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Commit c509401a authored by Laura Meier's avatar Laura Meier
Browse files

Update README.md

parent 2cad1f3c
...@@ -12,7 +12,7 @@ Eclipse IDE for Java Developers (2019-09 R, 4.13.0) ...@@ -12,7 +12,7 @@ Eclipse IDE for Java Developers (2019-09 R, 4.13.0)
Open model GUI via: Open model GUI via:
1. Run Main.java (in ...\MODEL_MASTIFF\Mastiff\Java model project\src\application) as Java application (e.g. via Eclipse IDE) 1. Run Main.java (in ...\MODEL_MASTIFF\Mastiff\Java model project\src\application) as Java application (e.g. via Eclipse IDE)
2. Double-click runMASTIFF.jar (if it does not open, check in 'Registrierungs-Editor' under 'Computer\HKEY_CLASSES_ROOT\jarfile\shell\open\command' the path points on the right java version) 2. Double-click [runMASTIFF.jar](https://git.ufz.de/oesa/mastiff/-/blob/main/runMASTIFF.jar) (if it does not open, check in 'Registrierungs-Editor' under 'Computer\HKEY_CLASSES_ROOT\jarfile\shell\open\command' the path points on the right java version)
3. via command line (cmd): 'java -jar runMASTIFF.jar' (check 'java -version' for version) 3. via command line (cmd): 'java -jar runMASTIFF.jar' (check 'java -version' for version)
...and choose scenarios options via GUI. ...and choose scenarios options via GUI.
...@@ -24,19 +24,19 @@ Open model GUI via: ...@@ -24,19 +24,19 @@ Open model GUI via:
Mastiff is modular in design. Therefore, you can switch on and off different processes in the GUI Mastiff is modular in design. Therefore, you can switch on and off different processes in the GUI
interface, including options/functions/processes that are not included in ODD protocol yet. interface, including options/functions/processes that are not included in ODD protocol yet.
Left side: Left side:
- Simulation parameters (amount segments, simulation time in months), initialisation for biofilm biomass and abundances (x:y defines the range, e.g. increasing intial abundance, if x = y every segmen has the same abundance) - Simulation parameters (amount segments, simulation time in months), initialisation for biofilm biomass and abundances (x:y defines the range, e.g. increasing intial abundance, if x = y every segmen has the same abundance)
- Button for intialize parameters (save parameters) and Button for run the model - Button for intialize parameters (save parameters) and Button for run the model
- Number runs, Name Scenario, Path in which the output should be saved - Number runs, Name Scenario, Path in which the output should be saved
Middle: Middle:
- Environmental parameters: air temperature, land use profile by defining land use types for each segment (options: individual by A-F, sequence (Holtemme), load file), minimum nutrient factor (min eN) - Environmental parameters: air temperature, land use profile by defining land use types for each segment (options: individual by A-F, sequence (Holtemme), load file), minimum nutrient factor (min eN)
- Biofilm parameters (growth rate, B0) and compartments (epsilon, my), Eutrophication parameters (thresholds beta0 and beta 1, pfmax, betaf) - Biofilm parameters (growth rate, B0) and compartments (epsilon, my), Eutrophication parameters (thresholds beta0 and beta 1, pfmax, betaf)
- Species characteristics: Mortality(mortality rates, scale, drift mortality), Reproduction (offspring, dispersal probability and distances) - Species characteristics: Mortality(mortality rates, scale, drift mortality), Reproduction (offspring, dispersal probability and distances)
- Trohic interaction - Trohic interaction
Right side: Right side:
- Stressors: constant input of herbicides and insecticides in segments with agriculture and WWTP, input of pesticides by event - Stressors: constant input of herbicides and insecticides in segments with agriculture and WWTP, input of pesticides by event
- Output Files (see OUTPUT/RESULT FILES) - Output Files (see OUTPUT/RESULT FILES)
Table (lower right): Table (lower right):
- segment specific parameters (number, land use type, maximal shading factor, epsilon, my, drift mortality, nutrient factor, biofilm biomass, abundance for each species, constant herbicide/insecticide input, beta1) - segment specific parameters (number, land use type, maximal shading factor, epsilon, my, drift mortality, nutrient factor, biofilm biomass, abundance for each species, constant herbicide/insecticide input, beta1)
-> double-click: change a parameter in a segment individually -> double-click: change a parameter in a segment individually
...@@ -53,7 +53,7 @@ Press Run multiple. ...@@ -53,7 +53,7 @@ Press Run multiple.
## OUTPUT/RESULT FILES ## OUTPUT/RESULT FILES
Output files could be choosen on the mid right. Possible are air temperature, water temperature, biofilm biomass, biofilm condition, probability of filamentous algae (pf), abundance of each species, demand of each species, Available feed, inflow and outflow of organisms, dispersal loss, abundance in biomass, diffusive herbicide and insecticides, event herbicide and insecticides. Output files could be choosen on the mid right. Possible are air temperature, water temperature, biofilm biomass, biofilm condition, probability of filamentous algae (pf), abundance of each species, demand of each species, Available feed, inflow and outflow of organisms, dispersal loss, abundance in biomass, diffusive herbicide and insecticides, event herbicide and insecticides.
You can find result files starting with .jar in [MODEL_MASTIFF\Data\Results](https://git.ufz.de/oesa/mastiff/-/blob/main/runMASTIFF.jar) You can find result files starting with [.jar](https://git.ufz.de/oesa/mastiff/-/blob/main/runMASTIFF.jar) in MODEL_MASTIFF\Data\Results
You can find result files starting manually in MODEL_MASTIFF\Mastiff\Java model project\data\Results You can find result files starting manually in MODEL_MASTIFF\Mastiff\Java model project\data\Results
...@@ -61,3 +61,5 @@ You can find result files starting manually in MODEL_MASTIFF\Mastiff\Java model ...@@ -61,3 +61,5 @@ You can find result files starting manually in MODEL_MASTIFF\Mastiff\Java model
A few options/function shown in GUI are implemented and tested but not relevant for publications and not mentioned in ODD. For further studies interfaces are build (e.g. predator 'Stonefly' eating on grazers, pesticide module) but not coupled or tested sufficiently. A few options/function shown in GUI are implemented and tested but not relevant for publications and not mentioned in ODD. For further studies interfaces are build (e.g. predator 'Stonefly' eating on grazers, pesticide module) but not coupled or tested sufficiently.
## ODD protocol
A complete, detailed model description, following the ODD protocall is provided [here](https://git.ufz.de/oesa/mastiff/-/blob/main/Model%20description.pdf)
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