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Modelling sediments for Algae BLOOM

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Fernando Aguilar, modified 4 Years ago.

Modelling sediments for Algae BLOOM

Youngling Posts: 22 Join Date: 2/7/13 Recent Posts
Dear all,

I'm modelling algae bloom in a reservoir and I need to add more features, like sediments. As I understood, the more complete way to do so is not S1/S2 nor SWITCH, but the third way.

I have read "D-Water_Quality_Sediment_Water_Userr_Manual" but is not very clear for me. Let's give you an example:

- I would like to model Phosphorus in water and sediment. First of all I modelled Phosphorus as a process in water, but no sediment is added.

- I have a map (.xyz) with phosphorus concentrations in bed layer. I would like to include it in my model.

So, my questions are:

- How can I definde that I want to model phosphorus in sediment? Is it already defined in my substance file?
- How can I add a input for Phosphorus concentrations as a map?
- Parameters such as sediment porosity, bioturbation, etc. Are mandatory?

If you have an example of a model with this features it would be very useful for me.

Thanks in advance,

Fernando
Mathieu Chatelain, modified 4 Years ago.

RE: Modelling sediments for Algae BLOOM

Padawan Posts: 28 Join Date: 12/13/12 Recent Posts
Hi Fernando,
if you want to model phosphorus in the sediment, you need to add a sediment grid to your water grid. This feature isn't supported by the Delwaq user interface yet, and has to be done manually by editing the INP-file. To achieve that, you can start to set-up a water model using the GUI (which you probably have done already), and then edit the INP-file by following what is described in "D-Water_Quality_Sediment_Water_User_Manual". Just add the relevant sections in block 3, after the number of water segments. It should look like:

MULTIGRID
  NOLAY 4 ; sigma-layer with 4 layers (after aggr)
 
  SUBGRID 'water-grid'
  INCLUDE '../../grids/water-grid.grd'

  SUBGRID 'water-zone'
  INCLUDE '../../grids/water-zone.grd'
 
  BOTTOMGRID 'sediment-grid'
  REFERENCEGRID 'Base grid'
  INCLUDE '../../grids/sediment-grid.grd'

  BOTTOMGRID 'sediment-zone'
  REFERENCEGRID 'sediment-grid'
  INCLUDE '../../grids/sediment-zone.grd'
 
  BOTTOMGRID 'sediment-default'
  REFERENCEGRID 'sediment-grid'
  INCLUDE '../../grids/sediment-default.grd'
   
  NOBOTTOMLAY INPUTGRID sediment-default 7 ; number of sediment layers
END_MULTIGRID


Follow the instructions in the manual to define the various GRD-files.

Then, you need to define boundary conditions (block 5) and initial conditions (block 8) in both the sediment and the water column. Again, best way is to follow the manual and come back here if you run into troubles. Block 8 is where you can use your phosphorus map as an initial condition in the sediment, yielding something like:

INITIALS PO4 INPUTGRID sediment-default DATA "your_file.inc"


Finally, you need to include processes and parameters linked to the sediment substances (block 7). As you mentioned, sediment porosity (PorInp), bioturbation (TURCOEF), bio-irrigation (DIFCOEF), layer thicknesses (FixTh), cells surface (SURF) and depth (bottomdept) are mandatory to properly define vertical transport in the sediment grid (note that there is no horizontal transport in the sediment). They can be defined as constants, parameters (i.e. space-varying time-constant) or segment functions (space-varying time-varying) on the sediment grid. To give you an example:

CONSTANTS 'minth'            DATA 1.00000e-006 ; minimum sediment layer thickness
PARAMETERS 'fixth'    INPUTGRID  'sediment-default' DATA 0.001 0.002 0.004 0.033 0.06 0.1 0.2 ; layers thicknesses
PARAMETERS 'maxth'    INPUTGRID  'sediment-default' DATA 0.001 0.002 0.004 0.033 0.06 0.1 0.2 ; max layers thicknesses
PARAMETERS PORINP     INPUTGRID 'water-zone'        DEFAULTS   1.0 ; porosity water
PARAMETERS PORINP     INPUTGRID 'sediment-default'  DEFAULTS   0.8 ; porosity sediment
PARAMETERS pH         INPUTGRID 'water-zone'        DEFAULTS   8.1 ; ph water
PARAMETERS pH         INPUTGRID 'sediment-default'  DEFAULTS   7.5 ; ph sediment
SEG_FUNCTIONS TurCoef INPUTGRID 'sediment-default' DATA INCLUDE '../../sediment/turcoef.inc' ; biorturbation
SEG_FUNCTIONS DifCoef INPUTGRID 'sediment-default' DATA INCLUDE '../../sediment/difcoef.inc' ; bioirrigation


Hope that helps,
Cheers,
-Mathieu.
FA
Fernando Aguilar, modified 4 Years ago.

RE: Modelling sediments for Algae BLOOM

Youngling Posts: 22 Join Date: 2/7/13 Recent Posts
Thank you very much Mathieu, I think it's very helpful. I'm trying to do a simple example with your tips, so I probably ask for more help soon.

Thank you!

Fernando
FA
Fernando Aguilar, modified 4 Years ago.

RE: Modelling sediments for Algae BLOOM

Youngling Posts: 22 Join Date: 2/7/13 Recent Posts
Hi again,

I have a problem with the first step of defining grids. By default, the number of segments I get when I create the .inp file with the GUI is 92190. However, when I create the .dwq file with DIDO tool i get a file with 11590 segments. Mi grid has 122 x 95 cells and it is a Z model with 35 layers. What I am doing wrong?

Thanks in advance,
Mathieu Chatelain, modified 4 Years ago.

RE: Modelling sediments for Algae BLOOM

Padawan Posts: 28 Join Date: 12/13/12 Recent Posts
Hi Fernando,
I'm not very famliar with Z-layer models, but I believe the aggregation file gives you the number of segments (=11,590) in the top layer. Note that there is an extra keyword to give when defining the sediment grid for a Z-layer model. Keyword ZMODEL appears between the MULTIGRID statement and the number of layers in the water column (NOLAY):
MULTIGRID
; z layer model with 4 layers
ZMODEL
NOLAY 4


I would need more details of the error you get to help you further.

However, you might want to consider the S1/S2 approach before jumping into the layered-sediment approach. The latter is much more complex than the former, has a much higher computational burden, and is only required for very specific studies. Although the latter might be more "accurate" to depict vertical profiles in the top sediment layer, it will require a huge time-investment to set it up and parametrize it correctly (especially since it isn't supported by the GUI yet). Given the information you provided (number of segments, number of layers), and your original question, I'm not sure you would benefit from using the layered-sediment approach at the stage where you are right now.

Therefore, could you please clarify your intentions? You mentioned that you have a MAP file of phosphorus concentration in the sediment, and that you want to use it. But you also stated that you want to compute phosphorus concentrations in both the water column and the sediment. That seems a bit contradictory to me. Does this mean that you want to use the MAP as (a) initial phosphorus concentrations in the sediment or (b) forcing of a phosphorus sediment flux or (c) for something else?

If you choose the S1/S2 approach, you can then select the substances you want to model by using the Process Library Configuration Tool (e.g. AAPS1, adsorbed O-PO4 in layer S1).

Cheers,
-Mathieu.
FA
Fernando Aguilar, modified 4 Years ago.

RE: Modelling sediments for Algae BLOOM

Youngling Posts: 22 Join Date: 2/7/13 Recent Posts
Hi Mathieu,

Thanks again for your helpful answer.

Yes, it seems the aggregation file that DIDO exports is only for the first layer, but the model doesn't work corretly. I realised that the number of segment I need is 92190, that is the number of computational cells x number of layers (35). Active computational layers are not 122 x 95 actually.

I've also used NOLAY and ZMODEL keywords, so this was not the problem.

I understood S1/S2 was a little deprecated but maybe I should have a look on it if it works fine. On the other hand, I understood this multigrid approach is much more complete and accurate.

Finally, I want to use my map as (a), initial conditions file.

Thank you so much. I probably back here when a new problem comes ;)

Fernando
Mathieu Chatelain, modified 4 Years ago.

RE: Modelling sediments for Algae BLOOM

Padawan Posts: 28 Join Date: 12/13/12 Recent Posts
Hey Fernando,
I don't think it's fair to say that the S1/S2 approach is deprecated. I have been using it for the past 4 years, and it has been useful many times. It is true that the layered-sediment approach is more "elegant" if you're interested in early diagenesis in the sediment upper layer, and ergo in quantifying the resulting fluxes across the sediment-water interface. However, it requires a number of additional parameters (porosity, bioturbation, etc.) that may be very cumbersome to calibrate if you don't have the correct data. It also involves features that are not fully supported by Delwaq GUI, and therefore can be very time-consuming and error-prone. Additionally, layered-sediment approach requires longer computational time, forcing you to compromise on other parts (like aggregation). All in all, both approaches are valuable.

I hope you're making progress in your setup. Seems to me like the S1/S2 approach will already give you some good insight for your study. Nonetheless, for both approaches, you can use your spatial distribution of phosphorus as a forcing for your initial conditions (block 8), as I mentioned in my first post.

Cheers & happy modeling,
-Mathieu.