3D/2D modelling suite for integral water solutions

Delft3D

Functional Description
Delft3D

Functional Specifications

Version: 2.20
SVN Revision: 52614

October 1, 2017
Delft3D, Functional Specifications

Published and printed by:

Deltares telephone: +31 88 335 82 73
Boussinesqweg 1 fax: +31 88 335 85 82
2629 HV Delft e-mail: info@deltares.nl
P.O. 177 www: https://www.deltares.nl
2600 MH Delft
The Netherlands

For sales contact: For support contact:

telephone: +31 88 335 81 88 telephone: +31 88 335 81 00
fax: +31 88 335 81 11 fax: +31 88 335 81 11
e-mail: sales@deltaressystems.nl e-mail: support@deltaressystems.nl
www: http://www.deltaressystems.nl www: http://www.deltaressystems.nl

Copyright © 2017 Deltares

All rights reserved. No part of this document may be reproduced in any form by print, photo
print, photo copy, microfilm or any other means, without written permission from the publisher:
Deltares.
 Contents

Contents
List of Figures v

1 Introduction 1
1.1 Areas of application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Delft3D framework overview . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.3 Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

2 Hydrodynamic module 3
2.1 Module description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.2 Applications areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.3 Coupling with other modules . . . . . . . . . . . . . . . . . . . . . . . . . 4

3 Water quality module 7

3.1 General introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.2 Module description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3.3 Application areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.4 Coupling with other modules . . . . . . . . . . . . . . . . . . . . . . . . . 10

4 Sediment transport module 13

4.1 Module description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
4.1.1 Cohesive sediment . . . . . . . . . . . . . . . . . . . . . . . . . . 13
4.1.2 Non-cohesive sediment . . . . . . . . . . . . . . . . . . . . . . . . 14
4.1.3 Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.2 Application areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.3 Coupling with other modules . . . . . . . . . . . . . . . . . . . . . . . . . 14

5 Ecological module 15
5.1 Module description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
5.2 Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
5.3 Coupling with other modules . . . . . . . . . . . . . . . . . . . . . . . . . 16

6 Particle tracking module 17

6.1 Module description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
6.2 Application areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

7 Wave module 19
7.1 Module description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
7.2 Application areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
7.3 Coupling with other modules . . . . . . . . . . . . . . . . . . . . . . . . . 20

8 Morphodynamic module 21
8.1 Module description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
8.2 Numerical aspects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
8.3 Application areas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

9 Pre-processing and post-processing 25

9.1 Visualisation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
9.1.1 GPP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
9.1.2 QUICKPLOT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
9.2 Grid generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
9.3 Grid data manipulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
9.4 Grid aggregation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
9.5 Tidal analysis and comparison with observations . . . . . . . . . . . . . . . 28
9.6 Tidal analysis and prediction . . . . . . . . . . . . . . . . . . . . . . . . . 28

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Delft3D, Functional Specifications

9.7 Nesting of Delft3D-FLOW models . . . . . . . . . . . . . . . . . . . . . . . 29

9.8 Nesting of D-Water Quality models . . . . . . . . . . . . . . . . . . . . . . 29
9.9 Interfaces with other programs . . . . . . . . . . . . . . . . . . . . . . . . 30
9.9.1 Interface to GIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
9.9.2 Interface to Matlab . . . . . . . . . . . . . . . . . . . . . . . . . . 30

10 Hardware configuration 33

References 35

iv Deltares
 List of Figures

List of Figures
1.1 System architecture of Delft3D . . . . . . . . . . . . . . . . . . . . . . . . 1

3.1 General overview of substances included in D-Water Quality. Substances are

organised in functional groups indicated by a grey header, except for some
substances that form a group of their own. Major processes between sub-
stances are indicated by arrows; note that many links are omitted . . . . . . . 7

6.1 Example of a D-Waq PART oil spill simulation . . . . . . . . . . . . . . . . . 18

9.1 Example QUICKPLOT figure: 3D view of bed level . . . . . . . . . . . . . . 26

9.2 Example QUICKPLOT figure: Depth-averaged velocity vectors and drying and
flooding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
9.3 Example QUICKPLOT figure: Depth-averaged velocity vectors and tidal ellips . 31

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Delft3D, Functional Specifications

vi Deltares
 1 Introduction
Deltares has developed a unique, fully integrated modelling framework for a multi-disciplinary
approach and 3D computations for coastal, river, lake and estuarine areas. It can carry out
numerical modelling of flows, sediment transport, waves, water quality, morphological devel-
opments and ecology. It has been designed for experts and non-experts alike. The Delft3D
framework is composed of several modules, grouped around a mutual interface, while being
capable to interact with one another.

Delft3D can switch between the 2D vertically averaged and 3D mode simply by changing the
number of layers. This feature enables to set up and investigate the model behaviour in 2D
mode before going into full 3D simulations.

1.1 Areas of application

Delft3D can be applied, but is not limited, to the following areas of applications:

 flows due to tide, wind, density gradients and wave induced currents;
 propagation of directionally spreaded short waves over uneven bathymetries, including
wave-current interaction;
 advection and dispersion of effluents;
 online morphodynamic computations (local scour, short time and length scales);
 sediment transport of cohesive and non-cohesive sediment;
 water quality phenomena including ecological modelling, the prediction of heavy metal
concentrations, interaction with organic and inorganic suspended sediment, interaction
between the water and bottom phase (such as sediment oxygen demand), algae blooms;
 particle tracking, including oil spill and dredging plume modelling;
 initial and/or dynamic (time varying) 2D-morphological changes, including the effects of
waves on sediment stirring and bed-load transport.

1.2 Delft3D framework overview

Delft3D is composed of a number of modules (see Figure 1.1), each addressing a specific
domain of interest, such as flow, near-field and far-field water quality, wave generation and
propagation, morphology and sediment transport, together with pre-processing and post-
processing modules. All modules are dynamically interfaced to exchange data and results
where process formulations require. In the following chapters these modules are described in
more detail.

Overall Menu

Flow/Mor Wave Water Quality Ecology Particles/Oil

Tools

Figure 1.1: System architecture of Delft3D

All features are embedded in Graphical User Interface suitable for Linux or the MS Windows.
An application (model) can be completely defined, inspected and analysed through a menu-
driven, user-friendly, graphical interface.

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The basic processes covered by each of the modules are:

Delft3D-FLOW and MOR 2D and 3D hydrodynamic, salinity, temperature, transport and online
sediment transport and morphology
Delft3D-WAVE short wave propagation (using SWAN)
D-Water Quality general water quality
Delft3D-SED cohesive and non-cohesive sediment transport
Delft3D-ECO complex eutrophication and ecological modelling
D-Waq PART particle tracking, oil spill modelling

1.3 Utilities
The following utility programs are available for pre-processing and post-processing:

RGFGRID: for generating orthogonal curvilinear grids, in Cartesian or spherical co-ordinates

QUICKIN: for preparing and manipulating grid oriented data, such as bathymetry, initial condi-
tions for water levels, salinity, constituents and other parameters
Delft3D-TRIANA: for performing off-line tidal analysis of time-series generated by Delft3D-
FLOW
Delft3D-TIDE: for performing tidal analysis on time series of measured water levels or veloci-
ties
GPP: for visualisation and animation of simulation results
Delft3D-QUICKPLOT: for visualisation and animation of simulation results
GISVIEW: ArcGIS extension to export GIS-coverages to Delft3D format and to read, visualise
and process results from Delft3D (ArcGIS is not included)
Delft3D-MATLAB: user interface and Matlab functions to read Delft3D files and to visualise or
process results in Matlab environment (Matlab is not included)
D-Waq DIDO: interactive grid aggregation editor for coupling FLOW with WAQ models

For more information please contact:

e-mail: delft3d.info@deltares.nl
www: www.deltares.nl

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 2 Hydrodynamic module
The hydrodynamic module, Delft3D-FLOW, is a multi-dimensional hydrodynamic simulation
program that calculates non-steady flow and transport phenomena resulting from tidal and
meteorological forcing on a curvilinear, boundary-fitted grid. In 3D simulations, the hydrody-
namic module applies the so-called sigma co-ordinate transformation in the vertical, which
results in a smooth representation of the bottom topography. It also results in a high comput-
ing efficiency because of the constant number of vertical layers over the whole computational
domain.

2.1 Module description

The hydrodynamic module is based on the full Navier-Stokes equations with the shallow water
approximation applied. The equations are solved with a highly accurate unconditionally stable
solution procedure. The supported features are:

 two co-ordinate systems, i.e. Cartesian and spherical, in the horizontal directions
 two grid systems in the vertical direction; the boundary fitted sigma grid and the horizontal
layer Z-grid
 domain decomposition both in the horizontal and vertical direction
 tide generating forces (only in combination with spherical grids);
 simulation of drying and flooding of inter-tidal flats (moving boundaries);
 density gradients due to a non-uniform temperature and salinity concentration distribution
(density driven flows);
 for 2D horizontal large eddy simulations the horizontal exchange coefficients due to circu-
lations on a sub-grid scale (Smagorinsky concept);
 turbulence model to account for the vertical turbulent viscosity and diffusivity based on the
eddy viscosity concept;
 selection from four turbulence closure models: k-ε, k-L, algebraic and constant coefficient;
 shear stresses exerted by the turbulent flow on the bottom based on a Chézy, Manning or
White-Colebrook formulation;
 enhancement of the bottom stresses due to waves;
 automatic conversion of the 2D bottom-stress coefficient into a 3D coefficient;
 wind stresses on the water surface modelled by a quadratic friction law;
 space varying wind and barometric pressure (specified on the flow grid or on a coarser
meteo grid), including the hydrostatic pressure correction at open boundaries (optional);
 simulation of the thermal discharge, effluent discharge and the intake of cooling water at
any location and any depth in the computational field (advection-diffusion module);
 the effect of the heat flux through the free surface;
 online analysis of model parameters in terms of Fourier amplitudes and phases enabling
the generation of co-tidal maps;
 drogue tracks;
 advection-diffusion of substances with a first order decay rate;
 online simulation of the transport of sediment (silt or sand) including formulations for ero-
sion and deposition and feedback to the flow by the baroclinic pressure term, the turbu-
lence closure model and the bed changes;
 the influence of spiral motion in the flow (i.e. in river bends). This phenomenon is espe-
cially important when sedimentation and erosion studies are performed;
 modelling of obstacles like 2D spillways, weirs, 3D gates, porous plates and floating struc-
tures;
 wave-current interaction, taking into account the distribution over the vertical;
 many options for boundary conditions, such as water level, velocity, discharge and weakly
reflective conditions;
 several options to define boundary conditions, such as time series, harmonic and astro-

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nomical constituents;
 option for linear decay of conservative substances
 online visualisation of model parameters enabling the production of animations.

2.2 Applications areas

Delft3D-FLOW can be applied to the following application areas:

 salt intrusion in estuaries;

 fresh water river discharges in bays;
 thermal stratification in lakes and seas;
 cooling water intakes and waste water outlets;
 sediment transport including feedback on the flow;
 transport of dissolved material and pollutants;
 short-term sediment transport including feedback on the flow;
 storm surges, combined effect of tide and wind/typhoon;
 river flows, meandering and braided rivers;
 floodplains, with or without vegetation;
 reservoir siltation and degradation below dams;
 bottom vanes, spurs, groynes, bridges, weirs and levees.

2.3 Coupling with other modules

The results of the hydrodynamic module are used in all other modules of Delft3D. The results
are dynamically exchanged between the modules through the use of a so-called commu-
nication file. Basic (conservative) water quality parameters like concentrations of dissolved
material and pollutants, can be included in the computations. But, for more dedicated wa-
ter quality simulations, the hydrodynamic module is coupled with the far-field water quality
module (D-Water Quality) , the nutrient phytoplankton module (Delft3D-ECO) and the near-
field particle tracking module (D-Waq PART). A coupling with the sediment transport module
(Delft3D-SED) is available to simulate cohesive and non-cohesive sediment transport pro-
cesses, e.g. in the case of erosion and sedimentation studies. For wave-current interaction a
dynamic coupling is provided with the wave module (Delft3D-WAVE) and for morphodynamic
simulations the hydrodynamic module is integrated with the wave module and a sedimentation
and erosion module into a morphodynamic module.

To simulate a model defined on a curvilinear grid system, an orthogonal grid must be provided.
To generate such a grid the program RGFGRID is provided, though the grid can be generated
by any grid generator program as long as the grid is delivered in the prescribed (ASCII) file
format. The generation of a curvilinear grid is an important and somewhat complex task.
Along with the main model parameters, the grid will ultimately determine the accuracy of the
final model results.

To prepare the bottom topography or other grid-related data, such as a non-constant initial
condition file, the program QUICKIN is provided. This program interpolates the scattered,
digitised chart data to depth-values at the grid points in the model. Many powerful interactive
processing options to further adjust the topography are supported, e.g. manual adjustment
of the values at individual points, selection of the domain of influence, group adjustments,
and smoothing. The output of this program (ASCII-file) can be imported into other Delft3D
modules.

Analysis and interpretation of a hydrodynamic simulation in terms of tidal quantities can be

performed by the program Delft3D-TRIANA. Delft3D-TRIANA performs off-line tidal analyses
of time-series of either water levels and/or velocities. The results from these analyses can be

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 Hydrodynamic module

subsequently compared with observation data supplied by you.

In case the open boundaries of a (detailed) Delft3D-FLOW model are located within the model
domain of a coarser Delft3D-FLOW model, the coarse model can generate the boundary
conditions of the detailed, nested model. The offline generation of boundary conditions is
done by Delft3D-NESTHD.

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6 of 38 Deltares
 3 Water quality module

3.1 General introduction

The transport of substances in surface and ground water is commonly represented by the
so-called advection-diffusion equation. The water quality module, D-Water Quality, is based
on this equation and it offers different computational methods to solve it numerically on an
arbitrary irregular shaped grid, on a grid of rectangles, triangles or curvilinear computational
elements. D-Water Quality can be applied just as easily on 0D, 1DV, 1DH, 2DV, 2DH and 3D
schematisations of a water body. D-Water Quality includes the complete natural cycles of C,
N, P, Si and O2, as well as cohesive sediments, bacteria, salinity, temperature, heavy metals
and organic micro-pollutants (see Figure 3.1).

Atmosphere

Salinity
Dissolved Oxygen Oxygen Demand
Chloride BOD COD Water
Temperature

Conservative
Tracers
Phytoplankton Grazers Heavy Metals
1 2 3 4 5
Nutrients C N P Si C N P Si
As Cd Cr Cu Hg

NO 3 NH 4 PO 4 Si Inorganic Matter Ni Pb V Zn
Decayable
Tracers Organic Matter Organic Matter IM1 IM2 IM3
(particulate) (dissolved)
Organic micro-
1 2 3 4 5 Adsorbed PO 4
pollutants
C N P Si DOC DON DOP
Atr BaP Diu Flu
Coli Bacteria
HCB HCH PCB-153
E.Coli FColi TColi

pH
CO 2 Alkalinity

Sediment
Sediment Oxygen Organic Matter Micro- Inorganic Matter
Demand (particulate) phytobenthos Heavy Metals
IM1 IM2 IM3
C N P Si C N P Si Organic micro-
pollutants

Figure 3.1: General overview of substances included in D-Water Quality. Substances are
organised in functional groups indicated by a grey header, except for some
substances that form a group of their own. Major processes between sub-
stances are indicated by arrows; note that many links are omitted

To proceed one step in time (t + ∆t), D-Water Quality solves equation 3.1 (a simplified
representation of the advection-diffusion-reaction equation) for each computational cell and
for each state variable.
     
∆M ∆M ∆M
Mit+∆t = Mit + ∆t × + ∆t × + ∆t × (3.1)
∆t Tr ∆t P ∆t S

The mass balance has the following components:

1 the mass at the beginning of a time step: Mit
2 the mass at the end of a time step: Mit+∆t
∆M


3 changes by advective and dispersive transport: ∆t T r
∆M


4 changes by physical, (bio)chemical or biological processes: ∆t P

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 Delft3D, Functional Specifications

∆M


5 changes by sources (e.g. waste loads, river discharges): ∆t S

The basic principles of D-Water Quality are the same whether you have one state variable
and only two computational cells, or you have several tens of state variables and thousands
of computational cells. The only difference is the number of times that D-Water Quality has to
solve equation 3.1. D-Water Quality is capable of describing any combination of constituents
and is not limited with respect to the number and complexity of the water quality processes.

Water quality processes are described by linear or non-linear functions of selected state vari-
ables and model parameters. Many process formulations are available in the form of a library,
which smoothly interfaces with the water quality module. The library contains over 50 wa-
ter quality process routines covering 140 standard substances. A graphical user interface
within the WAQ module enables you to select any combination of substances and associated
water quality processes. Also, for less experienced users pre-defined sets are available to
jump-start the water quality modelling.

3.2 Module description

D-Water Quality simulates a physical system that consists of a surface or ground water body.
Strictly speaking, it models a body of a medium that is able to transport passive constituents.
In this respect, "passive" means that the influence of the concentration of the constituents on
the transport coefficients may be neglected.

The transporting medium is characterised by its spatial and time dependent content (mass) of
the modelled constituents. Some are transportable; some are non-transportable. An example
of the latter is the bottom sediment in a surface water model. The concentration of the trans-
portable constituents is computed by dividing the mass by the water volume. The mass is the
state variable and the model is mass conserving by definition.

Waste disposals are specified either as mass units per time unit or as a combination of waste
flow and concentration. They represent either point sources (urban, industrial, rivers) or dif-
fuse sources (run-off, atmospheric deposition). The case of recirculating flows, as with cooling
water studies, is also taken care of: the water that was let in, will have the same quality at the
outlet.

The hydrodynamic characteristics of the transporting medium are expressed in terms of the
volume and the flux of the transporting medium ("flow"). The combination of water volumes
and flows must be consistent, i.e. an increase of the water volume must be balanced by a dif-
ference between inflow and outflow. D-Water Quality repeats hydrodynamic characteristics to
extend to simulation times beyond the available hydrodynamic simulation time. Also, D-Water
Quality can combine several hydrodynamic simulations into a single water quality simulation.
For example, a representative neap tide and a representative spring tide hydrodynamic simu-
lation can be combined to create a complete spring-neap cycle.

As part of Delft3D, the coupling module can derive a set of consistent hydrodynamic flows
automatically from Delft3D-FLOW, but the methods involved can be applied equally well to
third-party hydrodynamic models outside Delft3D.

In many cases, the water quality processes in the model are determined by meteorological
conditions, by other (modelled or non-modelled) constituents or by other (modelled or non-
modelled) processes. Examples are wind, water temperature, acidity (pH), primary production
and the benthic release of nutrients. These entities are referred to as "forcing functions".
Water quality process formulations are often of an empirical or semi-empirical nature and

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 Water quality module

contain "model parameters" which are subject to tuning or calibration. Because of this, D-
Water Quality allows complete freedom in selecting the set of water quality processes and the
relevant forcing functions and model parameters may vary between individual applications. It
therefore provides flexible input facilities for constants, spatially varying parameters, functions
of time and functions of space and time.

The physical system is affected by two types of processes:

 transport processes: these processes involve the movement of substances;

 water quality processes: these processes involve a transformation of one or more sub-
stances.

The transport of substances in surface and ground water is commonly represented by the
so-called advection diffusion equation. Advection is determined by the velocity field and dis-
persion by the dispersion coefficient. These basic transport processes operate on all trans-
portable substances in the same way. D-Water Quality offers the possibility to model other
transport phenomena as well which may differ between individual substances. Examples are
the gravity induced settling of particles and the autonomous motion of fish. These additional
transport processes must be expressed as an extra, substance dependant velocity or disper-
sion coefficient.

Water quality processes are incorporated in the advection diffusion equation by adding an
additional source in the mass balance (equation 3.1). Examples of water quality processes
are:

 exchange of substances with the atmosphere (oxygen, volatile organic substances, tem-
perature);
 adsorption and desorption of toxicants and ortho-phosphorous;
 deposition of particles and adsorbed substances to the bed;
 re-suspension of particles and adsorbed substances from the bed;
 mortality of bacteria;
 biochemical reactions like the decay of BOD and nitrification;
 growth of algae (primary production);
 predation (e.g. zooplankton on phytoplankton).

Special attention is paid to the treatment of the interaction with the bottom:

 all suspended sediment is modelled as cohesive sediment that can be transported with
the water flow just like a dissolved substance;
 all particulate inorganic matter can be represented by three size fractions or components;
 all particulate organic matter is represented by separate components, namely detritus
carbon, other organic carbon, diatoms, non-diatom algae (Green), adsorbed phosphorus
and organic carbon from loads;
 the bottom sediment is modelled via two separate layers. Each layer is considered homo-
geneous (well mixed). The different layers can have different compositions. The density
of a layer is variable depending on the sediment layer composition, which is also variable.
The porosity within a given layer is constant (user-defined).
 a third (deeper) layer exists (but is not explicitly modelled) which can supply sediment for
upward sediment transport ’digging’;
 sedimentation and resuspension are modelled using the Krone-Partheniades approach
(see the description of the sediment transport module Delft3D-SED).

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 Delft3D, Functional Specifications

3.3 Application areas

D-Water Quality can be applied to the following areas:

 Environmental Impact Assessment (EIA), objective evaluation of alternatives

 Water balance studies, including the identification of the origin of water, residence times
and flushing capabilities
 Swimming water quality, bacterial decay processes;
 Sewage and/or storm water outfall studies;
 Nutrient cycling and eutrophication;
 Sedimentation and resuspension of particulates, dredging plumes;
 Sediment-water interaction (including diffusive and benthic mixing);
 Bio-availability of heavy metals (and organic micro-pollutants;
 Recirculation of cooling water from power and desalination plants including the release of
bio-fouling chemicals such as chlorine

The processes always require input in the form of rate constants and/or simulation results
from other substances. The input could come from:

 one of the other modelled substances;

 a user-specified spatially distributed time function;
 a user-specified time function for the whole area;
 a user-specified spatially distributed constant;
 a user-specified constant for the whole area;
 a process flux originating from one of the water quality processes from the library;
 output from one of the other processes in the library;
 a default value from the database containing default values.

The pre-processor will report the origin of the input for each process. If information for a
process is missing, so that the process cannot be evaluated, it will detail what information is
actually required in addition.

Results can be presented as spatial patterns or time-series. Statistical processing can be

carried out during the simulation for minimum, average and maximum values, percentiles,
percentage of exceedance, geometric mean, etc. These values can be calculated for pre-
selected periods, so that it is possible to calculate for example winter and summer averages.

As a special type of output, mass balances can be generated. These can be used to analyse
the fate of substances (e.g. nutrients or heavy metals) or to quantify the contribution of waste
loads or certain processes to the ambient concentration of a substance.

3.4 Coupling with other modules

Hydrodynamic conditions can be prescribed by Delft3D-FLOW, SOBEK (Deltares 1D software
and SIMONA (2D/3D hydrodynamic model). Transfer of results goes via a so-called communi-
cation file. This file usually spans a representative period such as a tidal cycle, a spring-neap
cycle or even a full year. D-Water Quality is able to calculate beyond the period by repeating
the hydrodynamic cycle. Also, D-Water Quality is able to make use of multiple hydrodynamic
files by either combining them simultaneously or successively. For example, a representative
low river discharge hydrodynamic file and a high river discharge hydrodynamic file may be
combined to simulate all river discharges in between.

The grid aggregation tool D-Waq DIDO can be used to fit the grid resolution to the specific
needs of the application. D-Waq DIDO allows regular and irregular aggregation (in the hori-

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 Water quality module

zontal) and will reduce the number of computational elements and therefore computation time.
D-Waq DIDO is frequently used to reduce the grid resolution in areas far away from the area
of interest, while keeping the area of interest at the highest possible resolution.

QUICKIN can be used to generate space-varying initial conditions or space-varying process

parameters (e.g. wind speed).

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12 of 38 Deltares
 4 Sediment transport module
The sediment transport module, Delft3D-SED, can be applied to model the transport of cohe-
sive and non-cohesive sediments, i.e. to study the spreading of dredged materials, to study
sedimentation/erosion patterns, to carry out water quality and ecology studies where sediment
is the dominant factor.

It is in fact a sub-module of the water quality module, that is all processes contained in the
sediment transport module are also present in the water quality module. For a detailed de-
scription of the general aspects we refer to the description of the water quality module.

4.1 Module description

4.1.1 Cohesive sediment

This section describes the implementation of the physical processes in some detail. For co-
hesive sediment transport sedimentation, erosion, burial and digging are taken into account.

For sedimentation the following assumptions apply:

 sedimentation takes place when the bottom shear stress drops below a critical value;
 there is no correlation between the sediment components (i.e. each of the particulate
fractions can settle independently);
 sedimentation always results in an increase of sediment in the uppermost sediment layer;
 the total shear stress is the linear sum of the shear stresses caused by water velocity and
wind effects. Effects of shipping and fisheries can also be included.

The effects of ’hindered settling’ (i.e. decrease in sedimentation velocity at very high sus-
pended solids concentration) can be included.

For resuspension the assumptions are:

 the bottom sediments are homogenous within a layer. Therefore, the composition of the
resuspending sediment is the same as that of the bottom sediment;
 the resuspension flux is limited based on the available amount of sediment in a sediment
layer for the variable layer option. The resuspension is unlimited if the fixed layer option is
used;
 as long as mass is available in the upper sediment layer, resuspension takes place from
that layer only;
 resuspension flux is zero if the water depth becomes too small.

Burial is the process in which sediment is transferred downward to an underlying layer. The
sediment layer is assumed to be homogeneous, therefore the composition of the sediment
being buried is the same as that of the (overlying) sediment layer.

Digging is the process in which sediment is transferred upward from an underlying layer. The
sediment layers are homogeneous, therefore the composition of the sediment being trans-
ported upwards is the same as that of the (underlying) sediment layer. A third and deeper
layer allows for an unlimited ’digging’ flux to the second layer. The quality of this third layer
must be defined by you and is not modelled by Delft3D-SED.

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4.1.2 Non-cohesive sediment

For non-cohesive sediment (sand) the transport rate is calculated according to the transport
formulae of Engelund-Hansen and Ackers-White. These (semi-)empirical relations describe
the total transport (bed load and suspended load) in the situation of local equilibrium.

The implementation recognises two options: unlimited supply of sand via the boundaries and
the presence or absence of bedrock.

4.1.3 Limitations
To apply the sediment transport module the following limitations must be observed:

 in the sedimentation process, there is no correlation between the cohesive and non-
cohesive components, i.e. between sand and silt; each is treated independently;
 the effect of short waves must be taken into account through the hydrodynamic module
or through a localised wave effect estimation (that is, the waves are considered to be in
equilibrium with local circumstances);
 Delft3D-SED should only be used for short- or medium-term (days, weeks, months) mod-
elling of erosion and sedimentation process as the changes on bottom topography and
its effects on the flow are neglected. For long-term processes (years), whereby the flow
changes induced by changing bottom topography is significant, the separate morpholog-
ical and sediment module (Delft3D-MOR) should be used. This module has advanced
online coupling capabilities with the hydrodynamic flow and wave modules.

4.2 Application areas

Delft3D-SED can be applied to the following application areas:

 effects of dredging on the environment;

 sedimentation and resuspension of sediment in general;
 sand transport.

4.3 Coupling with other modules

See Section 3.4.

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 5 Ecological module
The far-field water quality module D-Water Quality models algae using an approach based
on Monod kinetics and is routinely included in the process library. The Delft3D-ECO module
contains the more sophisticated algae model BLOOM II (Los, 1991, 2009a,b) that is based on
an optimisation technique.

5.1 Module description

Delft3D-ECO distributes the available resources (nutrients and light) in an optimal way among
the different types of algae. A large number of groups and/or species of algae and even dif-
ferent phenotypes within one species can be considered. In the same way, algae living in
the water column (phytoplankton) and algae and water plants living on the sediment (benthic
species) can be included with their specific ecophysiological characteristics. With BLOOM
II, apart from the calculation of biomass concentrations, the dynamics of algae communi-
ties including competition for light and nutrients, adaptation to environmental conditions and
species composition can be simulated. The eutrophication processes in Delft3D-ECO can be
combined with the general water quality processes in D-Water Quality.

Delft3D-ECO can be used to calculate eutrophication phenomena, including:

 the competition between several groups of algae species;

 adaptation of algae to changes in the environment, in terms of stoichiometry and growth
characteristics. (This can be of particular importance if the simulation of possible devel-
opment of nuisance algae is an aim of the modelling.)
 steep gradients in algae biomass due to temporal or spatial variations;
 phytoplankton blooms;
 chlorophyll concentrations;
 species composition;
 limiting factors for algae growth;
 oxygen kinetics, including daily cycles;
 nutrient concentrations.

Algae blooms usually consist of various species of phytoplankton belonging to different taxo-
nomic or functional groups such as diatoms, microflagellates and dinoflagellates. They have
different requirements for resources (nutrients; light) and they have different ecological prop-
erties. Some species are considered to be objectionable for various reasons. Among these
are phaeocystis, which causes foam on the beaches and various species of dinoflagellates,
which among others may cause diurethic shell fish poisoning. To deal with these phenomena
it is necessary to distinguish different types of phytoplankton in the algae model.

Delft3D-ECO is based upon the principle of competition between different species, or groups
of species. The basic variables of this module are called types. A type represents the physi-
ological state of a species under strong conditions of limitation. Usually a distinction is made
between three different types: an N-type for nitrogen limitation, a P-type for phosphorus limi-
tation and an E-type for light energy limitation. Usually for each (group of) species the three
different types are modelled.

The solution algorithm of the model considers all potentially limiting factors and first selects
the one, which is most likely to become limiting. It then selects the best adapted type for
the prevailing conditions. The suitability of a type (its fitness) is determined by the ratio of
its requirement and its growth rate. This means that a type can become dominant either be-
cause it needs a comparatively small amount of a limiting resource (it is efficient) or because
it grows rapidly (it is opportunistic). Then the algorithm considers the next potentially limiting

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factor and again selects the best adapted phytoplankton type. This procedure is repeated
until it is impossible to select a new pair of a type and limiting factor without violating (i.e.
over-exhausting) some limiting factor. Thus the model seeks the optimum solution consisting
of n types and n limiting factors. The optimal distribution of biomass over the types cannot
always be reached within one time step due to growth and mortality limitations. Special time
dependency constraints are imposed upon all types to take their potential growth and mortal-
ity rates into account. As they represent different stages of the same species, the transition
of one type to another is a rapid process with a characteristic time step in the order of a day.
Transitions between different species is a much slower process as it depends on mortality
and net growth rates. It is interesting that the principle just described, by which each phyto-
plankton type maximises its own benefit, effectively means that the total net production of the
phytoplankton community is maximised.

5.2 Applications
The BLOOM model has been extensively used to model the Southern North Sea and has
been validated for 25 years of data in the Dutch coastal zone. Furthermore the model results
have been validated for a wide range of both freshwater and marine systems. The following
(groups of) algae or macrophyte species have been modelled using the BLOOM module for
salt waters:

 Diatoms
 Flagellates
 Dinoflagellates
 Phaeocystis
 Ulva (on the bottom)
 Ulva (floating)

For Ulva two life forms are distinguished: Ulva that is rooted in the sediment and Ulva that
floats on the water after it has been cut loose by strong winds or currents. The process of
cutting loose has been incorporated in the model. Up to now 6 types of algae or macrofytes
have been modelled and calibrated. As in BLOOM the properties of the algae are adjusted to
the light climate and nutrient availability, you do not need to adjust the parameters for this by
calibration. The default parameter values obtained by calibration of one model can therefore
be applied in a wide range of other model applications. For this reason, if one needs to
model an area that resembles a water system that has been modelled with BLOOM II before,
choosing the model that has proven successful under those conditions can be particularly
helpful.

5.3 Coupling with other modules

See Section 3.4.

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 6 Particle tracking module
The particle tracking module, D-Waq PART, is a 3-dimensional mid-field water quality model. It
estimates a dynamic concentration distribution by following the tracks of thousands of particles
in time. The model is fit for a detailed description of concentration contours of instantaneous
or continuous releases of salt, oil, or other conservative or simple decaying substances. This
section gives a brief introduction to the computer module and its applications.

6.1 Module description

D-Waq PART simulates transport processes and simple chemical reactions of substances.
The module allows the simulation of detailed shapes of patches of wasted material.

D-Waq PART can operate in a 2.5DH or 3D mode, in which D-Waq PART is coupled to
a 2-dimensional (one layer) or 3-dimensional (multi-layer) Delft3D-FLOW model. In the 2-
dimensional mode, the flow is extended with an analytical vertical velocity profile for bottom
shear and wind. The module calculates concentrations with a resolution that is higher than
that of the underlying hydrodynamic grid.

In D-Waq PART, two modules are available:

 Tracer module: simulation of conservative or first order decaying substances;

 Oil spill module: simulation of oil spills with floating and dispersed oil fractions (special
license required).

The physical components in the system are:

 the water system: a lake, estuary, harbour or river, possibly with open boundaries to other
water systems. Tidal variations are included;
 discharges due to human activities that may be instantaneous and/or continuous;
 chemical substances like rhodamine dyes, salt, oil or suspended solids;
 wind fields;
 settling and erosion of suspended matter;
 concentration dependent settling velocity.

In terms of physical processes or phenomena D-Waq PART can represent:

 the dynamics of patches close to an outfall location;

 simple first-order decay processes like the decay of several fractions of oil;
 vertical dispersion for well-mixed systems;
 horizontal dispersion due to turbulence. According to turbulence theory this dispersion
increases in time.
 the effects of time-varying wind fields on the patches;
 the effects of bottom-friction on the patches;
 the existence of a plume at the outfall (rather than a point-source) by starting the simulation
from a circular plume with an estimated or field-measured radius.
 settling of particles, where a concentration dependent settling, subject to a minimum and
maximum settling velocity, can be specified;
 transport and fate of spilled oil. Processes that are included in the oil module are: advec-
tion of floating oil by wind and currents, dispersion (entrainment in water) of oil induced by
wind waves (depending on wind speed and oil characteristics), evaporation of floating oil,
emulsification, decay, sticking of oil to the coastline or seabed. Changes of oil properties
(density, viscosity, water content) due to these processes are included in the oil module.
Additional advection due to wind drag is implemented in 3D (for 2D the logarithmic profile

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 Delft3D, Functional Specifications

of the current speed results in a similar wind driven transport), whilst in 3D a deflection
angle is included to represent the Coriolis effect of wind induced advection due to waves.

.
Figure 6.1: Example of a D-Waq PART oil spill simulation

 the model may be started from a known initial distribution of oil, e.g. a remote sensing
image of an oil spill.

D-Waq PART can in theory simulate an unlimited number of particles and substances. The
only restriction is the available memory of the hardware. For an application with approximately
400,000 particles and 8 substances, about 64 Mbytes internal (hard core) computer memory
is required. Under these conditions, a computer simulation requires for most applications less
than one hour, and takes most often less than 200 Mbytes of disk space. The requirements
can increase significantly when the numbers of particles and substances increase. Post-
processing is done with the general post-processing program GPP or QUICKPLOT. Graphical
maps can also be generated with advanced methods like point spread functions. Visualisation
is off-line. The coupling between the hydrodynamic module, Delft3D-FLOW, and D-Waq PART
is streamlined, but is off-line.

6.2 Application areas

D-Waq PART can be applied to cases in which the effects of the discharge from a limited
number of discharge points (sources) are studied and that focus on the behaviour of the
effluent plume within the mid-field range (order of 1-10 kilometers). Simulation periods are
generally in the order of days-weeks.

Note that in all applications the results of a dynamic two- or three-dimensional flow calculation
(including an accurate description of tidal variations), such as from Delft3D-FLOW, have been
coupled with the PART module.

Examples of applications are:

 dilution of conservative tracers (e.g. from effluent discharges);
 dispersion of first-order decaying substances (such as BOD, coliforms);
 dispersion of suspended solids resulting from dredging or dumping operations, including
the effects of settling and resuspension;
 effects of continuous or instantaneous spills;
 oil spill simulations

18 of 38 Deltares
 7 Wave module
To simulate the evolution of random, short-crested wind-generated waves in coastal waters
(which may include estuaries, tidal inlets, barrier islands with tidal flats, channels etc.) the
wave module Delft3D-WAVE can be used. This wave module computes wave propagation,
wave generation by wind, non-linear wave-wave interactions and dissipation, for a given bot-
tom topography, wind field, water level and current field in waters of deep, intermediate and
finite depth.

7.1 Module description

At present the wave model SWAN is available in the wave module of Delft3D. This is a third-
generation wave model (Ris, 1997; Booij et al., 1999). Where the previously available HISWA
wave model was a second-generation wave model, (Holthuijsen et al., 1989).

The SWAN model, which is an acronym for Simulating WAves Nearshore, is a spectral third-
generation wave model (see e.g. Holthuijsen et al. (1993); Ris (1997). The SWAN model is
the successor of the stationary second-generation HISWA model (Holthuijsen et al., 1989)
and has the great advantage, compared to HISWA, that the physics are explicitly represented
with state-of-the-art formulations and that the model is unconditionally stable (fully implicit
schemes). Moreover, the SWAN model can perform computations on a curvilinear grid (better
coupling with the flow-module of Delft3D) and it can - for instance - generate output in terms of
one- and two-dimensional wave spectra. In addition, the wave forces, as computed by SWAN
on the basis of the gradient of the radiation stress tensor (instead of the dissipation rate as
in HISWA), can be used as driving force to compute the wave-induced currents and set-up in
the flow module.

The SWAN model is based on the discrete spectral action balance equation and is fully spec-
tral (in all directions and frequencies). This latter implies that short-crested random wave fields
propagating simultaneously from widely different directions can be accommodated. SWAN
computes the evolution of random, short-crested waves in coastal regions with deep, inter-
mediate and shallow water and ambient currents. The SWAN model accounts for (refractive)
propagation - as the HISWA model - and represents the processes of wave generation by
wind, dissipation due to white-capping, bottom friction and depth-induced wave breaking and
non-linear wave-wave interactions (both quadruplets and triads) explicitly with state-of-the-art
formulations. To avoid excessive computing time and to achieve a robust model in practical
applications, fully implicit propagation schemes have been applied. It should be noted here,
however, that although an efficient numerical technique has been implemented in SWAN the
computing time for a typical wave computation may significantly be larger than that of the
HISWA model. The SWAN model has successfully been validated and verified in laboratory
and (complex) field cases (see e.g. Ris (1997); Ris et al. (1999)). It is noted that the SWAN
model (as the HISWA model) does not account for diffraction effects.

The SWAN model has been developed at Delft University of Technology (the Netherlands)
and where it is undergoing further enhancements. It is specified as the new standard for
nearshore wave modelling and coastal protection studies Therefore, Deltares has integrated
the SWAN model into Delft3D and is applying SWAN in its research and consultancy projects.
The SWAN model has been released under public domain.

You can download the source code, documentation and installation guide lines from the
SWAN-website: http://swan.ct.tudelft.nl. User support is provided by the Delft University of
Technology. As agreed with the SWAN group Deltares can provide the SWAN version that is
currently supported in Delft3D-WAVE. Upgrades must be downloaded from the SWAN web-
site.

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 Delft3D, Functional Specifications

7.2 Application areas

The wave module can be used for harbour and offshore installation design and for coastal
development and management related projects. It can also be used as a wave hindcast
model. Typical areas for the application of the wave module lie in the range between 2 by 2
km to 50 by 50 km.

The wave module can optionally be coupled with the other modules of Delft3D. In this way an
efficient and direct coupling is obtained between e.g. the flow module (wave driven currents)
and the sediment transport module (stirring by wave breaking).

7.3 Coupling with other modules

The wave computations are carried out in Delft3D on a on a regular rectilinear grid or a curvi-
linear grid. The curvilinear grid can be the same as the grid used in the hydrodynamic module
Delft3D-FLOW. The Delft3D system will automatically transfer all the relevant information to
and from (2-way coupling) the hydrodynamic module Delft3D-FLOW, which simulates the flow
on a curvilinear grid. The curvilinear grid can be generated with the grid generator RGFGRID
.

20 of 38 Deltares
 8 Morphodynamic module
The sediment transport module, integrates the effects of waves, currents, sediment transport
on morphological development, related to sediment sizes ranging from silt to gravel. It is
designed to simulate the morphodynamic behaviour of rivers, estuaries and coasts on time-
scales of days to years.

The typical problems to be studied using the morphological module involve complex interac-
tions between waves, currents, sediment transport and bathymetry. To allow such interactions,
the individual modules within Delft3D all interact through a well-defined common interface.

The computational modules within Delft3D are identical to their stand-alone counterparts and
each offer the full range of physical processes. In this way, Deltares combined experience of
over thirty years in computer modelling is built into this system.

A morphological simulation in Delft3D is defined as a tree structure of processes and sub-

processes down to elementary processes which contain calls to the computational modules.
You are free to build up processes of increasing complexity, from a single call to the flow model
to morphodynamic simulations spanning years, with varying boundary conditions. This mod-
ule simulates the processes on a curvilinear grid system used in the hydrodynamic module,
which allows a very efficient and accurate representation of complex areas.

8.1 Module description

Delft3D-MOR contains or is able to utilise the following components:

Wave
At present also the SWAN model is available in the wave module of Delft3D. The SWAN model
is fully spectral (in all directions and frequencies) and computes the evolution of random,
short-crested waves in coastal regions with shallow water and ambient currents. The SWAN
model accounts for (refractive) propagation and represents the processes of wave generation
by wind, dissipation due to white-capping, bottom friction and depth-induced wave breaking
and non-linear wave-wave interactions (both quadruplets and triads) explicitly with state-of-
the-art formulations. It is noted that the SWAN model does not account for diffraction effects.

Hydrodynamics
The hydrodynamic module (Delft3D-FLOW) used by Delft3D-MOR is based on the shallow
water equations, including effects of tides, wind, density currents, waves, and turbulence mod-
els up to k-ε. The module includes a transport solver for salinity, temperature and conserva-
tive substances. The effects of salinity and temperature on the density and on the momentum
balance are taken into account automatically.

The module uses a curvilinear grid in the horizontal plane. The vertical grid sizes are propor-
tional to the local water depth.

For efficient morphological computations a one-layer, depth-averaged approach is used. The

effects of spiral flow, i.e. in river bends, are computed by a secondary flow module which takes
into account the advection of spiral flow intensity and the effect of the secondary flow on the
primary current.

Wave effects in the model include radiation stress gradients associated with wave dissipation,
wave-induced mass flux and enhanced bed shear stress, computed by a choice of formula-

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 Delft3D, Functional Specifications

tions.

Sediment transport
The sediment transport module computes the bed-load and suspended-load sediment trans-
port field over the curvilinear model grid, for a given period of time.

The bed-load transport is computed as a local function of wave and flow properties and the
bed characteristics. The equilibrium suspended load is also computed as a local function
of these parameters. The module then recognises two modes of transport: total transport
(equilibrium) mode, or suspended load mode. In the first, the total transport is simply the
addition of bed-load and equilibrium suspended-load transport. In the second mode, the
entrainment, deposition, advection and diffusion of the suspended sediment is computed by a
transport solver. Here, a quasi-3D approach is followed, where the vertical profiles of sediment
concentration and velocity are given by shape functions.

The bed-load and equilibrium suspended-load transport can be modelled by a range of for-
mulations, among which are Engelund-Hansen, Meyer-Peter-Muller, Bijker, Bailard and Van
Rijn for sand, and a separate formulation for silt transport.

Effects of the bed slope on magnitude and direction of transport, and effects of non-erodible
layers can be taken into account for all formulations.

Bottom change
The bottom update module contains several explicit schemes of Lax-Wendroff type for updat-
ing the bathymetry based on the sediment transport field. Options are available for fixed or
automatic time-stepping, fixed (non-erodible) layers, various boundary conditions, and dredg-
ing.

8.2 Numerical aspects

All modules operate on the same rectangular or curvilinear, orthogonal grid. Fully implicit ADI
schemes are applied in the hydrodynamic module for the momentum and continuity equations.
The solver has robust drying and flooding procedures for both 2D and 3D cases. In the
transport solver a Forrester filter can be applied which guarantees positive concentrations
throughout.

The same transport solver is applied for suspended sediment computations.

The wave model HISWA operates on rectangular grids, and uses an implicit scheme in propa-
gation direction, combined with a forward marching technique. The wave module takes care of
all transformations and interpolations between these rectangular grids and the curvilinear flow
and transport grid. The wave model SWAN can perform computations directly on a curvilinear
grid.

The bottom update model uses an explicit scheme of Lax-Wendroff type. This leads to a
Courant type stability criterion. However, cheap intermediate "continuity correction" steps
keep the computational effort at a reasonable level.

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 Morphodynamic module

8.3 Application areas

Delft3D-MOR is designed to simulate wave propagation, currents, sediment transport and
morphological developments in coastal, river and estuarine areas.

Coastal areas including beaches, channels, sand bars, harbour moles, offshore breakwaters,
groynes and other structures. The coastal areas may be intersected by tidal inlets or rivers;
parts of it may be drying and flooding.

Rivers including bars, river bends (spiral flow effect), bifurcations, non-erodible layers, dredg-
ing operations and having arbitrary cross-sections (with overbank flow). Various structures
may be represented. Special features for 2D river applications are presently being developed
and validated, such as a bottom-vanes and graded-sediment.

Estuarine areas including estuaries, tidal inlets and river deltas influenced by tidal currents,
river discharges and density currents. Sediment can be non-cohesive (sandy) or cohesive
(silt). The areas may include tidal flats, channels and man-made structures, e.g. docks, jetties
and land reclamations.

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24 of 38 Deltares
 9 Pre-processing and post-processing
In this chapter several pre-processing and post-processing programs available in Delft3D are
described in some details. These programs concern visualisation, grid generation, manipula-
tion of grid related data and data analysis and manipulation.

9.1 Visualisation

9.1.1 GPP
The general post-processor (GPP) module of Delft3D allows uniform access to all kinds of
data files to select and visualise simulation results and measurement data. More specifically
the program allows to:

 select the map and/or time histories you want to visualise;

 select the lay-out and composition of the plot figure to be produced;
 select the type of output medium, i.e. screen for inspection, plotter or printer for hard copy
output.

The type of presentation depends on the character of the data set:

 vector plots for flow velocities, bottom shear stress and other vector quantities, with auto-
matic or user-defined scaling of s-axis, y -axis and vector scale;
 time history plots, from a single run, from various runs in the same plot or simulation
results in combination with measurement data. Depending on the data files, these can be
typical hydrodynamic quantities, such as water levels, velocity magnitude and direction,
but also water quality parameters like salinity, temperature and E.coli concentration. The
scaling can be determined automatically or set by you;
 contour and isoline plots of scalar quantities like the depth, water levels or algae growth
rates. Again you can choose automatic scaling or set the contour classes manually;
 vertical profiles for quantities defined on a three-dimensional grid;
 geometric plots of the grid itself, tidal flats, land boundaries;
 mass balances and limiting factors for displaying the details of water quality models.

Data sets can be plotted in any (sensible) combination, as long as there is a common co-
ordinate system. Layouts may contain more than one viewport, allowing several independent
plots on one page. It is noted that the overview above is by no means complete but it gives a
general idea about the possibilities.

The program has been designed to be general enough to handle different kinds of underlying
geometries and data files of widely varying formats.

The program is capable of producing high quality colour plots. It is also able to produce a plot
file in various standard formats. At the same time a print-out of the results in ASCII format can
be made, enabling the data to be imported in other post-processing programs.

For the use of ArcView and Matlab to visualise and further process Delft3D results, see Sec-
tion 9.9.

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 Delft3D, Functional Specifications

9.1.2 QUICKPLOT
The post-processing program Delft3D-QUICKPLOT allows you to easily plot and animate data
from most output files and some input files of Delft3D and several other software packages of
WL | Delft Hydraulics (such as SOBEK and PHAROS). Furthermore, it supports some simple
ASCII formats such that you can combine model output and measurement data in one plot,
and it is possible to load bitmap data as a backdrop for your 1D or 2D plots.

Typical plots created using Delft3D-QUICKPLOT are 2DH or 2DV plots and time-series plots,
although it also has basic support for 3D plots. Scalar results may be presented using con-
tour lines, contour patches, grid cell based patches, interpolated continuous shades, coloured
marker or value fields. Vector results may be presented as vectors, coloured vectors or nor-
malised vectors or as scalar quantities by selecting a single component (e.g. x-component,
y -component, magnitude, direction) of the vector.

Data sets can be linked to animate single or multiple data sets in a figure. Animation frames
can be stored in various bitmap formats. Data sets can be exported to various in-house or 3rd
party formats.

Delft3D-QUICKPLOT is a standalone program based on technology of The MathWorks Inc.

It can be seamlessly integrated with the MATLAB environment via the Delft3D-MATLAB inter-
face.

.
Figure 9.1: Example QUICKPLOT figure: 3D view of bed level

9.2 Grid generation

RGFGRID is a program to generate orthogonal, curvilinear grids of variable grid size, that are
to be used in combination with each of the modules of the Delft3D suite. The grid-generator
includes a graphical interface and an orthogonalisation module, providing easy control of the
grid generation process.

RGFGRID supports the following features:

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 Pre-processing and post-processing

.
Figure 9.2: Example QUICKPLOT figure: Depth-averaged velocity vectors and drying
and flooding

 graphical user interface;

 generation of grids in Cartesian or Spherical co-ordinate systems
 display of grid features as orthogonality, smoothness, aspect ration etc.;
 several user-functions have been implemented to provide easy control over the grid shape;
 keyboard and mouse driven events are supported;
 iterative way of working, each cycle providing more definition in the grid shape.
 generation of multi-domain interfaces.

9.3 Grid data manipulation

To create, visualise and modify grid based data, such as bathymetries, and other grid related
data the program QUICKIN is provided. QUICKIN is used in combination with the modules of
Delft3D.

QUICKIN supports the following features:

 graphical user interface;

 several interpolation options (averaging, triangulation, diffusion);
 suitable for different ratios of grid-density versus sample-density;
 various display possibilities: isolines, dots, perspective, etc.;
 implementation of various user-functions to provide easy control over the final bathymetry;
 sample data from different sources can be interpolated in sequence, thus, starting with
the best quality data available, an optimal bathymetry can be created.
 Definition of dredge and dump sites with their characterristics.

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9.4 Grid aggregation

The program DIDO enables you to span coarser, irregularly shaped, grid segments for water
quality modelling, starting from the fine grid of e.g. the grid used by the hydrodynamic model.
For ecological modelling with large numbers of state variables, a coarser schematisation, fol-
lowing ecological and transport separation lines rather than grid lines, is often preferable. The
fine grid of the hydrodynamic model serves as input, integer multiples of the input grid are
used for the description of the coarse grid. The procedure is fully mass-conserving. Aggrega-
tion is only supported in a plane surface.

DIDO provides the following features:

 zoom in locally;
 separate a working area from the remainder of the schematisation;
 aggregate regularly (e.g. every 2 segments in the one and 3 in the other direction);
 aggregate irregularly (by rubber band lines comparable to the bulls hide);
 fine tune by point and click on single elements;
 select a subset of the hydrodynamic area for water quality modelling;
 display information of a selected segment;
 save intermediate results on the fly;
 resume unfinished work from saved files;
 save the final result for water quality simulation.

The final result of DIDO will be used as input to the coupling program between the hydro-
dynamic module Delft3D-FLOW and the water quality module D-Water Quality enabling the
latter to run on a coarser grid using the fine grid hydrodynamic database. Water quality simu-
lations are converted back to the fine grid in post-processing software. This gives spatial plots
with the fine resolution (although aggregated areas will still show equal concentration values).

9.5 Tidal analysis and comparison with observations

Analysis and interpretation of a hydrodynamic simulation in terms of tidal amplitudes and
phases can be performed by the program Delft3D-TRIANA. Delft3D-TRIANA performs of-
fline tidal analyses on time-series of either water levels and/or velocities. Moreover, Delft3D-
TRIANA compares the results from these analyses with observation data supplied by you.
Amplitude ratios and phase differences as well as objective statistics are determined.

9.6 Tidal analysis and prediction

The program Delft3D-TIDE is used for the analysis of tidal recordings and the preparation of
tidal predictions.

The main module TIDE/ANALYSIS performs tidal analysis on time-series of water levels or
currents. A variety of features is included, such as:

 the coupling of closely positioned astronomical components;

 the simultaneous analysis of successive records of different instruments;
 the discrimination of sub-series to account for gaps in measurement recordings;
 the appreciation of linear trends and an accuracy analysis.

In a tidal analysis of a time-series of one year with a 10 minutes interval, 100 or more tidal
constituents can be prescribed simultaneously. The constituents are selected from the internal
database that contains 234 constituents that may be important at locations world-wide.

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The module TIDE/FOURIER performs Fourier-analyses on any type of time-series. This fea-
ture can be used to investigate the series of residual levels or velocities which has been
identified during the tidal analysis on remaining tidal components.

Using a set of tidal constants, such as computed in the analysis module, the TIDE/PREDICT
module predicts water levels or tidal currents as a function of time.

The module TIDE/HILOW may provide the production of tide tables with the dates, times and
heights of the High and Low Waters. Using a word-processor or desktop publishing software
package, the basic tide tables can be processed further and combined with other relevant
information like tidal stream data.

Whereas in the regular analysis part of the package you pre-define the constituents that will be
considered, the program also features an option (TIDE/ASCON) to compute the astronomic
arguments and node amplitude factors for all 234 internally defined constituents.

The package is accompanied with a comprehensive User Manual, exemplifying the use of the
program and its scientific backgrounds. A number of examples is added in the form of input
and data files.

9.7 Nesting of Delft3D-FLOW models

At the open boundaries of a Delft3D-FLOW model, boundary conditions are required for the
vertical and/or horizontal tide and the substances if applicable. In case these open boundaries
are located within a (coarser) overall Delft3D-FLOW model, then the overall model can be
used to generate the boundary conditions for the detailed model. In this case we say the
detailed model is nested within the overall model.

The procedure to generate nested boundary conditions consists of 3 steps:

1 Using the program Delft3D-NESTHD 1 a list of monitoring stations in the overall model,
needed for the interpolation, will be generated. In addition to this, the program generates
the nest administration, i.e. the link between the boundary support points in the detailed
(or nested) model and the monitoring stations in the overall model.
2 Run the overall model with the list of monitoring stations generated by Delft3D-NESTHD
1.
3 The actual boundary conditions for the nested model are generated by Delft3D-NESTHD
2 using the history file of the overall model and the nest administration.

9.8 Nesting of D-Water Quality models

The transfer of data from an encompassing or ’overall’ numerical model to an embedded
or ’nested’ numerical model is called nesting. In general the overall model has a coarse
resolution of grid cells, whereas the nested model has a higher resolution. At the boundary
locations of the nested model the results from the overall model are required as boundary
conditions for the nested model. The boundary conditions can be water levels, currents,
fluxes or discharges in case of hydrodynamic models, and water quality parameters in case
of water quality models.

The procedure of nesting through concentrations between D-Water Quality (or D-Waq PART)
models is performed by the system D-Waq NESTWQ. In this procedure two steps can be
distinguished which are handled by separate subsystems:

1 D-Waq NESTWQ 1, for the determination of nest segments and nest weights in the overall
model. The concentrations at these segments are used by the next subsystem.

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2 D-Waq NESTWQ 2, for the generation of boundary conditions for the boundary segments
in the nested model from the results at the nest segments in the overall model.

9.9 Interfaces with other programs

It should be emphasised that even though these extensions can be quite useful as a sup-
plement to the Delft3D tools, real benefits are gained mostly if you are familiar with both the
Delft3D environment and the external environment.

9.9.1 Interface to GIS

While pre-processing and post-processing can be done quite adequately using the specific
tools offered by Delft3D, recently a link have been established with ArcView. The link is in-
tended as a supplement to the existing tools rather than a replacement. It adds the ability to
view and manipulate model results and model input in a different environment.

The link to ArcView implies:

 exporting a GIS line coverage as land boundary outline and depth data as contained in
ArcInfo/ArcView map layers to a format suitable for RGFGRID and QUICKIN;
 importing the model grid and the corresponding depth field as generated by RGFGRID
and QUICKIN, so that they can be presented in a geographical context;
 importing the grid-based model results (scalar and vector quantities) with a user interface
quite similar to that of GPP in the ArcView environment for presentation or further analysis

All data files are read directly by this ArcView extension and stored as shape files. There is
no need to convert or process the model result files.

9.9.2 Interface to Matlab

In a similar way as with GIS it is possible to import the results produced with Delft3D directly
into Matlab. This gives the opportunity to visualise or use the results for further analysis using
the facilities offered by Matlab.

The Delft3D-MATLAB interface allows you to seamlessly integrate the simplicity of simulation
data access by Delft3D-QUICKPLOT with the flexibility of the MATLAB environment developed
by The MathWorks Inc. The combination of these two tools allows you to use the full power of
MATLAB for analysing, processing and visualising the simulation results.

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 Pre-processing and post-processing

.
Figure 9.3: Example QUICKPLOT figure: Depth-averaged velocity vectors and tidal ellips

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10 Hardware configuration
Delft3D and its accompanying programs is supported on the following platforms:

 Windows 32/64-bit platforms

 Linux Redhat 3.4

Configuration item Minimal Preferred

Processor IA32, 1 GHz IA32, 3 GHz or more

Internal memory 1024 MB 2 GB or more

Swap space 2.0 × internal memory 4.0 × internal memory

Hard disk 10 GB 80 GB or more

Monitor 17 inch colour 19 inch colour

Display 800 × 600 pixels 1280 × 1024 pixels

256 colours 16 million colours

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References
Booij, N., R. Ris and L. Holthuijsen, 1999. “A third-generation wave model for coastal regions,
Part I, Model description and validation.” Journal of Geophysical Research 104 (C4): 7649–
7666.

Holthuijsen, L., N. Booij and T. Herbers, 1989. “A prediction model for stationary, short-crested
waves in shallow water with ambient currents.” Coastal Engineering 13: 23–54.

Holthuijsen, L., N. Booij and R. Ris, 1993. “A spectral wave model for the coastal zone.” In
Proceedings of 2nd International Symposium on Ocean Wave Measurement and Analysis,
New Orleans, pages 630–641.

Los, F. J., 1991. Mathematical Simulation of algea blooms by the model BLOOM II. Tech.
Rep. T68, WL | Delft Hydraulics, Delft, The Netherlands. Version 2.

Los, F. J., 2009a. Eco-hydrodynamic modelling of primary production in coastal waters and
lakes using BLOOM. Ph.D. thesis, Wageningen University. ISBN 978-90-8585-329-9.

Los, F. J., 2009b. Eco-hydrodynamic modelling of primary production in coastal waters and
lakes using BLOOM. IOS Press Amsterdam. ISBN 978-1-58603-987-5.

Ris, R., N. Booij and L. Holthuijsen, 1999. “A third-generation wave model for coastal regions,
Part II: Verification.” Journal of Geophysical Research 104 (C4): 7649–7666.

Ris, R. C., 1997. Spectral Modelling of Wind Waves in Coastal Areas. Communications on
Hydraulic and Geotechnical Engineering, report 97-4. Delft University of Technology, Delft,
The Netherlands. Ph.D. thesis.

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PO Box 177 +31 (0)88 335 81 88
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Rotterdamseweg 185 www.deltaressystems.nl
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