but also
empirical formulae exist:
K ( ) = K sat S en
S e =  -  r /  s -  r 
K sat Saturated n- calibration
hydraulic parameter
different for different
conductivity soil types
Θr- residual Θs- saturated 62
31

 Continuity equation in vertical direction:
q 
 S 
z t
(where S is the sink term and represents root extraction
for transpiration, or soil evaporation)
 Darcy’s law: h
q   K ( )
z
 h 
 Combined:  ( K ( ) )  S 
z z t
 ( z  ) 
Knowing the relations K(Θ) ( K ( ) )S 
z z t
and Ψ(Θ), we can solve
  K ( ) 
the equation for Θ ( K ( ) ) S 
z z z t63

 By introducing the so-called soil water capacity (or soil
diffusivity): 
C

 We can write the equation expressed in the form:
  K ( ) 
( K ( ) ) S C
z z z t
 This is known as the Richard’s equation.
 The Richard equation (in Θ or in ψ) is solved numerically
by MIKE SHE in specified nodes (discretisation points) in
the vertical UZ column
 Flow through the UZ zone is also obtained
 These calculations include infiltration from overland flow
and recharge to the saturated zone 64
32
MIKE SHE UZ – boundary conditions

a) Boundaries are also related to the way of
linking UZ to other components
b)
 Top boundary:
a) Flux boundary (net rainfall)
rainfall), or
b) Head boundary (when ponding occurs in
the Overland Flow component - OL)
– Conditions are checked in each time step
(which is same for UZ and OL)
 Bottom boundary
– Groundwater table
– Integer multiplier of UZ time steps equals
one Saturated Zone (SZ) time step
– Groundwater table is updated after every
SZ time step calculation, which includes
the calculated recharge from UZ 65
MIKE SHE UZ – links with Evapotranspiration comp.
Et
Esoil
 Evapotranspiration component
determines sink terms for the UZ
 It takes water from the UZ for two
processes:
– Root uptake for transpiration (from
several nodes, depending on the
defined depth in the root zone)
– Soil evaporation (taken from the
first node in the UZ, just below the
soil surface)
66
33
MIKE SHE Unsaturated zone – data specification

 For each soil type, the two characteristic curves need to be
specified [ K(Θ) and Ψ(Θ) ]
 This is done in a soil property database
 Each vertical UZ computational column may contain several
different soils extending over different depths
 These combinations of soils need to be specified as UZ
profiles
 Each profile is discretised in vertical direction into a number
off computational
t ti l nodes,
d in
i which
hi h th
the numerical
i l solutions
l ti (f
(for
Θ and ψ) are obtained.
 The distribution of different profiles in space is specified as
a grid map (.dfs2) with different grid codes
67
MIKE SHE UZ - Soil Property Database
Soil properties for

individual soils
68
34
MIKE SHE UZ – Profile definition

Computational nodes Two different soil types
69
MIKE SHE UZ - Profile distribution

Spatial distribution of UZ profiles specified as a grid map
70
35
MIKE SHE UZ - Lumped calculations
 If UZ calculations need to be carried out for every profile the

calculations may be very time consuming
 Veryy often the flow conditions in g
groups
p of UZ p
profiles may
y
be assumed equal for ‘similar’ types of profiles.
 UZ profiles can then be classified in categories with similar
flow behaviour
 In this case the UZ calculations are carried out for one
profile of the same category, and the results are used for all
profiles in the same category
71
MIKE SHE UZ - Lumped calculations

Conditions for classification of lumped UZ calculations:
Rainfall stations
Soil profiles
Land Use/Vegetation
Groundwater Table
Calculation/Transfer Columns 72
36
MIKE SHE ET - Evapotranspiration

 Kristensen and Jensen model
– Uses the Potential (reference) evapotranspiration as
maximum
– Empirical model calculating ET from 4 water storages
 Canopy, Surface, Soil, Transpiration
 Processes Interception
 Interception of rainfall by the canopy

 Drainage from the canopy
Evaporation Transpiration
 Evaporation from the canopy surface
Infiltration
 Ponded Water
 Soil evaporation
 Transpiration Percolation
ET actual = ET canopy + ET transpiration + ET soil +ET pond

73
MIKE SHE ET – Theoretical concepts
Imax
a = Cintt * LAI
where Interception
Imax- max interception storage capacity (mm)
LAI – leaf area index
Cint – interception coefficient
ETcanopy= min
i (Imax, Ep*∆t)
where
Ep – potential evapotranspiration
∆t - ET time step
74
37

Transpiration
Water for transpiration is

taken from the root zone,
Water content at field capacity - f depending on the available
Water content at wilting point - w water in the soil and the
Actual water content -  properties of the plants 75
E at = f 1 (LAI) f 2 (  ) RDF E P
C3
  - E p
f 2 (  ) = 1 -  F 
f 1 (LAI) = C2  C1 LAI   F - W 
C1, C2, C3 – empirical C3=const C3-variable

parameters Ep-variable Ep=const 76
38

E at = f 1 (LAI) f 2 (  ) RDF E P
log R(z) = log R o - AROOTz
z2 Lr
RDF i =  z1 R(z)dz /  o R(z)dz
R0- root extraction at the surface
R(z) – root extraction at depth z
AROOT – root density parameter
RDFi- root depth extraction
for a computational UZ layer i
Lr – actual root depth
z1, z2, bounds of the UZ layer i
Root distribution in time
z1 Root zone of a UZ profile
z2 i and depth
77

E s = E p f 3 (  ) + E p - E at - E p f 3 (  ) f 4 (  )1 - f 1 (LAI)
 
C2  for  M     W LAI
A =0
0
 W
f 3 ( )  C2 for    W
0 for   
 M

  - ½ W +  F 
 for   ½ W +  F 
f 4 ( )   F - ½ W +  F 
 0 otherwise
Epond –taken from within the OL component at rate equal to potential

evapotranspiration, as long as there is available ponded water 78
39
MIKE SHE ET – data specification

 Specification of Reference (potential) evapotranspiration
– Can be spatially uniform or distributed
79

 Spatial distribution of vegetation types
80
40

 Evapotranspiration parameters
– Can be default or vegetation specific
81

 Vegetation properties (LAT, Root depth, other ET
parameters) are obtained from in vegetation property
database
82
41
River-aquifer exchange
(for Integrated model) - Exercise 4

 Mike 11 network is interpolated into a MIKE SHE
‘river’ links located in between computational cells
 From Mike 11 H-points

water levels are
interpolated to MIKE
SHE river links
 Exchange flows
between OL and SZ
component are
calculated on the basis of
the interpolated
p water
levels in MIKE SHE river
links
 These flows are
returned back to MIKE 11
as lateral inflows into
corresponding H-points84
42

 All branches, or a selected number of Mike 11 branches can be
linked to MIKE SHE. This information is specified in the MIKE
11 network file
85
MIKE SHE – exchange between river and SZ

 The flow exchange is governed by the water levels in MIKE
SHE river links, the groundwater levels calculated by the
SZ, and specified flow conductance
 Simplified cross section is used for the MIKE SHE river link 86
43

 Exchange flow is calculated as:
Q  Ch
where :
Q - exchange flow
C  conductance (L2 T -1 )
h - head difference between
grounwater level and river water level
 This is calculated for both sides of the simplified river
cross section
 If groundwater level drops below the river bed, the
head difference is between the river water level and
the bottom of the river
87

 Three options for calculating the conductance value:
– the conductivity of the aquifer material only (Aquifer only),
or
– both the conductivity of the river bed and the aquifer
materials [Aquifer + River], or
– the conductivity of the river bed material only [River only]
Aquifer only Aquifer + River River only
1
Kd a d x C
C ds 1 C  Lc wd x
ds 
Kd a d x Lc wd x
K – aquifer material hydraulic conductivity ( LT-1) Lc –leakage coefficient of the
da – vertical distance available for exchange river bed material (T-1)
dx – grid cell size w –approximate wetted
ds – flow distance (middle of grid cell to perimeter of the simplified 88
middle of river link) cross section (da + lhi)
44

 The type of contact for calculating the conductance is also
specified in MIKE 11 network file
89
45
Exercise 1. Saturated zone

This section shows the step-by-step procedure to be used in order to build a MIKE SHE model.
The example used for showing the steps is a simple model of the saturated zone of the Karup
catchment.
STARTING MIKE SHE AND CREATING A FLOW MODEL
First it is recommendable that you create a “working directory”, where you will save the work and
where the data needed for the model construction is stored.
The step by step procedure is as follows:
STEP 1. OPENING THE SOFTWARE

Select ‘Start menu Programs  MIKE BY DHI  MIKE ZERO’ and select ‘MIKE ZERO. The
general interface for all DHI software products will start. This interface is called ‘Mike Zero’
This interface is also the starting point for creating different types of files in DHI formats. In the
following steps we will only use Mike She and Mike11 files.
STEP 2. CREATE THE MSHE SETUP FILE

2.a Select ‘File NewFile’. Select the ‘MIKE SHE’ tab on the left panel. Select ‘Flow model’
46
on the right panel and click ‘OK’.
After clicking OK the following window appears:
Save the (still empty) configuration file in the working directory you have created. Close the
“Project Explorer” window, located on the right. Save the configuration file under the name ‘SZ-
ex1.SHE’.
STEP 3. SETTING UP A FLOW MODEL

Mike She is a modular system. You can select the components to be included in the model
(saturated, or unsaturated, or overland/channel flow modules) depending on the complexity of the
47
model you are building.

No matter what is the model set-up, there are a number of elements, which need to be defined. These
are:
- The model domain (the area covered by the model on which the computation is done),
- The topography (in the form of a DEM),
- The simulation parameters (simulation time step, length)
The order in which the model is built is the order in which the menus appear in the left window. We
will take each menu one by one:
3.a. The ‘Display’ menu for adding graphical overlays using bitmaps, ArcView.shp files.
Under ‘Display->Foreground” add an item by pressing the button ( upper right part of
the screen) and select item type as image. The Foreground menu item is now extended with
the Image Item. Select from the left panel the “Foreground->Image” menu. Load the image
from the file Karup0.bmp, located in the Bitmaps folder of your working directory. Set the
coordinates for the image as displayed in the following figure:
Xmin=832 Ymin= -1860

Xmax=32835 Ymax= 33260
Add as a new item to the foreground the shape file catchment-meter.shp, located in the folder
GIS-data. Set the line thickness of the shapefile as 1.
48
Your display should look like the following picture.
49
3.b. The ‘Simulation specification’ menu interface.

In the Simulation specification menu the components of the model are defined:
- Click on ‘Simulation specification’ on the left panel. Select the flow modules to be included
in the simulation. For this particular example we have selected the box ‘Saturated flow (SZ)’
with ‘Finite Differences’ numeric engine.
Expand the Simulation Specification menu to see the following sub-menus:

- Submenu: ‘Simulation title’- where you may fill in any information you would like to
define the model
50
- Submenu ‘Simulation period’- where. you can specify the start and end date of the simulation. You
can use either calendar mode or to increment the date using the small ‘up/down’ arrows next to the
window box
Set the dates as follows:

o Start date: 1 January 1980, 00hr00,
o End date: 1 February 1980, 00hr00.
- Submenu ‘Time step control’: Following values have to be set:

o Initial time step: 6 hours.
o Maximum allowed SZ time step: 24 hour
o Increment of reduced time step length: 0.05
o Max precipitation depth per time step (unit: mm): 10. The time step will be adjusted
automatically (when necessary) in such a way that the amount of precipitation falling
within one time step will not exceed this value.
o Max infiltration amount per time step (unit: mm): 10.The time step will be adjusted
automatically (if needed) such that the amount of water that infiltrates to the unsaturated
zone does not exceed this value.
o Input precipitation rate requiring its own timestep: 0.1 (unit: mm/hr): if the rainfall
intensity is larger than this precipitation rate, the computational time step is going to follow
the time steps at which the rainfall rates are specified
51
- In the submenu ‘SZ computational control parameters’ the values remain the default ones
52
3c. The ‘Model domain and grid’ menu

In this menu the catchment area, is given, in the form of a map. Select “catchement defined by Dfs
File” and then browse to locate the map in the “\Maps\Domain_1000m.dfs2”.
The map is of type ‘dfs2’.The extent of the computational domain is given by the grid codes. A
code 1, in a cell, means that the grid is part of the computational domain, and a grid code 2
stands for a boundary cell. Press the ‘Edit’ button to see the grid codes.
3.d. The menu ‘Topography’.

Select Grid File for Spatial distribution. The topography is stored in the file ‘Topography.dfs2’,
stored in the ‘Maps’ directory.
53
You can edit this grid by selecting the ‘Edit’ button . The following screen will become
available:
The grid editor is a generic grid tool, which is split in two windows. You can drag rightwards the
window to make the map larger. The table of values on the right side reflects the highlighted grid
shown on the left map. There are a series of tools available in the top menu of the grid editor, which
allows selection of values and changing them.
54
Close the grid editor.

Change the topography input to XYZ distributed data by changing the spatial distribution to ‘Point
XYZ(.txt)’ and loading the file topo-meter-xyz.txt from the GIS directory. Select ‘Bilinear
interpolation of 1000m radius. Unselect the Show shape raw data to better see the interpolated
values.
55
3.d. The menu ‘Climate’.

The option for snowmelt should not be checked.
- In the submenu ‘Precipitation rate’ following should be done:

o Spatial distribution: select ‘Uniform’;
o Temporal distribution: select ‘Time varying’. Load the precipitation time series
file: ‘SZA_rain’ located in the folder ‘Time’.
At the end of the step the screen should look as follows:
56
- In the submenu: ‘Net rainfall fraction’: choose ‘uniform’ and a value of 1. This value
shows the amount of precipitation which will reach the ground. Evapotranspiration module (ET)
is not included in this model.
STEP 4. THE SATURATED ZONE MODULE

Unfold the menu ‘Saturated zone’, several submenus appear.
- Menu ‘Geological layers’;
- Menu ‘Geological lenses’;
- Menu ‘Computational Layers’
a. Basic SZ data: Select ‘Include subsurface drainage’ and ‘Assign parameters via
geological layers’.
57
b. Use the name ‘Geolayer1’ for the geological layer. Assign the lower levels of the
geolayer1 via a map file named Lay1L.dfs2, located in the MAPS folder. (The top of the
layer is defined by the topography).
Set the following values for the parameters of the aquifer (spatially uniform):
o Horizontal Hydraulic conductivity : Khor = 0.0001 [m/s]
o Vertical Hydraulic conductivity : Kver = 0.00001 [m/s]
o Specific yield = 0.2 [-]
o Storage coefficient = 0.0001[1/m]
c. Introduce a set of geological lenses with lower hydraulic conductivity. Name the lenses
layer as ‘Clay’. Load the shape file specifying the horizontal extent of the lenses-
len03_grid_meter.shp, located in the GIS-DATA folder
58
Set the upper layer of the lenses using the file len03_u.shp, locate in the GIS-DATA folder
Set the lower level of the lenses using the file len03_l.shp, located in the GIS-DATA folder
59
Use Bilinear interpolation with search radius of 1500 m for both upper and lower level.
Set the following parameters for the geological lenses:
o Horizontal Hydraulic conductivity : Khor = 1e-7 [m/s]

o Vertical Hydraulic conductivity : Kver = 5e-8 [m/s]
o Specific yield = 0.1 [-]
o Storage coefficient = 1e-5 [1/m]
d. Define the computational layers by the geological layers, and keep the default minimum
aquifer thickness as 0.5 m
Set the initial groundwater heads to be 3.5m below the surface (Remark: Tick ‘values relative to
the ground’)
60
Define the whole outer boundary of the aquifer as a non-permeable (Zero Flux) boundary. Just
select ZeroFlux as boundary type, and click one point on the boundary cells. Do not specify any
internal boundary
e. Specify the drains to be ‘Drainage not routed, but removed from the model’
61
Use the following data for the drains specification

o Drain level : -0.8 (relative to the soil surface)
o Drain time constant: 5.6e-7
62
STEP 5. SPECIFICATION OF STORING OF RESULTS

The last step before pre-processing and running the model is to specify what results will be stored:
o Expand the menu ‘Storing of results’. Activate ‘Storing of water balance’ and specify the
storing interval as 24
o Submenu ‘Detailed time series output’ allows you to store the time series of computed flow
variables at specific points. Click on the ‘Add item’ icon to add an item. Select as ‘Data
type’ the ‘head elevation in saturated zone’ from the drop-down menu.
Define the X, Y and depth of the point to extract simulation data from, as:
X=7890 m
Y=24900m
Depth=14 m
Make sure the ‘Incl.Obs.Data’ is selected and upload the file with observed data
‘obs_head.dfs0’ (located in Time folder).
63
o Repeat the same steps as in the previous step and select ‘Precipitation rate’ in the same
point. Make sure that ‘Incl Obs.Data’ is not selected.
64
o Select the ‘Grid Series output’ to define what results you need to see as maps. Let the default
selection as is and add the ‘Depth to phreatic surface’. Outputs are stored as dfs2 files.
Save the model !
STEP 6. PREPROCESSING AND RUNNING THE MODEL

6a. In the upper bar menu select ‘Run’, than select ‘Preprocessing’ in order to compile the
model data. Select ‘Run’ than ‘Execute’
6b. In the upper bar menu select ‘Run’, than select ‘Water Movement’. Select ‘Run’ than
‘Execute’.
The status bar indicates the progress of the task. The shortcut menus from the second menu bar can
be used, for the same tasks.
where PP is for the preprocessing, and WM is for water movement, respectively.
65
STEP 7. VISUALISING SIMULATION RESULTS

After the simulation the computed results can be visualised in the form of maps (at a given time) or
time series (at a given point).
7.1. Visualising the results in Result viewer
Press the Result Tab from the Mike SHE Environment. and then select ‘Mike SHE
detailed time series’ . The screen with results is.
You can see both computed and observed groundwater heads.
7. 2. Map visualisation : Select ‘Gridded Data Result viewer’ in order to visualise the results
stored in the form of maps. The computed variables stored in the result files are displayed in the
right-hand side window. The simulation results are stored in a time-varying map file (dfs2 type of
file). Select the result you want to view and press ‘View result’ button. The results will be shown on
a map. (The XY flow vectors check box adds velocity flow vectors calculated for each cell)
66
After pressing ‘View result’ the following screen appears:
By using the forward arrow, you can visualise the time variation of the computed variables and of
the input data, over the domain of computation.
7.3. Extract simulated time series from MikeShe results.
If you use the time series button , of the result viewer you can see the variation in time in a
selected cell.
67
68
STEP 8. WATER BALANCE TOOL

The result file you will obtain after running a model will have the extension “Sheres” and will be located in
the folder with the same name as the model with the extension Result. (see figure)
In order to use the Water Balance facility of MikeShe you will have to do the following steps:
- Launch the Water Balance tool
From MikeZero editor follow the path File->New ->File. Select MikeSHE on the left panel and then Water
Balance Calculation tool on the right panel.
69
- Upload the Result file from where water balance data is extracted
You have to upload the Sheres file from which the data for water balance will be extracted
70
- Define the type of water balance to be computed

Types of water balances to be used with this exercise are:
- Total water balance – chart representation with results in a txt file
- Total water balance – accumulated with results in a time series file
Click on the Post processing tab and name the water balances you wish to extract from the result file.
71
In this case we will define three water balances: Chart water balance, Total Water Balance Incrremental and
Total Water Balance Accumulated. In order to add new items to the post processing, just press the add item
button on the top right of the panel.
Expand the Postprocessing menu on the left pane and select each named water balance, in order to further
define and specify it’s type.
Chart Water Balance has the following specifications:
Important remark: Always press the browse button in order to select the folder and name the file where the
data for the particular water balance will be stored.
72
Total water balance accumulated has the following specifications
Total water balance inccremented has the following specifications
73
Extraction and processing of data
Press the Result tab. Extract and process data (use the extract and process button for this).
- Visualise the results

Select the result Tab from the left pane and then select the water balance to be visualised.
Press the ‘Open’ button.
A total Water balance – Chart type for the Saturated zone model will look:
74
Comment on the result.
75
The Total Water balance Accumulated will look like:
The Total Water balance Inccremental will look like:
76
Exercise 2. Overland flow and river network

The present exercise shows the step-by-step procedure to be used in order to build a MIKE SHE
model.
The example used for showing the steps is the Var catchment model. It is a simple model for
rainfall-runoff modelling. The model will incorporate the overland part and the river part of the
hydrological cycle. The river network will first be modelled for a small part, next to the outlet, only
the last 20 km. It is necessary to have this small part of river network in the model, in order to show
the discharges generated by runoff in the downstream part of the catchment.
Incorporation of the whole river network will be in the second example of this model.

where the data needed for the model construction is stored.

Select ‘Start menu Programs  MIKE BY DHI  MIKE ZERO’ and select ‘MIKE ZERO. The
general interface for all DHI software products will start. This interface is called ‘Mike Zero’
This interface is the starting point for creating different types of files in DHI formats. In the
following steps we will only use Mike She and Mike11 files.
77

2.a Select ‘File New’. Select the ‘MIKE SHE’ tab. Select ‘Flow model’ and click ‘OK’.
Save the (still empty) configuration file in the working directory you have created. Close the
“Project Explorer” window, located on the right.
Save the configuration file under the name ‘VarShortRiver.SHE’.
78

Mike She is a modular system. You can select the components to be included in the model
(saturated, or unsaturated, or overland/channel flow modules) depending on the complexity of the
model you are building.
No matter what is the model set-up, there are a number of elements, which need to be defined. These
are:
- The model domain (the area covered by the model on which the computation is done),
- The topography (in the form of a DEM),
- The simulation parameters (simulation time step, length)
The order in which the model is built is the order in which the menus appear in the left window. We
will take each menu one by one:
3.a. The ‘Simulation specification’ menu interface: Here the components of the model are
defined:
- Click on ‘Simulation specification’. Select the flow modules to be included in the simulation.
For the particular example we select the boxes ‘Overland (OL)’ and ‘River and Lakes’(OC)
(see figure below). Uncheck any other boxes, which are checked by default.
79
- In the submenu: ‘Simulation title’ you may fill in any information you would like to define
the model
- In the sub-menu ‘Simulation period’. you can specify the start and end date of the
simulation. You can use either calendar mode or to increment the date using the small ‘up/down’
arrows next to the window box.

o Start date: 5 November 1994, 00hr00,
o End date 6 November 1994, 00hr00.
- In the submenu ‘Time step control’ following values have to be set:

o Initial time step: 0.1 hours (6 minutes).
o Maximum allowed time step: 0.5 hour
o Increment of reduced time step length: 0.05
o Max precipitation depth per time step (unit: mm): 0.5. The time step will be adjusted
automatically (when necessary) in such a way that the amount of precipitation falling within
one time step will not exceed this value.
o Max infiltration amount per time step (unit: mm): 0.5.The time step will be adjusted
automatically (if needed) such that the amount of water that infiltrates to the unsaturated zone
does not exceed this value. In the present model, there are no sub-surface components so this
parameter is not used by the model.
80
o Input precipitation rate requiring its own time step: 0.05 (unit: mm/hr): if the rainfall intensity
is larger than this precipitation rate, the computational time step is going to follow the time
steps at which the rainfall rates are specified
- In the Submenu ‘OL Computational Control Parameters’ set the parameters as

follows:
o max iteration no: 50
o iteration stop criteria: 510–5 m
o water depth threshold: 10–4 m (for the rest see the figure below)
81
3b. The ‘Model domain and grid’ menu

In this menu the catchment area, is given, in the form of a map. Select “catchment defined by Dfs
File” and then browse to locate the map in the “\Maps\Grid.dfs2”.
The map is of type ‘dfs2’.The extent of the computational domain is given by the grid codes. A
code 1, in a cell, means that the grid is part of the computational domain, and a grid code 2
stands for a boundary cell. Press the ‘Edit’ button to see the grid codes.
3.c. The menu ‘Topography’.
The topography is stored in the file ‘Topography.dfs2’, also stored in the ‘Maps’ directory
82
3.d. The menu ‘Climate’.

The option for snowmelt should not be checked.
- In the submenu ‘precipitation rate’ the following should be done:

o Spatial distribution: select ‘Station-based’;
o Data type: select ‘Grid codes’. Load the precipitation code file: ‘RainThiessen.dfs2’ located in
the folder ‘Maps’. The number of precipitation stations is automatically read by the software
and the menu in the main interface expands into as many submenus as there are rainfall station
codes. Each of them must be filled in with the time series corresponding to the station code.
83
o For each rainfall grid code: select the Temporal distribution option: ‘Time varying (.dfs0)’.
The data file is called ‘Prates.dfs0’ and is located in the folder ‘Time’. When you load the file,
select Item 1 for station 1, Item 2 for station 2, etc. The screen dump below was made for the
3rd station.
At the end of the step, for Grid code 1, the screen should look as follows:
- In the submenu: ‘Net rainfall fraction’: choose ‘uniform’ and a value of 0.9. This value
shows the amount of precipitation which will reach the ground. Evapotranspiration module (ET)
is not included in this model.
84
STEP 4. THE RIVER AND LAKES MODULE

In the the ‘Rivers and lakes’ menu, you upload (select) the Mike11 simulation file that
contains the description and simulation parameters of the river network to be used with the
model. In this case the path to the file is ‘..\Mike11\Var_Just20km\var_Just20km.sim11’ .
By clicking the ‘Edit’ button you can open the MIKE 11 interface and check the model.
The ‘Flood codes’and Bathymetry’should be unchecked.
STEP 5. THE OVERLAND (OL) FLOW MODULE

Unfold the menu ‘Overland’. Several submenus appear.
- Menu ‘Overland’: ‘Separated overland flow areas’ should not be selected
- Submenu ‘Manning number’: assign a uniform value of 20 (which is the Strickler friction
coefficient)
- Detention storage: 0
- Initial water depth: 0

o Unfold the menu ‘Storing of results’. Activate ‘Storing of water balance’. Specify storing
of results for OL and Prec at every 1 hour
o Submenu ‘Detailed time series output’ allows you to store the computed flow variables at
each time step at specific points
Save the model !
85

7a. In the upper bar menu select ‘Run’, than select ‘Preprocessing’ in order to compile the
model data. Select ‘Run’ than ‘Execute’
7b. In the upper bar menu select ‘Run’, than select ‘Water Movement’. Select ‘Run’ than
‘Execute’.
The status bar indicates the progress of the task. The shortcut menus from the second menu bar can
be used, with the same purpose, where PP is for the preprocessing, and WM is for water movement,
respectively

After the simulation the computed results can be visualised in the form of maps (at a given time) or
time series (at a given point).
8.1. Visualising the results of of the river Network (Mike 11 result files), using Mike View.
Time series at a selected point
In order to visualise the results of the computed flow variables as a function of time at a given point,
you must perform the following steps:
1. Open Mike View (from your programs select MIKE by DHI-> MIKE VIEW->MIKE
VIEW;
2. Open the result file name in MikeView
3. Click on the icon that symbolises a time series graph: . You will be asked to select the
variable that you want to visualise. It can be either a water level or a discharge.
4. Select a point of the river network. If you want to visualise the discharge, it should be a red
point. If you want to visualise the water level, it should be a blue point. The cursor takes the
form of a time series graph hen the selected point is a valid one.
5. Click on the left button of the mouse when you have selected a suitable point. The computed
hydrograph appears in the window, as shown below.
86
6. You can save the values of the hydrograph in time (your time series file) in several ways, two of
which are detailed here:
- by pressing the second mouse button and select ‘Copy values’. You can open Excel
and paste the values you just copy in an Excel spreadsheet.
- create a new time series file (dfs0), using MikeZero main menu and paste your copied
values there. In that file you can add as many time series as you need.
8.2. Visualising results of Mike SHE using the Result Viewer from Mike SHE.
In order to visualise the results of the computed flow variables as a function of time at a given point,
you must perform the following steps:
1. Activate the ‘Result ‘at the bottom of the left-hand side window. Select ‘Gridded Data Result
viewer’ in order to visualise the results stored in the form of maps
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2. Map visualisation.: The computed variables stored in the result files are displayed in the right-
hand side window. The simulation results are stored in a time-varying map file (dfs2 type of file).
Select the result you want to view and press ‘View result’ button. The results will be shown on a
map.
By using the forward arrow, you can visualise the time variation of the computed variables and of
the input data, over the domain of computation.
8.3. Adding a River model result file to the Mike SHE viewer.
In the above viewer of results, results from Mike 11 runs can be added, in the following way:
- Select ‘ Projects-> Add files to the
project’ from the main menu bar. The
screen on the left part of the page will
pop-up:
- Select the ‘Add files’ to the project
button
- Select the type of file to be

loaded, as ‘res11’ type of file (Mike11 result file), and than browse to the directory,
where the file is located and specify the name of this file.
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- Press OK. The river network will appear on the screen over the domain of computation.
- The computational points from Mike 11 can be made visible if you select
‘ProjectsActive view settings HorizontalBranchesGraphics’ and you check
the ‘Displayed’ box, for the computational points
- Press OK. The following screen will appear:
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The red points are the computational points of the Mike 11 model.
- In order to view the MIKE 11 results in this interface, you have to select the time series
result viewer button from the menu, and then select a point in the computational
domain, which coincides with a MIKE11 computational point. (you may need to zoom
in to select a MIKE 11 computational point at the outlet of the catchment)
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- Select the variables to be viewed and press OK.
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STEP 8. WATER BALANCES

Follow the steps from exercise 1, for building a total Water Balance. Following is the Total water
Balance as Chart for the Var Catchment.
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STEP 9. SECOND EXAMPLE-VAR RIVER – 100KM

In the river and lakes module change the Mike11 simulation file, with the file Var_BranchVar,
located in the Var_BranchVar folder. This river network is 100km long. Run the model again with
this Mike11 network. Compare the two hydrographs of the Var river ( the 20 km long and this one
of 100 km long), at the outlet of the catchment and comment the results.
The Total Water Balance – Chart type for this case is:
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STEP 10. THIRD EXAMPLE-VAR RIVER – THE WHOLE RIVER NETWORK

In the river and lakes module change the Mike11 simulation file, with the file Var_All.sim11,
located in the Var_AllBranches folder . This river network represents the full river network. Run the
model again with this Mike11 network. Compare the three hydrographs of the Var river (the 20 km
long, the 100km, and this full river network), at the outlet of the catchment and comment the results.
The Total Water Balance – Chart type for this case is:
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Exercise 3. Single column unsaturated zone model

The present exercise shows the step-by-step procedure for building MIKE SHE model of the
Unsaturated Zone. The example used is an imaginary single column Unsaturated Zone model. It is
a simple model for understanding the set-up and processes description in the unsaturated zone. The
model will incorporate the unsaturated zone and the evapotranspiration components of the water
cycle. There will be no flow exchanges in the horizontal directions, and only the flow through the
vertical column representing the unsaturated zone will be considered, coupled with the
evapotranspiration processes.

where the data needed for the model construction is stored. Copy the whole directory structure from
the exercise data folder (provided to you) in a working directory of your own choice.

Select ‘Start menu Programs  MIKE BY DHI  MIKE ZERO’ and select ‘MIKE ZERO’.
The general interface for all DHI software products will start. This interface is called ‘Mike Zero’
This interface is the starting point for creating different types of files in DHI formats.
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2.a Select ‘File NewFile’. Select the ‘MIKE SHE’ tab. Select ‘Flow model’ and click ‘OK’.
Save the (still empty) configuration file in the working directory you have created
Go to your working directory and save the configuration file under the name ‘UZ-Ex3.SHE’.
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3.a. The ‘Simulation specification’ menu interface is the following:
Here the components of the model are defined:
- Click on ‘Simulation specification’. Select the flow modules to be included in the simulation.
For this model we select the following ‘Water movement’ components : ‘Unsaturated flow
(UZ)’ and ‘Evapotranspiration’(see figure below). For UZ components select ‘Richards
equation’. Uncheck any other component which is checked by default.
- In the submenu: ‘Simulation title’ you may fill in any information you would like to define
the model
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- In the sub-menu ‘Simulation period’ specify the following:

o Start date: 1 January 1990, 00hr00,
o End date 1 March 1990, 00hr00.
We will simulate a period of 2 months.

- In the submenu ‘Time step control’ following values have to be set:
 Initial time step: 2 hours.
 Maximum allowed UZ time step: 2 hours
 Increment of time step: 0.05
 Max precipitation depth per time step (unit: mm): 1.
 Max infiltration amount per time step (unit: mm): 1
 Input precipitation rate requiring its own timestep: 0.1 (unit: mm/hr)
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- In the Submenu ‘UZ Computational Control Parameters’ set the parameters as follows:
 max profile water balance error: 0.001

 max number of iterations: 50
 iteration stop criteria ( fraction of Psi): 0.002
 max water balance error in node (fraction): 0.03
3b. The ‘Model domain and grid’ menu

In this menu Create a new model domain and grid with size 3 x 3 cells and each cell having 1000m.
Press the ‘Create’ button.
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In the following screen specify the data. Give the grid file a name, for example ‘UZ1-grid’(in
the ‘Maps’ folder of your working directory) and press the button ‘Create file’:
The grid is now saved as a dfs2 file that can be loaded as needed.
The final grid will be shown on the screen as:
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3.c. The menu ‘Topography’.

For this single column model we have uniform topography. The top of the column is at 10m.
3.d. The menu ‘Climate’ ( precipitation and reference evapotranspiration).

The option for snowmelt should be not checked.
- In the submenu ‘Precipitation rate’ the following should be done:
o Spatial distribution: ‘Uniform’;
o Temporal distribution: ‘Time varying (dfs0)’.
o Select the time series file ‘Precipitation.dfs0’ from the ‘time’ folder in your
working directory. You can edit this file with the ‘Edit’ button.
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- In the submenu ‘Reference Evapotranspiration’ specify a constant value of 5 mm/day:
STEP 4. LAND USE AND VEGETATION PROPERTIES

In the ‘Land use’ menu select the Vegetation sub-menu and specify the following:
- Spatial distribution: ‘uniform’
- Data type: ‘Constant’
- LAI constant value: 3 (Leaf area index)
- RD constant value: 500 mm
- Specify the evapotranspiration parameters as they are given in the figure below:
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STEP 5. THE UNSATURATED ZONE COMPONENT

In the first menu of Unsaturated zone select: ‘Calculated in all grid points’ (only one point for this
model) and no Bypass flow.
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In the ‘Soil profile definitions’ select the Spatial Distribution to be ‘Uniform’. Select the ‘Global’
sub-menu.
- In the top part of the screen ‘Soil Profile’: From the DBase folder of your working directory
select the data base file with soil properties ‘UZexercise1.uzs and choose the soil named ‘Fine
Sand’. Specify the depth of this soil to be from 0 to 10m
- In the bottom part of the screen ‘Vertical discretization’ specify the computational grid points as
presented in the following figure.
In the ‘Groundwater table for lower UZ bounds’ submenu select values relative to the ground and
specify a value of -8m.

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o Activate ‘Storing of water balance’ and specify 2 hours for the ‘Storing Interval for grid
series output’
o Submenu ‘Detailed time series output’ allows you to store the computed flow variables at
each time step at specific points
- In the ‘Time series output sub-menu select ‘water content in the unsaturated
zone’, select any point in the middle of the active cell and give a depth of 0.1.
In the grid series output select all default values, plus:

- average water content in the root zone
- actual evapotranspiration
- water content in unsaturated zone
- unsaturated zone flow
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o MikeSHE creates a default output folder for storage of results. This folder is located in
your working directory with a name ‘UZ –Ex3-Result’

7a. Select ‘Run →Pre-processing→ Execute’ in order to compile the model data
7b. Select ‘Run → Water Movement→ Execute’ in order to run the model
The shortcut menus from the second menu bar can be used, with the same purpose

8a. After the simulation the computed results can first be visualised as time series. We have selected
to see the time series of ‘water content in the unsaturated zone’ at depth of 0.1:
Check if these results seem logical given the input precipitation.

8.b. In order to see results from other components go to Gridded Data Results viewer and select
‘water content in the unsaturated zone’. In the opened grid select the ‘Time Series’ button. Click
inside the grid cell. The following menu appears.
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We will look at two graphs prepared with the following selections

a. Select cells numbered from 43 to 53 ( computational cells from 1 to 10) -the last ones in the
list. The graph obtained is:
b. Repeat the previous step and select cells from 10 to 16 (computational cells 38 to 44),
unselect cell 53 (the last one in the list). The result is the following graph:
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Discuss the result.
8.c. Follow the same steps as in 8B. and select the UZ plot button to see the Depth/Time graph (a
kind of a map) of water content in the UZ. Check the results if they are reasonable!
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8d. In the next step we will see time series results of several different components:
In the Gridded Data Results Viewer select the precipitation item:
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From here we can see precipitation results. In order to see results from other components, we need to
add result files to this file. Through the menu ‘Projects’ - >Add Files to Projects we will add result
files to the current file. We want to see the following items:
1. Actual evapotranspiration
2. Transpiration
3. Soil evaporation
4. Evaporation from intercepted water
5. Canopy storage
6. Infiltration to the UZ
The first 5 items are in the result file ‘UZ-ex3_ET_UzCells.dfs2’, located in the output folder of
your working directory. Therefore this file needs to be added 5 times to your current file. The last
item is found in the result file ‘UZ-ex3_2DUZ_AllCells.dfs2’. This file needs to be added once. (see
following figure)
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After this step, in order to select the actual items for viewing, we need to go to the menu sequence:
Projects-> Active view settings –> Horizontal. For each gridded file, we select one unique item:
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After the items selection with the time series button we can generate time series plots of all the items
together. The results should look something like the figure below:
Try to analyse these results, by posing questions like:

- Which one is the dominant evapotranspiration component?
- Can we explain the behaviour of transpiration and soil evaporation from the graphs in
relation to other components?
- When is infiltration taking place?
- From where comes the water that contributes to soil evaporation in the beginning of the
simulation.
STEP 9: MAKE A WATER BALANCE OF THIS MODEL AND SEE IF YOUR

ANALYSIS CAN BE CONFIRMED
The results for different water balances for the initial model when the canopy interception was
C=0.05, are :
- Total Water Balance ( Chart)
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-UZ Water Balance – Accumulated
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-UZ Water Balance – Incremental
STEP 10: RE-RUN THE MODEL WITH LARGER LEAF AREA INDEX:
LAI=3.
If you repeat Step 8d, the obtained result is:
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STEP 11: RE-RUN THE MODEL WITH 10 TIMES LARGER INTERCEPTION

STORAGE CAPACITY C=0.5 (CANOPY INTERCEPTION) AND COMPARE THE
RESULTS WITH THE ORIGINAL MODEL.
If you repeat Step 8d, the obtained result is:
Comment the obtained results.
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Exercise 4. Simple integrated catchment modelling

The present exercise shows the step-by-step procedure for building MIKE SHE model of a Simple
Integrated catchment model.
It is a simple model for understanding the set-up and processes description for an integrated model.
The model will incorporate all the components, the river and lakes, the unsaturated zone and the
saturated zone. In order to save computational time the overland component is not actually taken
into consideration, simply by setting the Manning coefficient to 0.
The step by step procedure to build such a model is as follows:
STEP 1. CREATE A NEW EMPTY MIKE SHE CONFIGURATION AND SAVE

IT AS ‘INTEGRATED-EX4’ IN YOUR WORKING DIRECTORY
STEP 2. ADD AN IMAGE TO YOUR DISPLAY
Under ‘Display->Foreground” add an image from the file Karup0.bmp, located in the
Bitmaps folder of your working directory. Set the coordinates for the image as displayed in
the following figure:
Xmin=832 Ymin= -1860
Xmax=32835 Ymax= 33260
Select Blend colors for Display style
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STEP 3. ADD THE SHAPE OF THE CATCHMENT BOUNDARY IN YOUR

DISPLAY
Add the shape file catchment-meter.shp, located in the folder GIS-data.
Your display should look like the following picture.
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STEP 4. SET THE MODEL DOMAIN AND GRID

Define the model domain with the same shape file as in the previous step. Define the grid
with 35 by 35 grid cells and each grid cell with a size of 1000m.
STEP 5. SIMULATION SPECIFICATION SET-UP:

The values should be set-up as follows:
a. Select all components as displayed
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b. Select title and description,
c. Simulation period: 1 Jan 1980 to 1 Jan 1983 -3 years of simulation
d. Set-time step controls as displayed in the picture
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e. Keep default OL, UZ, SZ computational parameters
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STEP 6. DEFINE THE TOPOGRAPHY OF THE CATCHMENT

Topography is defined by a Topography.dsf2 file located in the ‘Maps’ folder.
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STEP 7. SELECT PRECIPITATION IN THE CLIMATE MENU

Use the station based spatial distribution with the file Thissen polygons.dsf2, located in the
MAPS folder.
STEP 8. SELECT PRECIPITATION TIME SERIES RECORDS

For each station select precipitation time series from the file Precipitation2.dfs0, located in
the TIME folder.
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STEP 9. SELECT REFERENCE EVAPOTRANSPIRATION IN CLIMATE

MENU.
Set spatially uniform reference evapotranspiration, but time varying. Use the file
PotentialEvap.dfs0, located in TIME folder.
STEP 10. LAND USE - VEGETATION

a. Select the VegetationCodes.dfs2 file, from the Maps folder, for the ‘Station based’ spatial
distribution of vegetation.
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b. Set vegetation properties from vegetation properties data-base file: Vegetation-

properties.ETV for each vegetation type, located in the DBASE folder.
Extend the time series if necessary, to cover the whole simulation period..
STEP 11. SETTING UP RIVER MODEL

Load Mike 11 simulation file Karup.sim11 ( check the Mike 11 input files)
The river network will look as in the picture below:
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STEP 12. OVERLAND FLOW COMPONENT
When the river component is used, it is necessary to include the overland flow component.
However, we will set all the parameters to zero, which will effectively exclude the overland
flow and any excess precipitation will infiltrate.
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STEP 13. UNSATURATED ZONE

a. Definition of unsaturated zone calculation classification type: Calculated in all grid points
b. Spatial distribution of soil profiles

Load soil-profiles as spatial distribution, from the file SoilProfileDefinitions.dfs2, located in
the MAPS folder.
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c. Set the vertical profile soil composition and vertical discretisation in the profile.
We use 3 different soil profiles: fine sand, coarse sand and a combination of both.
Use the UZExercise1.uzs database file for the soil properties.
Use the vertical discretization specified in the picture below for all three profiles:
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STEP 14. SATURATED ZONE SET-UP
b. Basic SZ data: ‘Include subsurface drainage’ and ‘Assign parameters via geological
layers’.
b. Use default name for the layer ‘Aquifer’. Assign the lower levels of the Aquifer via a map
file named lay1L.dfs2, located in the MAPS folder. The top of the layer is defined by the
topography
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Set the following values for the parameters of the aquifer
o Horizontal Hydraulic conductivity : Khor = 0.0001

o Vertical Hydraulic conductivity : Kver = 0.00001
o Specific yield = 0.2
o Storage coefficient = 0.0001
d. Introduce a set of geological lenses with lower hydraulic conductivity. Name the lenses
layer as ‘Clay’. Load the shape file specifying the horizontal extent of the lenses-
len03_grid_meter.shp, located in the GIS-DATA folder
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Set the upper layer of the lenses using the file len03_u.shp, locate in the GIS-DATA folder
Set the lower level of the lenses using the file len03_l.shp, located in the GIS-DATA folder
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Set the following parameters for the geological lenses:
o Horizontal Hydraulic conductivity : Khor = 1e-7

o Vertical Hydraulic conductivity : Kver = 5e-8
o Specific yield = 0.1
o Storage coefficient = 1e-5
d. Define the computational layers b y the geological layers, and keep the default minimum
aquifer thickness
Set the initial groundwater heads to be 3.5m below the surface
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Define the whole outer boundary of the aquifer as a non-permeable (Zero Flux) boundary. Just
select ZeroFlux as boundary type, and click one point on the boundary cells.
Do not specify any internal boundary
e. Specify the drains to be defined by grid codes
Use the following data for the drains specification

o Drain level : -0.5 (relative to the soil surface)
o Drain time constant: 5.6e-7
o Drain codes: 1
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STEP 15. STORING OF RESULTS

Check the calculation of water balance, and specify the storage time step as 24 hours for all
components.
Don’t specify and detailed time series output

o Grid series output: select all default data types, and add the following types:
o Water content in unsaturated zone
o Unsaturated zone flow
o Depth to phreatic surface
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STEP 16. PRE-PROCESSING

After pre-processing you can check some of the pre-processed data. The example below
shows the model domain and grid with the MIKE SHE river links:
STEP 17. RUNNING THE MODEL AND VIEWING RESULTS
Run the model. (It should take around 5-10 minutes). You can now view any results, but our
focus will be on the hydrograph at the outlet of the catchment. In gridded results view load
the depth to phreatic surface. You can view the time evolution of the groundwater table in
the map.
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Load the MIKE11 result file (karup.res11), in MikeView and select the outlet discharge
point to plot the hydrograph.
STEP 18. CALCULATE THE WATER BALANCE FOR THE MODEL

Try to see from the water balance calculations which components are main contributors to
the flow in the river.
Examples of Water Balances for the integrated model are:
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-Total water Balance –Chart
-Total Water Balance – Accumulated
Analyse the water balance results!
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ASSIGNMENT-RELATED TASKS (SEE TASK 2 OF THE ASSIGNMENT

AT THE END OF THIS GUIDE):
STEP 19. LAND USE CHANGES

Change the land use by converting the forest and wetland into agricultural use. Analyse the
effect of this change on the system behavior.
STEP 20. RIVER-AQUIFER EXCHANGE CHANGES

Introduce the “Aquifer only” option for the river-aquifer exchange on the initial model.
Analyse the effect of this change on the system behavior. Plot the hydrograph at the outlet of
the catchment, for both the initial model and this one. Comment on the obtained result.
STEP 21. INTRODUCE PUMPING WELLS

Analyse a case when wells are used for pumping water from the saturated zone. Introduce 8
wells at the coordinates specified in table below, and with extraction rates specified in the file
“Wells.wel”. Compare the system behaviour of the initial model and this one and explain the
components changes.
Cell Well X Y Rate of extraction Filter definition

Top (m) Bottom (m)
(8,31) Well1 7500 30500 0.03 15 5
(8,30) Well2 7500 29500 0.03 15 5
(9,31) Well3 8500 30500 0.03 15 5
(9,30) Well4 8500 29500 0.05 20 3
(9,29) Well5 8500 28500 0.03 15 5
(10,30) Well6 9500 29500 0.03 25 15
(10,29) Well7 9500 28500 0.03 25 15
(11,29) Well8 10500 28500 0.03 25 10
For cell (9,30) make a single cell Water Balance and explain it.
In order to view the position of these wells in all your result screens you will need to include the
well description file in the menu Display-> Foreground (see figure below)
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Guides
141
142
Mike SHE – Explanation of drainage
143
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MIKE SHE allows for flow through drains in the soil. Drainage flow occurs only in the top layer of
the ground water model when the water table is above the position of the drains. In MIKE SHE the
drainage system is conceptually modelled as one 'big' drain within a grid square. The outflow
depends on the height of the water table above the drain and a specified time constant, and is
computed as a linear reservoir. The time constant characterises the density of the drainage system
and the permeability conditions around the drains.
In MikeSHE drainage is described through:

 Drainage codes - areas considered to be drained.
 Drain levels - distributed maps of effective drainage levels i.e. groundwater table
elevation above which drainage flow occurs.
 Drainage time constant
 Drainage options - routing of drainage water from drain levels, directly to rivers
local depressions, or model boundaries.
Drainage from each computational cell is a function of the drainage level and the time constant. The
drainage outflow from the individual cells, Qdr, is calculated from a linear reservoir approximation
depending on the actual water table, hsz, above drain level, hdr, and the specified time constant, Cdr :
Qdr = Cdr (hsz - hdr) A
where Qdr is calculated in m3/s , Cdr is specified in s-1, the levels in m and the area, A, in m2.
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Drainage codes
If the drainage routing is specified by Drain Codes, a grid code map is required that is used to link
the drain flow producing cells to recipient grid cells. The drain levels are still used to calculate the
amount of drain flow produced in each node, but the routing is based only on the code values in the
drain code file.
The Drain Code can be any integer value, but the different values have the following special
meanings:
 grid cells with an Drain Code value of zero will not produce any drain flow and
will not receive any drain flow.
 grid cells with positive Drain Code values will drain to the nearest river,
boundary or local depression in the drain level - in that priority - located next to
a cell with the same Drain Code value. Thus, if a grid cell produces drainage,
 the drain flow will be routed to the nearest river link located next
to a grid cell with the same Drain Code value.
 if there are no grid cells with the same Drain Code located next to
a river link, then the drain flow will be routed to the nearest
boundary cell with the same Drain Code value.
 if there are no boundary cells with the same Drain Code value, the
drain flow will be routed to the cell with the lowest drain level that
has the same Drain Code value (which may create a lake).
 grid cells with negative Drain Code values will drain to either a boundary or a
local depression. Thus, if a grid cell produces drainage,
 the drain flow will be routed to the nearest boundary cell with the
same negative Drain Code value.
 if there are no boundary cells with the same negative Drain Code
value, the drain flow will be routed to the cell with the lowest
drain level that has the same Drain Code value (which may create
a lake).
Example
For the following drain code mapping:
- The grid cells with Drain Code 3 drain to a

local depression since no boundary or river
link is found adjacent to a grid with the same
drain code.
- The grid cells with Drain Code 1 or 2 drain to
nearest river link located adjacent to a grid
with the same drain code.
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- The grid cells with drain code 0 do not contain drains and thus no drainage is produced.
- The grid cells with Drain Code -1 drains to local depression since no boundary is found
adjacent to a grid with the same drain code.
- The grid cells with Drain Code -2 drains to nearest boundary grid with the same drain code.
One method that is often used is to specify only one Drain Code for the entire model area (e.g. Drain
Code 1). Thus, all grids can drain and any drain flow is routed to the nearest river link. If there are
no rivers, the drain flow will be routed to the nearest boundary. If you want to route all drain flow to
the boundaries instead of the rivers, a negative drain code can be specified for the entire area (e.g.
Drain Code -1).
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MIKE SHE – MIKE 11 coupling
River-Aquifer Exchange
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MIKE SHE – MIKE 11 Coupling

The coupling between MIKE 11 and MIKE SHE is made via river links, which are located on
the edges that separate adjacent grid cells. The river link network is created by MIKE SHE's set-
up program, based on a user-specified sub-set of the MIKE 11 river model, called the coupling
reaches. The entire river system is always included in the hydraulic model, but MIKE SHE will
only exchange water with the coupling reaches. Figure 1 shows part of a MIKE SHE model grid
with the MIKE SHE river links, the corresponding MIKE 11 coupling reaches, and the MIKE 11
H-points (points where MIKE 11 calculates the water levels).
The location of each of MIKE SHE river link is determined from the co-ordinates of the MIKE 11
river points, where the river points include both digitised points and H-points on the specified
coupling reaches. Since the MIKE SHE river links are located on the edges between grid cells, the
details of the MIKE 11 river geometry can be only partly included in MIKE SHE, depending on the
MIKE SHE grid size. The more refined the MIKE SHE grid, the more accurately the river network
can be reproduced.
If flooding is not allowed, the MIKE 11 river levels at the H-points are interpolated to the MIKE
SHE river links, where the exchange flows to overland flow and the saturated and unsaturated zones
are calculated.
Figure 1: MIKE 11 Branches and H-points in a MIKE SHE Grid with River
Links
If flooding is allowed, then the water levels at the MIKE 11 H-points are interpolated to specified
MIKE SHE grid cells to determine if ponded water exists on the cell surface. If ponded water exists,
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then the unsaturated or saturated exchange flows are calculated based on the ponded water level
above the cell.
In both cases, the calculated exchange flows are fed back to MIKE 11 as lateral flow to or from the
corresponding H-points.
Cross-section of the River Link
For each river link, a simplified cross-section is used for calculating the exchange flows in MIKE
SHE. This cross-section is triangular in shape, based on the river bank width, the highest bank
elevation and deepest bed elevation. The river link cross-section is interpolated (distance weighted)
from the nearest MIKE 11 cross-sections. The simplified cross-sections are only used for the River-
Aquifer exchange calculations. The MIKE 11 (HD) hydraulic model uses the precise cross-sections,
as defined in the MIKE 11 .xns11 (cross-section) file.
Figure 2 illustrates the relationship between the simplified river link cross-section and the MIKE 11
cross-section. In Figure 2, the MIKE 11 cross-section is irregular in shape, while the river link cross-
section is triangle. The lowest point of point cross-sections are equal, as is the total width. The depth
of the river link cross-section equals the depth of the MIKE 11 cross-section measured from the
highest bank elevation (left side). If the MIKE 11 river cross-section is wider than the cell width,
then the river link cross-section is reduced to the cell width.
Figure 2: A typical simplified MIKE SHE river link cross-section

compared to the equivalent MIKE 11 cross-section.
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In Figure 2, there is a groundwater gradient across the river and a lateral flow through the river from
left to right. Since the water table elevations on the left and right sides of the river are different, the
active area for exchange flow (thickened line) is also different.
RIVER-AQUIFER EXCHANGE
Calculation of River-Aquifer Exchange Flows
When the river width is smaller than the grid-size in MIKE SHE, the exchange flow, Q, between a
saturated zone grid cell and the river link is calculated as a conductance, C, multiplied by the head
difference between the river and the grid cell.
(1)
where the subscript, i, refers to either of the two cells adjacent to the river link.
Head difference
Referring to Figure 2, the head difference between a grid cell and the river is calculated as
(2)
where hi is the head in the grid cell and hriv is the head in the river link, as interpolated from the
MIKE 11 H-points.
If the ground water level drops below the river bed elevation, the head difference is calculated as
(3)
where zbot is the bottom of the simplified river link cross section, which is equal to the lowest point
in the MIKE 11 cross-section.
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If the MIKE SHE simulation is run as a steady-state simulation there is an additional `Canyon'
option for calculating the difference in head when a river with a narrow, deep channel crosses
multiple model layers. In this case, the head difference in layers above the river level is limited by
the bottom elevation of the layer. Thus,
(4)
where zi is the bottom of the current layer.
Without the `Canyon' option, MIKE SHE effectively assumes that the river is hydraulically
connected to the upper most model layer, since MIKE SHE calculates the exchange flow with all
layers that intersect the river based on the difference between the river level and the water table.
In transient and steady-state simulations, MIKE SHE automatically switches between Eqs. (2) and
(3), but MIKE SHE must be specifically instructed to use Eq. (4) as an option during steady-state
simulations. The transition between the heads in Eq. (1) is illustrated in Figure 3.
Figure 3: Water table elevation versus the head difference using Eqs.
(2), (3), and (4).
154
Conductance
In Eq. (1), the conductance, C, between the cell and the river link can depend on
 the conductivity of the aquifer material only (Full contact), or

 the conductivity of the river bed material only [Reduced contact (b)], or
 both the conductivity of the river bed and the aquifer materials [Reduced contact (a)].
Referring to Figure 2, the typical relationship is illustrated between a MIKE 11 cross-section and a
MIKE SHE river link, with the variables used in the calculation of the conductance on both sides of
the river link.
Full Contact - Flow Resistance Only From the Aquifer Material
When the river is in full contact with the aquifer material, it is assumed that there is no low
permeable lining of the river bed. The only head loss between the river and the grid node is that
created by the flow from the grid node to the river bed itself. Thus, the conductance, Ci, between the
grid node and the river link is given by
(5)
where Ki is the horizontal conductivity in the grid cell, dai is the maximum vertical surface available
for exchange flow, dx is the grid size used in the SZ component, and ds is the average flow length,
which is assumed to be the distance from the grid node to the middle of the river bank in the
simplified cross-section.
If the water table is higher than the river level, da is the saturated thickness above the bottom of the
river bed. If the water table is below the river level, then da is the depth of water in the river.
If the river cross-section crosses multiple model layers, then da (and therefore C) is limited by the
thickness of the layer. Note, however, that da is not limited by the bank elevation of the river cross-
section, which means that if the water table in the cell is above the bank of the river, da accounts for
overland seepage above the bank of the river.
155
Reduced Contact (a) - Flow Resistance From Both the Aquifer and Riverbed Materials
If there is a river bed lining, then there will also be a head loss across the lining. In this case, the
conductance is a function of both the aquifer conductivity and the conductivity of the river bed.
Thus, the conductance can be calculated as a serial sum of the individual conductances. Thus, the
conductance, Ci, between the grid node and the river link is given by
(6)
where Ki is the horizontal conductivity in the grid cell, dai is the maximum vertical surface available
for exchange flow, dx is the grid size used in the SZ component, ds is the average flow length
(assumed to be the distance from the grid node to the middle of the river bank in the simplified
cross-section), Lci is the leakage coefficient [1/T] of the bed material, and wi is the wetted perimeter
of the cross-section (da + lhi).
If the water table is higher than the river level, da is the saturated thickness above the bottom of the
river bed. If the water table is below the river level, then da is the depth of water in the river.
If the river cross-section crosses multiple model layers, then dai (and therefore C) is limited by the
thickness of the layer. Note, however, that dai is not limited by the bank elevation of the river cross-
section, which means that if the water table in the cell is above the bank of the river, dai accounts for
overland seepage above the bank of the river.
In Eq. (6), the wetted perimeter, wi, is assumed to be equal to the sum of the vertical and horizontal
areas available for exchange flow. From Figure 2, this is equal to dai and lhi, respectively. As noted
above, dai is not limited by the river bank elevation, but lhi is limited to one half of the river link
width. Thus, the assumed wetted perimeter more closely approximates the wetted perimeter of
natural channels, rather than the simplified cross-section of the river link.
156
Reduced Contact (b) - Flow Resistance Only From the Riverbed Material
If there is a river bed lining, then there will also be a head loss across the lining. In this case, the
conductance is a function of both the aquifer conductivity and the conductivity of the river bed.
However, in some circumstances, the conductance of the aquifer material can be ignored (e.g. if the
bed material has a very low conductance and the aquifer material is very coarse). In this case, the
conductance, Ci, between the grid node and the river link is given by
(7)
where dx is the grid size used in the SZ component, Lci is the leakage coefficient [1/T] of the bed
material, and wi is the wetted perimeter of the cross-section (da + lhi).
In Eq. (7), the wetted perimeter, wi, is assumed to be equal to the sum of the vertical and horizontal
areas available for exchange flow. From Figure 2, this is equal to dai and lhi, respectively. Thus, the
assumed wetted perimeter more closely approximates the wetted perimeter of natural channels,
rather than the simplified cross-section of the river link.
If the water table is higher than the river level, dai is the saturated thickness above the bottom of the
river bed. If the water table is below the river level, then dai is the depth of water in the river. If the
river cross-section crosses multiple model layers, then dai is limited by the thickness of the layer.
However, dai is not limited by the bank elevation of the river cross-section, which means that if the
water table in the cell is above the bank of the river, dai accounts for overland seepage above the
bank of the river. Although, dai is not limited by the river bank elevation, lhi is limited to one half of
the river link width.
157
158
MIKE SHE
Available types of Water Balances
159
160
Table 1 below summarizes the 31 standard water balance types defined in the MikeSHE water balance
configuration file. Some of the water balances cannot be used in certain conditions and these restrictions
are listed in the description
Table 1. Standard Water balances
161
Table 1 ( cont). Standard Water balances
162
The various water balances items are listed in the tables below:
Table 2- SM - Precipitation and snowmelt items
Table 3 - CI - Canopy interception items
163
Table 4. - OL - Overland flow items
164
Table 4 (cont).- OL - Overland flow items
Table 5- UZ - Unsaturated Zone items
165
Table 5(cont)- UZ - Unsaturated Zone items
Table 6 - SZ - Saturated Zone items
166
Table 6( cont) - SZ - Saturated Zone items
167
Table 6(cont) - SZ - Saturated Zone items
168
Catchment modeling
Assignment - Karup catchment – Fully Integrated

model
169
170
This refers to the case of a fully integrated Mike She model built for the Karup catchment.
Task 1.
a) Build the integrated Karup model as described in the handout “Exercises in Catchment Modelling”
(Exercise 4).
Note:
i) Precipitation is not uniform any longer, but defined in the time series file Precipitation2.dfs0,
in folder Time
ii) Precipitation distribution is in the grid file Thiessen Polygons.dfs2, in folder Maps.
iii) Simulation period for the model is of three years: 1 January 1980 till 1 January 1983.
iv) Evapotranspiration option should be included in the simulation specification. The files
needed for this option are vegetation distribution and vegetation properties, for “Land Use”.
The corresponding files are VegetationCodes.dfs2 (a grid file in folder Maps) and
VegetationPropertiesKarup.ETV, respectively (in folder Dbase)
v) The river-aquifer exchange should be set to “Aquifer +Bed” option, in the MikeSHE
network links with the river.
vi) Unsaturated flow option has to be included in the simulation specification with the
Calculation Column Classification Type option set on 3. – Calculation in all grid points. For
inclusion of the UZ component you need the soil classification distribution and soil
properties. The files are Soil profile definitions.dfs2 (in Maps folder), and UZexercise1.uzs
respectively (in Dbase folder). Discretisation has to be prepared for each soil profile as
specified in the handout.
b) Run the model
c) Make Total Water Balances for the model built at point a) and explain the results you have obtained in
terms of overall system behaviour. Describe the contribution and the interaction of different components in
time.
Support your explanation with any water balances calculations or other data that you find appropriate.
171
TASK 2
Change the model setup from Task 1 in order to see the effects on the system behaviour. Use the following
options one by one, and compare the effects with the initially built model:
a) Change the land use by converting the forest and wetland into agricultural use
b) Use “Aquifer only” option for the river-aquifer exchange.
For these different options explain the changes in the overall system behaviour (using the total water balance
results) (with reference to Task 1c).
In case of task 2b) compare the hydrograph obtained at the outlet of the catchment with the same hydrograph
from initial model of Task 1 and comment the results.
c) In the model developed under task 2b) introduce 8 wells at the coordinates specified in table
below, and with extraction rates specified in the file “Wells.wel”. Compare the system behaviour of
the models built under 2b) and 2c) and explain the components changes. Again, use Water Balance
calculations and any other data you find appropriate for your explanations.
Cell Well X Y Rate of Filter definition

extraction
Top (m) Bottom (m)
(8,31) Well1 7500 30500 0.03 15 5
(8,30) Well2 7500 29500 0.03 15 5
(9,31) Well3 8500 30500 0.03 15 5
(9,30) Well4 8500 29500 0.05 20 3
(9,29) Well5 8500 28500 0.03 15 5
(10,30) Well6 9500 29500 0.03 25 15
(10,29) Well7 9500 28500 0.03 25 15
(11,29) Well8 10500 28500 0.03 25 10
For cell (9,30) make a single cell Water Balance and explain it.
Note: The cell coordinates in the above table refer to the numbering used in the water balance tool (which
starts with 1,2…)! In the results viewer of MIKE SHE the same cells have different cell coordinates
(numbering starts with 0,1..) For example Cell (9,30) from the above table (and in water balance tool) will be
Cell (8,29) in MIKE SHE results viewer.
Assignment submission is not required.
172

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A.

Jonoski, PhD, MSc Hand-out

OVERVIEW OF CATCHEMENT MODELLING WITH MIKESHE ................................... 1

EXERCISE 1. SATURATED ZONE............................................................................... 46

EXERCISE 2. OVERLAND FLOW AND RIVER NETWORK ........................................ 77

EXERCISE 3. SINGLE COLUMN UNSATURATED ZONE MODEL............................. 95

EXERCISE 4. SIMPLE INTEGRATED CATCHEMENT MODELLING........................ 117

GUIDES ....................................................................................................................... 141

GUIDE 1. DRAINS ...................................................................................................... 143

GUIDE 2. MIKESHE - MIKE 11 COUPLING ............................................................... 149

GUIDE 3. MIKESHE – AVAILABLE TYPES OF WATER BALANCES ...................... 159

ASSIGNMENT DESCRIPTION ................................................................................... 169

Overview of Catchment Modelling with MikeSHE

Department of Integrated Water Systems and Governance

Types of catchment models

 Model seen as a system:

Types of catchment models

Types of catchment models

 Classification on the basis of description of

Types of catchment models

Types of catchment models

Types of catchment models

Use of different types of catchment models

 Empirical models : easy to calibrate, very fast, little

Use of different types of catchment models

 When the only objective is simulation of runoff

Use of different types of catchment models

Spatially distributed catchment models

 Since physical processes are spatially distributed,

Combination of lumped conceptual models with

Combination of lumped conceptual models with

Hydrological Response Units

Hydrological Response Units

Grid-based spatial distribution

Rainfall stations etc. 17

Integrated catchment modelling – MIKE SHE

Infiltration 2-D overland and

3-D saturated flow Exchange across18

The pre- and post-processing module has:

 Graphical editing functionalities

 3-D Boussinesq equation for saturated flow

MIKE SHE WM - Components

MIKE SHE applications and typical set-up

MIKE SHE processes description

Integrated catchment modelling – MIKE SHE

Infiltration 2-D overland and

3-D saturated flow Exchange across27

 Main physical processes included at

MIKE SHE general data types

Grid files:2-D maps 1D river

MIKE SHE - Precipitation

MIKE SHE Frame component

OVERLAND AND infiltration UNSATURATED ZONE

river base drain flow groundwater recharge / discharge

 Controls the sequence of computation of different

Saturated zone – Exercise 1

MIKE SHE Saturated zone component - Theory

MIKE SHE Saturated zone component - Theory

MIKE SHE Saturated zone component - Theory

 Exchange with other components:

MIKE SHE SZ – Data specification

 Data requirements for setting-up the SZ

MIKE SHE SZ – Data specification