Deltares-research · Carsopre · Apr 13, 2022 · Mar 16, 2022 · Mar 16, 2022 · Mar 21, 2022
diff --git a/.idea/CoralModel.iml b/.idea/CoralModel.iml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/README.md b/README.md
@@ -1,75 +1,48 @@
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-
-# Official Documentation.
-Check our official GitHub pages documentation at [https://deltares.github.io/NBSDynamics/](https://deltares.github.io/NBSDynamics/).
-
-# CoralModel
-A biophysical model framework written in Python to make simulations 
-on coral development based on four environmental factors: 
-(1) light; (2) flow; (3) temperature; and (4) acidity. 
-For the hydrodynamics, the model can be coupled to Delft3D Flexible Mesh; 
-a hydrodynamic model developed at Deltares 
-([more information](https://oss.deltares.nl/web/delft3dfm)). 
-To enable this online coupling, certain configurations of Python are required 
-([more details](#python-code)).
-
-**Note:** This model is still in its beta and further development is still being done. 
-``coral_model_v0`` is used for the study and is rewritten (``coral_model``) to enhance collaboration.
-(The original version has not been written efficiently and is hard to follow for outsiders.)
-More information on this version control [here](#version-control).
-
-## Biophysics <a name="biophsics"></a>
-This biophysical model framework is part of the result of a 
-[master thesis](https://repository.tudelft.nl/islandora/object/uuid%3Ae211380e-3f92-4afe-b371-f1e87b0c3bbd?collection=education) 
-of which the key findings are published in *Environmental Modelling and Software*
-(the paper can be found [here](https://www.sciencedirect.com/science/article/pii/S1364815221001468?via%3Dihub)).
-
-The biophysical relations used in the biophysical model framework are mainly process-based, 
-where for the acidity the proxy of the aragonite saturation state is used. 
-Furthermore, both photo- and thermal-acclimatisation are included, 
-which result in a dynamic behaviour of the corals to their environment. 
-Hence, the corals are modelled such that they can adapt to changing environmental conditions over time.
-
-For more details on the biophysics, reference is made to the 
-[master thesis](https://repository.tudelft.nl/islandora/object/uuid%3Ae211380e-3f92-4afe-b371-f1e87b0c3bbd?collection=education) 
-and the [paper](https://www.sciencedirect.com/science/article/pii/S1364815221001468?via%3Dihub) that substitute this
-repository.
-
-## Python code <a name="python-code"></a>
-The Python code is written in Python 3 and makes use of various packages. 
-Not all of these packages are automatically included in the standard library of Python, 
-such as ``NetCDF4`` ([download](http://www.ldf.uci.edu/~gohlke/pythonlibs/#netcdf4)). 
-In case the biophysical model framework is to be coupled to Delft3d Flexible Mesh, 
-the ``bmi.wrapper`` package is also required  ([download](https://github.com/openearth/bmi-python)).
-
-The settings of Python and other packages for the online coupling to work properly are the following:
-* Python version 3.6.5
-* NumPy version 1.14.3
-* SciPy version 1.1.0
-* NetCDF4 version 1.4.2
-* Matplotlib version 2.2.2
-* BMI-Python
-
-**Note:** These requirements are only required in case the biophysical model framework is to be coupled 
-with Delft3D Flexible Mesh.
-
-
-# Version control <a name="version-control"></a>
-There are two versions of the CoralModel: ``coral_model_v0`` and ``coral_model``.
-The first (``coral_model_v0``) is the original code as used in the study (i.e. 
-[master thesis](https://repository.tudelft.nl/islandora/object/uuid%3Ae211380e-3f92-4afe-b371-f1e87b0c3bbd?collection=education) 
-and [paper](https://www.sciencedirect.com/science/article/pii/S1364815221001468?via%3Dihub)).
-The latter (``coral_model``) is an updated version, which is rewritten such that it enhances collaboration.
-This collaboration was one of the goals to further develop this model, 
-and the biophysical modelling of coral development.
-
-``coral_model_v0`` will be depreciated in the future, when ``coral_model`` is fully operational
-and possibly even incorporates more aspects of coral (reef) development.
+# How to run a Vegetation simulation in NBSDynamics
+
+
+## Simulation structure.
+
+The simulation is started using the [simtest_saltmars_test](../../test/test_data/simtest_saltmarsh_test.py) file. 
+Here the different paths need to be specified. 
+An object of the class [VegFlowFmSimulation](../../src/core/simulation/veg_delft3d_simulation.py) (which inherits from the BaseSimulation) is created. 
+Within the object, the vegetation species (in constants and vegetation) are required as an input. 
+Different species are defined through different constants. 
+In [Constants](../../src/core/common/constants_veg.py) a json file is called which contains the species specific vegetation parameters. 
+Additional time related constants (e.g. start time and ecological time steps) are defined in [Constants](../../src/core/common/constants_veg.py) and can be changed manually there.  
+Further species can be added by defining their specific parameters using [constants_json_create](../../src/core/common/constants_json_create.py).
+
+With those parameters assigned to the object, the simulation is started by using the following methods (specified in the [BaseSimulation](../../src/core/simulation/veg_base_simulation.py)):
+
+* initiate
+  * configures hydrodynamics and output
+  * validates simulation directories 
+  * initiated vegetation characteristics for all life stages in the class [LifeStages](../../src/core/vegetation/veg_lifestages.py)
+  * initializes the output ([VegOutputWrapper](../../src/core/output/veg_output_wrapper.py))
+
+* run
+  * when calling the run method (sim_run.run()), the duration of the simulation needs to be specified (in years) (e.g. sim_run.run(5))
+  * if duration is not given, the duration specified in the [Constants](../../src/core/common/constants_veg.py) class will be used 
+  * the start date is set to the date specified in [Constants](../../src/core/common/constants_veg.py)
+  * end date = start date + duration 
+  * a loop is started over the duration of the simulation (years)
+  * inside of that loop another loop iterates over the number of ecological time steps per year (coupling times per year) specified in [Constants](../../src/core/common/constants_veg.py)
+  * to get the hydro and morphological variables from Delft-FM, the hydro-morphodynamics are retrieved every day.
+    * the coupling and retrieving of the values is specified in the class [Delft3D](../../src/core/hydrodynamics/delft3d.py)
+  * aggregated values are then created in the class [Hydro_Morphodynamics](../../src/core/bio_process/hydromorphodynamics.py) and retrieved via the method 'get_hydromorph_values'
+  * the vegetation dynamics are initiated: 
+    * [Mortality and Growth](../../src/core/bio_process/veg_mortality.py)
+      * criteria for mortality and mortality fractions are determined based on the species and the morpho- &  hydrodynamics 
+      * vegetation growth is initiated based on the number of growth days within the current ecological time step
+    * [Colonization](../../src/core/bio_process/veg_colonisation.py)
+      * method is only called when colonization is possible during the specific period of the ecological time step 
+      * criteria for colonization are determined based on the species and the morpho- &  hydrodynamics
+      * the vegetation characteristics of the initial lifestage are updated based on the possible colonization
+    * [Update_Lifestages](../../src/core/vegetation/veg_model.py)
+      * the life stages are updates (initial to juvenile and juvenile to mature)
+      * initial to juvenile always occurs when new vegetation colonized 
+      * juvenile to mature only occurs when vegetation in the juvenile stage reached the maximum years in that life stage
+      * if the maximum age of vegetation is reached, the vegetation is removed
+  * The results are exported using the methods defined in [MapOutput](../../src/core/output/veg_output_model.py) and [HisOutput](../../src/core/output/veg_output_model.py)
+
+* finalize (Finalize simulation)
diff --git a/docs/guides/run_simulation_veg.md b/docs/guides/run_simulation_veg.md
@@ -0,0 +1,48 @@
+# How to run a Vegetation simulation in NBSDynamics
+
+
+## Simulation structure.
+
+The simulation is started using the [simtest_saltmars_test](../../test/test_data/simtest_saltmarsh_test.py) file. 
+Here the different paths need to be specified. 
+An object of the class [VegFlowFmSimulation](../../reference/simulation/vegetation_simulation/#src.core.simulation.veg_delft3d_simulation) (which inherits from the BaseSimulation) is created. 
+Within the object, the vegetation species (in constants and vegetation) are required as an input. 
+Different species are defined through different constants. 
+In [Constants](../../reference/common/common/#src.core.common.constants_veg) a json file is called which contains the species specific vegetation parameters. 
+Additional time related constants (e.g. start time and ecological time steps) are defined in [Constants](../../src/core/common/common/#src.core.common.constants_veg) and can be changed manually there.  
+Further species can be added by defining their specific parameters using [constants_json_create](../../src/core/common/common/#src.core.common.constants_json_create).
+
+With those parameters assigned to the object, the simulation is started by using the following methods (specified in the [BaseSimulation](../../reference/simulation/vegetation_simulation/#src.core.simulation.veg_base_simulation)):
+
+* initiate
+  * configures hydrodynamics and output
+  * validates simulation directories 
+  * initiated vegetation characteristics for all life stages in the class [LifeStages](../../reference/vegetation/vegetation_model/#src.core.vegetation.veg_lifestages)
+  * initializes the output ([VegOutputWrapper](../../reference/output/vegetation_output/#src.core.output.veg_output_wrapper))
+
+* run
+  * when calling the run method (sim_run.run()), the duration of the simulation needs to be specified (in years) (e.g. sim_run.run(5))
+  * if duration is not given, the duration specified in the [Constants](../../reference/common/common/#src.core.common.constants_veg) class will be used 
+  * the start date is set to the date specified in [Constants](../../reference/common/common/#src.core.common.constants_veg)
+  * end date = start date + duration 
+  * a loop is started over the duration of the simulation (years)
+  * inside of that loop another loop iterates over the number of ecological time steps per year (coupling times per year) specified in [Constants](../../reference/common/common/#src.core.common.constants_veg)
+  * to get the hydro and morphological variables from Delft-FM, the hydro-morphodynamics are retrieved every day.
+    * the coupling and retrieving of the values is specified in the class [Delft3D](.../../reference/hydrodynamics/hydromodels/#delft3d)
+  * aggregated values are then created in the class [Hydro_Morphodynamics](../../reference/bio_process/vegetation_processes/#src.core.bio_process.veg_hydro_morphodynamics) and retrieved via the method 'get_hydromorph_values'
+  * the vegetation dynamics are initiated: 
+    * [Mortality and Growth](../../reference/bio_process/vegetation_processes/#src.core.bio_process.veg_mortality)
+      * criteria for mortality and mortality fractions are determined based on the species and the morpho- &  hydrodynamics 
+      * vegetation growth is initiated based on the number of growth days within the current ecological time step
+    * [Colonisation](../../reference/bio_process/vegetation_processes/#src.core.bio_process.veg_colonisation)
+      * method is only called when colonisation is possible during the specific period of the ecological time step 
+      * criteria for colonisation are determined based on the species and the morpho- &  hydrodynamics
+      * the vegetation characteristics of the initial lifestage are updated based on the possible colonisation
+    * [Update_Lifestages](../../reference/vegetation/vegetation_model/#src.core.vegetation.veg_model)
+      * the life stages are updates (initial to juvenile and juvenile to mature)
+      * initial to juvenile always occurs when new vegetation colonized 
+      * juvenile to mature only occurs when vegetation in the juvenile stage reached the maximum years in that life stage
+      * if the maximum age of vegetation is reached, the vegetation is removed
+  * The results are exported using the methods defined in [MapOutput](../../reference/output/vegetation_output/#src.core.output.veg_output_model) and [HisOutput](../../reference/output/vegetation_output/#src.core.output.veg_output_model)
+
+* finalize (Finalize simulation)
diff --git a/docs/reference/bio_process/vegetation_processes.md b/docs/reference/bio_process/vegetation_processes.md
@@ -0,0 +1,13 @@
+## Biophysical processes
+
+### Colonisation
+::: src.core.bio_process.veg_colonisation
+
+### Hydro morphodynamics
+::: src.core.bio_process.veg_hydro_morphodynamics
+
+### Mortality and growth
+::: src.core.bio_process.veg_mortality
+
+
+
diff --git a/docs/reference/common/common.md b/docs/reference/common/common.md
@@ -10,4 +10,11 @@
 ::: src.core.common.space_time
 
 ### Singletons
-::: src.core.common.singletons
+::: src.core.common.singletons
+
+## Vegetation Constants
+:: src.core.common.constants_veg
+
+## Create json file
+:: src.core.common.constants_json_create
+
diff --git a/docs/reference/output/vegetation_output.md b/docs/reference/output/vegetation_output.md
@@ -0,0 +1,10 @@
+## Output classes for the NBSDynamics vegetation model.
+
+### Protocol
+::: src.core.output.veg_output_protocol
+
+### Wrapper
+::: src.core.output.veg_output_wrapper
+
+### Output models
+::: src.core.output.veg_output_model
diff --git a/docs/reference/simulation/vegetation_simulation.md b/docs/reference/simulation/vegetation_simulation.md
@@ -0,0 +1,10 @@
+## Classes representing the available simulation modes.
+
+### Simulation Protocol
+::: src.core.simulation.simulation_protocol
+
+### Base simulation.
+::: src.core.simulation.veg_base_simulation
+
+### Vegetation Delft3D (FlowFM / DIMR)
+::: src.core.simulation.veg_delft3d_simulation
diff --git a/docs/reference/vegetation/vegetation_model.md b/docs/reference/vegetation/vegetation_model.md
@@ -0,0 +1,7 @@
+## Vegetation Model
+
+:: src.core.vegetation.veg_model
+
+## Update lifestages
+
+:: src.core.vegetation.veg_lifestages
diff --git a/pyproject.toml b/pyproject.toml
@@ -50,7 +50,7 @@ version_files = [
     "pyproject.toml:version"
 ]
 
-[tool.commitizen.custommize]
+[tool.commitizen.customize]
 bump_pattern = "^(break|new|fix|hotfix|refactor|docs)"
 bump_map = {"break" = "MAJOR", "new" = "MINOR", "fix" = "PATCH", "hotfix" = "PATCH", "refactor"="PATCH", "docs" = "PATCH"}
 

diff --git a/sm_plot.py b/sm_plot.py
@@ -0,0 +1,103 @@
+import os
+
+import matplotlib.pyplot as plt
+import netCDF4
+import numpy as np
+
+# plt.style.use('seaborn-whitegrid')
+
+
+out_dir = os.path.join(
+    "C:\\",
+    "Users",
+    "toledoal",
+    "NBSDynamics",
+    "test",
+    "test_data",
+    "sm_testcase2",
+    "input",
+    "MinFiles",
+    "fm",
+    "output",
+)
+
+# read map file and plot
+url = os.path.join(out_dir, "VegModel_map.nc")
+nc = netCDF4.Dataset(url)
+nc.variables.keys()
+limdict = {
+    "cover": [0, 9999],
+    "height": [300, 304],
+    "diaveg": [295, 297],
+    "rnveg": [302, 304],
+    "veg_frac_j": [0, 9999],
+    "veg_frac_m": [0, 1.05],
+    "max_tau": [0, 1.05],
+    "max_u": [0, 1.05],
+    "max_wl": [0, 1.05],
+    "min_wl": [0, 1.05],
+    "bl": [9999, 9999],
+}
+
+teller = 0
+for vv in nc.variables.keys():
+    teller = teller + 1
+    if teller > 3:
+
+        VT = nc.variables[vv]
+        VarT = VT[:]
+
+        fig = plt.figure()
+        ax = plt.axes()
+        plt.xlim(0, 100)
+        ylims = limdict[vv]
+        if ylims[0] == 9999:
+            ylims[0] = 0.95 * np.min(VarT)
+        if ylims[1] == 9999:
+            ylims[1] = 1.05 * np.max(VarT)
+        plt.ylim(ylims)
+        plt.title(VT.long_name)
+        plt.xlabel("Time (years)")
+        plt.ylabel(VT.units)
+
+        x = np.linspace(1, 100, 100)
+
+        ax.plot(x, VarT[:, 1], "-g", label="Cell 1")
+        ax.plot(x, VarT[:, 100], "-r", label="Cell 100")
+        ax.plot(x, VarT[:, 300], "-c", label="Cell 300")
+        plt.legend()
+
+nc.close()
+
+# read his file and plot
+url = os.path.join(out_dir, "VegModel_his.nc")
+nc = netCDF4.Dataset(url)
+nc.variables.keys()
+
+teller = 0
+for vv in nc.variables.keys():
+    teller = teller + 1
+    if teller > 3:
+
+        VT = nc.variables[vv]
+        VarT = VT[:]
+
+        fig = plt.figure()
+        ax = plt.axes()
+        plt.xlim(0, 100)
+        ylims = limdict[vv]
+        if ylims[0] == 9999:
+            ylims[0] = 0.95 * np.min(VarT)
+        if ylims[1] == 9999:
+            ylims[1] = 1.05 * np.max(VarT)
+        plt.title(VT.long_name)
+        plt.xlabel("Time (years)")
+        plt.ylabel(VT.units)
+
+        x = np.linspace(0, 100, 36525)
+        colors = iter(plt.cm.rainbow(np.linspace(0, 1, VarT.shape[1])))
+        for i in range(VarT.shape[1]):
+            ax.plot(x, VarT[:, i], color=next(colors), label=f"Point {i}")
+        plt.legend()
+
+nc.close()
diff --git a/src/core/bio_process/dislodgment.py b/src/core/bio_process/dislodgment.py
@@ -28,7 +28,7 @@ def update(self, coral: Coral, survival_coefficient=1):
         # # partial dislodgement
         Dislodgement.partial_dislodgement(self, coral, survival_coefficient)
         # # update
-        # ulation states
+        # population states
         for s in range(4):
             coral.p0[:, s] *= self.survival
         # morphology