Introductory MIKE 21 Hydrodynamic

(HD)Training Course
Dylon Tan / Ivy Voo
Coastal Modeller / Coastal Engineer
Objectives

• Understand background of coastal processes.

• Learn to set up MIKE 21 HD model via hands on exercises.
• Understand its results application via examples and real case studies

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Agenda

• 01 Introduction of Basic Hydrodynamics and Modelling

• 02 MIKE Pre Processing
• 03 MIKE 21 Hydrodynamics – Flexible Mesh
• 04 Case Study

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Day 1
Day 1
9:00 AM Coastal Process
10.15 AM Break
10.30 AM MIKE Modelling Introduction
12.00 PM Lunch
1.00 PM MIKE Pre-Processing
2.45 PM Break
3.00 PM MIKE Pre-Processing (cont.)
4.30 PM Day 1 Recap
5.00 PM End of Day 1

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Day 2
Day 2
9:00 AM Day 1 Recap
9.15 AM MIKE 21 Hydrodynamic Flow Model
10.45 AM Break
11.00 AM MIKE 21 Hydrodynamic Flow Model (cont.)
12.00 PM Lunch
1.00 PM MIKE 21 Hydrodynamic Flow Model (cont.)
2.45 PM Break
3.00 PM Case Study
4.00 PM Course Recap
4.30 PM Course Evaluation
5.00 PM End of course for MIKE 21 HD

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01.
Introduction to Coastal Processes

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Basics of Hydrodynamics
• If 24 plastic bottles were dropped from the Labuan ferry every day for a
year, where do you think they would go?

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Basics of Hydrodynamics

Input of Labuan Port

• 24 particles/day
• 8,470 particles/year

What governs the transport of

these plastic bottles?

Biological, physical or chemical

process?

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Basics of Hydrodynamics
Physical processes drive currents (or flows) in the coastal and marine
areas.

In general, flows are made up of two components:

• Tidal flows
• Non-tidal or residual flows (for example, wind driven flows)

But why are they different?

• Tidal flows are deterministic (i.e. not random, predictable)
• Non-tidal flows are stochastic (i.e. random, more difficult to predict)

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 Basics of Hydrodynamics: Tides
• Balance between
− Gravitational forces from Moon
and Sun
− Centrifugal forces from the
revolving Earth (around the
Sun)
Source from
Google Image

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Basics of Hydrodynamics: Tides
Tides are either semi-diurnal,
diurnal or mixed at a given location

• Semi-diurnal tide: Two lows

and two highs per day
• Diurnal tide: One low and one
high per day
• Mixed tide: A mixture between
semi-diurnal and diurnal

Source from Google Image

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Tidal Elevation (14days)
High tide

Tidal
Range

Low tide

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Basics of Hydrodynamics: Tides
• Spring tide: Moon and sun
are aligned, larger tidal
range.
• Neap tide: Moon and sun are
out of phase (not aligned, at
right angle from each other),
smaller tidal range Source from Google Image
• The spring and neap tidal
cycle occurs every 14 days
(i.e. moon revolving around
Earth).

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Basics of Hydrodynamics: Tides
• Tides are predictable
− As tides are predictable, the
tidal-generated currents can
also be predicted.
• Why is this important?
− Tide is a dominant force in
“moving” water mass.
− Being able to predict tidal
currents, you can then predict
water movement (in tidal-
dominant environment).

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Tidal flows
• Generally, tides (and tidal currents) are stronger in shallow water
• Also varies with location and dependent on seabed contour (bathymetry)

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Wind-Driven Flows
• Flows that are generated from wind forces exerted on the surface
• Typical wind conditions in the South China Sea are governed by the
monsoons:
− Northeast monsoon ( typically Nov-Mar)
− Southwest monsoon (typically May-Sep)
− Inter-monsoon (typically Apr & Oct)
• The onset and withdrawal of the monsoon vary from year to year
• Wind-driven current speeds are higher at surface and reduce with depth

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Influence of Wind Forcing in Tidal Currents

Tide + Wind
(Northeast Monsoon)
Tide only
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Current Flows
• In short, total flow = Tidal Flow + Non-Tidal Flows
• It is a complex system ☺
• Typically, for a given location, either the tidal and/or non-tidal flow governs
(i.e. the dominant force).
• For South China Sea, the non - tidal driven flow is typically dominant
deeper water whereas shallow/coastal areas then tidal driven flow is
dominant.
• For Singapore Strait, the tidal flow is dominant.

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02.
What is Model?

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What is a Model?
Modelling The Environment: An Introduction To System Dynamics
Andrew Ford 2009
• A model is a substitute for a real system.
• They represent some aspect of a real system.
• Models are used when it is easier to work with a substitute than with the actual
system.
• Example of models:
− Conceptual model (e.g. flow charts)
− Empirical model (e.g. regression analysis)
− Physical model (e.g. lab-scale experiments)
− Numerical model
• Modelling is the process of solving problems by appropriate simplification
of reality.
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 What is Numerical Modelling?
• A numerical model solves basic
mathematical equations (as we
know them).
• Describing (or resolving) an area by Source from Google Image

a calculation grid:
− Structured grid
− Unstructured grid

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Type of Coastal Numerical Model ?
Examples of numerical models in coastal and marine water environment:
• Hydrodynamics or flow models
• Wave models
• Advection and dispersion model
• Particle tracking model
• Sediment transport model
• Oil spill model
• Ecological model
• Underwater acoustics model

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Steps in Numerical Modelling
1. Define problem – what is of importance
2. Choose a model that can adequately describe the physical problems
with appropriate assumptions and define a modelling strategy
3. Typical data collected to drive the model :
• Bathymetry
• Wind and Air pressure
• Tide
• Air Temperature, humidity, cloud cover
• Seawater salinity and temperature
• River discharges
Remember GIGO (Garbage In Garbage Out)
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4. Pre-Processing of inputs. Example: Generate grid or mesh with
consideration of spatial resolution requirements
5. Set up and run the model
6. Calibrate and/or validate the model against measurements – will further
explained case study

Steps 4 to 6 could be an iterative procedure to achieve good model results

7. Produce the model results

8. Carry out statistical analysis, as required

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Steps in Numerical Modelling
• Data source for bathymetry:
− Navigation or sea charts
− Dedicated surveys
− Satellite-derived bathymetry
• Important bathymetric features
may need to be resolved to
resolve the local flow conditions
• Choose the optimal resolution
considering the computational
costs

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Steps in Numerical Modelling – Step No 4

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Steps in Numerical Modelling
Model calibration and/or validation
• Visual comparison
• Quality indices

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03.
MIKE Zero Modelling Platform

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Getting Familiar with File Formats

.DFS0
.DFS1
.DFS2
.DFS3
.MESH
.DFSU

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Getting Familiar with File Formats
*.DFS0
• Time varying data
(time series) at
specific point.

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Getting Familiar with File Formats
*.DFS1
• Profile series data
(combination of
time series along
line).

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Getting Familiar with File Formats
*.DFS2
• Grid series data
(2D map filled by
grid points);
• Store various
information e.g.
water depth

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Getting Familiar with File Formats

DFS2: Area series

Water Depth

DFS3: Volume series

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Length
Getting Familiar with File Formats
*.DFSU
• 2D map file
• Consists of multiple
elements
• Store information at
each element

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Getting Familiar with File Formats
*.MESH
• 2D map file for model
• Consists of multiple
nodes
• Store information of
the geographical
position and water
depth (bathymetry)
at each node

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Getting Familiar with File Formats
*.xyz
• Contains information
for each geographical
point (coordinate);
• Can be converted
from standard .txt or
.asc
• Load into mesh editor
(.mdf) or bathymetry
editor (.batsf) to
create mesh or DFS2
file.

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Exercise01: Create DFS0
1. New → Mike Zero → Time Series → Blank Time Series
2. Properties
• Title: Tide level
• Axis Type: Equidistant Calendar Axis
• Start date: 1 Jan 19 12 AM
• Time interval: 30 mins
• No of Timestep : 48
• Item name: Tidal elevation
• Type: Surface elevation
• Unit: meter
3. Copy data from txt into DFS0, then save it.
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Exercise01: Move around DFS0
4. Zoom-in, Zoom out, move around dfs0
• Right-click → Zoom In
• Drag across an area until appears
• Drag vertically until appears

• Hold down the “Shift” key, and pan around the DFS0.

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Exercise02: Boundary Condition for Kota Kinabalu
• New → Mike 21 → MIKE 21 Toolbox → Tidal → Tide Prediction of Heights
• Setup name: Kota Kinabalu
• Type: Timeseries prediction
• Station: Kota Kinabalu
• Longitude: 116.067, Latitude: 5.983
• Prediction Method: Admiralty
• Prediction Period: 1/1/2020 – 1/1/2021
• Interval: 0.1 hour
• Make Tide Table?: No Constituents from
RMN Tide Tables
• Number of constituents: 6 (default)
• Save output file
• Execute

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Exercise03: Plot Composer – Plot DFS0
• Plot PLC
1. New → Plot Composer
2. Plot → Insert New Plot
1. Checked: Single Plot Maximized
2. Highlight: Time Series Plot
3. Add the DFS0 created just now as new item

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What other tools are available (Mike Zero Toolbox)?
• Concatenation
− Combine several files into one file
− Same dimension, same items
− Combine files in sequence of time
• Extraction e.g.
− Profile series from 2D files
− Timeseries from 2D files
• Statistics
− Timeseries, profile series, matrix,
volume
− Max, min, mean, standard
deviation, median, exceedance
percentages
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04.
MIKE Mesh Generation

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FM : Flexible Mesh Domain

The “mesh” contains the

bathymetry (water depth) and
land boundaries
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Generate flexible mesh (.mdf)

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Generate flexible mesh (FM)
Mesh Generator
• Revolves around inserting and defining nodes, vertices, arcs
and polygons.
Node
• Defines the start and end point of an arc.
Vertex
• An internal point along an arc.
Arc
• Number of line segments composed of zero or more vertices
and one or two nodes.
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Generate flexible mesh (FM)
Polygon
• A closed loop composed of one closed arc, or two or more
open arcs;
• A zone can which can be included or excluded from the
domain.

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Generate flexible mesh (FM)

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Generate flexible mesh (FM)
Define and draw domain
• Use the drawing tool
(“Draw Arc”) in the mesh
editor to draw the land or
open boundaries extent;
• Insert nodes using “Insert
Node” tool;
• You can move and delete
the nodes.

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Generate flexible mesh (FM)
Defining Boundary
• Distinguish between closed (land) and open (water) boundaries
through the point attribute parameter;
• For each node in the mesh, you can specify an attribute value.
• Do this by right clicking and selecting properties;
• Open boundaries must be defined with a number >1.

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Generate flexible mesh (FM)
Generate and interpolate mesh
• In the mesh boundary area,
add a polygon;
• Click on the polygon and
specify type of mesh
(triangular or rectangular) and
the desired mesh element
length;
• Add the scatter data (.xyz or
other type of bathymetry data);
• Generate the mesh and
interpolate it.

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Generate flexible mesh (FM)
Export mesh or DFSU
• You can either export mesh of dfsu from the editor;
• When exporting dfsu file, specify the type of item to be stored into the
file.

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Obtaining the right resolution
Large element size Small element size

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Exercise04: Creating Bathymetry .mesh
Use Oresund Project Example – Bridge connecting Denmark to Sweden
• Step 1 – Create a New Mesh Generator Workspace
• Step 2 – Import Model Boundaries (land_modified.xyz)
• Step 3 – Define workspace area
Projection : UTM33
• Step 4 – Editing the Land Boundary Course Resolution – 1km
• Step 5 – Specification of Domain Area of Interest – 250m
• Step 6 – Specification of Boundaries Resolution size X2/2
• Step 7 – Defining and Optimizing mesh resolution
• Step 8 – Mesh Generation
• Step 9 – Load Scatter data (water.xyz)
• Step 10 – Interpolation of a Bathymetry to the Mesh
• Step 11 – Export Mesh

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Recap of Day 1

• Basic of Hydrodynamic
• Tidal Flow and Non Tidal Flow
• Types of Numerical Model
• Steps in Preparing a Model
• MIKE DFS formats
• Mesh Generation

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Thank you

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