Substance files - Delwaq - Delft3D
intro story DELWAQ
DELWAQ is the engine of the D-Water Quality and D-Ecology programmes of the Delft3D suite. It is based on a rich library from which relevant substances and processes can be selected to quickly put water and sediment quality models together.
The processes library covers many aspects of water quality and ecology, from basic tracers, dissolved oxygen, nutrients, organic matter, inorganic suspended matter, heavy metals, bacteria and organic micro-pollutants, to complex algae and macrophyte dynamics. High performance solvers enable the simulation of long periods, often required to capture the full cycles of the processes being modelled.
The finite volume approach underlying DELWAQ allows it to be coupled to both the structured grid hydrodynamics of the current Delft3D-FLOW engine and the upcoming D-Flow Flexible Mesh engine (1D-2D-3D) of the Delft3D Flexible Mesh Suite (or even other models such as TELEMAC).
'DELWAQ in open source' is our invitation to all leading experts to collaborate in further development and research in the field of water quality, ecology and morphology using Delft3D. Feel free to post your DELWAQ related questions or comments in this dedicated forum space. If you are new to DELWAQ, the tutorial (in the user manual) is a good place to start. A list of DELWAQ related publications is available here.
** PLEASE TAG YOUR POST! **
As the demand for example substance files is growing, we decided to use this thread as a collection point.
If you feel like sharing your substance files, just reply to this post with some basic information such as:
- quick description of subfile content
- what problems did you adress
- what kind of system did you apply it to (lake, coastal, estuarine, ...)
- anything you judge useful for other users
Here's an overview of all subfiles submitted so far. It will be updated as more are added.
Name Topic Original post
coli_04 coliform bacteria [url=http://oss.deltares.nl/web/delft3d/delwaq/-/message_boards/view_message/382457#_19_message_382457]here[/url]
oxy_general_04 dissolved oxygen [url=http://oss.deltares.nl/web/delft3d/delwaq/-/message_boards/view_message/382457#_19_message_382457]here[/url]
sed_1fraction_04 suspended sediment [url=http://oss.deltares.nl/web/delft3d/delwaq/-/message_boards/view_message/382457#_19_message_382457]here[/url]
bloom_basic BLOOM greens, diatoms & blue-greens [url=http://oss.deltares.nl/web/delft3d/delwaq/-/message_boards/view_message/382407#_19_message_487575]here[/url]
bloom_ulva BLOOM basic with ulva [url=http://oss.deltares.nl/web/delft3d/delwaq/-/message_boards/view_message/382407#_19_message_487575]here[/url]
- coliform bacteria (coli_04)
- dissolved oxygen (oxy_general_04)
- suspended sediment (sed_1fraction_04)
I just checked in the manual and saw that there is the possibility of including floculation in WAQfor cohesive sediment.
However when I added the 'CrSS'critical sediment concentration for floculation as an active processe in both .sub and .0 files
in .sub I added:
description 'contant for concentration effect on floculation'
description 'critical concentration of SS for floculation'
and in the .0
"abbrev 'CrSS' name 'critical concentration of SS for floculation' active 1"
name 'contant for concentration effect on floculation'
input_process ' '
name 'critical concentration of SS for floculation'
input_process ' '
I get the error:
" Found -P command line switch
WARNING: activated process not found in process definition file
process ID: CrSS "
Do you have an example file for floculation?
Editing *.sub files by hand files is quite error prone. You should either edit your input file directly or use the PLCT GUI to create your *.sub file (which will then be read by the Delwaq GUI to produce the input file).
Here's a quick and dirty set for one substance 'IM1'. You can load the *.0 file in the PLCT GUI to adapt it.
thanks for the reply, I had changed it in the .sub file because I could not find it in my PLCT Gui the
substance_group 'Particulate inorganic matter'
that I still don`t have it and this is the reason that I could not set the flocs.
Do you know if it is a closed library?
If you don't have a group called 'Particulate inorganic matter' in yout PLCT you might be using an older version (the substance groups have been reorganized somewhere in november 2013).
In that case you should still be able to configure similar processes in the PLCT:
- open the PLCT
- select group 'Suspended matter'
- select substance 'inorganic matter (IM1)'
- check process 'Sedimentation IM1 (Sed_IM1)' and click the 'Edit...' button next to the checkbox
- set 'sedimentation velocity IM1 (VSedIM1)' from constant to CalVS_IM1 and click the bottom-left OK button
- click the bottom-left OK button again (now in the 'Select Processes' window)
- at the bottom of the 'Make selection of substance groups' window click the 'Edit...' button next to 'Extra processes'
- you now see 'Specify...' next to the CalVS_IM1 process you activated previously, click on it
- you now see several floculation related parameters (CrSS, nIM1). Set them to editable so you can modify their value in the WAQ GUI.
- you also see that V0SedIM1 is set to NODEFAULT, which requires you to set it to editable as well
- click OK
- click OK
- click READY
- Save your sub file.
If you update Delwaq to a more recent version, the procedure will be the same except that IM1 will be located in the substance group 'Particulate inorganic matter'
thanks very much for the detailed instructions, I run a test case and the settings does change the sediment concentration
A while ago you were mentioning of providing an example coastal-open ocean primary production .sub files. Any news on that matter?
Yes, the example files I got were used with an older version of Delwaq, hence some processes are not present in the current processes library.
As soon as these issues are fixed, the files will be uploaded.
A while back ago I wondered whether an example open ocean primary productivity example substance files would be released. Is there any input about the matter? I already have a solid hydrodynamics run for the Mediterranean and it would be great if I can couple it with a basic eco model with several primary producers.
They will be uploaded later today.
Sorry for all delays, but finally here are two examples of BLOOM setups using the GUI. I've created .0+.sub files using the PLCT. If you open the .0 file in the PLCT you should be able to modify the model yourself.
Furthermore I setup test cases using examples\06_delwaq from the Delft3D oss-repository (you could also download the hydrodynamics from below). Please notice that some of the parameters in these test case setups are different from the default values in the sub-files.
The basic setup contains green algae, diatoms and blue green algae. In the other example Ulva are added, including sedimentation/resupension of Ulva. There was a problem with the sedimentation/resupension of Ulva that only has been resolved recently, so if you want to use this second example, please use a build of DELWAQ with revision 4051 or later.
I have successfully loaded the bloom_basic.sub file in the precompiled free gui in windows. I wanted to make some changes by using the .0 file. The thing is, i do not have a compiled delft3d in windows. I have it on my linux machine. I was planning to send the input file to linux machine.
From the extracted files of gui in windows, the plct library did not load with some files missing (files did not show/fit in the window, i do not know which). So i copied my bloom.spe, bloominp.d09, proc_def.dat, proc_def.def files to waq/default folder. The plct loaded fine, but when i try to load your .0 file, no errors but no response either. Basically, the problem is that i cannot load your .0 file, and cannot make modifications.
I have the tag3185 version compiled in my linux. Is this a version incompatibility issue? or something else is missing in my windows gui?
You can very well use the windows GUI's to prepare the input for running on Linux. So that shouldn't be a problem.
I think that you copied all the files correctly. Could it be that you try to start the PLCT directly by click on the executable? Because you should start it from the Deflt3D menu (c:\Program Files (x86)\Deltares\Delft3D 4.01.00\win32\d3d_menu.bat in a default installation). Oh, and start it in ECO mode if you want to work with BLOOM.
If you have quite an older version of the open source GUI it could be that you have to run another batch-file to make some modifications to the PLCT-ini files, maybe that could be the problem. Check the instaaltion document that came with your version of the GUI.
The way i followed is this.
I saved a random .sub file from gui. Copied its version number to your .0 and modifed the description of the parameter 'CONSELAC' in reference to mine. Seemed to work. What i realised in my runs is that, even though the layer S1 is active in your .sub file, there is no interaction with the water column and the S1 layer. Maybe i am missing something.