First applications
Before you get started with your first applications, you should read the installation and preparation instructions for your operating system, if you haven’t already done so.
This is especially recommended for beginners who have little experience with Python and the input console.
Instructions are provided for Windows and Ubuntu and should be applicable to other operating systems with minor tweaks.
1 Setup without OpenGeoSys
Here, we explain how to run a simple pyMANGA setup.
In this setup, 10 black mangrove trees grow at seawater salinity.
Tree growth follows the BETTINA approach.
Model output is written to the folder ‘ModelOutput’ in the same directory.
More examples can be found here and in our benchmark gallery.
After following the installation section, pyMANGA is installed and tested by running py MANGA.py -h in the command line. We can now provide a project file to pyMANGA and execute an example setup.
To do so, you need to add the path to the pyMANGA project file as input.
For Windows type:
py -3.7 MANGA.py -i Benchmarks/ExampleSetups/FirstApplication/example_setup.xml
respectively for Ubuntu:
python MANGA.py -i Benchmarks/ExampleSetups/FirstApplication/example_setup.xml
-i refers to the index or path of the file in which the input to be used for this example is defined.
This code calls pyMANGA with the control file ’example_setup.xml’. For detailed information on the structure of control files see Control File or the pyMANGA documentation.
2 Setup with OpenGeoSys
Here, we explain how to run the complex pyMANGA setup ‘OGS3D_SAZOI_BETTINA’ from our benchmark gallery. More information on our benchmarks can be found here, and a detailed OGS setup can be found here.
This setup uses OpenGeoSys (OGS), which is a scientific open source project for the development of numerical methods for the simulation of thermo-hydro-mechanical-chemical (THMC) processes in porous and fragmented media. To use OGS, you need to download and install it. Again the installation is different for windows and ubuntu.
Installing OGS
To use OGS, you have to download and install it first. pyMANGA has been tested with OGS version 6.4.0. On this homepage you will find several variants of OGS version 6.4.0. Select the variant with ‘Python bindings’ and ‘Utilities’.
Please make sure that you download exactly this version of OGS.
Unzip the archive and move all folders it contains to:
./ResourceLib/BelowGround/Individual/OGS/
The files must be located directly in this folder.
To check if OGS is executable on your computer, open a terminal in the pyMANGA root directory and enter the following:
./ResourceLib/BelowGround/Individual/OGS/bin/ogs.exe
If OGS runs correctly, you will get the following output:
PARSE ERROR:
Required argument missing: project-file
Brief USAGE:
./ogs [--enable-fpe] [--unbuffered-std-out]
[--config-warnings-nonfatal] [-l <LOG_LEVEL>] [-o <PATH>] [-r
<PATH>] [--] [--version] [-h] <PROJECT_FILE>
If this does not work, first check if you have installed the Python module “vtk” in version 9.2.2.
Please read the section about installing pyMANGA on Ubuntu. If you encounter insurmountable problems at this point, please contact us.
First applications of pyMANGA with OGS
By opening a terminal in the pyMANGA main level and entering the following command, you can start the next application example:
python3 MANGA.py -i Benchmarks/ExampleSetups/OGSExampleSetup/OGS3D_SAZOI_BETTINA.xml
or
py MANGA.py -i Benchmarks/ExampleSetups/OGSExampleSetup/OGS3D_SAZOI_BETTINA.xml
Note: The computation time when using OGS can take several hours. You can reduce this time by opening
.\Benchmarks\ExampleSetups\OGSExampleSetup\OGS3D_SAZOI_BETTINA.xml
and changing the line 22 to
<delta_t_ogs> 604800 </delta_t_ogs>
This is the time step length (in seconds) that indicates how long the groundwater flow model calculates before extrapolating the rest of the BETTINA time step. From the results, the pore water distribution is extrapolated under steady state assumptions. Therefore, this parameter must be used very carefully, but it is a means to significantly reduce the computation time.
