... | @@ -10,6 +10,8 @@ The first part is the path to the OpenSimRoot executable. `-f `tells OpenSimRoot |
... | @@ -10,6 +10,8 @@ The first part is the path to the OpenSimRoot executable. `-f `tells OpenSimRoot |
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After the simulation is complete, the "OutputTest" directory contains (depending on what was specified) files called `tabled_output.tab`, `warnings.txt`, some .vtu files and some .pvd files. The `tabled_output.tab` contains the values of variables like the nitrogen depletion, the dry weight of the plant and the total root length on each day. `warnings.txt` has an obvious meaning. The .vtu and .pvd files contain the geometric root model and can be visualized with ParaView.
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After the simulation is complete, the "OutputTest" directory contains (depending on what was specified) files called `tabled_output.tab`, `warnings.txt`, some .vtu files and some .pvd files. The `tabled_output.tab` contains the values of variables like the nitrogen depletion, the dry weight of the plant and the total root length on each day. `warnings.txt` has an obvious meaning. The .vtu and .pvd files contain the geometric root model and can be visualized with ParaView.
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To do this, open ParaView and open `VisualizationRoots.pvd`, then click "Apply" in the "Properties" window on the left. You will probably not see anything because at time t=0 there is no root structure yet! Click the "Play" button in the top bar and you will see the root structure as it is growing. By default, the root structure is uniformly coloured so this only shows us the topology of the root system. To see more relevant information, in the properties window, under the header "Coloring", select something else instead of "Solid Color" to see the property you selected coloured (in the example below I chose rootClassID). By default the "Color Space" option (in the "Color Map Editor" on the right) is set to "Diverging", I prefer RGB but see what suits you the best. You can choose a different colour mapping and alter the sensitivity by adjusting the circles and curve in the "Mapping Data" section on the right. Double click on a circle in the bar at the bottom to choose a different colour.
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To do this, open ParaView and open `VisualizationRoots.pvd`, then click "Apply" in the "Properties" window on the left. You will probably not see anything because at time t=0 there is no root structure yet! Click the "Play" button in the top bar and you will see the root structure as it is growing. By default, the root structure is uniformly coloured so this only shows us the topology of the root system. To see more relevant information, in the properties window, under the header "Coloring", select something else instead of "Solid Color" to see the property you selected coloured (in the example below I chose rootClassID). By default the "Color Space" option (in the "Color Map Editor" on the right) is set to "Diverging", I prefer RGB but see what suits you the best. You can choose a different colour mapping and alter the sensitivity by adjusting the circles and curve in the "Mapping Data" section on the right. Double click on a circle in the bar at the bottom to choose a different colour.
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See the picture below for a sample visualization where the different colours indicate different types of roots (primary, seminal, lateral). |
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It is also possible to see the depletion of nutrients in the soil, assuming OpenSimRoot was told to output this, by also opening the relevant output file. More on this will follow as soon as I figure it out myself.
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See the following picture (it's a pdf) for a sample visualization where the different colours indicate different types of roots (primary, seminal, lateral).[test.pdf](/uploads/3e83438192d60b2145ee1fa40b96fddf/test.pdf) |
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