The pyMANGA project

pyMANGA is controlled via an xml file (see also this section). The content of the XML file to run this example is presented here. OGS specific adjustments and parameters are explained. A description of all other configurations can be found in the general documentation.

<?xml version="1.0" encoding="ISO-8859-1"?>
    <MangaProject>
        <random_seed>1</random_seed>
        <tree_dynamics>
        <aboveground_competition>
            <type>SimpleTest</type>
        </aboveground_competition>

For simulations with the underground concept OGSLargeScale3D, the following concept-specific tags must be defined:

•       the absolute path to the folder with all relevant OGS files (*ogs_project_folder*)
  

•       the OGS project file (*ogs_project_file*)
  

•       the source mesh (*source_mesh*)
  

•       the bulk mesh (*bulk_mesh*)
  

•       the time step length, which indicates how long the groundwater flow model calculates before the rest of the BETTINA time step is extrapolated(*delta_t_ogs*)
  

•       Script with Python boundary conditions (*python_script*)
  

The OGS project described in The OGS project must be specified as ogs_project_file. The previously defined python constraint is inserted under the name python_script. Definition and usage of time dependent boundary conditions are described in detail at the boundary conditions. delta_t_ogs defines for how long the groundwater flow model calculates before extrapolating the rest of the BETTINA time step. Creation of the required meshes is described in the groundwater domain section. The parameters seaward_salinity and landward_salinity are used in the python boundary conditions. Arbitrary parameters can be introduced here, as long as we use them again in our boundary condition definition. Spezifications of the tide, beginning with tide_ are used in the python boundary file.

    <belowground_competition>
        <type>OGSLargeScale3D</type>
        <ogs_project_folder>/ABSOLUTE/PATH/TO/pyMANGA/test/website_test/</ogs_project_folder>
        <ogs_project_file>ogs_projectfile.prj</ogs_project_file>
        <source_mesh>my_first_source.vtu</source_mesh>
        <bulk_mesh>my_first_model.vtu</bulk_mesh>
        <delta_t_ogs>500000</delta_t_ogs>
        <abiotic_drivers>
            <seaward_salinity>0.035</seaward_salinity>
            <landward_salinity>0.035</landward_salinity>
            <tide_daily_amplitude> 0 </tide_daily_amplitude>
            <tide_monthly_amplitude> 0 </tide_monthly_amplitude>
            <tide_daily_period> 60 * 60 * 12. </tide_daily_period>
            <tide_monthly_period> 60. * 60 * 24 * 31 / 2. </tide_monthly_period>
        </abiotic_drivers>
        <python_script>python_script.py</python_script>
    </belowground_competition>
    <tree_growth_and_death>
        <type>SimpleBettina</type>
    </tree_growth_and_death>
    </tree_dynamics>

For this example, we use an initial tree distribution.

    <initial_population>
        <group>
            <name>Initial</name>
            <species>Avicennia</species>
            <distribution>
                <type>GroupFromFile</type>
                <filename>/ABSOLUTE/PATH/TO/pyMANGA/test/website_test/initial_trees.csv</filename>
            </distribution>
        </group>
    </initial_population>
        <tree_time_loop>
        <type>Simple</type>
        <t_start>0</t_start>
        <t_end> 3e9 </t_end>
        <delta_t> 3e6</delta_t>
    </tree_time_loop>
    <visualization>
       <type>NONE</type>
    </visualization>
    <tree_output>
        <type>NONE</type>
    </tree_output>
</MangaProject>

The inital tree distribution is stored in a csv file and has the following content:

tree,	time,	x,	y,	r_stem,	h_stem,	r_crown,	r_root	
Initial_000000001,	0,	20,	5.0,	0.04,	3.5,	1.4,	0.7
Initial_000000002,	0,	22.5,	5.0,	0.04,	3.5,	1.4,	0.7