Tutorial 2: Building a basic 2D flow model

Note

This tutorial described the old route of building a 3Di model. After the Klondike release, you do not need Tortoise and Inpy anymore. This tutorial will be updated.

In this tutorial, we will build a basic 2D flow model in 3Di. We will start from scratch and build our model step by step. We will finish with a working model that you can play around with on the 3Di live site. This model is based on the Laugharne and Pendine Burrows in the United Kingdom. The burrows enclose a flat area of reclaimed salt marshes that are currently used as farmland. While this tutorial represents a real-world area, it is important to keep in mind that some processes will be simplified for the purpose of this tutorial.

You will learn the following skills in this tutorial:

• Prepare an empty 3Di model.

• Couple a digital elevation model (DEM) to your 3Di-model.

• Configure the settings of a 2D model.

• Validate your model input using the raster checker.

• Validate your model schematization using the schematization checker.

• Compile your model on the 3Di live site.

Before you start, please make sure to:

• Install the 3Di Modeller Interface. Please see Installation manual for instructions.

• Install the 3Di toolbox in the Modeller Interface. Please see Plugin Installation for instructions.

• Gain access to the 3Di Live Site. Please see Login to the Live Site for instructions.

• Download the Taf dataset for this tutorial, which contains an empty .sqlite and a digital elevation model (DEM).

  _{The digital elevation model contains United Kingdom public sector information licensed under the Open Government Licence v2.0.}

Model initialisation

Model preparation

Before we can start building our model, we need prepare our model and organize our data. The Taf dataset that you have downloaded contains an empty .sqlite database and a digital elevation model (DEM) of the Laugharne and Pendine Burrows called dem_2m_LPB.tif. The structured .sqlite database contains all elements that can be included in a 3Di model. It will slowly be filled in when you build a model. Rename empty.sqlite to LP_Burrows.sqlite.

Loading the model in the Modeller Interface

Our model must be imported in the Modeller Interface to view and modify its contents. The model can be loaded via the 3Di toolbar (part of the 3Di toolbox plug in) by following these steps:

1. Open the Modeller Interface.

2. Create a new project.

3. Click the Select 3Di results button on the 3Di Toolbar (white database icon). [1]

4. Select load in the model section, and select the LP_Burrows.sqlite database provided with this tutorial. [2]

5. You should now see the 3Di model as part of your the Modeller Interface layers. [3]

You can also import the DEM as a raster layer:

1. go to the folder where you downloaded the Taf dataset.

2. Select the .tif file.

3. Drag the .tif file from your folder into the Modeller Interface screen.

This can improve your feel with the data, but it is not strictly required.

It is advised that you set your project reference EPSG:27700 (British National Grid) for this tutorial. To do this, click on the current project reference at the bottom right and select the coordinate reference system you want.

Empty LP_burrows.sqlite and DEM loaded into the Modeller Interface and projected on a google satellite background map.

Model building

The most fundamental element to building a 3Di is choosing your correct settings. We will go through all settings that are required for a basic 2D flow model. A list of mandatory settings and detailed descriptions can be found in the database overview. We will introduce extra elements like 1D channels, levees or hydraulic structures in later tutorials.

Complete the global settings

The global settings are contained in the v2_global_settings table. Open the settings by

1. Right-click the v2_global_settings table. [1]

2. Select Open attribute table. [2]

3. Select Switch to form view in the bottom right corner. [1]

4. Select Toggle editing mode and in the top right corner. [2]

5. Select Add feature. [3]

Now we can start to configure all settings. 3Di requires you to complete all mandatory settings before changes can be saved. Attempts to save the settings before all mandatory field have been completed will result in an error message. A list of mandatory settings and detailed descriptions can be found in the database overview. Finally, please note that the following settings have been selected specifically for this tutorial.

Let us now fill in the settings of each tab in the global settings table.

General

Setting	Value for this tutorial	Comments
id	1
name	Tutorial_2D_flow
use_0d_inflow	0: do not use 0d inflow	Use only when point sources are present
use_1d_flow	No	This tutorial does not define 1D channels
use_2d_rain	Yes	Enables rainfall
use_2d_flow	Yes	Enables 2D flow

Grid

Setting	Value for this tutorial	Comments
grid_space	64	Minimum grid cell size in metres
kmax	1	See Computational grid
table_step_size	0.10	See Computational grid

Terrain information

Setting	Value for this tutorial	Comments
dem_file	dem_2m_LPB.tif
epsg_code	27700	British national grid
frict_coef_file	NULL	Only used for spatially varying friction
frict_coef	0.06	Farmland
frict_type	2: Manning
frict_avg	No
initial_groundwater_level_file	NULL	No groundwater
initial_groundwater_level	NULL
initial_groundwater_level_type	(NULL)
initial_waterlevel_file	NULL	Only for spatially varying initial water level
initial_waterlevel	-10	in metres; selected for a dry start
water_level_ini_type	max
interception_file	NULL	No interception
interception_global	NULL
wind_shielding_file	NULL	No wind

Time

Setting	Value for this tutorial	Comments
start_date	2020-01-01
start_time	2020-01-01 00:00:00
sim_time_step	30	in seconds
timestep_plus	No	Only when extra control over the timestep is required
minimum_sim_time_step	NULL
maximum_sim_time_step	NULL
nr_timesteps	240	for a 2 hour simulation
output_time_step	120	in seconds

Setting id’s

Setting	Value for this tutorial	Comments
interflow_settings_id	NULL	No interflow
groundwater_settings_id	NULL	No groundwater
numerical_settings_id	1	Reference to the model specific numerical settings
simple_infiltration_settings_id	1	Reference to the model specific infiltration settings
control_group_id	NULL	No control groups

Extra options 1D (not relevant as this tutorial does not contain 1D elements)

Setting	Value for this tutorial	Comments
advection_1d	0: Do not use advection 1d	No 1D elements
dist_calc_points	10000	No 1D elements
manhole_storage_area	NULL	No 1D elements
max_angle_1d_advection	NULL	No 1D elements
table_step_size_1d	NULL	No 1D elements

Extra options 2D

Setting	Value for this tutorial	Comments
advection_2d	1: Use advection 2d
dem_obstacle_detection	No
guess_dams	No
dem_obstacle_height	NULL	Obstacles not activated
embedded_cutoff_threshold	NULL
flooding_threshold	1e-06
table_step_size_volume_2d	NULL

Don’t forget to save your changes after completing all settings, by clicking on save edits in the top left corner.

Complete the infiltration settings

The settings for the infiltration mechanism are contained in the v2_simple_infiltration table.

Editing the table work in a similar manner as with the v2_global_settings table. Complete the following settings:

General

Setting	Value for this tutorial	Comments
id	1	Must match the simple_infiltration_settings_id in the v2_global_settings_table
display_name	infiltration
infiltration_rate	360	in mm/hour; uniform silty sand is assumed in this tutorial
infiltration_rate_file	NULL	Only used for spatially varying infiltration rates
max_infiltration_capacity_file	NULL	infinite infiltration capacity is assumed in this tutorial
infiltration_surface_option	0	See Infiltration

Complete the aggregation settings

The aggregation settings control the aggregation of model results. They are contained in the v2_aggregation_settings table.

As with the previous settings, open the attribute table, toggle the editing mode and add a feature. However, select switch to table view this time.

The different rows of the table refer to different model output categories. For each category, set the global_settings_id at 1. You can either do this manually by filling in 1’s in the column [1], or by:

1. Selecting the column global_settings_id in the drop down menu [2]

2. Typing a 1 in the bar [3]

3. Clicking update All [4]

4. And pressing save edits [5]

Retain the default values for all other settings.

Complete the numerical settings

The numerical settings are contained in the v2_numerical_settings table which can be found under advanced numerics.

As with the previous settings, open the attribute table, toggle the editing mode, switch to form view and add a feature. Complete the following settings:

General

Setting	Value for this tutorial	Comments
id	1	Must match the numerical_settings_id in the v2_global_settings_table

Limiters (not used in this tutorial, only for sloping areas)

Setting	Value for this tutorial	Comments
limiter_grad_1d	1
limiter_grad_2d	0
limiter_slope_crossectional_area_2d	0
limiter_slope_friction_2d	0

Matrix

Setting	Value for this tutorial	Comments
convergence_cg	1e-09
convergence_eps	1e-05
use_of_cg	20
use_of_nested_newton	0: when the schematisation does not include 1D-elements …
max_degree	5: for surface flow only
max_nonlin_iterations	20
precon_cg	1
integration_method	0

Thresholds

Setting	Value for this tutorial	Comments
flow_direction_threshold	1e-06
general_numerical_threshold	1e-08
thin_water_layer_definition	0.05
minimum_friction_velocity	0.05
minimum_surface_area	1e-08

Miscellaneous

Setting	Value for this tutorial	Comments
cfl_strictness_factor_1d	1
cfl_strictness_factor_2d	1
frict_shallow_water_correction	0
pump_implicit_ratio	1
preissmann_slot	0

With the completion of the numerical settings, we have built a basic working 2D flow model.

The overview of all settings for this tutorial can be referenced here.

Model validation

Verify the model rasters using the raster checker

Before sending our new model to the web portal, it is important to validate that our model contains no errors. The Raster checker is part of the 3Di toolbox and performs 18 checks to verify the quality of the DEM. For more information, see: Raster checker The raster checker can also be applied to other 3Di-related rasters when relevant.

A log of the performed test is written to the log file in the location as denoted in the result prompt. This location is typically the location of your DEM-file. The log file can be opened to view additional details of the checks performed.

Verify the model schematisation using the schematisation checker

The second validation is that of the model schematisation. This is checked with the Schematisation checker in the 3Di toolbox. It checks the model tables for many possible errors that could lead to crashes when the model is compiled.

Now open the log file at your specified location. You may find the error “Value in v2_aggregation_settings.aggregation_in_space should to be of type integer”. This is a known bug in the schematisation checker, which will be removed in a future update. You should not find any other warnings.

Log of the schematisation checker

If you do not get any further warnings or errors, your model is successfully validated and is ready for activation.

Model activation

Upload your model to the repository

The first stage towards running your model in the web portal is to upload you model to the 3Di model databank. Take the following actions:

Create a new .zip file with your new LP_Burrows.sqlite database and your DEM dem_2m_LPB.tif. Here we name it Tutorial_01_2D_flow.zip.

Be mindful that the folder structure in the .zip file matches that of your schematisation. Based on the settings in this tutorial, your .sqlite database and your DEM should be in the same folder. Exclude the log files from your .zip folder.

Go to https://models.lizard.net/model_databank/. Log in and select Upload new model.

Fill in the details of your models. Be sure to select 3Di-v2 as your model type. Select Submit when you have completed the form.

Compile your model

Now your model is stored in the model database, it is ready for compilation. It can take a couple minutes before your model appears in the list of available models.

1. Go to https://3di.lizard.net/models/.

2. Use to search function to retrieve your model. Search for the name that you gave your model in the previous step. You have to select also show repositories that do not have inp files yet.

3. Select initialize inp generation for your model.

Your model will now be compiled. After a few minutes the blue bar “no models” will turn to a green bar with the text “success” when the model is successfully compiled. You may have refresh the page. Once completed, you can select the model to view its details. The model is now also available on the 3Di Live Site.

Your screen after a successful compilation

Run your model

You can now run your model via the 3Di Live Site (Login to the Live Site) or via the 3Di Modeller Interface (Using the Modeller Interface). It will be available under the name you gave it.

Congratulations on building a 2D flow model from scratch!