@@ -3,7 +3,8 @@ In this exercise you will complete the setup of a case to run with SERGHEI. We w
This tutorial assumes that you have built SERGHEI and have managed to run some simple test case before.
# 1. Get some data for this case
Clone the GitLab repository which contains the basic data for this case, into a directory of your choice.
Clone the GitLab repository which contains the basic data for this case, into a directory of your choice. A suggestion is to use `$HOME/monaiTsnuami`.
The GitLab repository is [here]().
# 2. What do I need to set up?
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@@ -14,8 +15,39 @@ SERGHEI requires, a minimum set of 3 input files:
However, many other files can be defined. A tutorial on the input files is [here](https://gitlab.com/serghei-model/serghei/-/wikis/User-Guide/Quick-tutorial:-setup-a-model).
## What did you get already?
In the data which you cloned you will find the `dem.input` file with the experimental scale bathymetry and topography of the affected region. This is an ASCII raster file. You can inspect it by simply opening it as a text file.
Generating an appropriate DEM is a job in itself and will not be discussed here.
You also get a `wave.input` file containing a time-series definition of the input wave which serves as a forcing boundary and drives the tsunami into the computational domain.
You also get a `wave.input` file containing a time-series definition of the input wave which serves as a forcing boundary and drives the tsunami into the computational domain. You can also inspect this text file, which has a very simple and human readable structure.
## What's missing?
For all the points herein, you can refer to the aforementioned [Quick tutorial: setup a model](https://gitlab.com/serghei-model/serghei/-/wikis/User-Guide/Quick-tutorial:-setup-a-model#Simulation-Control) page for details.
To fully define this case we **don't need all** of the possible input files, only a few:
1.`parameters.input`
2.`sw.input`
3.`extbc.input`
## First setup
Let's first setup `parameters.input` and `sw.input`, which are mandatory. Remember to put these files inside the `input` directory.
### Simulation control `parameters.input`.
The simulation duration should be 30s, with a CFL value of 0.5, spatial output with a frequency of 1s and observation output frequency of 0.25s.
We will run this test on a single compute node, therefore ***no domain decomposition*** is necessary in either the x nor y directions. Consequently `parNx` and `parNy` should be 1.
We will use `NETCDF` output, default boundaries should be `REFLECTIVE`, and a reasonable screen output is between 200-1000.
### Shallow water model control `sw.input`
The initial conditions for the experiment are those of a quiescent (i.e., zero velocity) water surface at sea level. In the typical shallow water variable naming `h` is water depth, `z` is the elevation of the bed relative to some arbitrary datum, and therefore `h+z` is the elevation of the water surface relative to the same datum. This datum must be consistent with that of the DEM. In the DEM `z=0` is the mean sea level. With this information, set `initialMode` and `initialValue`.
This benchmark typically uses Manning's friction law, with a roughness value of 0.01. Set this up in the file. Finally, because of the small scale of the experiment, and because in a tsunami we are particularly interested on the advancement of the wave over dry land, we will use a dry depth tolerance of 0.
### Do a first run
Let's try to launch the job. Recall that the command looks like this
