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* new constants class * new class colonization start * new class vegetation * changes to veg_model * created get_hydromorphodynamics and import vegetation model * base_simulation.py - created initiate_hydromorphodynamics delft3d.py - created update_hydromorphodynamics * Addition of vegetation characteristics method, growth and mortality classes. New veg_base_simulation. * Addition of vegetation characteristics method, growth and mortality classes. New veg_base_simulation. * add class Hydro_Morphodynamics, process in veg_base_simulation.py * changes to Hydro_Morphodynamics, process in veg_base_simulation.py * changes to Hydro_Morphodynamics, process in veg_base_simulation.py, progress in the veg bio-processes * changes to Hydro_Morphodynamics, process in veg_base_simulation.py, progress in the veg bio-processes * progress in mortality * output * updates to output * progress in mortality * account for maxAge vegetation in veg_growth * account for maxAge vegetation in veg_growth * updates to output * changes after debugging * simtest * veg_delft3D_simulation file * changes to veg_model * updates veg_model * json file for constants and changes to constants class * changes to Vegetation * updates veg_model growth nogrowth * changes to Vegetation * updates veg_model and new veg_lifestages * updates veg_model and new veg_lifestages * changes to Vegetation * changes to Vegetation * Debugging * Debugging * Debugging * Debugging * Added README for the veg_model * Added README for the veg_model * Added README for the veg_model * delete old readme * Rename veg_model_README.md to README.md * delete entries in the initial life stage after passing it to juvenile * delete entries in the initial life stage after passing it to juvenile * add Puccinellia to species in constants, debugging * debugging * debugging * debugging * debugging * debugging and file to read output * debugging and output * debugging and output * debugging and additions for Salicornia * updates veg_mortality.py * changes in mortality * changes in update lifestages * changes in output * ci(pyproject.toml): Corrected tool typo * added test case * test(test/test_data/): Added missing data * test_acceptance.py * delete sim_test * test(test/test_acceptance.py): Fixed test * test(test/test_acceptance.py): Modified test to run on any machine * test(transect_case): Fixed missing test data for the transect case output * autoformat: isort & black * Documentation * autoformat: isort & black * fix bugs in veg_mortality.py * autoformat: isort & black Co-authored-by: DzimbaS <[email protected]> Co-authored-by: deboradta <[email protected]> Co-authored-by: DzimbaS <[email protected]> Co-authored-by: Carsopre <[email protected]> Co-authored-by: deboradta <[email protected]> Co-authored-by: DzimbaS <[email protected]>
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| [](https://github.com/Deltares/NBSDynamics/actions/workflows/ci.yml) | ||
| [](https://github.com/Deltares/NBSDynamics/actions/workflows/docs.yml) | ||
| [](https://sonarcloud.io/summary/new_code?id=Deltares_NBSDynamics) | ||
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| [](https://github.com/psf/black) | ||
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| # Official Documentation. | ||
| Check our official GitHub pages documentation at [https://deltares.github.io/NBSDynamics/](https://deltares.github.io/NBSDynamics/). | ||
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| # 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)). | ||
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| **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). | ||
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| ## 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)). | ||
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| 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. | ||
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| 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. | ||
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| ## 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)). | ||
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| 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 | ||
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| **Note:** These requirements are only required in case the biophysical model framework is to be coupled | ||
| with Delft3D Flexible Mesh. | ||
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| # 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. | ||
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| ``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 | ||
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| ## Simulation structure. | ||
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| 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). | ||
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| 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)): | ||
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| * 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)) | ||
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| * 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) | ||
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| * finalize (Finalize simulation) |
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| # How to run a Vegetation simulation in NBSDynamics | ||
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| ## Simulation structure. | ||
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| 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). | ||
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| 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)): | ||
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| * 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)) | ||
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| * 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) | ||
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| * finalize (Finalize simulation) |
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| ## Biophysical processes | ||
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| ### Colonisation | ||
| ::: src.core.bio_process.veg_colonisation | ||
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| ### Hydro morphodynamics | ||
| ::: src.core.bio_process.veg_hydro_morphodynamics | ||
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| ### Mortality and growth | ||
| ::: src.core.bio_process.veg_mortality | ||
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| ## Output classes for the NBSDynamics vegetation model. | ||
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| ### Protocol | ||
| ::: src.core.output.veg_output_protocol | ||
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| ### Wrapper | ||
| ::: src.core.output.veg_output_wrapper | ||
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| ### Output models | ||
| ::: src.core.output.veg_output_model |
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| ## Classes representing the available simulation modes. | ||
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| ### Simulation Protocol | ||
| ::: src.core.simulation.simulation_protocol | ||
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| ### Base simulation. | ||
| ::: src.core.simulation.veg_base_simulation | ||
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| ### Vegetation Delft3D (FlowFM / DIMR) | ||
| ::: src.core.simulation.veg_delft3d_simulation |
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| ## Vegetation Model | ||
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| :: src.core.vegetation.veg_model | ||
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| ## Update lifestages | ||
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| :: src.core.vegetation.veg_lifestages |
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| import os | ||
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| import matplotlib.pyplot as plt | ||
| import netCDF4 | ||
| import numpy as np | ||
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| # plt.style.use('seaborn-whitegrid') | ||
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| out_dir = os.path.join( | ||
| "C:\\", | ||
| "Users", | ||
| "toledoal", | ||
| "NBSDynamics", | ||
| "test", | ||
| "test_data", | ||
| "sm_testcase2", | ||
| "input", | ||
| "MinFiles", | ||
| "fm", | ||
| "output", | ||
| ) | ||
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| # 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], | ||
| } | ||
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| teller = 0 | ||
| for vv in nc.variables.keys(): | ||
| teller = teller + 1 | ||
| if teller > 3: | ||
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| VT = nc.variables[vv] | ||
| VarT = VT[:] | ||
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| 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) | ||
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| x = np.linspace(1, 100, 100) | ||
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| 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() | ||
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| nc.close() | ||
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| # read his file and plot | ||
| url = os.path.join(out_dir, "VegModel_his.nc") | ||
| nc = netCDF4.Dataset(url) | ||
| nc.variables.keys() | ||
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| teller = 0 | ||
| for vv in nc.variables.keys(): | ||
| teller = teller + 1 | ||
| if teller > 3: | ||
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| VT = nc.variables[vv] | ||
| VarT = VT[:] | ||
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| 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) | ||
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| 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() | ||
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| nc.close() |
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