Difference between revisions of "Tutorial Module06"

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(Adding a Polygon Input of Particles with Bed Interaction)
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*Add the following section to the PTM control file beneath our current definition of the microplastics particle group.
*Add the following section to the PTM control file beneath our current definition of the microplastics particle group.
  <font color="blue"><tt>group</tt></font><font color="red"><tt>==</tt></font> sediment
  <font color="blue"><tt>group</tt></font><font color="red"><tt> ==</tt></font> sediment
     <font color="blue"><tt>d50</tt></font><font color="red"><tt>==</tt></font> 0.000002
     <font color="blue"><tt>d50</tt></font><font color="red"><tt> ==</tt></font> 0.000002
     <font color="blue"><tt>particle density</tt></font><font color="red"><tt>==</tt></font> 2650
     <font color="blue"><tt>particle density</tt></font><font color="red"><tt> ==</tt></font> 2650
     <font color="blue"><tt>initial scalar mass</tt></font><font color="red"><tt>==</tt></font> 1
     <font color="blue"><tt>initial scalar mass</tt></font><font color="red"><tt> ==</tt></font> 1
     <font color="blue"><tt>settling model</tt></font><font color="red"><tt>==</tt></font> constant
     <font color="blue"><tt>settling model</tt></font><font color="red"><tt> ==</tt></font> constant
     <font color="blue"><tt>settling parameters</tt></font><font color="red"><tt>==</tt></font> 0.0002 !(m/s)
     <font color="blue"><tt>settling parameters</tt></font><font color="red"><tt> ==</tt></font> 0.0002 !(m/s)
     <font color="blue"><tt>horizontal dispersion model</tt></font><font color="red"><tt>==</tt></font> constant
     <font color="blue"><tt>horizontal dispersion model</tt></font><font color="red"><tt> ==</tt></font> constant
     <font color="blue"><tt>horizontal dispersion parameters</tt></font><font color="red"><tt>==</tt></font> 1.0
     <font color="blue"><tt>horizontal dispersion parameters</tt></font><font color="red"><tt> ==</tt></font> 1.0
     <font color="blue"><tt>vertical dispersion model</tt></font><font color="red"><tt>==</tt></font> HD model
     <font color="blue"><tt>vertical dispersion model</tt></font><font color="red"><tt> ==</tt></font> HD model
     <font color="blue"><tt>vertical dispersion parameters</tt></font><font color="red"><tt>==</tt></font> 1.0
     <font color="blue"><tt>vertical dispersion parameters</tt></font><font color="red"><tt> ==</tt></font> 1.0
     <font color="blue"><tt>erosion model</tt></font><font color="red"><tt>==</tt></font> Mehta
     <font color="blue"><tt>erosion model</tt></font><font color="red"><tt> ==</tt></font> Mehta
     <font color="blue"><tt>erosion parameters</tt></font><font color="red"><tt>==</tt></font> 0.1,0.2,1.0
     <font color="blue"><tt>erosion parameters</tt></font><font color="red"><tt> ==</tt></font> 0.1,0.2,1.0
     <font color="blue"><tt>deposition model</tt></font><font color="red"><tt>==</tt></font> Krone
     <font color="blue"><tt>deposition model</tt></font><font color="red"><tt> ==</tt></font> Krone
     <font color="blue"><tt>deposition parameters</tt></font><font color="red"><tt>==</tt></font> 0.25
     <font color="blue"><tt>deposition parameters</tt></font><font color="red"><tt> ==</tt></font> 0.25
  <font color="blue"><tt>end group</tt></font>
  <font color="blue"><tt>end group</tt></font>

Revision as of 19:52, 2 August 2020

Page Under Construction

Tutorial Description

The TUFLOW Particle Tracking Module (PTM) allows the 2D or 3D simulation of discrete Lagrangian particles as they are transported by the flow field (or other drivers such as wind or waves). Particle behavior such as settling, buoyancy, decay, sedimentation and re-suspension can all be simulated. The tracking of discrete particles can be used to output particle fate and age, which is useful for purposes of animal migration, search and rescue, environmental contaminants and oil spill modelling.

The PTM is invoked through the TUFLOW FV hydrodynamic engine which controls the overall simulation and supplies the hydrodynamic forcing to the particle transport module.

The tutorial will cover a number of aspects of the particle tracking model:

  • Add a single set of particles via a point source and simulate their fate
  • Review the outputs using the QGIS TUFLOW Viewer plugin
  • Add additional groups of particles via a polygon source
  • Add deposition and erosion to the particles to allow them to interact with the bed

    For the purposes of the particle tracking tutorial, we'll be using the hydrodynamic model created in Tutorial Module 5 (Estuary Application) and supplementing with additional information to represent the particles.

    Setting up a Point Source of a Group of Particles

    Creating a .FVPTM file

    The first step in the TUFLOW FV particle tracking module is to generate an .fvptm file which defines the commands to define particle characteristics and processes. This .fvptm file is then referenced via the TUFLOW FV control file (.fvc).

    • Use your preferred text editor to create a new file with extension .fvptm. Name the file PT_000.
    • Add the following commands to define a group of particles representing microplastics which enter our model via a combined sewer overflow within our estuarine reach and can flow out of the model at the downstream tidal boundary.
    !PTM to asses fate of Combined Sewer Overflow Outflow
    ! use nodestring definition from HD model to allow particles to leave model domain.
    Open boundary nodestring ==  2  !downstream tidal boundary
    !Time Commands
    langrangian timestep == 60.!seconds
    eulerian timestep == 60. !seconds
    !Global Commands
    Nscalar == 1
    !Particle Group Commands
    group ==  microplastics
         initial scalar mass == 1000
         settling model == none
         horizontal dispersion model ==  constant
         horizontal dispersion parameters == 1.0
         vertical dispersion model == HD model
         vertical dispersion parameters == 1.0
         erosion model == none
         deposition model == none
    end group
    seed particles== point,  159.09971,  -31.39463
        particle groups== microplastics
        timeseries file==  ..\bc_dbase\CSO.csv
        timeseries header== Date,microplastics
    end seed
    !Output Settings
    output dir== ..\results\
        output== ptm_netcdf
        output groups==  microplastics
        output interval== 1800.
        output parameters== uvw, depth, water_depth, uvw_water
    end output

    With the Nscalar command the scalar mass constituents are defined. These can be thought of as separate mass ‘containers’ that reside on a particle.

    With the Group settings we are specifying the characteristics of the particles. In this exercise the particles defined won't settle, deposit on the bed or be subject to erosion. We will use a constant horizontal dispersion model and use the hydrodynamic model to define the vertical dispersion.

    With the Seed Particles settings we are specifying that the particles are added to the model at a point inflow at co-ordinate 159.09971, -31.39463. The particles will be added to the model based on a mass flux time series defined in an CSO.csv file which we define in a later step.

    With the Output Settings settings, we're specifying the location and format of the outputted results as well as the output interval and type for our group of particles. These are Lagrangian outputs specific to the individual particles. Eulerian outputs, for example the concentration of particles within the water column, are specified in the TUFLOW FV Control File (.fvc)

    • Once the above commands have been added, save and close the PT_000.fvptm file.

    Mass Flux Time Series File

    Part of the commands added in the .fvptm, are to define the how many and where to seed (release) particles for the microplastics. In this instance, the particles to be tracked are added at a point within the model domain at 159.1269, -31.41123. There is also a reference to a csv file in the bc_dbase folder which is the mass flux time series file. This defines the temporal variation of the particle input into the model with the units in grams/second. This works in conjunction with the initial scalar mass value we defined in the PTM control file to determine the number of particles added to the model.

    The number of particles per second is equal to:-

    Time Series Mass (g/s)/Initial Scalar Mass (g)

    • Create a csv file called CSO.csv within the bc_dbase folder.
    • Add column headers ‘Date’ and ‘Plastics’ and populate with the following values:
    Date Microplastics
    01/05/2011 00:00:00 20
    01/05/2011 01:00:00 20
    01/05/2011 01:00:01 0

    Your CSV file should look like the below. This will introduce particles to our model at the beginning of the simulation for a period of 1 hour.

    CSO csv.PNG

    The time series mass flux value is 20g/s. The initial scalar mass defined in our particle group settings is 1000g. Therefore the number of particles released per second is:-

    20/1000=0.02 particles per second. Over the 1 hour release period, this equates to 72 particles being released in total.

    • Save and close the CSO.csv file.

    Update the TUFLOW FV Control File

    With the changes to the model, we now need to update our TUFLOW FV control file (.fvc) to read in the additional data which define our particle tracking module.

    • Copy the existing HYD_002.fvc file and rename to PT_000.fvc.
    • Add the following reference to the PT_000.fvc file in order to reference are TUFLOW FV particle tracking module control file.
    !Particle Tracking Input
    Particle Tracking Control File== PT_000.fvptm
    • Also within the output commands add the PTM_1 results parameter to the netcdf output parameters.
    output== netcdf
        output parameters== h,v,d, PTM_1
        output interval== 3600
    end output
    • Save and close the PT_000.fvc file

    Run the Simulation

    • Update the batch file to allow the PT_000.fvc simulation to be run. Run the simulation by running the batch file.

    Batch file.png

    Reviewing Results in QGIS

    There are two types of results which are available to review. The first is the Eulerian results which provide information about the 2D and 3D characteristics of the bulk flow and particles. There are also Lagrangian results which provide characteristics for the individual particles.

    Reviewing Eulerian Results in QGIS

    In the previous examples we assessed 3D results using MATLAB and Python libraries. Some of these tools are now available within the QGIS TUFLOW Viewer Plugin allowing a user interface to review TUFLOW FV 3D results. See the following Viewing 3D TUFLOW FV Results in QGIS page for instructions on how to review TUFLOW FV 3D results within QGIS.

    Reviewing Lagrangian Results in QGIS

    So far we have assessed Eulerian results in terms of the mass concentration of particles within the cells. The results of the particle tracking are also available as Lagrangian outputs, that is the location and characteristics of the individual particles.

    • Using the TUFLOW Viewer plugin, select File->Load Results – Particles. Animate through the results and you should see the presence of particles within the model output. Results are best viewed in conjunction with the map output, usually with depth and velocity vectors displayed.

    Particles 1.png

    • Right click on the PT_000_ptm.nc file which appears within the Layers panel with QGIS and go to Open attributes. You’ll see that there are 72 particles within the output once the simulation has got to 01/05/2011 01:00:00 (at 01/05/2011 00:30:00 there are 36 particles) which matches what we would expect from our mass flux time series and initial scalar mass value.
    • Within the layer attributes table are the 3D velocity values for the particle (uvw), the water (uvw_water), the depth to the particle and the water depth. Other output parameters are available (see the STM_PTM_User_Manual_2020).

    The individual parameters can also be seen using the info tool, Info tool.png

    Particles attributes.png

    Currently the particles are themed using a single icon and colour type. However, it is possible to theme based on particle characteristics.

    • Right click on the PT_000_ptm.nc and enter the Styles menu. Using the options here we can theme on particle age since release (in hours), the depth of the particle within the water depth, particle group ID, mass and particle state.

    Particles styles.png

    • Choose the 'stat' theme and animate the results. This will show the status of the particle as whether they are active in the water column, are active on dry land or within the bed.

    Particles styles 1.png

    • Choose the 'depth' theme which shows the depth of the particle. The darker the particle theme, the deeper the particle within the water column.

    Particles styles 2.png

    At this stage, we’ve added a point source of particles to are model representing an input of plastics which are neutrally buoyant and aren’t subject to deposition and erosion. In the next exercise, we will allow the particles to interact with the bed sediment.

    Adding a Polygon Input of Particles with Bed Interaction

    So far the particles that we've added have been neutrally buoyant, they don't sink and they don't interact with the estuary bed (sediment). Within the particle transport model, it is possible to allow the particles to interact with the bed and be subject to deposition and erosion. This can be useful for the representation of sediments for example determining the fate of contaminated sediments or similar.

    • Copy and paste the existing PT_000.fvptm as PT_001.fvptm.
    • Add the following section to the PTM control file beneath our current definition of the microplastics particle group.
    group == sediment
        d50 == 0.000002
        particle density == 2650
        initial scalar mass == 1
        settling model == constant
        settling parameters == 0.0002 !(m/s)
        horizontal dispersion model == constant
        horizontal dispersion parameters == 1.0
        vertical dispersion model == HD model
        vertical dispersion parameters == 1.0
        erosion model == Mehta
        erosion parameters == 0.1,0.2,1.0
        deposition model == Krone
        deposition parameters == 0.25
    end group

    In this instance we have defined a particle group called sediment which has a characteristic sediment size of 0.000002m. To add erosion, it's necessary to apply a settling model, erosion model and a deposition model. In this instance our settling model will be set to a constant particle settling rate of 0.0002 m/s, the erosion will be modelled using the Mehta erosion model and the deposition by the Kroene deposition model. For details, the reader is referred to the Sediment Transport and Particle Tracking User Manual

    In the previous examples we have provided point inputs of particles using a mass flux time series file. We will now define a polygon with a group mass of our contaminated sediment to an area within our model domain distributed throughout the water column.

    • Add a material block to define the default material block which defines the different bed characteristics within our model domain. For the purpose of this model, we will assume that the bed material is uniform with the bed material having a dry density of 1631 kg/m3.
    !This is required due to adding deposition and settling
    Material== 0 !Default material.  Can add additional material blocks for spatial distribution.
        Layer== 1
            dry density== 1631.,1631.
        End layer
    end material
    • Add the following section to the PTM control file beneath the current definition of the particle point release location.
    !Contaminated Sediment
    seed particles== polygon
        particle groups== sediment
        polygon file== ..\bc_dbase\wwtp_poly.csv
        Vertical coordinate type== depth
        Vertical distribution file== ..bc_dbase\vert_distr.csv
        group mass== 1000
    end seed
    • Within the 'Global Commands' section add the following lines to specify the bed roughness model and parameters to control bed shear stress as well as limiting erosion and deposition when flow depths are low:
    !Sediment Transport COMMANDS (required if a particle group interacts with bed)
    bed roughness model== ks
        bed roughness parameters== 0.01,0.01 !ksc, ksw
    !Depth Limit Commands
        erosion depth limits== 0.01,0.05
        deposition depth limits== 0.01,0.05
    • Add sediment to the output groups within the ptm_netcdf output. Also add state_age to the list of output parameters.
     output== netcdf
        output groups== microplastics, sediment
        output interval== 1800
        output parameters== uvw, depth, water_depth, uvw_water, state_age
     end output

    Polygon input

    In the previous model we applied a time-varying point source. In this example, we will apply a group mass to the a polygon at the beginning of the simulation. Firstly we will define the polygon to which the particles will enter the model and secondly we will define their vertical distribution within the water column.

    • In the bc_dbase folder, create a sediment_polygon.csv file. Add two columns called X,Y and populate with the following values.
    X Y
    159.124 -31.413
    159.127 -31.413
    159.127 -31.410
    159.124 -31.410

    This defines the vertices of the polygon using X, Y co-ordinates to where we will apply the particles.

    • Save and close the sediment_polygon.csv file.
    • In the same folder, create a Sediment_vertical_Ditribution.csv file. We will use this to define the distribution of our particles within the water column. The data takes the form of a Depth vs weight table with depth being the depth from the surface (also possible to use height, elevation and sigma level)and weight defines the relative distribution of the particles in the vertical profile.
    Depth Weight
    0 0
    1.4 0
    1.5 1
    2 1
    2.1 0
    9999 0

    This defines the distribution of the particles within the water column. In this instance are particles will be applied to the water column at a depth between 1.5m and 2.1m from the water surface.

    • Save and close the file.

    Update the TUFLOW FV Control File

    • Copy and paste PT_000.fvc as PT_001.fvc.
    • Update the reference to the updated PTM control file to PT_001.ptmfv

    In the output section, add PTM_2 and PTM_BED_2 in the netcdf output parameters.

    output== netcdf
       output parameters== h,v,d, PTM_1, PTM_2, PTM_BED_2
       output interval== 3600
    end output

    This will allow us to see the concentration of the contaminated sediment both within the water depth and the bed within the map output.

    • Save and close the file.
    • Update the reference to the updated TUFLOW FV control file, PT_001.fvc within the batch file, comment out the previous run command and run the PT_001.fvc simulation.

    Review the Results in QGIS

    • Open the map output and particle netcdf files within QGIS using the TUFLOW Viewer plugin tool.
    • Set the map output theme to include flow depth and the velocity vectors.
    • Right click on the PT_001_ptm.nc within the layers panel and in ‘Styles’ select the ‘stat’ attribute.

    The polygon input of particles should be visible at the beginning of the simulation.

    Polygon input.PNG

    In this run we now have two sets or particles, our buoyant microplastics from the first exercise and our decontaminated sediment that we’ve added within the second exercise. The contaminated sediments are free to deposit and erode throughout the simulation. By animating the results you will see that the particles added appear in suspension within the water column at the beginning of the event but start to deposit onto the ‘Bed’ Sediment.

    Particles styles 3.png

    After a while, the majority of the particles have deposited upon the bed although some particles have been transported and deposited downstream.

    Particles styles 4.png

    Around 22:00 on 1/05/2011, the particles that were on the bed are picked up and suspended into the water column due to erosion.

    Particles styles 5.png

    • Assess the map output Particle Group 2 Concentration. This will show concentrations at the beginning of the simulation. You can use the curtain plot tool to assess the distribution of the concentration through a cross-section. This shows the highest concentrations in the layers with a depth of between 1.5m and 2m.

    3D Concentration.PNG

    • Plot the Map Output, particle group 2 bed concentration. This shows increasing concentration within the bed on the outer banks of the channel close to where the contaminated sediment was added to the simulation.


    This tutorial has introduced the particle tracking functionality with TUFLOW FV, including how to set up models and review outputs, both Eulerian and Langrangian, within the QGIS TUFLOW Viewer plugin. Further functionality allows the input of moving point sources as well as applying particle motility to allow particles to move of their own accord without any hydrodynamic (or wind) forcing. This is useful where particle tracking is used to simulate animal migration.