ECOLAB UserGuide PDF

ECO LAB
ECO Lab
User Guide
MIKE by DHI 2009

2
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Printing History
June 2003
April 2004
August 2005
April 2006
October 2007
January 2009
3
4 MIKE Zero
CONTENTS
5
1 ABOUT THIS GUIDE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.1 Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.2 Assumed User Background . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3 GETTING STARTED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.1 Defining an ECO Lab Template . . . . . . . . . . . . . . . . . . . . . . . . 13
3.1.1 Specifying state variables . . . . . . . . . . . . . . . . . . . . . . 14
3.1.2 Specifying constants . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.1.3 Specifying forcings . . . . . . . . . . . . . . . . . . . . . . . . . . 21
3.1.4 Specifying auxiliary variables . . . . . . . . . . . . . . . . . . . . 24
3.1.5 Specifying processes . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.1.6 Specifying derived outputs . . . . . . . . . . . . . . . . . . . . . . 31
3.1.7 Very simple example: degradation of coliform bacteria . . . . . 33
4 REFERENCE MANUAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.1 Auxiliary Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
4.2 Built-in Constants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
4.3 Built-in Forcings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
4.4 Built-in Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.5 Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
4.5.1 EU Eutrophication template . . . . . . . . . . . . . . . . . . . . . 45
4.5.2 WQ Water Quality templates . . . . . . . . . . . . . . . . . . . . 45
4.6 Constants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
4.7 Derived Outputs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
4.8 Euler Integration Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
4.9 Eutrophication ECO Lab Template . . . . . . . . . . . . . . . . . . . . . . 47
4.10 Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
4.11 Forcings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
4.12 Heavy Metal ECO Lab Template . . . . . . . . . . . . . . . . . . . . . . . 47
4.13 Logical Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.14 Mathematical Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.15 Predefined ECO Lab Templates . . . . . . . . . . . . . . . . . . . . . . . 49
4.16 Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.17 Process Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
4.18 Process Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
4.19 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
4.20 Reserved Words . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
4.21 Runge Kutta 4th Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
4.22 Runge Kutta 5th Order with Quality Check . . . . . . . . . . . . . . . . . 52
4.23 Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
6 MIKE Zero
4.24 Semantic Rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4.24.1 State variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
4.24.2 Auxiliary variables . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
4.24.3 Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
4.24.4 Derived outputs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4.25 Spatial Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.26 State Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.27 Syntax Rules of Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.28 Temperature Dependencies . . . . . . . . . . . . . . . . . . . . . . . . . . 57
4.28.1 General description . . . . . . . . . . . . . . . . . . . . . . . . . . 57
4.28.2 Arrhenius temperature dependency factor . . . . . . . . . . . . . 57
4.28.3 Lassiter Temperature dependency factor . . . . . . . . . . . . . . 58
4.29 Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.30 Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.31 Water Quality ECO Lab Templates . . . . . . . . . . . . . . . . . . . . . . 59
7
8 MIKE Zero
Purpose
1 ABOUT THIS GUIDE
1.1 Purpose
The main purpose of this User Guide is to get you started in the use of
ECO Lab, for defining new ECO Lab templates or editing existing tem-
plates describing ecosystems. This User Guide is complemented by the
Online Help.
1.2 Assumed User Background

Although the ECO Lab interface for developing new ECO Lab templates
has been designed carefully with emphasis on a logical and user-friendly
interface without compromising on flexibility and functionality, and
although the User Guide and Online Help contain modelling procedures
and reference material, basic knowledge about ecological modelling and
ecosystems is always needed in any practical application. All knowledge
about ecosystems is found in the ECO Lab templates and the model devel-
opers head. The ECO Lab software itself has no knowledge of any ecosys-
tem before loading or creating a new template, and it is possible for the
model developer to make templates that can be calculated, but make no
sense. The interface is designed to catch some of these descriptions, which
from a logical point of view cannot take place, but the reliability of the
new ECO Lab templates, which are created by the model developer, is the
model developer's own responsibility.
In this case, basic knowledge about ecological modelling and ecosys-

tems means a background in environmental science problems, which is
sufficient for you to be able to know what processes take place and are
important in the ecosystem that ECO Lab should describe. This User
Guide is not intended as a substitute for a basic knowledge of the area in
which you are working: ecological modelling.
9
About This Guide
10 MIKE Zero
2 INTRODUCTION
ECO Lab is a numerical lab for Ecological Modelling. It is an open and
generic tool for customising Aquatic Ecosystem models to describe water
quality, eutrophication, heavy metals and ecology. The module is mostly
used for modelling water quality as part of an Environmental Impact
Assessment (EIA) of different human activities, but the tool is also applied
in aquaculture, e.g. for optimization the production of fish, seagrasses and
mussels. Another application area is in online forecasts of water quality.
The demand for tailor made ecosystem descriptions is great, because eco-
systems vary. The strength of this tool is the easy modification and imple-
mentation of mathematical descriptions of ecosystems into the
hydrodynamic engines of DHI.
The user can use Predefined ECO Lab Templates containing the mathe-
matical descriptions of ecosystems or can choose to develop own model
templates. A template is independent of grid systems and the same tem-
plate can be loaded in MIKE 11, MIKE 21, MIKE 3, MIKE 21 FM and
MIKE 3 FM. The template can describe dissolved substances, particulate
matter of dead or living material, living biological organisms and other
components (all referred to as state variables in this context).
The module is developed to describe chemical, biological, ecological

processes and interactions between state variables and also the physical
process of sedimentation of components can be described. State variables
included in ECO Lab can either be transported by advection-dispersion
processes based on hydrodynamics, or have a more fixed nature (e.g.
rooted vegetation or mussels).
11
Introduction
12 MIKE Zero
Defining an ECO Lab Template
3 GETTING STARTED
The user has the option of
1 Using predefined DHI supported templates

2 Creating own templates
3 Modifying existing templates
If the user chooses to use the predefined DHI supported templates directly,
it is not necessary to read this User Guide, but instead the User Guide for
MIKE 11/21/3 ECO Lab can be relevant for information about running
simulations with ECO Lab.
This manual is about creating new templates and editing existing tem-
plates.
If the user wishes to create a new template: Open MIKE Zero and choose:
File | New | ECO Lab.
If the user wishes to modify an existing ECO Lab template, simply click
on the file in the File Manager and the ECO Lab user interface will open
the chosen file. The MIKE Zero installation program has copied examples
of ECO Lab templates to your hard disk (the templates has the file exten-
sion *.ecolab): see under the path where MIKE Zero was installed
(default: C:\Program files\): DHI\MIKEZero\Templates\ECOLab\*.eco-
lab.
These files can be used as they are or be modified. They can also just be
used for inspiration.
3.1 Defining an ECO Lab Template

An ECO Lab template contains a mathematical description or a set of
ordinary differential equations of an ecosystem including the processes
affecting the ecosystem. In ECO Lab this mathematical description is
divided into 6 types of components, which can be used to describe the sys-
tem. The component types are:
1 State variables
2 Constants
3 Forcings
13
Getting started
4 Auxiliary Variables
5 Processes
6 Derived Output
3.1.1 Specifying state variables

Step one for the model developer in the development process of the model
is to decide which state variables that are necessary to include in the
model for describing a certain ecosystem. State variables represent those
variables that describe the state of the ecosystem and that the user wants to
predict the state of.
Thus, for example, if the model developer wants to make a model of Bio-
logical Oxygen Demand (BOD) and Dissolved Oxygen (DO) in the water
column it would be necessary to specify BOD and DO as state variables in
the ECO Lab user interface. This is done by choosing:
Edit | New Item... | State Variable
A dialog as shown in Figure 3.1 will appear.
Figure 3.1 Creating a new state variable in the ECO Lab dialog
The user should specify different characteristics about the state variable.
14 MIKE Zero
The 'Variable name' attribute should be filled with a short describing

name.
The name should not be too long, as the name specified in this box will be
used later when referring to this state variable in user specified expres-
sions. If the names are short, the expressions become shorter and easier to
read.
The user can specify a longer description than the above name in the
'Description' attribute. The text written in this box will also be printed in
the result files of the MIKE 11/21/3 ECO Lab simulations. The text will
also appear as 'fly by' text in the menus for the MIKE 11/21/3 ECO Lab.
The model developer has the option of publishing further information or

documentation of the state variable by specifying an address or a path to a
website or document in the box called 'Documentation'. By choosing
'Show' a browser will show the documentation.
An optional short text (256 characters) can also be supplied in the box
called 'Online help'.
Under the attribute 'Scope' it has to be specified where in the water envi-
ronment the state variable can be found. There are 4 options:
1 WC Water Column
2 WS Water Surface
3 WB Water Bed
4 SED Sediment
The specification in this attribute is most important in multilayered grid

systems like MIKE 3, because if a state variable is specified with scope
WB, WS or SED, this state variable will in the 3D model only be a 2D
state variable, but if specified with scope WC, the 3D model will reserve
memory for a 3D state variable. The attribute is also introduced to avoid
ECO Lab models introducing impossible descriptions. For example, it is
not possible to have a process interacting with the atmosphere in the sedi-
ment.
Under the 'Transport' attribute it has to be chosen if the state variable

should be transported by the advection-dispersion module of the MIKE
System. Examples of this kind of state variable are usually found in the
pelagic and could for instance be phytoplankton. The alternative is to have
15
Getting started
a state variable that has a fixed location. That would typically be different
seagrasses, or mussels that both have a stationary nature.
There are 3 unit types available for state variables in ECO Lab:
1 Concentrations, with default unit mg/l, the unit is compatible with the
EUM system
2 Mass per area, with default unit g/m2, the unit is compatible with the
EUM system
3 Undefined, with a user specified text string as unit
The user must specify a default value for the state variable. The value
should be the expected value for the state variable. The specified default
value is suggested as initial conditions in the MIKE 11/21/3 ECO Lab.
The user must also specify a realistic range in which the state variable can
be found. If the user specifies initial conditions in the MIKE 11/21/3 ECO
Lab that are outside this interval the user will be warned.
State variables defined in the ECO Lab model are always available for
output in the M11/21/3 ECO Lab menus.
The Expression box contains the ordinary differential equation for the
state variable. This differential equation summarises the processes that
influence the state variable.
The only legal arguments in the state variable expression are:
1 Process names
2 Stochiometric numbers that can be multiplied in the processes
An overview of all state variables and processes and their interaction can
be seen under 'Tools: Processmatrix'. If a state variable and a process has
interaction, the Process matrix will have a stochiometric coefficient speci-
fied at the relevant spot in the matrix. See Figure 3.2.
16 MIKE Zero
Figure 3.2 Tool for viewing the Process matrix of an ECO Lab template. This
example of an ECO Lab template has 6 state variables and 16 proc-
esses and gives an overview over their interaction. The tool is acti-
vated in the ECO Lab user interface by choosing:
Tool | Processmatrix
Another tool is available under 'Tools: References'. For the marked varia-
ble this tool gives an overview of dependencies to other variables. For
example, what other expressions that use this variable as argument and
which arguments that are used in the expression itself. See Figure 3.3.
17
Getting started
Figure 3.3 A tool for viewing references to other variables of a marked variable
is available. For the marked variable, this tool shows an overview of
dependencies to other variables. This example shows that the proc-
ess called phtsyn uses 6 other arguments defined elsewhere in
ECO Lab and phtsyn is used as argument itself when calculating the
expression for DO. The tool is activated in the ECO Lab user inter-
face by choosing: Tool | References
3.1.2 Specifying constants

Constants are used as arguments in the mathematical expressions of proc-
esses in an ECO Lab model. They are constant in time, but can vary in
space. Typical examples of constants are different specific rate coeffi-
cients, exponents, half saturation concentrations and also universal con-
stants such as gas constant and atomic weights.
Thus, for example, if the model developer wants to make a model of BOD
and DO in the water column it could be relevant to specify a process for
BOD degradation. This process could be described by an 1st order degra-
dation expression that uses a specific rate for degradation. This specific
rate could be described as a Constant in ECO Lab. The user does that by
choosing:
Edit | New Item... | Constant
A dialog as shown on Figure 3.4 will appear.
18 MIKE Zero
Figure 3.4 Creating a new Constant in the ECO Lab dialog. In this case a 1st
order decay rate for BOD
The user should specify different characteristics about the included con-
stants.
The 'Constant name' attribute should be filled with a short describing

name.
The name should not be too long because the name specified in this box is
used later when referring to this constant in user specified expressions. If
the names are short, the expressions become shorter and easier to read.
'Description' attribute. The text will appear as 'fly by' text in the menus for
the MIKE 11/21/3 ECO Lab.

documentation of the constant by specifying an address or path to a web-
site or document in the box called 'Documentation'. By choosing 'Show' a
browser will show the documentation.
19
Getting started
Under the attribute 'Spatial Variation' it has to be specified which variation

pattern the constant has. There are 3 options:
1 None: Global, with same value in all grid points

2 Horizontal: Possibly different values in each horizontal grid point, but
without variation in water column
3 Horizontal and Vertical: Possible different values in all grid points.
Relevant for multilayered grid systems
The attribute is introduced to avoid wasting computer memory, so that for

instance a global constant only allocates memory for one number.
The user has the option of using built-in constants that are specified else-
where in the MIKE system. The built-in constants are available, when
choosing the constant as not being user specified. See built-in constants in
Table 3.1.
Table 3.1 Built-in constants
Built-in Constants
Latitude
Longitude
Bed Level
Time step for advection-dispersion calculations
Time step for ECO Lab calculations
Grid Spacing
There are 2 unit types available for constants in ECO Lab:
1 1st order rate, with default unit: per day, the unit is compatible with the
EUM system
The user must specify a default value for the constant. The value should be
the expected value for the constant. The specified default value is also
suggested as the default value for the constant in the MIKE 11/21/3 ECO
Lab menus.
20 MIKE Zero
The user can also specify a realistic range if available where the constants
are usually found. If the user specifies constants in the MIKE 11/21/3
ECO Lab menus that are outside this interval, the user will be warned.
A tool is available under 'Tools: References'. For the marked variable, this
tool shows an overview of dependencies to other variables. For example,
what other expressions that use this variable as argument. See Figure 3.3.
3.1.3 Specifying forcings

Forcings are used as arguments in the mathematical expressions of proc-
esses in an ECO Lab model. They can vary in time and space. They repre-
sent variables of an external nature that affect the ecosystem. Typical
examples of forcings are temperature, solar radiation and wind.
BOD degradation. This process could be described by an expression
dependent on temperature. This temperature could be described as a Forc-
ing in ECO Lab. The user does that by choosing:
Edit | New Item... | Forcing
A dialog as shown in Figure 3.5 will appear.
21
Getting started
Figure 3.5 Creating a new Forcing in the ECO Lab dialog. In this case a built-in
forcing for temperature
The user should specify different characteristics about the included forc-
ing.
The 'Forcing name' attribute should be filled with a short describing name.
The name should not be too long because the name specified in this box is
used later when referring to this forcing in user specified expressions. If
the names are short, the expressions become shorter and easier to read.
'Description' attribute. The text will appear as 'fly by' text in the menus for
the MIKE 11/21/3 ECO Lab.

documentation of the forcing by specifying an address or a path to a
homepage or document in the box called Documentation. By choosing
22 MIKE Zero

pattern the forcing has. There are 3 options:

The attribute is introduced to avoid wasting computer memory, so that a

global forcing only allocates memory for one number.
The user has the option of using built-in forcings that are specified or cal-
culated elsewhere in the MIKE system (see example in Table 3.2). The
built-in forcings are available when choosing the forcing as not being user
specified.
There are 2 unit types available for forcings in ECO Lab:
1 1st order rate, with default unit: per day, the unit is compatible with the
EUM system
The user must specify a default value for the forcing. The value should be
the expected value for the forcing. The specified default value is also sug-
gested as the default value for the forcing in the MIKE 11/21/3 ECO Lab
menus.
The user can also specify a realistic range if available where the forcings
are usually found. If the user specifies forcings in the MIKE 11/21/3 ECO
Lab menus that are outside this interval, the user will be warned.
what other expressions that use this variable as argument. See Figure 3.3.
23
Getting started
Table 3.2 Built-in forcings in ECO Lab
Built-in forcings
Water Layer Height
Salinity
Temperature
Wind Velocity
Wind Direction
Water Surface Level
Water Depth
Horizontal Current Speed
Horizontal Current Direction
Vertical Current Speed
Water Surface Slope in Flow Direction
Bed Area of Grid Cell
Flooded Area of Grid Cell
Surface Area of Grid Cell
Volume of Grid Cell
Horizontal Grid Cell Flux
Vertical Grid Cell Flux
Water Density
Chezy No.
3.1.4 Specifying auxiliary variables

Auxiliary variables are mostly arguments in mathematical expressions'
processes in an ECO Lab model, but sometimes they are only used for
specifying results directly.
BOD degradation. This process could be described by an expression
dependent on temperature. This temperature could be described as a Forc-
ing in ECO Lab. The user does that by choosing:
24 MIKE Zero
Edit | New Item... | Auxiliary Variable
Figure 3.6 Creating a new Auxiliary Variable in the ECO Lab dialog. Note that a
built-in function is about to be inserted in the expression box. A list
of possible arguments including the built-in functions can be viewed
by pressing 'Ctrl' + 'Space'. In this case the list has been limited to
only include arguments that start with a capitol O.
The user should specify different characteristics about the auxiliary varia-
ble.
The 'Variable name' attribute should be filled with a short describing

name.
The name should not be too long, because the name specified in this box is
used later when referring to this auxiliary variable in user specified
expressions. If the names are short, the expressions become shorter and
easier to read.
description attribute. The text written in this box will also be printed in the
result files of the MIKE 11/21/3 ECO Lab simulations. The text will also
appear as 'fly by' text in the menus for the MIKE 11/21/3 ECO Lab.
25
Getting started

documentation of the auxiliary variable by specifying an address or a path
to a website or document in the box called 'Documentation'. By choosing
called 'Online help'. This text is at the moment only used as reference and
record of the ECO Lab model.
It can be specified in the 'Output' box that the auxiliary variable should be
available for output in the M11/21/3 ECO Lab model menus. If 'YES' is
chosen the user will be prompted in the M11/21/3 ECO Lab menus and
asked if the auxiliary variable should be included in the result file.

pattern the auxiliary variable has.
There are 3 options:

The attribute is introduced to avoid wasting computer memory and redun-

dant calculations, so that for instance a global auxiliary variable only allo-
cates memory for one number and is only calculated once per time step.
It is possible to specify user specified text as unit description for auxiliary

variables in ECO Lab.
The Expression box should be filled with the mathematical formulation of

the auxiliary variable.
The expression is formulated by a series of arguments, State Variables,

Constants, Forcings, Auxiliary variables separated by operators. A list of
possible arguments will be shown if the keys 'Ctrl' + 'Space' are stroked at
once. The list can be filtered by marking the beginning characters of an
argument before stroking 'Ctrl' + 'Space'.
The following argument types are possible to use in auxiliary variable

expressions:
26 MIKE Zero
1 Numbers
2 Already defined names of state variables, constants, forcings, and aux-
iliary variables. The names will turn from red to blue when recognised
as an already defined variable
3 Mathematical functions. The text will turn from red to green when rec-
ognised as a supported mathematical function
4 Built-in functions. The text will turn from red to green when recog-
nised as a predefined built-in function
5 Logical functions. If recognised as a logical function the text will turn
from red to black
6 Reserved words. If recognised as a reserved word the text will turn
from red to black
The following operators are possible to use in expressions:
1 Addition: +
2 Subtraction: -
3 Multiplication: *
4 Division: /
In addition to the above-mentioned, the expressions must follow a set of

semantic rules for how the arguments can be combined. Of course, the
expressions must also follow the syntax rules. See Reference Manual for
ECO Lab for details about these rules.
what other expressions that use this variable as argument and which argu-
ments that are used in the expression itself. See Figure 3.3.
The order in which the expressions in auxiliary variables are defined is

also the order in which they will be calculated. Arguments in an expres-
sion defined after the expression itself is therefore not legal. Therefore it
can often be necessary to change the order in which the variables are
defined when creating a template. This is done by simply dragging and
dropping the relevant variable with the mouse to a new position.
3.1.5 Specifying processes

Processes describe the transformations that affect the state variables. That
means processes are used as arguments in the differential equations that
27
Getting started
ECO Lab solves to determine the state of the state variables. These differ-
ential equations, which describe the interaction between state variables
and processes are specified under 'State Variables'. To add a new process
in ECO Lab choose:
Edit | New Item... | Process
Figure 3.7 Creating a new Process in the ECO Lab dialog. In this case it is a
process for BOD degradation. Note that a built-in function
(ARRHENIUS20) is used in the expression box along with other
arguments.
The user should specify different characteristics about the process.
The 'Process name' attribute should be filled with a short describing name.
The name should not be too long, because the name specified in this box is
used later when referring to this process in user specified expressions. If
the names are short the expressions become shorter and easier to read.
description attribute. The text written in this box will also be printed in the
28 MIKE Zero
result files of the MIKE 11/21/3 ECO Lab simulations. The text will also
appear as 'fly by' text in the menus for the MIKE 11/21/3 ECO Lab menus.

documentation of the process by specifying an address or path to a website
or document in the box called Documentation. By choosing 'Show' a
browser will show the documentation.
It can be specified in the 'Output' box that the process should be available
for output in the M11/21/3 ECO Lab model menus. If 'YES' is chosen the
user will be prompted in the M11/21/3 ECO Lab menus and asked if the
process should be included in the result file.
Under the attribute 'Spatial variation' it has to be specified which variation

pattern the process has. There are 3 options:

3 Horizontal and Vertical: Possibly different values in all grid points.

dant calculations, so that for instance a global process only allocates mem-
ory for one number and is only calculated once per time step.
It is possible to specify user specified text as unit description for processes

in the ECO Lab model.
The Expression box should be filled with the mathematical formulation of

the process.
The expression is formulated by a series of arguments, mathematical func-

tions, built-in functions, logical functions and reserved words separated by
operators. A list of possible arguments will be shown if the keys 'Ctrl' +
'Space' are stroked at once. The list can be filtered by marking the begin-
ning characters of an argument before stroking 'Ctrl' + 'Space'.
The following arguments are possible to use in process expressions:
29
Getting started
1 Numbers
2 Already defined names of state variables, constants, forcings, auxiliary
variables and Processes. The names will turn from red to blue when
recognised as an already defined variable
ognised as a supported mathematical function. The text will turn from
red to green when recognised as a supported mathematical function
4 Built-in functions. The text will turn from red to green when recog-
nised as a predefined built-in function. The text will turn from red to
green when recognised as a predefined built-in function
5 Logical functions. If recognised as a logical function the text will turn
from red to black
from red to black
1 Addition: +
2 Subtraction: -
3 Multiplication: *
4 Division: /

expressions must also follow the defined syntax rules. See Reference
Manual for ECO Lab for details about these rules.
The order in which the expressions in processes are defined is also the
order in which they will be calculated. Arguments in an expression
defined after the expression itself is therefore not legal. Therefore it can
often be necessary to change the order in which the variables are defined
when creating a template. This is done by simply dragging and dropping
the relevant variable with the mouse to a new position.
30 MIKE Zero
3.1.6 Specifying derived outputs

Derived outputs are outputs that as the name indicates are derived based
on other model results. An example could be an estimate of Total N,
which summarises the state variables containing nitrogen. The difference
between calculating Total N under 'Derived Outputs' and 'Auxiliary Varia-
bles' is that if state variables are included in the expressions, the values
will be based on values from the previous time step in the auxiliary varia-
bles, but in derived output the state variables will have updated values for
present time step. That is because the calculation of the derived output is
done after the differential equation has been integrated.
The user adds a derived output by choosing:
Edit | New Item... | Derived Outputs
Figure 3.8 Creating a new Derived Output in the ECO Lab dialog. In this case it
is a derived output for Total N that summarises the nitrogen contain-
ing state variables in the water column.
The user should specify different characteristics about the derived output.
Derived outputs do not have a name attribute, so derived outputs cannot be

referred to in other expressions.
31
Getting started
The user can specify a longer description in the description attribute. The
text written in this box will be printed in the result files of the MIKE
11/21/3 ECO Lab simulations. The text will also appear as 'fly by' text in
the menus for the MIKE 11/21/3 ECO Lab.

documentation of the derived output specifying an address or path to a
website or document in the box called 'Documentation'. By choosing
called 'Online help'. This text is at the moment only used as reference and
record of the ECO Lab model.

pattern the derived output has.
The are 3 options:


dant calculations, so that for instance a global derived output only allo-
cates memory for one number and is only calculated once per time step.
If derived outputs are defined, they will always be available in the

M11/21/3 ECO Lab menus, when specifying the result file.
It is possible to specify user specified text as unit description for a derived

output in ECO Lab.
The expression box should be filled with the mathematical formulation of

the derived output.
The expression is formulated by a series of arguments, mathematical func-

tions, built-in functions, logical functions and reserved words separated by
operators. A list of possible arguments will be shown if the keys 'Ctrl' +
'Space' are stroked at once. The list can be filtered by marking the begin-
ning characters of an argument before stroking 'Ctrl' + 'Space'.
32 MIKE Zero
The following arguments are possible to use in expressions:
1 Numbers
2 Already defined names of state variables, constants, forcings, auxiliary
variables and processes. Note that the values for the state variables will
be based on values after integration has taken place. The names will
turn from red to blue when recognised as an already defined variable
ognised as a supported mathematical function
4 Built-in Functions. The text will turn from red to green when recog-
nised as a predefined built-in function
5 Logical functions. If recognized as a logical function the text will turn
from red to black
from red to black
1 Addition: +
2 Subtraction: -
3 Multiplication: *
4 Division: /

expressions must also follow the defined syntax rules. See Reference
Manual for ECO Lab for details about these rules.
3.1.7 Very simple example: degradation of coliform bacteria

The following is a simple example with the purpose to illustrate how to
create a simple ECO Lab template. In this case it describes coliform bacte-
ria in an aquatic environment.
The bacteria are assumed to be degraded with a first order decay expres-
sion in the water and the degradation is dependent on temperature. For
33
Getting started
simplicity in this example the description does not include salinity and
solar radiation in the model even though it is known that these factors also
play a role in degradation of coliform bacteria in the water environment.
To define the above mentioned system the user should open the ECO Lab
user interface and create a template with the variables and characteristics
that can be seen in Table 3.3. Note that '---' in the table means that the
attribute is not necessary to specify for that variable type.
After typing the information into ECO Lab the file should be saved as a
ECO Lab template (*.ecolab file). When pressing 'Save' ECO Lab will
compile the contents of the template. At this stage the user might get an
error message if ECO Lab cannot compile the file. The ECO Lab template
is not complete from a technical point of view before it is possible to save
without error messages.
An often seen error message relates to illegal combinations of spatial vari-

ation. For example, an Auxiliary variable cannot have spatial variation =
'NONE', if arguments in its expression have spatial variations different
than 'None'. State variables with scope 'WC' always have the spatial varia-
tion = 'HORIZONTAL_AND_VERTICAL' (cannot be changed), so if a
state variable is used in an expression, the expression cannot have the spa-
tial variation = 'NONE'. However, it is legal to use arguments with the
spatial variation 'NONE' in expressions with the spatial variation
'HORIZONTAL_AND_VERTICAL'. See Reference Manual for ECO Lab
for details about semantic rules.
34 MIKE Zero
Table 3.3 Characteristics of a simple Faecal Coliform ECO Lab model
State variable Process Constant Constant Forcing Auxiliary

Variable
Variable name FC FCdegr KcoliF tetaT temp ftemp
Description Faecal Colif- Degradation of 1st order decay Temperature Temperature Factor for
orm Bacteria Faecal 20 C, coefficient for temperature
Coliform (faecal) decay rate influence
Scope WC WC --- --- --- ---
Transport ADVECTION_ --- --- --- --- ---

DISPERSION
Spatial Variation --- HORIZONTAL_ NONE NONE HORIZONTAL_ HORIZONTAL_

AND_VERTICAL AND_VERTICAL AND_VERTICAL
Process Type --- Transforma- --- --- --- ---

tion
EUM type Undefined 1st order rate Undefined Undefined Undefined

WQ model
Unit 1/100 ml per day Dimensionless degrees C Dimensionless
User specified --- --- Yes Yes No ---
Built-in ID --- --- --- --- TEMPERATURE ---
Default value 0 --- 0.8 1.09 10 ---
Min value 0 --- 0 1 0 ---
Max value 1000000000 --- 10 1.2 100 ---
Expression -FCdegr KcoliF*FC*fSAL* --- --- --- POW(tetaT,temp-

fTEMP 20)
Output --- Yes --- --- --- Yes
35
Getting started
36 MIKE Zero
4 REFERENCE MANUAL
It is intended that you use this manual when you are making model appli-
cations with ECO Lab and need to know how various inputs, outputs, etc.
can be specified. Also often used terms in ECO Lab are explained.
All the entries listed below are included in the Reference Manual in alpha-
betical order.
Auxiliary Variables (p. 38)

Built-in Constants (p. 38)
Built-in Forcings (p. 39)
Built-in Functions (p. 40)
Calibration (p. 44)
Constants (p. 46)
Derived Outputs (p. 46)
Euler Integration Method (p. 46)
Eutrophication ECO Lab Template (p. 47)
Expressions (p. 47)
Forcings (p. 47)
Heavy Metal ECO Lab Template (p. 47)
Logical Functions (p. 48)
Mathematical Functions (p. 48)
Predefined ECO Lab Templates (p. 49)
Processes (p. 49)
Process Matrix (p. 50)
Process Type (p. 50)
References (p. 51)
Reserved Words (p. 51)
Runge Kutta 4th Order (p. 51)
Runge Kutta 5th Order with Quality Check (p. 52)
Scope (p. 52)
Semantic Rules (p. 53)
Spatial Variation (p. 56)
State Variables (p. 56)
Syntax Rules of Expressions (p. 56)
Temperature Dependencies (p. 57)
Transport (p. 58)
Units (p. 58)
Water Quality ECO Lab Templates (p. 59)
37
Reference Manual
4.1 Auxiliary Variables

Auxiliary variables are mostly arguments in mathematical expressions of
Processes in an ECO Lab template, but sometimes they are only used for
specifying results directly.
They are defined as mathematical expressions themselves with a sequence

of arguments and operators.
Arguments in a auxiliary variable expression could be state variables, con-

stants, forcings, numbers, or other auxiliary variables. The auxiliary varia-
bles are calculated in the order they are defined in the ECO Lab model,
starting from top. So only auxiliary variables defined above the present
auxiliary variable expression can be used as argument in auxiliary variable
expressions.
The idea is to split long process expressions (see Processes) into sub-
expressions under auxiliary variables, so that the process expressions
become more simple and easier to read. However, only the model devel-
opers imagination limits the possible use of auxiliary variables, because
here you can calculate intermediate results. Typical examples of auxiliary
variables are dimensionless factors that can be multiplied by a process.
The factors could e.g. be a factor for primary productions' dependency of
light, or a factor for coliform bacteria's decay dependency of temperature.
The defined factor is then used as argument under processes. Other uses of
auxiliary variables are to use them in other auxiliary variables. For exam-
ple, an auxiliary variable for estimating light in the water column can be
used as argument in the auxiliary variable mentioned above for calculating
a factor for primary productions' dependency of light.
4.2 Built-in Constants

In ECO Lab templates it is possible to refer to constants that are specified
or calculated in the hydrodynamic engines of MIKE. The available built-
in constants are not the same in all the hydrodynamic engines. If it is spec-
ified that it should be a built-in constant and it is not available in the
engine, the engine dialog will prompt as if the constant was user specified.
It is possible to choose from the following list of built-in constants:
38 MIKE Zero
Built-in Forcings
1 Latitude
If available this built-in constant returns the latitude of the model area
2 Longitude
If available this built-in constant returns the longitude of the model
area
3 Bed level
If available this built-in constant returns the altitude of the model area
4 AD time step (AD_DT)
This built-in constant returns the time step in seconds between every
advection-dispersion calculation
5 ECO Lab time step (WQ_DT)
This built-in constant returns the time step in seconds between every
update by the ECO Lab module
4.3 Built-in Forcings

In ECO Lab templates it is possible to refer to forcings that are specified
or calculated in the hydrodynamic engines of MIKE. The available built-
in forcings are not the same in all the DHI hydrodynamical engines. If it is
specified that it should be a built-in forcing and it is not available in the
engine, the engine dialog will prompt as if the forcing was user specified.
It is possible to choose from the following list of built-in forcings:
1 Water Layer Height

This forcing returns the spatial distance between layers (in meters). In
one layered grid systems the water depth will be returned
2 Salinity
If available this forcing returns the salinity calculated in the hydrody-
namic setup
3 Temperature
If available this forcing returns the temperature calculated in the hydro-
dynamic setup
4 Wind Velocity
If available this forcing returns the wind velocity specified in the
hydrodynamic setup
5 Wind Direction
If available this forcing returns the wind direction specified in the
hydrodynamic setup
39
Reference Manual
6 Water Surface Level

This forcing returns the water level calculated in the hydrodynamic
setup
7 Water Depth
This forcing returns the water depth calculated in the hydrodynamic
setup
8 Horizontal Current Speed
This forcing returns the horizontal current speed in meters per second
calculated in the hydrodynamic setup
9 Horizontal Current Direction
This forcing returns the horizontal current direction in degrees calcu-
lated in the hydrodynamic setup
10 Vertical Current Speed
This forcing returns the vertical current speed in meters per second cal-
culated in the hydrodynamic setup
11 Water Surface Slope in Flow Direction
This forcing returns the slope of the water surface (meter per meter)
calculated in the hydrodynamic setup. Under normal conditions posi-
tive values.
12 Bed Area of Grid Cell
13 Flooded Area of Grid Cell
14 Surface Area of Grid Cell
15 Volume of Grid Cell
16 Horizontal Grid Cell Flux
17 Vertical Grid Cell Flux
18 Water Density
If available in hydrodynamic simulation this forcing returns a value for
water density
4.4 Built-in Functions

In the ECO Lab templates it is possible to choose a number of predefined
functions from a database and use them in the expressions. The database
contains the following functions:
1 DAYNUMBER(Year, Month, Day)

This function returns an integer between 1 and 365 representing the
40 MIKE Zero
Built-in Functions
day number in year
2 ARRHENIUS20(Temperature Coefficient, Temperature)

This function returns a temperature dependency based on the following
Arrhenius expression:
f ( a, b ) = a ( b 20 )
3 ARRHENIUS5(Temperature Coefficient, Temperature)

This function returns a temperature dependency based on the following
Arrhenius expression:
f ( a, b ) = a ( b 5 )
4 OXYGENSATURATION(Salinity, Temperature)
This function returns an estimate of the saturated dissolved oxygen
concentration in the water as function of salinity and temperature:

f (a,b) = 14, 65 0, 0841 a + b ( 0 , 00256 a 0, 41022 + b
( 0, 007991 0, 0000374 a 0, 000077774 b ) )
5 OXYGENSATURATION_WEISS(Salinity, Temperature)
This function returns an estimate of the saturated dissolved oxygen
concentration in water as function of salinity and temperature. Sug-
gested by Weiss:
ea
f ( sali, temp ) = -------------------
0.69997
where
100
a = 173.4292 + 249.6339 ------------------------------------ +
temp + 273.15
temp + 273.15 temp + 273.15
143.3483 log ------------------------------------ 21.8493 ------------------------------------ +
100 100
temp + 273.15 temp + 273.15 2
sali 0.033096 + 0.014259 ------------------------------------ 0.0017 ------------------------------------
100 100
6 LASSITER(Lassiter Constant, Growth Rate, Growth Optimum

Temperature, Growth Inhibition Temperature, Temperature)
This function returns a dimensionless temperature dependency factor
relevant for many biological processes
41
Reference Manual
a (d c)
d temp
---------------------
a ( temp c )
Lassiter ( a, b, c, d, temp ) = b e
dc
7 MICHAELIS_MENTEN1(Concentration, Halfsaturation Con-

stant):
a
f (a,b) = ------------
a+b
8 MICHAELIS_MENTEN2(Concentration, Constant):
2
a
f (a,b) = -------------
2
-
a +b
9 REVERSE_MICHAELIS_MENTEN(Concentration):
1
f ( a ) = ------------
a+1
10 SUNRISE(Year, Month, Day, Latitude, Correction For Summer

Time)
11 SUNSET (Year, Month, Day, Latitude, Correction For Summer

Time)
12 LAMBERT_BEER_1(Surface Light, Layer Height, Light Extinc-

tion Coefficient)
This function estimates the light penetration in water column based on
Lambert Beer expression. The light intensity in the top of each grid
layer is returned
13 LAMBERT_BEER_2(Surface Light, Layer Height, Light Extinc-

tion Coefficient)
This function estimates the light penetration in water column based on
Lambert Beer expression. The light intensity in the bottom of each grid
layer is returned
14 RELATIVE_DAYLENGTH(Month, Day, Latitude)

Returns a value for relative day length. The value equals 1 at equinox
(when day and night have same length)
15 SECCHI_DEPTH(Light Extinction Coefficient,
Dampening_Percentage)
42 MIKE Zero
Built-in Functions
Returns the secchi depth at a horizontal point as function of a vertically

variating light extinction (1/m). The dampening percentage is included,
so that the user can specify own definitions of secchi depth. Secchi
depth is the depth at which the lightintensity has been dampened by a
given percentage relative to the surface light intensity. Note that at
shallow water the secchi depth will not describe the transparency of the
water because the function can not return values higher than the water
depth. An alternative is to look at the extinction coefficient itself. An
often used definition of secchi depth uses a dampening percentage of
80. Important: The variable referring to this function must be specified
with spatial variation Horizontal and Vertical in order for the function
to use the vertical variating extinction coefficient. The calculated sec-
chi depth is returned in the top layer in output of multilayered model
systems, the values in the layers below can be ignored.
16 AVERAGE_WATER_COLUMN(name of variable)
Returns the average value in the water column of a specified variable
with vertical variation. Can be used for estimating primary production
per m2 if the average water column primary production per m3 is mul-
tiplied with water depth. Important: The variable referring to this func-
tion must be specified with spatial variation Horizontal and Vertical
in order for the function to find the average the vertical variating varia-
ble. The calculated average of the water column is returned in the top
layer in output of multilayered model systems, the values in the layers
below can be ignored.
17 SMOOTHING_AVERAGE(variable, weight of latest value of
the variable)
Returns a smooth value S of a variable that has been weighted against
both latest value of the variable Y and historical values of the variable.
Can be used in ecology when a variable does have immediate effect on
other variables. For instance can long periods of anoxia kill benthic
organisms, but maybe not the peaks of low oxygen concentrations.
Smoothing average is suitable for describing this phenomena. It has a
similar function as moving average, but it has the advantage that it uses
much less memory than the moving average function.
S(t) = Y(t) + ( 1 ) S(t 1)
18 MOVING_AVERAGE(variable, x number of timesteps to average)

Returns a moving average of a variable. The average is an average of
the x latest values of the variable. Can be used in ecology when a vari-
able does have immediate effect on other variables. For instance can
long periods of anoxia kill benthic organisms, but maybe not the peaks
of low oxygen concentrations. Moving average is suitable for describ-
43
Reference Manual
ing this phenomena. It has a similar function as smoothing average, but

be aware that it is very heavy on memory to use this function.
19 IF(conditional expression, expression if true, expression if false)
Returns 2 different values depending on a conditional expression. It is
an alternative to an IF THEN ELSE statement and can be formulated as
a function. This IF function is useful for nesting IF statements, which is
not possible with the other way of writing IF THEN ELSE statements
in ECO Lab. It is possile to make 8 nested IF statements in ECO Lab.
20 RAND()
Returns a random number between 0 and 1.
4.5 Calibration
By calibration of a ECO Lab model setup it is attempted to find the best
accordance between computed and observed state variables (model com-
ponents) by variation of a number of parameters.
Deviation between computed and observed state variables in ECO Lab

can be caused by a number of reasons. The most obvious are:
1 Inaccurate specification of concentrations at the model boundaries

2 Inaccurate specification of loadings to the ecosystem
3 Inaccurate initial concentrations
4 Inaccurate hydrodynamic setup
5 Limitations in the chosen ECO Lab process descriptions
6 Inaccurate calibration of coefficients in ECO Lab process equations
7 Wrong measurements
8 Instable numerical solution
The ECO Lab modeller should when calibrating an ECO Lab setup have
the above mentioned possible reasons for inaccuracy in the results in
mind, before changing parameters dramatically.
Calibrating coupled ordinary differential equations can be tricky, because

of the mutual dependency of the state variables. So if one state variable is
calibrated to fit the observed values, maybe it will not fit so well after cal-
ibrating other state variables in the ecosystem. Some dependencies are
stronger than others. Therefore it is advisable to calibrate the state varia-
bles with the least dependencies to other state variables first.
44 MIKE Zero
Calibration
For the DHI ECO Lab templates the following calibration order is sug-
gested:
4.5.1 EU Eutrophication template

Recommended calibration order
z Phytoplankton
Potential growth, shift diatoms-green algae
Sedimentation
Light extinction
Temperature dependency
z Nutrients
z Detritus sedimentation/decay
z Sediment (denitrification/immobilisation)
z Oxygen
z Macrophytes
4.5.2 WQ Water Quality templates

Recommended calibration order
z BOD-DO relations
degradation rates
re-aeration
production/respiration
(nitrification)
z Nutrients
content BOD
nitrification/denitrification
sorption processes
z Coliforms
45
Reference Manual
4.6 Constants
Constants are used as arguments in the mathematical expressions of proc-
esses in an ECO Lab template. They are constants in time, but can vary in
space. Typical examples of constants are different specific rate coeffi-
cients, exponents, half saturation concentrations and also universal con-
stants such as gas constants and atomic weights.
Some coefficients and transformation rates can be found in the literature,

but many have not been documented in literature. So this possible lack of
information is wise to investigate, before defining a complex ECO Lab
model.
4.7 Derived Outputs

Derived outputs are additional outputs that the user can specify in ECO
Lab templates. They are usually results, which are not given in the state
variables directly, but as can be derived from the state variables or proc-
esses.
Derived outputs are described as mathematical expressions with a

sequence of arguments and operators. Arguments in a derived output
expression could be state variables, constants, forcings, auxiliary varia-
bles, numbers, or processes. It is not possible to refer to derived outputs in
other expressions.
Examples of derived outputs in an ECO Lab model could be Total N or

Secchi depth, which both are not given directly through the state variables,
but can be derived from them. It shall be noted that the derived output is
calculated after the state variables have been integrated, so identical
expressions including state variables as arguments will not give the same
result if calculated under auxiliary variables instead of under derived out-
put.
4.8 Euler Integration Method

The Euler Integration Method is a very simple numerical solution method
for solving ordinary differential equations.
The formula for the Euler method is:
46 MIKE Zero
Eutrophication ECO Lab Template
y n + 1 = y n + hf ( x n, y n )
which advances a solution y from x n to x n + 1 = xn + h
4.9 Eutrophication ECO Lab Template

The Eutrophication ECO Lab Template is a predefined DHI supported
ECO Lab template, which is a model of eutrophication processes in
aquatic systems.
See Scientific Description of the EU Template under manuals in the instal-

lation. The pdf file can be viewed directly from the ECO Lab GUI when
the EU template is loaded.
4.10 Expressions
Expressions must be specified for state variables, auxiliary variables,
processes, and derived outputs in the ECO Lab templates. An expression
is a sequence of arguments and operators.
The expressions must follow the Syntax Rules of Expressions and the
Semantic Rules.
4.11 Forcings
Forcings are used as arguments in the mathematical expressions of proc-
esses in an ECO Lab template. They can vary in time and space. They rep-
resent variables of an external nature that affect the ecosystem. Typical
examples of forcings are temperature, solar radiation and wind.
If many measurements are available of a state variable, it is possible to

temporarily replace it with a forcing. This way a specific process can be
isolated and calibrated with less uncertainty. After calibrating the process,
the forcing can be transformed back into a state variable again.
4.12 Heavy Metal ECO Lab Template

The Heavy Metal ECO Lab Template is a predefined DHI supported ECO
Lab template, which is a model for estimating the spreading of heavy met-
als in aquatic systems.
47
Reference Manual
See Scientific Description of the ME Template under manuals in the instal-

lation. The pdf file can be viewed directly from the ECO Lab GUI when
the ME template is loaded.
4.13 Logical Functions

The IF THEN ELSE logical function is implemented in ECO Lab and can
be used in expressions in the ECO Lab templates. IF statements can be
expressed in 2 ways:
1 IF (conditional expression) THEN (expression) ELSE (expression)

2 IF(conditional expression,expression if true, expression if false)
4.14 Mathematical Functions

It is possible to use a number of mathematical functions in expressions in
the ECO Lab templates. Below is a list of the supported mathematical
functions.
The syntax below must be followed carefully with respect to capital letters
and number of arguments.
1 ABS(X)
2 ARCCOS(X)
3 ARCSIN(X)
4 ARCTAN(X)
5 ARCTAN2(X,Y)
6 COS(X)
7 COSH(X)
8 EXP(X)
9 LN(X)
10 LOG(X)
11 MAX(X,Y)
12 MIN(X,Y)
13 POW(X,Y)
14 SIN(X)
48 MIKE Zero
Predefined ECO Lab Templates
15 SINH(X)
16 SQR(X)
17 SQRT(X)
18 TAN(X)
19 TANH(X)
20 PI()
4.15 Predefined ECO Lab Templates

DHI has a number of standard ECO Lab templates that are supplied with
the installation.
1 EutrophicationModel1.ecolab: Eutrophication, a classic DHI model

2 EutrophicationModel1SedimentBenthicVegetation.ecolab: As
Eutrophication1.ecolab, but includes benthic vegetation and dynamics
of nutrients in sediment
3 EutrophicationModel2.ecolab: Eutrophication including diurnal DO
variations. It is also different from Eutrophication1.ecolab, because
inorganic N is split into ammonia and nitrate.
4 ME.ecolab: Heavy metal
5 WQSimple.ecolab: BOD-DO
6 WQNutrients.ecolab: BOD-DO, nutrients
7 WQlevel1.ecolab: BOD-DO (especially for MIKE 11!)
8 WQsimpleCOLI.ecolab: BOD-DO and Coliform bacteria
9 WQsimpleTandS.ecolab: BOD-DO and temperature and salinity
10 WQsimpleTandSCOLI.ecolab: BOD-DO, Coliform bacteria and tem-
perature and salinity
You can find the templates in the Templates directory under MIKE Zero,
e.g. 'c:\Program Files\DHI\MIKEZero\Templates\ECOLab'.
4.16 Processes
Processes are arguments in differential equations governing the state of
the state variables included in the ECO Lab templates.
49
Reference Manual
They are defined as mathematical expressions themselves with a sequence

of arguments and operators. Arguments in a process expression could be
state variables, constants, forcings, auxiliary variables, numbers, or other
processes. The processes are calculated in the order they are defined in the
ECO Lab model, starting from the top. So only processes defined above
the present process expression can be used as argument in process expres-
sions. Examples of processes in an ECO Lab model could be degradation,
death, or production of a state variable. All processes can be described as
rates, i.e. they relate to time.
4.17 Process Matrix

A process matrix show the interaction between state variables and proc-
esses. It is a simple way of getting an overview of the state variables of an
ECO Lab model and which processes affect them. All defined processes
are listed in rows and all state variables are listed in columns. Any interac-
tion between a state variable and a process is included by specifying a
coefficient at the appropriate place in the process matrix. A positive coef-
ficient should be specified if the process increases the state of the state
variable, and a negative value if the influence of a process decreases the
value of a state variable. The process matrix of a template can be seen in
the ECO Lab template editor by choosing 'Tools: Processmatrix'.
4.18 Process Type

The model developer has the following process types to choose from
when defining a process in an ECO Lab template:
1 Transformation. This is e.g. in situ degradation and production of mat-

ter. This process type transformates matter at the spot, and cannot
move or transport matter
2 Settling. This process moves matter down the water column, and in
multilayered grid systems the matter is moved from layer to layer. In
the bottom layer the matter is disappearing out of the water column.
3 Bouyancy. This process moves the matter up the water column, and in
multilayered grid systems the matter is moved from layer to layer. In
the top layer the transport stops and therefore an accumulation in the
water surface can take plac if the process continues to move the matter
upwards.
50 MIKE Zero
References
4.19 References
References is a tool for viewing dependencies of a symbol to other sym-
bols. The references of a symbol can be seen in the ECO Lab template edi-
tor by choosing 'Tools: references' when a symbol is marked.
4.20 Reserved Words

ECO Lab has reserved the following list of words for special functionality
in the expressions of an ECO Lab template. So they can only be used in
expressions for that functionality.
1 YEAR, returns present year in simulation

2 MONTH returns present month in simulation
3 DAY returns present day in simulation
4 HOUR returns present hour in simulation
5 MINUTE returns present minute in simulation
6 SECOND returns present second in simulation
7 PI() returns the value for pi: 3.14......
8 Logical Functions
9 Mathematical Functions
4.21 Runge Kutta 4th Order

The Runge Kutta 4th Order is a classical numerical solution method for
solving ordinary differential equations. Usually, it has a higher accuracy
than the Euler method, but requires longer simulation times. The fourth
order Runge-Kutta method requires four evaluations of the right hand side
per time step.
k 1 = hf ( x n, y n )
h k
k 2 = hf x n + ---, y n + ----1
2 2
h k
k 3 = hf x n + ---, y n + ----2
2 2
k 4 = hf ( x n + h, y n + k 3 )
51
Reference Manual
k k k k 5
y n + 1 = y n + ----1 + ----2 + ----3 + ----4 O ( h )
6 3 3 6
4.22 Runge Kutta 5th Order with Quality Check

The Runge Kutta 5th Order with Quality Check is a numerical solution
method for solving ordinary differential equations. The accuracy is evalu-
ated and the time step is adjusted if results are not accurate enough.
It requires 6 function evaluations for each time step to take a so-called

Cash-Karp Runge Kutta step and the error is estimated as the difference
between a Runge Kutta fourth order solution and the Runge Kutta fifth
order solution.
4.23 Scope
Scope is the ECO Lab way of specifying where a state variable or process
can be found in the water environment. By having this description of the
physical distribution of state variables and their processes it is possible to
control that the state variables are only affected by a process in locations,
where the state variables and the processes have overlapping occurrence.
A process or state variable with scope WS (water surface) has the physical
meaning that it is located in the upper part of the water column and it is
always in direct contact with the water surface. Note that a WS State vari-
able does not touch the water bed. An example of a WS state variable can
for instance be water hyacinths. An example of a WS process could be
reaeration (exchange of oxygen between water phase and atmosphere). A
WS process or state variable is only represented by one number per hori-
zontal grid point.
A process or state variable with scope WC (water column) has the physi-
cal meaning that it can be located in the whole water column. This means
that a WC state variable can both touch the water surface, the water bed,
or neither. An example of a WC state variable can for instance be phyto-
plankton Carbon concentration. An example of a WC process that takes
place in the whole water column could be BOD degradation. If a state var-
iable is specified as WC and it is affected by a WS process, the process
will only influence the state variable in the water surface layer. In all other
layers the process will be set to zero. A WC process or state variable is
represented by one number per vertical layer per horizontal grid point.
52 MIKE Zero
Semantic Rules
A process or state variable with scope WB (water bed) has the physical
meaning that it is located in the bottom part of the water column and it is
always in contact with the bed. Note that a WB state variable cannot touch
the water surface, but dependent on the discretization of the water column
in a specific model setup a situation where both state variables that are
confined to the bed and to the water surface can exist in the same model
point. This is always the case for depth integrated model systems. Exam-
ples of a WB state variable can for instance be eelgrass, macroalgae, or fil-
trators. An example of a WB process could be release of inorganic
nitrogen from the sediment. A WB process or state variable is only repre-
sented by one number per horizontal grid point.
A process or state variable with scope SED (sediment) has the physical
meaning that it is located in the sediment. Only transformation processes
are possible in the sediment and processes defined as WS processes (for
instance oxygen exchange with atmosphere) cannot influence a SED state
variable. SED state variables have a fixed nature and cannot be trans-
ported by the advection dispersion module of the hydrodynamic engines.
An example of a SED state variable can for instance be BOD in the sedi-
ment.
A SED process or state variable is only represented by one number per

horizontal grid point. Therefore, if the modeller wants the sediment to be
divided into layers, each layer should be defined as separate SED state
variables.
Example: State variable 1: ammonia in porewater (layer 1), State variable

2: ammonia in porewater (layer 2) etc.
4.24 Semantic Rules

The semantic rules define how arguments in expressions of an ECO Lab
template can be combined by excluding combinations that from a logical
point of view make no sense. The rules are about
z which spatial variation combinations that can be combined

z which scopes of processes and state variables that can be combined
The rules are as follows:
4.24.1 State variables

Spatial variation is not user specified for State Variables. Instead state var-
iables are assumed always to have the spatial variation
53
Reference Manual
'HORIZONTAL_AND_VERTICAL'. This cannot be changed by the user.

'Scope' is specified for the state variables. Legal arguments to an expres-
sion for a differential equation specified under state variables are only
numbers and Processes. The following arguments are legal in state varia-
ble expressions:
z Processes with spatial variation 'NONE', 'HORIZONTAL' or

'HORIZONTAL_AND_VERTICAL'. All scopes of the processes are
legal. If for instance scope of a process is chosen as WS and used in a
state variable expression. The process will have a value when calculat-
ing the top layer of the water column, but the process will have the
value zero in other layers
z Numbers
4.24.2 Auxiliary variables

Scope is not user specified for Auxiliary Variables, but spatial variation
must be specified and the options are 'NONE', 'HORIZONTAL', and
'HORIZONTAL_AND_VERTICAL'.
Legal arguments to an expression for an auxiliary variable with spatial

variation 'NONE' are:
z already defined auxiliary variables, constants, forcings with spatial

variation 'NONE'

variation 'HORIZONTAL' are:

variation 'NONE' or 'HORIZONTAL'
z state variables with scope 'WS', 'SED', or 'WB'

variation 'HORIZONTAL_AND_VERTICAL' are:

variation 'NONE' or 'HORIZONTAL' or
'HORIZONTAL_AND_VERTICAL'
z state variables with scope 'WS', 'SED', 'WB', or 'WC'
4.24.3 Processes
Both spatial variation and scope must be specified for processes. See sepa-
rate explanations for scope and spatial variation in separate paragraphs.
54 MIKE Zero
Semantic Rules
Legal arguments to an expression for a process with spatial variation

'NONE' are:
z already defined processes, auxiliary variables, constants, forcings with

spatial variation 'NONE' and all scope types are legal.

'HORIZONTAL' are:
z already defined processes, auxiliary variables, constants, forcings with

spatial variation 'NONE' or 'HORIZONTAL'
z already defined processes with spatial variation
'HORIZONTAL_AND_VERTICAL' with scope 'WS', 'SED', or 'WB'

'HORIZONTAL_AND_VERTICAL' are:
z already defined state variables, processes, auxiliary variables, con-

stants, and forcings. Conflicts between scope or spatial variation for
the arguments are not possible here.
4.24.4 Derived outputs

Scope is not user specified for Derived Outputs, but spatial variation must
be specified and the options are 'NONE', 'HORIZONTAL', and
'HORIZONTAL_AND_VERTICAL'.
Legal arguments to an expression for a derived output with spatial varia-

tion 'NONE' are:
z processes, auxiliary variables, constants, forcings with spatial variation

'NONE'

tion 'HORIZONTAL' are:

'NONE' or 'HORIZONTAL'

tion 'HORIZONTAL_AND_VERTICAL' are:
55
Reference Manual

'NONE' or 'HORIZONTAL' or 'HORIZONTAL_AND_VERTICAL'
z state variables with scope 'WS', 'SED', 'WB', or 'WC'
4.25 Spatial Variation

For constants, forcings, auxiliary variables, processes and derived outputs
the model developer has to specify in the ECO Lab template editor what
variation pattern that can be expected for the variable. The options are:
1 None
2 Horizontal
3 Horizontal and vertical
When specifying spatial variation for auxiliary variables, processes, and

derived outputs, which all contain expressions, the model developer
should be careful that the spatial variation of the variable is not conflicting
with the specified spatial variations of the used arguments in the expres-
sion. See Semantic Rules.
4.26 State Variables

State variables are usually the most important variables in an ECO Lab
model. State variables represent those variables that describe the state of
the ecosystem and that the user wants to predict the state of. So they are
also the main result after running an ECO Lab setup. The state variable
will change according to the processes that the model developer describes
affect it. So the critical task for the model developer is to describe the
processes in a way, so that the state of the state variable changes correctly,
also when forcings (external conditions such as e.g. wind, temperature)
change.
4.27 Syntax Rules of Expressions

Expressions in ECO Lab can be written in 2 ways:
z Logical function: IF (expression) THEN (expression) ELSE (expres-

sion)
z Normal expression: Expression
56 MIKE Zero
Temperature Dependencies
Expressions are sequences of arguments separated by operators.
List of legal arguments in expressions:
1 Symbols for state variables, constants, forcings, auxiliary variables,

processes defined in the ECO Lab model above the present expression
2 Built-in functions from ECO Lab database, see built-in functions
3 Mathematical functions written in capital letters, see mathematical
functions
4 Reserved words written in capital letters, see reserved words
5 Numbers
The legal operators are multiplication, division, subtraction, addition.
See also Semantic Rules.
4.28 Temperature Dependencies

4.28.1 General description
A large number of reactions in the environment are temperature depend-
ent. Reactions involving biological elements are directly affected due to
increased biological activity at higher temperatures. If the temperature
rises above the optimum temperature for the biological reaction, the proc-
ess rate will decrease. Chemical reactions can also increase with increas-
ing temperature partly owing to the higher molecular activity.
4.28.2 Arrhenius temperature dependency factor

The Arrhenius temperature dependency factor is an often used simple
expression for describing the temperature dependency of a process. It is
described by a reference temperature (in most cases 20 Celsius) and a
temperature coefficient:
The expression is available in the database of ECO Lab in a precompiled

version. See also Built-in Functions.
It shall be noted that this expression grows exponentially with tempera-

ture, so for biological processes it shall only be used for temperatures
below the optimum temperature.
57
Reference Manual
4.28.3 Lassiter Temperature dependency factor

An often used expression for describing the temperature dependency of a
biological process. The expression is available in the database of ECO Lab
in a precompiled version. See also Built-in Functions.
4.29 Transport
In ECO Lab the state variables that are present in the water column has the
option of using the advection-dispersion module for calculating the trans-
port based on hydrodynamics. If this option is not specified in the ECO
Lab Template, the state variable will have a fixed location and the calcula-
tion of its state will only be based on the processes defined in ECO Lab
template and not based on advection-dispersion processes.
State variables that are present in the sediment cannot be transported

based on the advection-dispersion module.
It is also possible to have state variables in the water column that have a
fixed nature. An example of that could be relevant in models involving
aquaculture, for instance cages of scallops in the water column.
4.30 Units
In ECO Lab it is possible to use a limited number of predefined unit types
that are supporting the EUM unit conversion system.
For state variables there are 3 unit types to choose from in the ECO Lab
template editor:
1 Volume Concentration [mg/l]. In the engine dialogs of ECO Lab this

unit can be converted to other units for mass and volume chosen by the
user
2 Area Concentration [g/m2]. In the engine dialogs of ECO Lab this unit
can be converted to other units for mass and area chosen by the user
3 Undefined, here some user specified text can be written that will be
written in e.g. output, but no conversion will take place by the EUM
unit conversion system
For processes the unit is always relating to time, so formally the unit is
[per second], but it should be understood as [undefined per second]. This
way the user has the option of changing the time unit to for instance [per
58 MIKE Zero
Water Quality ECO Lab Templates
hour] in the engine dialogs of ECO Lab, while the 'undefined' part of the
unit will not be converted according to the EUM system.
For constants, forcings and auxiliary variables the units are not supported
by the EUM unit conversion system, but it is possible to specify user spec-
ified text, which will be written in e.g. output and dialogs.
4.31 Water Quality ECO Lab Templates

Water Quality ECO Lab Templates are predefined DHI supported ECO
Lab templates that are a series of simple water quality models.
State variables that are modelled with the WQ templates are:
1 BOD
2 DO
3 Nitrate
4 Nitrite
5 Phosphate
6 Faecal Coliform
7 Total Coliform
See scientific description of the WQ template collection under manuals in

the installation. The pdf file can be viewed directly from the ECO Lab
user interface when a WQ template is loaded.
59
Reference Manual
60 MIKE Zero
A F
ABS(X) . . . . . . . . . . . . . . . . . . 48 Faecal coliform . . . . . . . . . . . . 59
AD time step (AD_DT) . . . . . . . . . 39 Flooded area of grid cell . . . . . . . 40
ARCCOS(X) . . . . . . . . . . . . . . . 48 Forcings . . . . . . . . . . . . . . . . 37
ARCSIN(X) . . . . . . . . . . . . . . . 48
ARCTAN(X) . . . . . . . . . . . . . . . 48 G
ARCTAN2(X,Y) . . . . . . . . . . . . . 48 Global . . . . . . . . . . 20, 23, 26, 29, 32
Arrhenius20 . . . . . . . . . . . . . . . 41
Arrhenius5 . . . . . . . . . . . . . . . . 41 H
Auxiliary variables . . . . . . . . . 24, 37 Heavy metal . . . . . . . . . . . . . . 49
Heavy Metal ECO Lab template . . . 37
B Horizontal . . . . . . . 20, 23, 26, 29, 32
Bed area of grid cell . . . . . . . . . . 40 Horizontal and vertical 20, 23, 26, 29, 32
Bed level . . . . . . . . . . . . . . . . . 39 Horizontal current direction . . . . . 40
BOD . . . . . . . . . . . . . . . . . . . 59 Horizontal current speed . . . . . . . 40
BOD-DO . . . . . . . . . . . . . . . . . 49 Horizontal grid cell flux . . . . . . . . 40
BOD-DO relations . . . . . . . . . . . 45 HOUR . . . . . . . . . . . . . . . . . . 51
Built-in constants . . . . . . . . . . 20, 37
Built-in forcings . . . . . . . . . . . 24, 37 L
Built-in functions . . . . . . . . . . . . 37 Lambert Beer1 . . . . . . . . . . . . . 42
Lambert Beer2 . . . . . . . . . . . . . 42
C Lassiter . . . . . . . . . . . . . . . . . 41
Calibration . . . . . . . . . . . . . . . . 37 Latitude . . . . . . . . . . . . . . . . . 39
Coliforms . . . . . . . . . . . . . . . . . 45 LN(X) . . . . . . . . . . . . . . . . . . 48
Constants . . . . . . . . . . . . . . 18, 37 LOG(X) . . . . . . . . . . . . . . . . . 48
COS(X) . . . . . . . . . . . . . . . . . . 48 Logical functions . . . . . . . . . 37, 51
COSH(X) . . . . . . . . . . . . . . . . . 48 Longitude . . . . . . . . . . . . . . . . 39
D M
DAY . . . . . . . . . . . . . . . . . . . 51 Macrophytes . . . . . . . . . . . . . . 45
Daynumber . . . . . . . . . . . . . . . 40 Mathematical functions . . . . . . 37, 51
Derived output . . . . . . . . . . . . . 31 MAX(X,Y) . . . . . . . . . . . . . . . 48
Derived outputs . . . . . . . . . . . . . 37 Michaelis Menten 1 . . . . . . . . . . 42
Detritus sedimentation/decay . . . . . 45 Michaelis Menten 2 . . . . . . . . . . 42
DO . . . . . . . . . . . . . . . . . . . . 59 MIN(X,Y) . . . . . . . . . . . . . . . . 48
MINUTE . . . . . . . . . . . . . . . . 51
E MONTH . . . . . . . . . . . . . . . . . 51
ECO Lab time step (WQ_DT) . . . . . 39
Euler integration method . . . . . . . . 37 N
EUM unit conversion . . . . . . . . 58, 59 Nitrate . . . . . . . . . . . . . . . . . . 59
Eutrophication . . . . . . . . . . . . . . 49 Nitrite . . . . . . . . . . . . . . . . . . 59
Eutrophication ECO Lab template . . 37 Nutrients . . . . . . . . . . . . . . . . 45
EXP(X) . . . . . . . . . . . . . . . . . . 48
Expressions . . . . . . . . . . . . . . . 37 O
Oxygen . . . . . . . . . . . . . . . . . 45
61
Oxygen saturation . . . . . . . . . . . 41 Temperature . . . . . . . . . . . . . . . 39
Oxygen saturation Weiss . . . . . . . 41 Temperature dependencies . . . . . . 37
Total coliform . . . . . . . . . . . . . . 59
P Transformation . . . . . . . . . . . . . 50
Phosphate . . . . . . . . . . . . . . . . 59 Transport . . . . . . . . . . . . . . . . 37
Phytoplankton . . . . . . . . . . . . . 45
PI() . . . . . . . . . . . . . . . . . . 49, 51 U
POW(X,Y) . . . . . . . . . . . . . . . . 48 Unit types . . . . . . . . . . . . . . 20, 23
Predefined ECO Lab templates . . . 37 Units . . . . . . . . . . . . . . . . . . . 37
Process matrix . . . . . . . . . . . 16, 37
Process type . . . . . . . . . . . . . . 37 V
Processes . . . . . . . . . . . . . . 27, 37 Variable . . . . . . . . . . . . . . . . . 17
Vertical current speed . . . . . . . . . 40
R Vertical grid cell flux . . . . . . . . . . 40
References . . . . . . . . . . . . . 17, 37 Volume of grid cell . . . . . . . . . . . 40
Relative Daylength . . . . . . . . . . . 42
Reserved words . . . . . . . . . . . . 37 W
Reverse Michaelis Menten . . . . . . 42 Water bed . . . . . . . . . . . . . . . . 15
Runge Kutta 4th Order . . . . . . . . 37 Water column . . . . . . . . . . . . . . 15
Runge Kutta 5th Order with quality Water density . . . . . . . . . . . . . . 40
check . . . . . . . . . . . . . . . . . . 37 Water depth . . . . . . . . . . . . . . . 40
Water layer height . . . . . . . . . . . 39
S Water Quality ECO Lab templates . . 37
Salinity . . . . . . . . . . . . . . . . . . 39 Water surface . . . . . . . . . . . . . . 15
Scope . . . . . . . . . . . . . . . . 15, 37 Water surface level . . . . . . . . . . . 40
SECOND . . . . . . . . . . . . . . . . 51 Water surface slope in flow direction . 40
Sediment . . . . . . . . . . . . . . . . 15 Wind direction . . . . . . . . . . . . . . 39
Sediment (denitrification/ Wind velocity . . . . . . . . . . . . . . 39
immobilisation) . . . . . . . . . . . . 45
Semantic rules . . . . . . . . . . . . . 37 Y
Settling . . . . . . . . . . . . . . . . . . 50 YEAR . . . . . . . . . . . . . . . . . . . 51
SIN(X) . . . . . . . . . . . . . . . . . . 48
SINH(X) . . . . . . . . . . . . . . . . . 49
Spatial variation . .20, 23, 26, 32, 37, 53
SQR(X) . . . . . . . . . . . . . . . . . 49
SQRT(X) . . . . . . . . . . . . . . . . 49
State variables . . . . . . . . . . . 14, 37
Sunrise . . . . . . . . . . . . . . . . . 42
Sunset . . . . . . . . . . . . . . . . . . 42
Surface area of grid cell . . . . . . . . 40
Syntax rules of expressions . . . . . . 37
T
TAN(X) . . . . . . . . . . . . . . . . . . 49
TANH(X) . . . . . . . . . . . . . . . . . 49
62 MIKE Zero

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ECO LAB

MIKE by DHI 2009

1 ABOUT THIS GUIDE

1.2 Assumed User Background

In this case, basic knowledge about ecological modelling and ecosys-

The module is developed to describe chemical, biological, ecological

1 Using predefined DHI supported templates

3.1 Defining an ECO Lab Template

3.1.1 Specifying state variables

Edit | New Item... | State Variable

A dialog as shown in Figure 3.1 will appear.

The 'Variable name' attribute should be filled with a short describing

The model developer has the option of publishing further information or

The specification in this attribute is most important in multilayered grid

Under the 'Transport' attribute it has to be chosen if the state variable

The only legal arguments in the state variable expression are:

3.1.2 Specifying constants

Edit | New Item... | Constant

A dialog as shown on Figure 3.4 will appear.

The 'Constant name' attribute should be filled with a short describing

The model developer has the option of publishing further information or

Under the attribute 'Spatial Variation' it has to be specified which variation

1 None: Global, with same value in all grid points

The attribute is introduced to avoid wasting computer memory, so that for

Table 3.1 Built-in constants

Time step for advection-dispersion calculations

Time step for ECO Lab calculations

There are 2 unit types available for constants in ECO Lab:

3.1.3 Specifying forcings

Edit | New Item... | Forcing

A dialog as shown in Figure 3.5 will appear.

The model developer has the option of publishing further information or

Under the attribute 'Spatial Variation' it has to be specified which variation

1 None: Global, with same value in all grid points

The attribute is introduced to avoid wasting computer memory, so that a

There are 2 unit types available for forcings in ECO Lab:

Table 3.2 Built-in forcings in ECO Lab

Water Layer Height

Water Surface Level

Horizontal Current Speed

Horizontal Current Direction

Vertical Current Speed

Water Surface Slope in Flow Direction

Bed Area of Grid Cell

Flooded Area of Grid Cell

Surface Area of Grid Cell

Volume of Grid Cell

Horizontal Grid Cell Flux

Vertical Grid Cell Flux

3.1.4 Specifying auxiliary variables

Edit | New Item... | Auxiliary Variable

A dialog as shown on Figure 3.6 will appear.

The 'Variable name' attribute should be filled with a short describing

The model developer has the option of publishing further information or

Under the attribute 'Spatial Variation' it has to be specified which variation

There are 3 options:

1 None: Global, with same value in all grid points

The attribute is introduced to avoid wasting computer memory and redun-

It is possible to specify user specified text as unit description for auxiliary

The Expression box should be filled with the mathematical formulation of

The expression is formulated by a series of arguments, State Variables,

The following argument types are possible to use in auxiliary variable

The following operators are possible to use in expressions:

Expression -FCdegr KcoliFFCfSAL* --- --- --- POW(tetaT,temp-