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Add idealized marsh flooding case with vegetation drag #651
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sbrus89
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MPAS-Dev:ocean/coastal
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caozd999:coastal/marshFlooding_PR_cherrypick
Aug 18, 2020
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16 changes: 16 additions & 0 deletions
16
testing_and_setup/compass/ocean/drying_slope/forward_idealized_transect.xml
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|---|---|---|
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| <template> | ||
| <namelist> | ||
| <option name="config_Rayleigh_friction">.false.</option> | ||
| <option name="config_Rayleigh_damping_depth_variable">.false.</option> | ||
| <option name="config_use_implicit_bottom_drag">.false.</option> | ||
| <option name="config_use_implicit_bottom_drag_variable">.false.</option> | ||
| <option name="config_use_implicit_bottom_drag_variable_mannings">.true.</option> | ||
| <option name="config_thickness_flux_type">'centered'</option> | ||
| <option name="config_dt">'0000_00:00:05'</option> | ||
| <option name="config_run_duration">'0000_48:00:01'</option> | ||
| <option name="config_tidal_forcing_monochromatic_amp">1.5</option> | ||
| <option name="config_tidal_forcing_monochromatic_period">1.0</option> | ||
| <option name="config_tidal_forcing_monochromatic_phaseLag">0.0</option> | ||
| <option name="config_tidal_forcing_monochromatic_baseline">3.0</option> | ||
| </namelist> | ||
| </template> |
24 changes: 24 additions & 0 deletions
24
testing_and_setup/compass/ocean/drying_slope/forward_vegetation_properties.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| <template> | ||
| <streams> | ||
| <stream name="forcing"> | ||
| <attribute name="type">input</attribute> | ||
| <attribute name="input_interval">initial_only</attribute> | ||
| <attribute name="filename_template">forcing.nc</attribute> | ||
| <add_contents> | ||
| <member type="var" name="vegetationMask"/> | ||
| <member type="var" name="vegetationDiameter"/> | ||
| <member type="var" name="vegetationHeight"/> | ||
| <member type="var" name="vegetationDensity"/> | ||
| </add_contents> | ||
| </stream> | ||
| <stream name="output"> | ||
| <attribute name="type">output</attribute> | ||
| <attribute name="clobber_mode">truncate</attribute> | ||
| <attribute name="filename_template">output.nc</attribute> | ||
| <attribute name="output_interval">0000-00-00_00:12:00</attribute> | ||
| <add_contents> | ||
| <member type="var" name="vegetationManning"/> | ||
| </add_contents> | ||
| </stream> | ||
| </streams> | ||
| </template> |
20 changes: 20 additions & 0 deletions
20
testing_and_setup/compass/ocean/drying_slope/init_idealized_transect.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| <template> | ||
| <namelist> | ||
| <option name="config_use_variable_drag">.true.</option> | ||
| <option name="config_use_idealized_transect">.true.</option> | ||
| <option name="config_idealized_transect_Lcoast">0.3</option> | ||
| <option name="config_idealized_transect_Scoast">0.00125</option> | ||
| <option name="config_idealized_transect_Lshore">0.2</option> | ||
| <option name="config_idealized_transect_Sshore">0.0025</option> | ||
| <option name="config_idealized_transect_Lmarsh">0.5</option> | ||
| <option name="config_idealized_transect_Smarsh">0.0</option> | ||
| <option name="config_idealized_transect_roughness">0.025</option> | ||
| <option name="config_idealized_transect_roughness_marsh">0.025</option> | ||
| <option name="config_tidal_boundary_left_bottom_depth">0.0</option> | ||
| <option name="config_tidal_boundary_left_value">0.0</option> | ||
| <option name="config_tidal_boundary_right_value">8.0e3</option> | ||
| <option name="config_tidal_forcing_monochromatic_baseline">3.0</option> | ||
| <option name="config_alter_ICs_for_pbcs">.true.</option> | ||
| <option name="config_thickness_flux_type">'centered'</option> | ||
| </namelist> | ||
| </template> | ||
16 changes: 16 additions & 0 deletions
16
testing_and_setup/compass/ocean/drying_slope/init_vegetation_properties.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| <template> | ||
| <streams> | ||
| <stream name="forcing_data_init"> | ||
| <attribute name="type">output</attribute> | ||
| <attribute name="filename_template">forcing.nc</attribute> | ||
| <attribute name="clobber_mode">truncate</attribute> | ||
| <attribute name="output_interval">0000_00:00:01</attribute> | ||
| <add_contents> | ||
| <member name="vegetationMask" type="var"/> | ||
| <member name="vegetationDiameter" type="var"/> | ||
| <member name="vegetationHeight" type="var"/> | ||
| <member name="vegetationDensity" type="var"/> | ||
| </add_contents> | ||
| </stream> | ||
| </streams> | ||
| </template> |
84 changes: 84 additions & 0 deletions
84
testing_and_setup/compass/ocean/drying_slope/marsh_flooding/idealized_transect/comparison.py
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| #!/usr/bin/env python | ||
| # coding: utf-8 | ||
| # Authors: Zhendong Cao, Phillip Wolfram | ||
| # Date: May 2020 | ||
|
|
||
| # import libs | ||
| import numpy as np | ||
| import xarray as xr | ||
| import matplotlib.pyplot as plt | ||
| import os | ||
| #import cv2 | ||
| # plot tidal amplitude at open boundary | ||
|
|
||
| fname1 = 'NoVegetation' | ||
| fname2 = 'ConstantVegManning' | ||
| fname3 = 'VegManningEquation' | ||
|
|
||
| # mpas-o | ||
| ds1 = xr.open_dataset(fname1+'.nc') | ||
| ds2 = xr.open_dataset(fname2+'.nc') | ||
| ds3 = xr.open_dataset(fname3+'.nc') | ||
|
|
||
| x = np.linspace(0, 1.0, len(ds1.xtime))*48.0 | ||
| ympas1 = ds1.ssh.where(ds1.tidalInputMask).mean('nCells').values | ||
| ympas2 = ds2.ssh.where(ds2.tidalInputMask).mean('nCells').values | ||
| ympas3 = ds3.ssh.where(ds3.tidalInputMask).mean('nCells').values | ||
|
|
||
| plt.plot(x, ympas1, marker='o', label=fname1) | ||
| plt.plot(x, ympas2, marker='^', label=fname2) | ||
| plt.plot(x, ympas3, marker='*', label=fname3) | ||
|
|
||
| # analytical | ||
| x = np.linspace(0,48.0,100) | ||
| y = 1.5*np.sin(x*np.pi/12.0) - 3.0 | ||
| plt.plot(x, y, 'k-', lw=3, label='analytical') | ||
|
|
||
| plt.legend(frameon=False, loc='upper right', fontsize=8) | ||
| plt.ylabel('Tidal amplitude (m)') | ||
| plt.xlabel('Time (hrs)') | ||
| plt.suptitle('Tidal amplitude forcing for test cases and analytical') | ||
| plt.savefig('tidalcomparison.png',dpi=300) | ||
| plt.close() | ||
|
|
||
| # extract bottomDepth | ||
| bottomDepth = ds1.bottomDepth.values.reshape((116, 4))[:,1] | ||
| x_along = np.linspace(0,8,116) | ||
| # plot water elevation at selected time slices | ||
| times = np.linspace(0.0,2.0,41) | ||
| ii = 0 | ||
| figname_prefix = 'Waterlevel' | ||
| for atime in times: | ||
| plt.figure(figsize=(12,6)) | ||
| plt.xlim(0, 8) | ||
| plt.ylim(-4, 0) | ||
| plottime = int((float(atime)/0.2)*24.0) | ||
| timestr = ds1.isel(Time=plottime).xtime.values | ||
| ymean = ds1.isel(Time=plottime).groupby('yCell').mean(dim=xr.ALL_DIMS) | ||
| x = ymean.yCell.values/1000.0 | ||
| y = ymean.ssh.values | ||
| plt.plot(x, y,'-k',label=fname1) | ||
|
|
||
| ymean = ds2.isel(Time=plottime).groupby('yCell').mean(dim=xr.ALL_DIMS) | ||
| x = ymean.yCell.values/1000.0 | ||
| y = ymean.ssh.values | ||
| plt.plot(x, y,'-b',label=fname2) | ||
|
|
||
| ymean = ds3.isel(Time=plottime).groupby('yCell').mean(dim=xr.ALL_DIMS) | ||
| x = ymean.yCell.values/1000.0 | ||
| y = ymean.ssh.values | ||
| plt.plot(x, y,'-g',label=fname3) | ||
|
|
||
| plt.fill_between(x=x_along,y1=-10*np.ones(x_along.shape), y2=-bottomDepth, color='grey',zorder=9) | ||
| plt.xlabel('Cross shore distance (km)') | ||
| plt.ylabel('Bathymetry (m)') | ||
| atime='%.2f'%atime | ||
| plt.title('time='+atime+'days') | ||
| plt.legend(frameon=False, loc='upper right') | ||
| figname = '{}{:02d}.png'.format(figname_prefix,ii) | ||
| plt.savefig(figname, dpi=100) | ||
| plt.close() | ||
| print('Time '+atime+ ' done!') | ||
| ii += 1 | ||
| # make a movie | ||
| os.system("ffmpeg -r 1 -i Waterlevel%02d.png -vcodec mpeg4 -y movie.mp4") |
28 changes: 28 additions & 0 deletions
28
...nd_setup/compass/ocean/drying_slope/marsh_flooding/idealized_transect/config_analysis.xml
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|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| <?xml version="1.0"?> | ||
| <config case="analysis"> | ||
| <add_link path_base="script_test_dir" source="comparison.py" dest="comparison.py"/> | ||
| <add_link source="../forward1/output.nc" dest="NoVegetation.nc"/> | ||
| <add_link source="../forward2/output.nc" dest="ConstantVegManning.nc"/> | ||
| <add_link source="../forward3/output.nc" dest="VegManningEquation.nc"/> | ||
|
|
||
| <run_script name="run.py"> | ||
| <step executable="./comparison.py"> | ||
| </step> | ||
| <step executable="paraview_vtk_field_extractor.py"> | ||
| <argument flag="-f">output1.nc</argument> | ||
| <argument flag="-o">vtk_output1</argument> | ||
| <argument flag="-v">allOnCells</argument> | ||
| <argument flag="-d">maxEdges=0</argument> | ||
| <argument flag="">nVertLevels=0:10</argument> | ||
| <argument flag="--combine"></argument> | ||
| </step> | ||
| <step executable="paraview_vtk_field_extractor.py"> | ||
| <argument flag="-f">output2.nc</argument> | ||
| <argument flag="-o">vtk_output2</argument> | ||
| <argument flag="-v">allOnCells</argument> | ||
| <argument flag="-d">maxEdges=0</argument> | ||
| <argument flag="">nVertLevels=0:10</argument> | ||
| <argument flag="--combine"></argument> | ||
| </step> | ||
| </run_script> | ||
| </config> |
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