Module 2: Overview
The transport flag iupwind_t=0 signals the Eulerian-Lagrangian method of transport. Because it is not conservative for salt, this numerical method is not common in practice. Instead, we want to use the hybrid second order (TVD, iupwind_t=2) finite volume scheme with upwind being preferred in water shallower than 6m total depth. In the simplified grid example, which has a sea level of about a meter above the bathymetric datum, a total depth of 6m will occur at about 5m nominal bathymetric depth.
Warning
The information on iupwind_t variable needs to be updated
Setting iupwind_t=2 is a single flag change in param.nml. However, because it is a hybrid scheme, SCHISM expects a property file called tvd.prop of 0 and 1 values describing where TVD can be used potentially. Keep in mind, even with this file TVD will only be used if H > 6m.
The .prop file format just pairs element numbers and values. We are controlling TVD entirely with depth, so we just need a prop file full of ones. There are 4636 elements in the domain (you can get this number from first number on the second line of hgrid.gr3). So this file will be two columns, the first of which will be the numbers 1 to 4636 and the second of which will be the number 1:
The task is also a soft introduction to the preprocessor:
Navigate to the m2_preprocessor folder (./Module_Data/m2_preprocessor”)
Inspect the directory. The launch file for the preprocessor is called input.yaml in all our examples. There are two variants of the simple bay mesh, which differ only in depth. We will use the 16m version this time. Go to the “mesh” section of input.yaml and following the amount of indentation in the file (preferably using spaces), set the mesh input file to hgrid_16m.gr3.
mesh_inputfile: hgrid_16.gr3
We want to tell the preprocessor to build a .prop file based on a polygon. So at the outer level of indentation add:
prop:
tvd.prop: !include tvd.yaml
Now we need to create a trivial tvd.yaml, which will contain a default and one polygon. Because the default will assign 1.0 to anything we miss, the actual specification of the polygon doesn’t matter. However, we will add one that amply contains the whole domain (the “All” part is just a label). Here are the contents of tvd.yaml
default: 1
polygons:
- attribute: '1'
name: All
vertices:
- [0.0, -100000.0]
- [100000.0, -100000.0]
- [100000.0, 100000.0]
- [0.0, 100000.0]
Now you should be able to run the preprocessor. You will either need to be in the schism conda environment created in the Getting Started section or you’ll need to specify the script location.
With conda (Preferred):
conda activate schism
cd <PATH TO M2_PREPROCESSOR FOLDER>
prepare_schism input.yaml
Without conda:
Navigate to the m2_preprocessor folder in your file explorer. Type “cmd” in the navigation bar to open a command prompt terminal in this directory. If you downloaded schimpy and placed it in the scripts folder (see the Python section of Getting Started) you should be able to do the following command: .. code-block:: console
python ../../scripts/schimpy-master/schimpy/prepare_schism.py input.yaml
At this point, you have recreated the Hello SCHISM tutorial with an added prop file. Only a few more changes are needed. Locate and open the files param.barotropic.nml. Set iupwind_t = 2 and rnday=5 in param.barotropic.nml. This changes the transport method to TVD2 and the runtime in days to 5.
Then save the param.barotropic.nml file as param.nml and the bctides.in.barotropic file as bctides.in. SCHISM is looking for a specific files called param.nml and bctidess.in, so depending on wether you’re running 2D or 3D you’ll want to save the barotropic/baroclinic param file out as those file names, or use symbolic links.
Launch the run (note, you’ll need the windows build of SCHISM to be set in your system Path):
mpiexec -np 8 pschism_PREC_EVAP_GOTM_TVD-VL.exe 4