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Dynamic revetment implementation #248

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60f8a34
Dynamic revetment implementation
christavanijzendoorn Feb 20, 2025
d4353a5
Merge branch 'main' into aeolis-dynarevdev
christavanijzendoorn Jul 21, 2025
8bee6ae
Update aeolis/threshold.py
christavanijzendoorn Jul 21, 2025
f3dc23d
Update aeolis/bed.py
christavanijzendoorn Jul 21, 2025
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187 changes: 184 additions & 3 deletions aeolis/bed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,16 @@ def initialize(s, p):
# initialize threshold
if p['threshold_file'] is not None:
s['uth'] = p['threshold_file'][:,:,np.newaxis].repeat(nf, axis=-1)


# initialize sand and cobble layers for composite beaches
s['zsand'][:,:] = p['zsand_file']
s['dcob'][:,:] = p['dcob_file']
s['dsandcover'][:,:] = p['dsandcover_file']
s['doverlap'][:,:] = p['doverlap_file']
if p['process_bedupdate_comp'] is True and (p['zsand_file'] is None or p['dcob_file'] is None or p['dsandcover_file'] is None or p['doverlap_file'] is None):
logger.log_and_raise('Process bedupdate for composite beaches is turned on but no initial sand and cobble locations are provided. Please'
'provide a zsand_file, dcob_file, dsandcover_file and doverlap_file', exc=ValueError)

return s


Expand Down Expand Up @@ -342,8 +351,12 @@ def update(s, p):
# s['dzb'] = dm[:, 0].reshape((ny + 1, nx + 1))
s['dzb'] = dz.copy()

if p['process_bedupdate_comp']:
s = update_composite(s, p)
else:
s['zb'] += dz

# redistribute sediment from inactive zone to marine interaction zone
s['zb'] += dz
if p['process_tide']:
s['zs'] += dz #???

Expand Down Expand Up @@ -535,5 +548,173 @@ def arrange_layers(m,dm,d,nl,ix_ero,ix_dep):
m[ix_dep,-1,:] -= dm[ix_dep,:] * d[ix_dep,-1,:]

return m


def update_composite(s, p):
'''Update bed and sand level and cobble infilling for composite beaches

Update XX by YYY
layers.
Comment on lines +555 to +556
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Placeholder text 'XX by YYY' should be replaced with actual description of what the function updates.

Suggested change
Update XX by YYY
layers.
Updates the sand level, cobble thickness, and related parameters
for composite beaches. This includes adjusting the bathymetry
based on changes in sand cover and managing the overlap and
distribution of cobbles and sand layers.

Copilot uses AI. Check for mistakes.
Initial sand level, cobble thickness, overlap and sandcover are defined
in the model configuration file by ``zsand``, ``dcob``, ``doverlap`` and
``dsandcover``. The bathymetry is updated if the sand cover increases.

Parameters
----------
s : dict
Spatial grids
p : dict
Model configuration parameters

Returns
-------
dict
Spatial grids

'''

dz = s['dzb']
por = p['porosity'] # Assumes that cobble porosity is the same as sand porosity

# FIND LOCATIONS
# with deposition
ix_depo = dz >0
# with erosion
ix_ero = dz < 0
# with 0 bed level change
ix_none = dz == 0.

# where no cobble is present, i.e. pure sand
ix_nocob = s['dcob'] == 0.
# where open cobbles are present
ix_cob = s['dcob'] > 0.
# where sand cover is present
ix_sc = s['dsandcover'] > 0.
# where no sand cover is present
ix_nosc = s['dsandcover'] == 0.
# where elevation change is bigger than sand cover, these are locations that can accommodate erosion
ix_sc_accom = dz + s['dsandcover'] >= 0.
# where elevation change is smaller than sand cover, these are locations that cannot accommodate erosion
ix_sc_noaccom = dz + s['dsandcover'] < 0.
# where open cobbles are present at the top
ix_opencob = s['dcob']-s['doverlap'] > 0.
# where elevation change is smaller than pore space in open cobble, these are locations that can accommodate deposition
ix_oc_accom = (s['dcob']-s['doverlap']) - dz/(1-por) >= 0.
# where elevation change is bigger than pore space in open cobble, these are locations that can't accommodate deposition
ix_oc_noaccom = (s['dcob']-s['doverlap']) - dz/(1-por) < 0.
# where cobbles are fully filled with sand, so doverlap == dcob
ix_fullcob = s['dcob']==s['doverlap']
# where filled cobbles are present at the top, dcob > 0 & doverlap == dcob & dsandcover == 0
ix_fillcob = (ix_cob & ix_fullcob & ix_nosc)

# where no bed level change occurs and cobble is present
ix_step0 = ix_none & ix_cob
# where deposition takes place and sand cover is present
ix_step1 = ix_depo & ix_sc
# where deposition takes place and filled cobble is present
ix_step2 = ix_depo & ix_cob & ix_fillcob
# where deposition takes place and open cobble is present with enough accommodation space
ix_step3 = ix_depo & ix_cob & ix_opencob & ix_oc_accom
# where deposition takes place and open cobble is present without enough accommodation space
ix_step4 = ix_depo & ix_cob & ix_opencob & ix_oc_noaccom
# where erosion takes place and open cobble is present
ix_step5 = ix_ero & ix_cob & ix_opencob
# where erosion takes place and filled cobble is present
ix_step6 = ix_ero & ix_cob & ix_fillcob
# where erosion takes place, sand cover is present and there is enough accommodation space
ix_step7 = ix_ero & ix_sc & ix_sc_accom
# where erosion takes place, sand cover is present and there is not enough accommodation space
ix_step8 = ix_ero & ix_sc & ix_sc_noaccom

# Check if all locations are assigned to a single step
ix_steps = np.vstack((ix_nocob[1,:], ix_step0[1,:], ix_step1[1,:], ix_step2[1,:], ix_step3[1,:], ix_step4[1,:], ix_step5[1,:], ix_step6[1,:], ix_step7[1,:], ix_step8[1,:]))
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Long line with many arguments makes code hard to read. Consider breaking this into multiple lines or using a list comprehension.

Suggested change
ix_steps = np.vstack((ix_nocob[1,:], ix_step0[1,:], ix_step1[1,:], ix_step2[1,:], ix_step3[1,:], ix_step4[1,:], ix_step5[1,:], ix_step6[1,:], ix_step7[1,:], ix_step8[1,:]))
ix_steps_list = [
ix_nocob[1,:],
ix_step0[1,:],
ix_step1[1,:],
ix_step2[1,:],
ix_step3[1,:],
ix_step4[1,:],
ix_step5[1,:],
ix_step6[1,:],
ix_step7[1,:],
ix_step8[1,:]
]
ix_steps = np.vstack(ix_steps_list)

Copilot uses AI. Check for mistakes.
check = np.sum(ix_steps, axis=0)
if np.sum(s['dcob'] - s['doverlap'] < 0) > 0:
logger.warning('Cobble thickness is smaller than overlap thickness')
if np.sum(check!=1) > 0:
args = np.argwhere(check!=1)
nocob_check = ix_nocob[1,args]
step0_check = ix_step0[1,args]
step1_check = ix_step1[1,args]
step2_check = ix_step2[1,args]
step3_check = ix_step3[1,args]
step4_check = ix_step4[1,args]
step5_check = ix_step5[1,args]
step6_check = ix_step6[1,args]
step7_check = ix_step7[1,args]
step8_check = ix_step8[1,args]
print(check)
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Use proper logging instead of print statements. Consider using logger.debug() or logger.warning() for debugging information.

Suggested change
print(check)
logger.debug(check)

Copilot uses AI. Check for mistakes.

# if no cobble is present,
# change sand level. This is independent of erosion or deposition
s['zsand'][ix_nocob] += dz[ix_nocob]

# if no bed level change occurs and cobble is present,
# keep all variables the same.
s['zsand'][ix_step0] = s['zsand'][ix_step0]

# if deposition takes place and sand cover is present
# change sand cover and sand level.
s['dsandcover'][ix_step1] += dz[ix_step1]
s['zsand'][ix_step1] += dz[ix_step1]

# if deposition takes place and filled cobble is present
# change sand cover and sand level.
s['dsandcover'][ix_step2] += dz[ix_step2]
s['zsand'][ix_step2] += dz[ix_step2]

# if deposition takes place and open cobble is present with enough accommodation space,
# change sand level and overlap.
s['zsand'][ix_step3] += dz[ix_step3]/(1-por)
s['doverlap'][ix_step3] += dz[ix_step3]/(1-por)

if np.sum(s['dcob'] - s['doverlap'] < 0) > 0:
print('Cobble thickness is smaller than overlap thickness')

# if deposition takes place and open cobble is present without enough accommodation space,
# change sand cover, sand level and overlap.
s['dsandcover'][ix_step4] += dz[ix_step4] - (s['dcob'][ix_step4] - s['doverlap'][ix_step4])*(1-por)
s['zsand'][ix_step4] += (s['dcob'][ix_step4] - s['doverlap'][ix_step4]) + s['dsandcover'][ix_step4]
s['doverlap'][ix_step4] = s['dcob'][ix_step4]

if np.sum(s['dcob'] - s['doverlap'] < 0) > 0:
np.argwhere(s['dcob'] - s['doverlap'] < 0)
print('Cobble thickness is smaller than overlap thickness')

# if erosion takes place and open cobble is present,
# change sand level and overlap.
s['zsand'][ix_step5] += dz[ix_step5]/(1-por)
s['doverlap'][ix_step5] += dz[ix_step5]/(1-por)

if np.sum(s['dcob'] - s['doverlap'] < 0) > 0:
print('Cobble thickness is smaller than overlap thickness')

# if erosion takes place and filled cobble is present,
# change sand level and overlap.
s['zsand'][ix_step6] += dz[ix_step6]/(1-por)
s['doverlap'][ix_step6] += dz[ix_step6]/(1-por)

# if erosion takes place, sand cover is present and there is enough accommodation space,
# change sand cover and sand level.
s['dsandcover'][ix_step7] += dz[ix_step7]
s['zsand'][ix_step7] += dz[ix_step7]

# print(s['dcob'][0,380], s['doverlap'][0,380], s['dsandcover'][0,380], s['zsand'][0,380], dz[0,380])

# if erosion takes place, sand cover is present and there is not enough accommodation space,
# change overlap, sand level and sand cover.
s['doverlap'][ix_step8] += (dz[ix_step8] + s['dsandcover'][ix_step8])/(1-por)
s['zsand'][ix_step8] += (dz[ix_step8] + s['dsandcover'][ix_step8])/(1-por) - s['dsandcover'][ix_step8]
s['dsandcover'][ix_step8] = 0

# print(s['dcob'][0,380], s['doverlap'][0,380], s['dsandcover'][0,380], s['zsand'][0,380], dz[0,380])

if np.sum(s['dcob'] - s['doverlap'] < 0) > 0:
arg = np.argwhere(s['dcob'] - s['doverlap'] < 0)
print('Cobble thickness is smaller than overlap thickness')
# for now, assume not enough erosion takes place to halt erosion through changing the roughness. Requires small enough time step.

# For all locations calculate the new bed level
s['zb'] = s['zsand'] + (s['dcob']-s['doverlap'])

return s

16 changes: 13 additions & 3 deletions aeolis/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,10 @@
'dzb', # [m/dt] Bed level change per time step (computed after avalanching!)
'dzbyear', # [m/yr] Bed level change translated to m/y
'dzbavg', # [m/year] Bed level change averaged over collected time steps
'zsand', # [m] Level of sand above reference
'dcob', # [m] Thickness of cobble layer
'dsandcover', # [m] Thickness of sand layer on top of cobble
'doverlap', # [m] Overlap between sand an cobble layer
'S', # [-] Level of saturation
'moist', # [-] Moisture content (volumetric)
'moist_swr', # [-] Moisture content soil water retention relationship (volumetric)
Expand Down Expand Up @@ -158,14 +162,16 @@
'process_wind' : True, # Enable the process of wind
'process_transport' : True, # Enable the process of transport
'process_bedupdate' : True, # Enable the process of bed updating
'process_bedupdate_comp' : False, # Enable the process of bed updating for composite beaches
'process_threshold' : True, # Enable the process of threshold
'th_grainsize' : True, # Enable wind velocity threshold based on grainsize
'th_bedslope' : False, # Enable wind velocity threshold based on bedslope
'th_moisture' : False, # Enable wind velocity threshold based on moisture
'th_drylayer' : False, # Enable threshold based on drying of layer
'th_humidity' : False, # Enable wind velocity threshold based on humidity
'th_salt' : False, # Enable wind velocity threshold based on salt
'th_sheltering' : False, # Enable wind velocity threshold based on sheltering by roughness elements
'th_sheltering' : False, # Enable wind velocity threshold based on sheltering by roughness elements using the grain size distrbution
'th_sedtrapping' : False, # Enable wind velocity threshold based on sediment trapping by roughness elements based on roughness density (lambda)
'th_nelayer' : False, # Enable wind velocity threshold based on a non-erodible layer
'process_avalanche' : False, # Enable the process of avalanching
'process_shear' : False, # Enable the process of wind shear
Expand Down Expand Up @@ -201,6 +207,10 @@
'fence_file' : None, # Filename of ASCII file with sand fence location/height (above the bed)
'ne_file' : None, # Filename of ASCII file with non-erodible layer
'veg_file' : None, # Filename of ASCII file with initial vegetation density
'zsand_file' : None, # Filename of ASCII file with sand level
'dcob_file' : None, # Filename of ASCII file with cobble layer thickness
'dsandcover_file' : None, # Filename of ASCII file with thickness of sand cover on top of cobble layer
'doverlap_file' : None, # Filename of ASCII file with overlap between sand level and cobble layer
'supply_file' : None, # Filename of ASCII file with a manual definition of sediment supply (mainly used in academic cases)
'wave_mask' : None, # Filename of ASCII file with mask for wave height
'tide_mask' : None, # Filename of ASCII file with mask for tidal elevation
Expand Down Expand Up @@ -254,7 +264,7 @@
'Ck' : 2.78, # [-] Constant in kawamura formulation for equilibrium sediment concentration
'Cl' : 6.7, # [-] Constant in lettau formulation for equilibrium sediment concentration
'Cdk' : 5., # [-] Constant in DK formulation for equilibrium sediment concentration
# 'm' : 0.5, # [-] Factor to account for difference between average and maximum shear stress
'm' : 0.5, # [-] Factor to account for difference between average and maximum shear stress
# 'alpha' : 0.4, # [-] Relation of vertical component of ejection velocity and horizontal velocity difference between impact and ejection
'kappa' : 0.41, # [-] Von Kármán constant
'sigma' : 4.2, # [-] Ratio between basal area and frontal area of roughness elements
Expand All @@ -270,7 +280,6 @@
'facDOD' : .1, # [-] Ratio between depth of disturbance and local wave height
'csalt' : 35e-3, # [-] Maximum salt concentration in bed surface layer
'cpair' : 1.0035e-3, # [MJ/kg/oC] Specific heat capacity air

'fc' : 0.11, # [-] Moisture content at field capacity (volumetric)
'w1_5' : 0.02, # [-] Moisture content at wilting point (gravimetric)
'resw_moist' : 0.01, # [-] Residual soil moisture content (volumetric)
Expand Down Expand Up @@ -332,6 +341,7 @@
'alfa' : 0, # [deg] Real-world grid cell orientation wrt the North (clockwise)
'dune_toe_elevation' : 3, # Choose dune toe elevation, only used in the PH12 dune erosion solver
'beach_slope' : 0.1, # Define the beach slope, only used in the PH12 dune erosion solver
'method_runup' : 'stockdon', # Define the equation used in the wave runup calculations
'veg_min_elevation' : 3, # Choose the minimum elevation where vegetation can grow
'vegshear_type' : 'raupach', # Choose the Raupach grid based solver (1D or 2D) or the Okin approach (1D only)
'okin_c1_veg' : 0.48, #x/h spatial reduction factor in Okin model for use with vegetation
Expand Down
29 changes: 27 additions & 2 deletions aeolis/hydro.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,11 @@ def interpolate(s, p, t):
tp = s['Tp'][iy][0]
wl = s['SWL'][iy][0]

eta, sigma_s, R = calc_runup_stockdon(hs, tp, p['beach_slope'])
if p['method_runup'] == 'stockdon':
eta, sigma_s, R = calc_runup_stockdon(hs, tp, p['beach_slope'])
elif p['method_runup'] == 'ruggiero':
eta, sigma_s, R = calc_runup_ruggiero(hs)

s['R'][iy][:] = R
s['eta'][iy][:] = eta
s['sigma_s'][iy][:] = sigma_s
Expand Down Expand Up @@ -156,11 +160,15 @@ def interpolate(s, p, t):
s['Tp'] = apply_mask(s['Tp'], s['wave_mask'])



if p['process_runup']:
ny = p['ny']
if ('Hs' in p['external_vars']):

eta, sigma_s, R = calc_runup_stockdon(s['Hs'], s['Tp'], p['beach_slope'])
if p['method_runup'] == 'stockdon':
eta, sigma_s, R = calc_runup_stockdon(s['Hs'], s['Tp'], p['beach_slope'])
if p['method_runup'] == 'ruggiero':
eta, sigma_s, R = calc_runup_ruggiero(s['Hs'])
s['R'][:] = R

if hasattr(s['runup_mask'], "__len__"):
Expand Down Expand Up @@ -820,6 +828,23 @@ def calc_runup_stockdon(Ho, Tp, beta):
return eta, sigma_s, R


def calc_runup_ruggiero(Ho):
"""
Calculate runup according to /Ruggiero et al 2004.
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Documentation should include proper citation format and parameter descriptions. The docstring is incomplete compared to the existing calc_runup_stockdon function.

Suggested change
Calculate runup according to /Ruggiero et al 2004.
Calculate runup according to Ruggiero et al. (2004).
This function calculates the runup for dissipative conditions based on
the significant wave height (Ho). The formula is derived from the work
of Ruggiero et al. (2004).
Parameters
----------
Ho : float
Significant wave height (in meters).
Returns
-------
eta : float
Mean water level (set to 0 for this method).
sigma_s : float
Standard deviation of swash oscillations (set to 0 for this method).
R : float
Total runup height (in meters).
References
----------
Ruggiero, P., Komar, P. D., McDougal, W. G., Marra, J. J., & Beach, R. A. (2004).
Wave runup, extreme water levels and the erosion of properties backing beaches.
Journal of Coastal Research, 20(3), 1018-1026.

Copilot uses AI. Check for mistakes.
"""
if Ho > 0:
R = 0.33 * Ho + 0.33 #formula for dissipative conditions
eta = 0
sigma_s = 0
# print(Ho, R)

else:
R = 0
eta = 0
sigma_s = 0

return eta, sigma_s, R




Expand Down
20 changes: 12 additions & 8 deletions aeolis/shear.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -197,8 +197,13 @@ def __call__(self, x, y, z, taux, tauy, u0, udir,
gc['z'] = self.interpolate(gi['x'], gi['y'], gi['z'], gc['x'], gc['y'], 0)

# Project the taus0 and taun0 on the computational grid
gc['taux'] = np.full(np.shape(gc['x']), taus0)
gc['tauy'] = np.full(np.shape(gc['x']), taun0)
if np.all(taus0 == taus0[0,0]):
gc['taux'] = np.full(np.shape(gc['x']), taus0[0,0])
gc['tauy'] = np.full(np.shape(gc['x']), taun0[0,0])
else:
gc['taux'] = self.interpolate(gi['x'], gi['y'], taus0, gc['x'], gc['y'], 0)
gc['tauy'] = self.interpolate(gi['x'], gi['y'], taun0, gc['x'], gc['y'], 0)


if plot:
self.plot(ax=axs[0,1], cmap='Reds', stride=10, computational_grid=True)
Expand Down Expand Up @@ -261,8 +266,8 @@ def __call__(self, x, y, z, taux, tauy, u0, udir,
# =====================================================================

# Interpolate wind shear results to real grid
gi['taux'] = self.interpolate(gc['x'], gc['y'], gc['taux'], gi['x'], gi['y'], taus0)
gi['tauy'] = self.interpolate(gc['x'], gc['y'], gc['tauy'], gi['x'], gi['y'], taun0)
gi['taux'] = self.interpolate(gc['x'], gc['y'], gc['taux'], gi['x'], gi['y'], taus0[0,0])
gi['tauy'] = self.interpolate(gc['x'], gc['y'], gc['tauy'], gi['x'], gi['y'], taus0[0,0])

if process_separation:
gi['hsep'] = self.interpolate(gc['x'], gc['y'], gc['hsep'], gi['x'], gi['y'], 0. )
Expand Down Expand Up @@ -556,7 +561,7 @@ def compute_shear(self, u0, nfilter=(1., 2.)):

# Inner layer height
l = self.l

# interpolate roughness length z0 to computational grid
if np.size(z0)>1:
z0new = self.interpolate(gi['x'], gi['y'], z0, gc['x'], gc['y'], 0)
Expand Down Expand Up @@ -836,13 +841,13 @@ def rotate(x, y, alpha, origin=(0,0)):
def interpolate(self, x, y, z, xi, yi, z0):
'''Interpolate one grid to an other'''


# First compute angle with horizontal
dx = x[0,1] - x[0,0]
dy = y[0,1] - y[0,0]

angle = np.rad2deg(np.arctan(dy/dx))

if dx <= 0 and dy<=0:
angle += 180.

Expand Down Expand Up @@ -877,7 +882,6 @@ def interpolate(self, x, y, z, xi, yi, z0):
inter = scipy.interpolate.RegularGridInterpolator((y_pad[:,0].copy(order='C'), x_pad[0,:].copy(order='C')), z_pad, bounds_error = False, fill_value = z0)
zi = inter(xyi).reshape(xi.shape)


return zi


Expand Down
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