Merge branch 'main' into 1d2d-patch

openearth · Jul 27, 2024 · 9a714dc · 9a714dc
2 parents 9fdcfc2 + c640ea7
commit 9a714dc
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diff --git a/aeolis/bed.py b/aeolis/bed.py
@@ -202,7 +202,7 @@ def mixtoplayer(s, p):
 
 
 def wet_bed_reset(s, p):
-    ''' Text
+    ''' Reset wet bed to initial bed level if the total water level is above the bed level.
 
 
 
@@ -332,6 +332,9 @@ def update(s, p):
     # reshape mass matrix
     s['mass'] = m.reshape((ny+1,nx+1,nl,nf))
 
+    # Store toplayer of 'mass' variable (ilayer = 0)
+    s['masstop'][:,:,:] = s['mass'][:,:,0,:].copy()
+
     # update bathy
     if p['process_bedupdate']:
 

diff --git a/aeolis/constants.py b/aeolis/constants.py
diff --git a/aeolis/examples/README.md b/aeolis/examples/README.md
@@ -0,0 +1,77 @@
+This folder contains a variation of AeoLiS simulation setups.
+
+
+1D - (simple) One-dimensional examples:
+
+1D/case1_small_waves
+<description>
+
+1D/case2_larger_waves
+<description>
+
+1D/case3_erosion_avalanching
+<description>
+
+1D/case4_surface_moisture
+<description>
+
+
+2D - (simple) Two-dimensional examples
+
+2D/Barchan_dune
+<description>
+
+2D/Parabolic_dune
+<description>
+
+2D/Carrara_Coast
+<description>
+
+
+deVries2023 - Simulations describing ...
+
+deVries2023/Run 1 - Fetch effects and spatial variability in supply
+<description>
+
+deVries2023/Run 2 - Fetch effects and wind directionality
+<description>
+
+deVries2023/Run 3 - Fetch effects and temporal variability in supply
+<description>
+
+deVries2023/Run 4 - Predictions of decadal development
+<description>
+
+
+grainsizevariations - SHORT DESCRIPTION
+<description>
+
+
+sandengine_small_grids - Fast Sand Engine simulation
+Simulation of the subaerial Sand Engine evolution, describing supply-limiting effects like moisture and sediment sorting on a larger scale
+
+
+vanWesten2024 - Landform simulations as described in the AeoLiS landform publication (van Westen, 2024)
+
+vanWesten2024/barchan_morocco
+<description>
+
+vanWesten2024/barchan_rotate
+<description>
+
+vanWesten2024/blowout
+<description>
+
+vanWesten2024/embryo
+<description>
+
+vanWesten2024/parabolic
+<description>
+
+
+
+
+
+
+
+
diff --git a/aeolis/examples/README.txt b/aeolis/examples/README.txt
@@ -0,0 +1,77 @@
+This folder contains a variation of AeoLiS simulation setups.
+
+
+1D - (simple) One-dimensional examples:
+
+1D/case1_small_waves
+<description>
+
+1D/case2_larger_waves
+<description>
+
+1D/case3_erosion_avalanching
+<description>
+
+1D/case4_surface_moisture
+<description>
+
+
+2D - (simple) Two-dimensional examples
+
+2D/Barchan_dune
+<description>
+
+2D/Parabolic_dune
+<description>
+
+2D/Carrara_Coast
+<description>
+
+
+deVries2023 - Simulations describing ...
+
+deVries2023/Run 1 - Fetch effects and spatial variability in supply
+<description>
+
+deVries2023/Run 2 - Fetch effects and wind directionality
+<description>
+
+deVries2023/Run 3 - Fetch effects and temporal variability in supply
+<description>
+
+deVries2023/Run 4 - Predictions of decadal development
+<description>
+
+
+grainsizevariations - SHORT DESCRIPTION
+<description>
+
+
+sandengine_small_grids - Fast Sand Engine simulation
+Simulation of the subaerial Sand Engine evolution, describing supply-limiting effects like moisture and sediment sorting on a larger scale
+
+
+vanWesten2024 - Landform simulations as described in the AeoLiS landform publication (van Westen, 2024)
+
+vanWesten2024/barchan_morocco
+<description>
+
+vanWesten2024/barchan_rotate
+<description>
+
+vanWesten2024/blowout
+<description>
+
+vanWesten2024/embryo
+<description>
+
+vanWesten2024/parabolic
+<description>
+
+
+
+
+
+
+
+
diff --git a/examples/deVries2023/2D_Domain.PNG → aeolis/examples/deVries2023/2D_Domain.PNG b/examples/deVries2023/2D_Domain.PNG → aeolis/examples/deVries2023/2D_Domain.PNG
diff --git a/...ial variability in supply/Run1-play.ipynb → ...ial variability in supply/Run1-play.ipynb b/...ial variability in supply/Run1-play.ipynb → ...ial variability in supply/Run1-play.ipynb
diff --git a/... spatial variability in supply/Run1.ipynb → ... spatial variability in supply/Run1.ipynb b/... spatial variability in supply/Run1.ipynb → ... spatial variability in supply/Run1.ipynb
diff --git a/...nd spatial variability in supply/Run1.png → ...nd spatial variability in supply/Run1.png b/...nd spatial variability in supply/Run1.png → ...nd spatial variability in supply/Run1.png
diff --git a/...nd spatial variability in supply/Run1.txt → ...nd spatial variability in supply/Run1.txt b/...nd spatial variability in supply/Run1.txt → ...nd spatial variability in supply/Run1.txt
diff --git a/...atial variability in supply/Run1_play.txt → ...atial variability in supply/Run1_play.txt b/...atial variability in supply/Run1_play.txt → ...atial variability in supply/Run1_play.txt
diff --git a/...tial variability in supply/Run1_play2.txt → ...tial variability in supply/Run1_play2.txt b/...tial variability in supply/Run1_play2.txt → ...tial variability in supply/Run1_play2.txt
diff --git a/...spatial variability in supply/Run1b.ipynb → ...spatial variability in supply/Run1b.ipynb b/...spatial variability in supply/Run1b.ipynb → ...spatial variability in supply/Run1b.ipynb
diff --git a/...d spatial variability in supply/Run1b.txt → ...d spatial variability in supply/Run1b.txt b/...d spatial variability in supply/Run1b.txt → ...d spatial variability in supply/Run1b.txt
diff --git a/...spatial variability in supply/callback.py → ...spatial variability in supply/callback.py b/...spatial variability in supply/callback.py → ...spatial variability in supply/callback.py
diff --git a/... variability in supply/cmap_sandmotor.txt → ... variability in supply/cmap_sandmotor.txt b/... variability in supply/cmap_sandmotor.txt → ... variability in supply/cmap_sandmotor.txt
diff --git a/...atial variability in supply/copyright.png → ...atial variability in supply/copyright.png b/...atial variability in supply/copyright.png → ...atial variability in supply/copyright.png
diff --git a/... in supply/figure_grid_initialization.png → ... in supply/figure_grid_initialization.png b/... in supply/figure_grid_initialization.png → ... in supply/figure_grid_initialization.png
diff --git a/...n supply/figure_params_initialization.png → ...n supply/figure_params_initialization.png b/...n supply/figure_params_initialization.png → ...n supply/figure_params_initialization.png
diff --git a/...pply/figure_timeseries_initialization.png → ...pply/figure_timeseries_initialization.png b/...pply/figure_timeseries_initialization.png → ...pply/figure_timeseries_initialization.png
diff --git a/...nd spatial variability in supply/logo.png → ...nd spatial variability in supply/logo.png b/...nd spatial variability in supply/logo.png → ...nd spatial variability in supply/logo.png
diff --git a/...ability in supply/plot_tools_sandmotor.py → ...ability in supply/plot_tools_sandmotor.py b/...ability in supply/plot_tools_sandmotor.py → ...ability in supply/plot_tools_sandmotor.py
diff --git a/...ariability in supply/supply_animation.mp4 → ...ariability in supply/supply_animation.mp4 b/...ariability in supply/supply_animation.mp4 → ...ariability in supply/supply_animation.mp4
diff --git a/...ial variability in supply/supply_file.txt → ...ial variability in supply/supply_file.txt b/...ial variability in supply/supply_file.txt → ...ial variability in supply/supply_file.txt
diff --git a/...nd spatial variability in supply/wind.txt → ...nd spatial variability in supply/wind.txt b/...nd spatial variability in supply/wind.txt → ...nd spatial variability in supply/wind.txt
diff --git a/...patial variability in supply/wind_var.txt → ...patial variability in supply/wind_var.txt b/...patial variability in supply/wind_var.txt → ...patial variability in supply/wind_var.txt
diff --git a/... spatial variability in supply/x_grid.txt → ... spatial variability in supply/x_grid.txt b/... spatial variability in supply/x_grid.txt → ... spatial variability in supply/x_grid.txt
diff --git a/...spatial variability in supply/x_grid2.txt → ...spatial variability in supply/x_grid2.txt b/...spatial variability in supply/x_grid2.txt → ...spatial variability in supply/x_grid2.txt
diff --git a/... spatial variability in supply/y_grid.txt → ... spatial variability in supply/y_grid.txt b/... spatial variability in supply/y_grid.txt → ... spatial variability in supply/y_grid.txt
diff --git a/...spatial variability in supply/y_grid2.txt → ...spatial variability in supply/y_grid2.txt b/...spatial variability in supply/y_grid2.txt → ...spatial variability in supply/y_grid2.txt
diff --git a/... spatial variability in supply/z_grid.txt → ... spatial variability in supply/z_grid.txt b/... spatial variability in supply/z_grid.txt → ... spatial variability in supply/z_grid.txt
diff --git a/...spatial variability in supply/z_grid2.txt → ...spatial variability in supply/z_grid2.txt b/...spatial variability in supply/z_grid2.txt → ...spatial variability in supply/z_grid2.txt
diff --git a/...ffects and wind directionality/Run2.ipynb → ...ffects and wind directionality/Run2.ipynb b/...ffects and wind directionality/Run2.ipynb → ...ffects and wind directionality/Run2.ipynb
diff --git a/... effects and wind directionality/Run2.png → ... effects and wind directionality/Run2.png b/... effects and wind directionality/Run2.png → ... effects and wind directionality/Run2.png
diff --git a/... effects and wind directionality/Run2.txt → ... effects and wind directionality/Run2.txt b/... effects and wind directionality/Run2.txt → ... effects and wind directionality/Run2.txt
diff --git a/...d wind directionality/Run2_nautical.ipynb → ...d wind directionality/Run2_nautical.ipynb b/...d wind directionality/Run2_nautical.ipynb → ...d wind directionality/Run2_nautical.ipynb
diff --git a/...s and wind directionality/Run2_play.ipynb → ...s and wind directionality/Run2_play.ipynb b/...s and wind directionality/Run2_play.ipynb → ...s and wind directionality/Run2_play.ipynb
diff --git a/...fects and wind directionality/Run2b.ipynb → ...fects and wind directionality/Run2b.ipynb b/...fects and wind directionality/Run2b.ipynb → ...fects and wind directionality/Run2b.ipynb
diff --git a/...effects and wind directionality/Run2b.txt → ...effects and wind directionality/Run2b.txt b/...effects and wind directionality/Run2b.txt → ...effects and wind directionality/Run2b.txt
diff --git a/...ts and wind directionality/Run2b_play.txt → ...ts and wind directionality/Run2b_play.txt b/...ts and wind directionality/Run2b_play.txt → ...ts and wind directionality/Run2b_play.txt
diff --git a/...s and wind directionality/Run2b_play2.txt → ...s and wind directionality/Run2b_play2.txt b/...s and wind directionality/Run2b_play2.txt → ...s and wind directionality/Run2b_play2.txt
diff --git a/...effects and wind directionality/Run2c.txt → ...effects and wind directionality/Run2c.txt b/...effects and wind directionality/Run2c.txt → ...effects and wind directionality/Run2c.txt
diff --git a/...effects and wind directionality/Run2d.txt → ...effects and wind directionality/Run2d.txt b/...effects and wind directionality/Run2d.txt → ...effects and wind directionality/Run2d.txt
diff --git a/...effects and wind directionality/Run2e.txt → ...effects and wind directionality/Run2e.txt b/...effects and wind directionality/Run2e.txt → ...effects and wind directionality/Run2e.txt
diff --git a/...cts and wind directionality/copyright.png → ...cts and wind directionality/copyright.png b/...cts and wind directionality/copyright.png → ...cts and wind directionality/copyright.png
diff --git a/...ctionality/figure_grid_initialization.png → ...ctionality/figure_grid_initialization.png b/...ctionality/figure_grid_initialization.png → ...ctionality/figure_grid_initialization.png
diff --git a/...ionality/figure_params_initialization.png → ...ionality/figure_params_initialization.png b/...ionality/figure_params_initialization.png → ...ionality/figure_params_initialization.png
diff --git a/...lity/figure_timeseries_initialization.png → ...lity/figure_timeseries_initialization.png b/...lity/figure_timeseries_initialization.png → ...lity/figure_timeseries_initialization.png
diff --git a/... effects and wind directionality/logo.png → ... effects and wind directionality/logo.png b/... effects and wind directionality/logo.png → ... effects and wind directionality/logo.png
diff --git a/...s and wind directionality/supply_file.txt → ...s and wind directionality/supply_file.txt b/...s and wind directionality/supply_file.txt → ...s and wind directionality/supply_file.txt
diff --git a/... and wind directionality/supply_file2.txt → ... and wind directionality/supply_file2.txt b/... and wind directionality/supply_file2.txt → ... and wind directionality/supply_file2.txt
diff --git a/...d wind directionality/supply_wind_var.mp4 → ...d wind directionality/supply_wind_var.mp4 b/...d wind directionality/supply_wind_var.mp4 → ...d wind directionality/supply_wind_var.mp4
diff --git a/... effects and wind directionality/wind.txt → ... effects and wind directionality/wind.txt b/... effects and wind directionality/wind.txt → ... effects and wind directionality/wind.txt
diff --git a/...effects and wind directionality/wind0.txt → ...effects and wind directionality/wind0.txt b/...effects and wind directionality/wind0.txt → ...effects and wind directionality/wind0.txt
diff --git a/...ts and wind directionality/wind0_naut.txt → ...ts and wind directionality/wind0_naut.txt b/...ts and wind directionality/wind0_naut.txt → ...ts and wind directionality/wind0_naut.txt
diff --git a/...ffects and wind directionality/wind30.txt → ...ffects and wind directionality/wind30.txt b/...ffects and wind directionality/wind30.txt → ...ffects and wind directionality/wind30.txt
diff --git a/...ts and wind directionality/wind30_neg.txt → ...ts and wind directionality/wind30_neg.txt b/...ts and wind directionality/wind30_neg.txt → ...ts and wind directionality/wind30_neg.txt
diff --git a/...ffects and wind directionality/wind45.txt → ...ffects and wind directionality/wind45.txt b/...ffects and wind directionality/wind45.txt → ...ffects and wind directionality/wind45.txt
diff --git a/...ffects and wind directionality/wind60.txt → ...ffects and wind directionality/wind60.txt b/...ffects and wind directionality/wind60.txt → ...ffects and wind directionality/wind60.txt
diff --git a/...ffects and wind directionality/wind75.txt → ...ffects and wind directionality/wind75.txt b/...ffects and wind directionality/wind75.txt → ...ffects and wind directionality/wind75.txt
diff --git a/...fects and wind directionality/wind_SS.txt → ...fects and wind directionality/wind_SS.txt b/...fects and wind directionality/wind_SS.txt → ...fects and wind directionality/wind_SS.txt
diff --git a/...ects and wind directionality/wind_var.txt → ...ects and wind directionality/wind_var.txt b/...ects and wind directionality/wind_var.txt → ...ects and wind directionality/wind_var.txt
diff --git a/...ffects and wind directionality/x_grid.txt → ...ffects and wind directionality/x_grid.txt b/...ffects and wind directionality/x_grid.txt → ...ffects and wind directionality/x_grid.txt
diff --git a/...ffects and wind directionality/y_grid.txt → ...ffects and wind directionality/y_grid.txt b/...ffects and wind directionality/y_grid.txt → ...ffects and wind directionality/y_grid.txt
diff --git a/...ffects and wind directionality/z_grid.txt → ...ffects and wind directionality/z_grid.txt b/...ffects and wind directionality/z_grid.txt → ...ffects and wind directionality/z_grid.txt
diff --git a/...temporal variability in supply/Run3.ipynb → ...temporal variability in supply/Run3.ipynb b/...temporal variability in supply/Run3.ipynb → ...temporal variability in supply/Run3.ipynb
diff --git a/...d temporal variability in supply/Run3.png → ...d temporal variability in supply/Run3.png b/...d temporal variability in supply/Run3.png → ...d temporal variability in supply/Run3.png
diff --git a/...d temporal variability in supply/Run3.txt → ...d temporal variability in supply/Run3.txt b/...d temporal variability in supply/Run3.txt → ...d temporal variability in supply/Run3.txt
diff --git a/...emporal variability in supply/Run3b.ipynb → ...emporal variability in supply/Run3b.ipynb b/...emporal variability in supply/Run3b.ipynb → ...emporal variability in supply/Run3b.ipynb
diff --git a/... temporal variability in supply/Run3b.txt → ... temporal variability in supply/Run3b.txt b/... temporal variability in supply/Run3b.txt → ... temporal variability in supply/Run3b.txt
diff --git a/...poral variability in supply/copyright.png → ...poral variability in supply/copyright.png b/...poral variability in supply/copyright.png → ...poral variability in supply/copyright.png
diff --git a/... in supply/figure_grid_initialization.png → ... in supply/figure_grid_initialization.png b/... in supply/figure_grid_initialization.png → ... in supply/figure_grid_initialization.png
diff --git a/...n supply/figure_params_initialization.png → ...n supply/figure_params_initialization.png b/...n supply/figure_params_initialization.png → ...n supply/figure_params_initialization.png
diff --git a/...pply/figure_timeseries_initialization.png → ...pply/figure_timeseries_initialization.png b/...pply/figure_timeseries_initialization.png → ...pply/figure_timeseries_initialization.png
diff --git a/...d temporal variability in supply/logo.png → ...d temporal variability in supply/logo.png b/...d temporal variability in supply/logo.png → ...d temporal variability in supply/logo.png
diff --git a/...ral variability in supply/supply_file.txt → ...ral variability in supply/supply_file.txt b/...ral variability in supply/supply_file.txt → ...ral variability in supply/supply_file.txt
diff --git a/...riability in supply/supply_large_file.txt → ...riability in supply/supply_large_file.txt b/...riability in supply/supply_large_file.txt → ...riability in supply/supply_large_file.txt
diff --git a/... variability in supply/supply_limited.mp4 → ... variability in supply/supply_limited.mp4 b/... variability in supply/supply_limited.mp4 → ... variability in supply/supply_limited.mp4
diff --git a/...riability in supply/supply_small_file.txt → ...riability in supply/supply_small_file.txt b/...riability in supply/supply_small_file.txt → ...riability in supply/supply_small_file.txt
diff --git a/... variability in supply/supply_surplus.mp4 → ... variability in supply/supply_surplus.mp4 b/... variability in supply/supply_surplus.mp4 → ... variability in supply/supply_surplus.mp4
diff --git a/...d temporal variability in supply/tide.txt → ...d temporal variability in supply/tide.txt b/...d temporal variability in supply/tide.txt → ...d temporal variability in supply/tide.txt
diff --git a/...d temporal variability in supply/wind.txt → ...d temporal variability in supply/wind.txt b/...d temporal variability in supply/wind.txt → ...d temporal variability in supply/wind.txt
diff --git a/...mporal variability in supply/wind_var.txt → ...mporal variability in supply/wind_var.txt b/...mporal variability in supply/wind_var.txt → ...mporal variability in supply/wind_var.txt
diff --git a/...temporal variability in supply/x_grid.txt → ...temporal variability in supply/x_grid.txt b/...temporal variability in supply/x_grid.txt → ...temporal variability in supply/x_grid.txt
diff --git a/...temporal variability in supply/y_grid.txt → ...temporal variability in supply/y_grid.txt b/...temporal variability in supply/y_grid.txt → ...temporal variability in supply/y_grid.txt
diff --git a/...temporal variability in supply/z_grid.txt → ...temporal variability in supply/z_grid.txt b/...temporal variability in supply/z_grid.txt → ...temporal variability in supply/z_grid.txt
diff --git a/...edictions of decadal development/Run2.txt → ...edictions of decadal development/Run2.txt b/...edictions of decadal development/Run2.txt → ...edictions of decadal development/Run2.txt
diff --git a/...ictions of decadal development/Run4.ipynb → ...ictions of decadal development/Run4.ipynb b/...ictions of decadal development/Run4.ipynb → ...ictions of decadal development/Run4.ipynb
diff --git a/...edictions of decadal development/Run4.txt → ...edictions of decadal development/Run4.txt b/...edictions of decadal development/Run4.txt → ...edictions of decadal development/Run4.txt
diff --git a/...ctions of decadal development/Run4_42.txt → ...ctions of decadal development/Run4_42.txt b/...ctions of decadal development/Run4_42.txt → ...ctions of decadal development/Run4_42.txt
diff --git a/... decadal development/Run4_42_10yr_new.txt → ... decadal development/Run4_42_10yr_new.txt b/... decadal development/Run4_42_10yr_new.txt → ... decadal development/Run4_42_10yr_new.txt
diff --git a/...ions of decadal development/Run4_42_2.txt → ...ions of decadal development/Run4_42_2.txt b/...ions of decadal development/Run4_42_2.txt → ...ions of decadal development/Run4_42_2.txt
diff --git a/...s of decadal development/Run4_42_long.txt → ...s of decadal development/Run4_42_long.txt b/...s of decadal development/Run4_42_long.txt → ...s of decadal development/Run4_42_long.txt
diff --git a/...ctions of decadal development/Run4_90.txt → ...ctions of decadal development/Run4_90.txt b/...ctions of decadal development/Run4_90.txt → ...ctions of decadal development/Run4_90.txt
diff --git a/... decadal development/Run4_90_10yr_new.txt → ... decadal development/Run4_90_10yr_new.txt b/... decadal development/Run4_90_10yr_new.txt → ... decadal development/Run4_90_10yr_new.txt
diff --git a/...f decadal development/Run4_90_1yr_new.txt → ...f decadal development/Run4_90_1yr_new.txt b/...f decadal development/Run4_90_1yr_new.txt → ...f decadal development/Run4_90_1yr_new.txt
diff --git a/... decadal development/Run4_90_1yr_new2.txt → ... decadal development/Run4_90_1yr_new2.txt b/... decadal development/Run4_90_1yr_new2.txt → ... decadal development/Run4_90_1yr_new2.txt
diff --git a/...ions of decadal development/Run4_90_2.txt → ...ions of decadal development/Run4_90_2.txt b/...ions of decadal development/Run4_90_2.txt → ...ions of decadal development/Run4_90_2.txt
diff --git a/...s of decadal development/Run4_90_long.txt → ...s of decadal development/Run4_90_long.txt b/...s of decadal development/Run4_90_long.txt → ...s of decadal development/Run4_90_long.txt
diff --git a/... decadal development/Run4_90_long_new.txt → ... decadal development/Run4_90_long_new.txt b/... decadal development/Run4_90_long_new.txt → ... decadal development/Run4_90_long_new.txt
diff --git a/...decadal development/Run4_90_long_new2.txt → ...decadal development/Run4_90_long_new2.txt b/...decadal development/Run4_90_long_new2.txt → ...decadal development/Run4_90_long_new2.txt
diff --git a/...decadal development/Run4_90_long_new3.txt → ...decadal development/Run4_90_long_new3.txt b/...decadal development/Run4_90_long_new3.txt → ...decadal development/Run4_90_long_new3.txt
diff --git a/... of decadal development/Run4_constant.txt → ... of decadal development/Run4_constant.txt b/... of decadal development/Run4_constant.txt → ... of decadal development/Run4_constant.txt
diff --git a/...ns of decadal development/Run4_long.ipynb → ...ns of decadal development/Run4_long.ipynb b/...ns of decadal development/Run4_long.ipynb → ...ns of decadal development/Run4_long.ipynb
diff --git a/...ons of decadal development/Run4_new.ipynb → ...ons of decadal development/Run4_new.ipynb b/...ons of decadal development/Run4_new.ipynb → ...ons of decadal development/Run4_new.ipynb
diff --git a/...ns of decadal development/Run4_play.ipynb → ...ns of decadal development/Run4_play.ipynb b/...ns of decadal development/Run4_play.ipynb → ...ns of decadal development/Run4_play.ipynb
diff --git a/...ions of decadal development/Run4_play.txt → ...ions of decadal development/Run4_play.txt b/...ions of decadal development/Run4_play.txt → ...ions of decadal development/Run4_play.txt
diff --git a/...ons of decadal development/Run4_play2.txt → ...ons of decadal development/Run4_play2.txt b/...ons of decadal development/Run4_play2.txt → ...ons of decadal development/Run4_play2.txt
diff --git a/...ons of decadal development/Run4_play3.txt → ...ons of decadal development/Run4_play3.txt b/...ons of decadal development/Run4_play3.txt → ...ons of decadal development/Run4_play3.txt
diff --git a/...ons of decadal development/Run4_play4.txt → ...ons of decadal development/Run4_play4.txt b/...ons of decadal development/Run4_play4.txt → ...ons of decadal development/Run4_play4.txt
diff --git a/...ons of decadal development/Run4_play5.txt → ...ons of decadal development/Run4_play5.txt b/...ons of decadal development/Run4_play5.txt → ...ons of decadal development/Run4_play5.txt
diff --git a/...dictions of decadal development/Run4b.txt → ...dictions of decadal development/Run4b.txt b/...dictions of decadal development/Run4b.txt → ...dictions of decadal development/Run4b.txt
diff --git a/...ons of decadal development/Run4b_corr.txt → ...ons of decadal development/Run4b_corr.txt b/...ons of decadal development/Run4b_corr.txt → ...ons of decadal development/Run4b_corr.txt
diff --git a/...dictions of decadal development/Run4c.txt → ...dictions of decadal development/Run4c.txt b/...dictions of decadal development/Run4c.txt → ...dictions of decadal development/Run4c.txt
diff --git a/...dictions of decadal development/Run4d.txt → ...dictions of decadal development/Run4d.txt b/...dictions of decadal development/Run4d.txt → ...dictions of decadal development/Run4d.txt
diff --git a/...ns of decadal development/Run4d_m_err.txt → ...ns of decadal development/Run4d_m_err.txt b/...ns of decadal development/Run4d_m_err.txt → ...ns of decadal development/Run4d_m_err.txt
diff --git a/...ons of decadal development/Run4d_stat.txt → ...ons of decadal development/Run4d_stat.txt b/...ons of decadal development/Run4d_stat.txt → ...ons of decadal development/Run4d_stat.txt
diff --git a/...dictions of decadal development/Run4e.txt → ...dictions of decadal development/Run4e.txt b/...dictions of decadal development/Run4e.txt → ...dictions of decadal development/Run4e.txt
diff --git a/...tions of decadal development/Run4e_EF.txt → ...tions of decadal development/Run4e_EF.txt b/...tions of decadal development/Run4e_EF.txt → ...tions of decadal development/Run4e_EF.txt
diff --git a/...ns of decadal development/Run4e_m_err.txt → ...ns of decadal development/Run4e_m_err.txt b/...ns of decadal development/Run4e_m_err.txt → ...ns of decadal development/Run4e_m_err.txt
diff --git a/...evelopment/figure_grid_initialization.png → ...evelopment/figure_grid_initialization.png b/...evelopment/figure_grid_initialization.png → ...evelopment/figure_grid_initialization.png
diff --git a/...elopment/figure_params_initialization.png → ...elopment/figure_params_initialization.png b/...elopment/figure_params_initialization.png → ...elopment/figure_params_initialization.png
diff --git a/...ment/figure_timeseries_initialization.png → ...ment/figure_timeseries_initialization.png b/...ment/figure_timeseries_initialization.png → ...ment/figure_timeseries_initialization.png
diff --git a/...redictions of decadal development/knmi.py → ...redictions of decadal development/knmi.py b/...redictions of decadal development/knmi.py → ...redictions of decadal development/knmi.py
diff --git a/...edictions of decadal development/logo.png → ...edictions of decadal development/logo.png b/...edictions of decadal development/logo.png → ...edictions of decadal development/logo.png
diff --git a/...ctions of decadal development/supply3.txt → ...ctions of decadal development/supply3.txt b/...ctions of decadal development/supply3.txt → ...ctions of decadal development/supply3.txt
diff --git a/...ns of decadal development/supply_file.txt → ...ns of decadal development/supply_file.txt b/...ns of decadal development/supply_file.txt → ...ns of decadal development/supply_file.txt
diff --git a/... decadal development/supply_file1min7.txt → ... decadal development/supply_file1min7.txt b/... decadal development/supply_file1min7.txt → ... decadal development/supply_file1min7.txt
diff --git a/... decadal development/supply_file1min8.txt → ... decadal development/supply_file1min8.txt b/... decadal development/supply_file1min8.txt → ... decadal development/supply_file1min8.txt
diff --git a/...ecadal development/supply_file1min8_2.txt → ...ecadal development/supply_file1min8_2.txt b/...ecadal development/supply_file1min8_2.txt → ...ecadal development/supply_file1min8_2.txt
diff --git a/... decadal development/supply_file5min5.txt → ... decadal development/supply_file5min5.txt b/... decadal development/supply_file5min5.txt → ... decadal development/supply_file5min5.txt
diff --git a/... decadal development/supply_file5min6.txt → ... decadal development/supply_file5min6.txt b/... decadal development/supply_file5min6.txt → ... decadal development/supply_file5min6.txt
diff --git a/... decadal development/supply_file5min7.txt → ... decadal development/supply_file5min7.txt b/... decadal development/supply_file5min7.txt → ... decadal development/supply_file5min7.txt
diff --git a/...adal development/uurgeg_235_2001-2010.txt → ...adal development/uurgeg_235_2001-2010.txt b/...adal development/uurgeg_235_2001-2010.txt → ...adal development/uurgeg_235_2001-2010.txt
diff --git a/...adal development/uurgeg_235_2011-2020.txt → ...adal development/uurgeg_235_2011-2020.txt b/...adal development/uurgeg_235_2011-2020.txt → ...adal development/uurgeg_235_2011-2020.txt
diff --git a/...ions of decadal development/wind_10yr.txt → ...ions of decadal development/wind_10yr.txt b/...ions of decadal development/wind_10yr.txt → ...ions of decadal development/wind_10yr.txt
diff --git a/...decadal development/wind_10yr_onshore.txt → ...decadal development/wind_10yr_onshore.txt b/...decadal development/wind_10yr_onshore.txt → ...decadal development/wind_10yr_onshore.txt
diff --git a/...ecadal development/wind_2006_2016_312.txt → ...ecadal development/wind_2006_2016_312.txt b/...ecadal development/wind_2006_2016_312.txt → ...ecadal development/wind_2006_2016_312.txt
diff --git a/...decadal development/wind_2006_2016_42.txt → ...decadal development/wind_2006_2016_42.txt b/...decadal development/wind_2006_2016_42.txt → ...decadal development/wind_2006_2016_42.txt
diff --git a/...decadal development/wind_2006_2016_90.txt → ...decadal development/wind_2006_2016_90.txt b/...decadal development/wind_2006_2016_90.txt → ...decadal development/wind_2006_2016_90.txt
diff --git a/...al development/wind_2006_2016_onshore.txt → ...al development/wind_2006_2016_onshore.txt b/...al development/wind_2006_2016_onshore.txt → ...al development/wind_2006_2016_onshore.txt
diff --git a/...ons of decadal development/wind_const.txt → ...ons of decadal development/wind_const.txt b/...ons of decadal development/wind_const.txt → ...ons of decadal development/wind_const.txt
diff --git a/...ctions of decadal development/x2_grid.txt → ...ctions of decadal development/x2_grid.txt b/...ctions of decadal development/x2_grid.txt → ...ctions of decadal development/x2_grid.txt
diff --git a/...ictions of decadal development/x_grid.txt → ...ictions of decadal development/x_grid.txt b/...ictions of decadal development/x_grid.txt → ...ictions of decadal development/x_grid.txt
diff --git a/...ctions of decadal development/y2_grid.txt → ...ctions of decadal development/y2_grid.txt b/...ctions of decadal development/y2_grid.txt → ...ctions of decadal development/y2_grid.txt
diff --git a/...ictions of decadal development/y_grid.txt → ...ictions of decadal development/y_grid.txt b/...ictions of decadal development/y_grid.txt → ...ictions of decadal development/y_grid.txt
diff --git a/...ctions of decadal development/z2_grid.txt → ...ctions of decadal development/z2_grid.txt b/...ctions of decadal development/z2_grid.txt → ...ctions of decadal development/z2_grid.txt
diff --git a/...ictions of decadal development/z_grid.txt → ...ictions of decadal development/z_grid.txt b/...ictions of decadal development/z_grid.txt → ...ictions of decadal development/z_grid.txt
diff --git a/...ries2023/Series of AeoLiS animations.pptx → ...ries2023/Series of AeoLiS animations.pptx b/...ries2023/Series of AeoLiS animations.pptx → ...ries2023/Series of AeoLiS animations.pptx
diff --git a/examples/deVries2023/Sweep_tests/Run1.txt → ...examples/deVries2023/Sweep_tests/Run1.txt b/examples/deVries2023/Sweep_tests/Run1.txt → ...examples/deVries2023/Sweep_tests/Run1.txt
diff --git a/examples/deVries2023/Sweep_tests/Run_q1.txt → ...amples/deVries2023/Sweep_tests/Run_q1.txt b/examples/deVries2023/Sweep_tests/Run_q1.txt → ...amples/deVries2023/Sweep_tests/Run_q1.txt
diff --git a/...deVries2023/Sweep_tests/Run_q1_supply.txt → ...deVries2023/Sweep_tests/Run_q1_supply.txt b/...deVries2023/Sweep_tests/Run_q1_supply.txt → ...deVries2023/Sweep_tests/Run_q1_supply.txt
diff --git a/examples/deVries2023/Sweep_tests/Run_q2.txt → ...amples/deVries2023/Sweep_tests/Run_q2.txt b/examples/deVries2023/Sweep_tests/Run_q2.txt → ...amples/deVries2023/Sweep_tests/Run_q2.txt
diff --git a/...deVries2023/Sweep_tests/Run_q2_supply.txt → ...deVries2023/Sweep_tests/Run_q2_supply.txt b/...deVries2023/Sweep_tests/Run_q2_supply.txt → ...deVries2023/Sweep_tests/Run_q2_supply.txt
diff --git a/examples/deVries2023/Sweep_tests/Run_q3.txt → ...amples/deVries2023/Sweep_tests/Run_q3.txt b/examples/deVries2023/Sweep_tests/Run_q3.txt → ...amples/deVries2023/Sweep_tests/Run_q3.txt
diff --git a/...deVries2023/Sweep_tests/Run_q3_supply.txt → ...deVries2023/Sweep_tests/Run_q3_supply.txt b/...deVries2023/Sweep_tests/Run_q3_supply.txt → ...deVries2023/Sweep_tests/Run_q3_supply.txt
diff --git a/examples/deVries2023/Sweep_tests/Run_q4.txt → ...amples/deVries2023/Sweep_tests/Run_q4.txt b/examples/deVries2023/Sweep_tests/Run_q4.txt → ...amples/deVries2023/Sweep_tests/Run_q4.txt
diff --git a/...deVries2023/Sweep_tests/Run_q4_supply.txt → ...deVries2023/Sweep_tests/Run_q4_supply.txt b/...deVries2023/Sweep_tests/Run_q4_supply.txt → ...deVries2023/Sweep_tests/Run_q4_supply.txt
diff --git a/...deVries2023/Sweep_tests/Sweep_tests.ipynb → ...deVries2023/Sweep_tests/Sweep_tests.ipynb b/...deVries2023/Sweep_tests/Sweep_tests.ipynb → ...deVries2023/Sweep_tests/Sweep_tests.ipynb
diff --git a/...s/deVries2023/Sweep_tests/supply_file.txt → ...s/deVries2023/Sweep_tests/supply_file.txt b/...s/deVries2023/Sweep_tests/supply_file.txt → ...s/deVries2023/Sweep_tests/supply_file.txt
diff --git a/examples/deVries2023/Sweep_tests/wind_q1.txt → ...mples/deVries2023/Sweep_tests/wind_q1.txt b/examples/deVries2023/Sweep_tests/wind_q1.txt → ...mples/deVries2023/Sweep_tests/wind_q1.txt
diff --git a/examples/deVries2023/Sweep_tests/wind_q2.txt → ...mples/deVries2023/Sweep_tests/wind_q2.txt b/examples/deVries2023/Sweep_tests/wind_q2.txt → ...mples/deVries2023/Sweep_tests/wind_q2.txt
diff --git a/examples/deVries2023/Sweep_tests/wind_q3.txt → ...mples/deVries2023/Sweep_tests/wind_q3.txt b/examples/deVries2023/Sweep_tests/wind_q3.txt → ...mples/deVries2023/Sweep_tests/wind_q3.txt
diff --git a/examples/deVries2023/Sweep_tests/wind_q4.txt → ...mples/deVries2023/Sweep_tests/wind_q4.txt b/examples/deVries2023/Sweep_tests/wind_q4.txt → ...mples/deVries2023/Sweep_tests/wind_q4.txt
diff --git a/examples/deVries2023/Sweep_tests/x_grid.txt → ...amples/deVries2023/Sweep_tests/x_grid.txt b/examples/deVries2023/Sweep_tests/x_grid.txt → ...amples/deVries2023/Sweep_tests/x_grid.txt
diff --git a/examples/deVries2023/Sweep_tests/y_grid.txt → ...amples/deVries2023/Sweep_tests/y_grid.txt b/examples/deVries2023/Sweep_tests/y_grid.txt → ...amples/deVries2023/Sweep_tests/y_grid.txt
diff --git a/examples/deVries2023/Sweep_tests/z_grid.txt → ...amples/deVries2023/Sweep_tests/z_grid.txt b/examples/deVries2023/Sweep_tests/z_grid.txt → ...amples/deVries2023/Sweep_tests/z_grid.txt
diff --git a/examples/deVries2023/tide_screenshot.PNG → .../examples/deVries2023/tide_screenshot.PNG b/examples/deVries2023/tide_screenshot.PNG → .../examples/deVries2023/tide_screenshot.PNG
diff --git a/aeolis/hydro.py b/aeolis/hydro.py
@@ -92,12 +92,6 @@ def interpolate(s, p, t):
             interp = NearestNDInterpolator(np.transpose(mask), s['SWL'][mask])
             s['SWL'] = interp( * np.indices(s['SWL'].shape))
 
-            # fig, ax = plt.subplots()
-            # pc = plt.pcolormesh(s['x'], s['y'], s['SWL'])#, vmin=1, vmax=1.3)
-            # ax.set_aspect('equal')
-            # fig.colorbar(pc, ax=ax)
-            # plt.show()
-
             print('!Be carefull, according to current implementation of importing waterlevel from Flexible Mesh, SWL is equal to DSWL = zs!')
             logger.warning('!Be carefull, according to current implementation of importing waterlevel from Flexible Mesh, SWL is equal to DSWL = zs!')
 
@@ -416,7 +410,37 @@ def update(s, p, dt,t):
 @njit
 def Boussinesq (GW, DSWL, ds, GW_stat, K_gw, ne_gw, D_gw,shl_ix, bound,zb,process_seepage_face):
     '''
-    Add description
+    Boussinesq equation for groundwater level change
+
+    Parameters
+    ----------
+    GW : numpy.ndarray
+        Groundwater level
+    DSWL : numpy.ndarray
+        Dynamic seawater level 
+    ds : numpy.ndarray
+        Cell size
+    GW_stat : float
+        Static groundwater level
+    K_gw : float
+        Hydraulic conductivity
+    ne_gw : float
+        Effective porosity
+    D_gw : float
+        Aquifer depth
+    shl_ix : numpy.ndarray
+        Index of shoreline location
+    bound : int
+        Landward boundary condition
+    zb : numpy.ndarray
+        Bed level
+    process_seepage_face : bool
+        Process seepage face
+
+    Returns 
+    -------
+    numpy.ndarray
+        Groundwater level change
     
     '''
 
@@ -468,8 +492,26 @@ def Boussinesq (GW, DSWL, ds, GW_stat, K_gw, ne_gw, D_gw,shl_ix, bound,zb,proces
 @njit
 def runup_overheight_distr(fx, fx_ix,shl_ix,runup_ix, x):
     '''
-    Add description
+    Compute distribution of infiltrated water due to wave runup according to Nielsen (1990)
+
+    Parameters
+    ----------
+    fx : numpy.ndarray
+        Distribution of infiltrated water
+    fx_ix : numpy.ndarray
+        Index of peak f(x)
+    shl_ix : numpy.ndarray
+        Index of shoreline location
+    runup_ix : numpy.ndarray
+        Index of runup limit
+    x : numpy.ndarray
+        x-coordinate
     
+    Returns
+    -------
+    numpy.ndarray
+        Distribution of infiltrated water
+
     '''
     for i in range(len(fx[:,0])):
         #Define index of peak f(x)
@@ -482,6 +524,61 @@ def runup_overheight_distr(fx, fx_ix,shl_ix,runup_ix, x):
 
 @njit
 def hdelta(wetting, scan_w, gw,gw_prev,scan_d,h_delta,zb,scan_w_moist,scan_d_moist,w_h,satd_moist,d_h,satw_moist,alfaw_moist,alfad_moist,resw_moist,resd_moist,mw_moist,md_moist,nw_moist,nd_moist):
+    '''
+    Compute suction at reversal between wetting/drying conditions
+
+    Parameters
+    ----------
+    wetting : numpy.ndarray
+        Flag indicating wetting or drying of soil profile
+    scan_w : numpy.ndarray
+        Flag indicating that the moisture is calculated on the wetting scanning curve
+    gw : numpy.ndarray
+        Groundwater level
+    gw_prev : numpy.ndarray
+        Groundwater level in previous timestep
+    scan_d : numpy.ndarray
+        Flag indicating that the moisture is calculated on the drying scanning curve
+    h_delta : numpy.ndarray
+        Suction at reversal between wetting/drying conditions
+    zb : numpy.ndarray
+        Bed level
+    scan_w_moist : numpy.ndarray
+        Moisture content on wetting scanning curve
+    scan_d_moist : numpy.ndarray
+        Moisture content on drying scanning curve
+    w_h : numpy.ndarray
+        Moisture content on wetting curve
+    satd_moist : float
+        Moisture content at saturation on drying curve
+    d_h : numpy.ndarray
+        Moisture content on drying curve
+    satw_moist : float
+        Moisture content at saturation on wetting curve
+    alfaw_moist : float
+        Inverse of the air-entry value for a wetting branch of the soil water retention function
+    alfad_moist : float
+        Inverse of the air-entry value for a drying branch of the soil water retention function
+    resw_moist : float
+        Residual moisture content on wetting curve
+    resd_moist : float
+        Residual moisture content on drying curve
+    mw_moist : float
+        Shape parameter for the wetting branch of the soil water retention function
+    md_moist : float
+        Shape parameter for the drying branch of the soil water retention function
+    nw_moist : float
+        Pore-size distribution index in the soil water retention function, wetting branch
+    nd_moist : float
+        Pore-size distribution index in the soil water retention function, drying branch
+
+    Returns
+    -------
+    numpy.ndarray
+        Suction at reversal between wetting/drying conditions
+
+    '''
+
     for i in range(len(wetting[:,0])):
         for j in range(len(wetting[0,:])):
             #Compute h delta on the main drying and wetting curve
@@ -512,6 +609,39 @@ def hdelta(wetting, scan_w, gw,gw_prev,scan_d,h_delta,zb,scan_w_moist,scan_d_moi
 
 @njit
 def SWR_curve(wetting,gw,gw_prev,scan_w,moist_swr,w_h,scan_d,scan_w_moist,d_h,scan_d_moist):
+    '''
+    Compute moisture content due to capillary processes
+
+    Parameters
+    ----------
+    wetting : numpy.ndarray
+        Flag indicating wetting or drying of soil profile
+    gw : numpy.ndarray
+        Groundwater level
+    gw_prev : numpy.ndarray
+        Groundwater level in previous timestep
+    scan_w : numpy.ndarray
+        Flag indicating that the moisture is calculated on the wetting scanning curve
+    moist_swr : numpy.ndarray
+        Moisture content due to capillary processes
+    w_h : numpy.ndarray
+        Moisture content on wetting curve
+    scan_d : numpy.ndarray
+        Flag indicating that the moisture is calculated on the drying scanning curve
+    scan_w_moist : numpy.ndarray
+        Moisture content on wetting scanning curve
+    d_h : numpy.ndarray
+        Moisture content on drying curve
+    scan_d_moist : numpy.ndarray
+        Moisture content on drying scanning curve
+
+    Returns
+    -------
+    numpy.ndarray
+        Moisture content due to capillary processes
+
+    '''
+
     for i in range(len(wetting[:,0])):
         for j in range(len(wetting[0,:])):
             #Wetting conditions main curve
@@ -625,6 +755,25 @@ def saturation_pressure(T):
 def calc_runup_stockdon(Ho, Tp, beta):
     """
     Calculate runup according to /Stockdon et al 2006.
+
+    Parameters
+    ----------
+    Ho : float or numpy.ndarray
+        Significant wave height
+    Tp : float or numpy.ndarray
+        Peak period
+    beta : float
+        Beach slope
+
+    Returns
+    -------
+    eta : float or numpy.ndarray
+        Runup height
+    sigma_s : float or numpy.ndarray
+        Setup height
+    R : float or numpy.ndarray
+        Total runup height
+
     """
 
     if hasattr(Ho, "__len__"):