def run(self):
# self.timers[0].tic()
self.logger.info('Running module StaticAvailability')
################################################################################################################
## Init
################################################################################################################
jmax = self.input.v('grid', 'maxIndex', 'x')
kmax = self.input.v('grid', 'maxIndex', 'z')
fmax = self.input.v('grid', 'maxIndex', 'f')
L = self.input.v('L')
self.x = self.input.v('grid', 'axis', 'x')
self.zarr = ny.dimensionalAxis(self.input.slice('grid'), 'z')[:, :, 0]-self.input.v('R', x=self.x/L).reshape((len(self.x), 1)) #YMD 22-8-17 includes reference level; note that we take a reference frame z=[-H-R, 0]
c00 = np.real(self.input.v('hatc0', 'a', range(0, jmax+1), range(0, kmax+1), 0))
c04 = np.abs(self.input.v('hatc0', 'a', range(0, jmax+1), range(0, kmax+1), 2))
# c20 = np.real(self.input.v('hatc2', 'a', range(0, jmax+1), range(0, kmax+1), 0)) # NB. do not include hatc2 in the definition of alpha1 here
alpha1 = ny.integrate(c00, 'z', kmax, 0, self.input.slice('grid'))[:, 0]
alpha1[-1] += alpha1[-2] # correct alpha1 at last point to prevent zero value
alpha2 = ny.integrate(c04, 'z', kmax, 0, self.input.slice('grid'))[:, 0]/(alpha1+1e-10) + 1.e-3
# self.timers[0].toc()
################################################################################################################
## Compute T and F
################################################################################################################
# self.timers[1].tic()
d = self.compute_transport()
G = self.compute_source()
# self.timers[1].toc()
################################################################################################################
## 4. Calculate availability
################################################################################################################
# self.timers[2].tic()
# Add all mechanisms to datacontainer
dctrans = DataContainer(d)
# Calculate availability
a, f0, f0x = self.availability(dctrans.v('F', range(0, jmax+1)), dctrans.v('T', range(0, jmax+1)), G, alpha1, alpha2)
f0 = f0.reshape(jmax+1, 1)
f0x = f0x.reshape(jmax+1, 1)
d['a'] = a
nfu = ny.functionTemplates.NumericalFunctionWrapper(f0[:, 0], self.input.slice('grid'))
nfu.addDerivative(f0x[:, 0], 'x')
d['f'] = nfu.function
# self.timers[2].toc()
################################################################################################################
# 5. Calculate concentrations, i.e. a*hatc(a) + ax*hatc(ax)
################################################################################################################
# self.timers[3].tic()
d['c0'] = {}
d['c1'] = {}
d['c2'] = {}
# Calculate c0=f*hatc0
for submod in self.input.getKeysOf('hatc0', 'a'):
c0_comp = self.input.v('hatc0', 'a', submod, range(0, jmax+1), range(0, kmax+1), range(0, fmax+1))
d['c0'][submod] = {}
tmp = f0[:, None] * c0_comp
d['c0'][submod] = tmp
# Calculate c1 = f*hatc1_f + fx*hatc1_fx
for submod in self.input.getKeysOf('hatc1', 'a'):
if submod == 'erosion':
for subsubmod in self.input.getKeysOf('hatc1', 'a', 'erosion'):
c1_comp = self.input.v('hatc1', 'a', 'erosion', subsubmod, range(0, jmax+1), range(0, kmax+1), range(0, fmax+1))
d['c1'] = self.dictExpand(d['c1'], 'erosion', subsubmod)
tmp = f0[:, None] * c1_comp
d['c1']['erosion'][subsubmod] = tmp
elif submod == 'sedadv':
c1_comp_a = self.input.v('hatc1', 'a', 'sedadv', range(0, jmax+1), range(0, kmax+1), range(0, fmax+1))
c1_comp_ax = self.input.v('hatc1', 'ax', 'sedadv', range(0, jmax+1), range(0, kmax+1), range(0, fmax+1))
d['c1'][submod] = {}
tmp = f0[:, None] * c1_comp_a + f0x[:, None] * c1_comp_ax
d['c1'][submod] = tmp
else:
c1_comp = self.input.v('hatc1', 'a', submod, range(0, jmax+1), range(0, kmax+1), range(0, fmax+1))
d['c1'][submod] = {}
tmp = f0[:, None] * c1_comp
d['c1'][submod] = tmp
# Calculate c2 = f*hatc2
for subsubmod in self.input.getKeysOf('hatc2', 'a', 'erosion'):
c2_comp = self.input.v('hatc2', 'a', 'erosion', subsubmod, range(0, jmax+1), range(0, kmax+1), range(0, fmax+1))
d['c2'] = self.dictExpand(d['c2'], 'erosion', subsubmod)
tmp = f0[:, None] * c2_comp
d['c2']['erosion'][subsubmod] = tmp
# self.timers[3].toc()
# self.timers[0].disp('time availability - init')
# self.timers[1].disp('time availability - T, F')
# self.timers[2].disp('time availability - a, f')
# self.timers[3].disp('time availability - to dict')
# self.timers[4].disp('time availability - cap')
# self.timers[5].disp('time availability - trap')
# [self.timers[i].reset() for i in range(0, len(self.timers))]
return d
def run(self):
""" """
self.logger.info('Running module DynamicAvailability_upwind')
################################################################################################################
# Init
################################################################################################################
jmax = self.input.v('grid', 'maxIndex', 'x')
kmax = self.input.v('grid', 'maxIndex', 'z')
fmax = self.input.v('grid', 'maxIndex', 'f')
self.x = ny.dimensionalAxis(self.input.slice('grid'), 'x')[:, 0, 0]
self.dx = (self.x[1:] - self.x[:-1])
self.zarr = ny.dimensionalAxis(self.input.slice('grid'), 'z')[:, :, 0]
self.B = self.input.v('B', range(0, jmax + 1))
self.Bx = self.input.d('B', range(0, jmax + 1), dim='x')
self.Kh = self.input.v('Kh')
self.u0tide_bed = self.input.v('u0', 'tide', range(0, jmax + 1), kmax,
1)
c00 = np.real(
self.input.v('hatc0', range(0, jmax + 1), range(0, kmax + 1), 0))
c04 = np.abs(
self.input.v('hatc0', range(0, jmax + 1), range(0, kmax + 1), 2))
c04_int = np.trapz(c04, x=-self.zarr)
hatc2 = np.abs(
self.input.v('hatc2', range(0, jmax + 1), range(0, kmax + 1), 0))
alpha1 = np.trapz(c00 + hatc2, x=-self.zarr, axis=1)
if alpha1[-1] == 0:
alpha1[-1] = alpha1[-2]
alpha2 = c04_int / alpha1 + 1e-3
## load time series Q
t = self.interpretValues(self.input.v('t'))
toutput = self.interpretValues(self.input.v('toutput'))
toutput[0] = t[
0] # correct output time; first time level is always equal to initial computation time
Qarray = self.interpretValues(self.input.v('Q1'))
if len(Qarray) != len(t):
from src.util.diagnostics.KnownError import KnownError
raise KnownError(
'Length of Q does not correspond to length of time array.')
################################################################################################################
# Compute transport, source and BC
################################################################################################################
## Transport
d = self.compute_transport()
dc = DataContainer(d)
# change size of those components that depend on the river discharge and put init value in first element
T_r = copy(dc.v('T', 'river', range(0, jmax + 1)))
T_rr = copy(dc.v('T', 'river_river', range(0, jmax + 1)))
T_dr = copy(dc.v('T', 'diffusion_river', range(0, jmax + 1)))
F_dr = dc.v('F', 'diffusion_river', range(0, jmax + 1))
d['T']['river'] = np.zeros((jmax + 1, 1, 1, len(toutput)))
d['T']['river'][:, 0, 0, 0] = T_r
d['T']['river_river'] = np.zeros((jmax + 1, 1, 1, len(toutput)))
d['T']['river_river'][:, 0, 0, 0] = T_rr
d['T']['diffusion_river'] = np.zeros((jmax + 1, 1, 1, len(toutput)))
d['T']['diffusion_river'][:, 0, 0, 0] = T_dr
d['F']['diffusion_river'] = np.zeros((jmax + 1, 1, 1, len(toutput)))
d['F']['diffusion_river'][:, 0, 0, 0] = F_dr
T = dc.v('T', range(0, jmax + 1), 0, 0, 0)
F = dc.v('F', range(0, jmax + 1), 0, 0, 0)
## Source
G = self.compute_source() #NB does not change over long time scale
## Seaward boundary condition
if self.input.v('sedbc') == 'csea':
csea = self.input.v('csea')
fsea = csea / alpha1[0] * (
self.input.v('grid', 'low', 'z', 0) -
self.input.v('grid', 'high', 'z', 0)
) #NB does not change over long time scale
else:
from src.util.diagnostics.KnownError import KnownError
raise KnownError(
'incorrect seaward boundary type (sedbc) for sediment module')
## compute TQ, uQ, hatc2Q: quantities relative to the river discharge
u1river = np.real(
self.input.v('u1', 'river', range(0, jmax + 1), range(0, kmax + 1),
0))
Q_init = -np.trapz(u1river[-1, :], x=-self.zarr[-1, :]) * self.B[
-1] # initial discharge
self.TQ = T_r / Q_init # river transport per discharge unit
self.uQ = u1river / Q_init # river velocity per discharge unit
################################################################################################################
# Initialise X = (f, S)
################################################################################################################
if self.input.v('initial') == 'erodibility':
finit = self.input.v('finit', range(0, jmax + 1))
Sinit = self.init_stock(finit, alpha1, alpha2)
elif self.input.v('initial') == 'stock':
Sinit = self.input.v('Sinit', range(0, jmax + 1))
finit = self.erodibility_stock_relation(alpha2, Sinit / alpha1)
elif self.input.v('initial') == 'equilibrium':
_, finit, _ = self.availability(F, T, G, alpha1, alpha2)
Sinit = self.init_stock(finit, alpha1, alpha2)
else:
from src.util.diagnostics.KnownError import KnownError
raise KnownError(
'incorrect initial value for sediment module. Use erodibility, stock or equilibrium'
)
X = np.concatenate((finit, Sinit))
f = np.zeros((jmax + 1, 1, 1, len(toutput)))
S = np.zeros((jmax + 1, 1, 1, len(toutput)))
f[:, 0, 0, 0] = finit
S[:, 0, 0, 0] = Sinit
################################################################################################################
# Time integrator
################################################################################################################
T_base = dc.v('T', range(0, jmax + 1), 0, 0, 0) - dc.v(
'T', 'river', range(0, jmax + 1), 0, 0, 0) - dc.v(
'T', 'river_river', range(0, jmax + 1), 0, 0, 0) - dc.v(
'T', 'diffusion_river', range(0, jmax + 1), 0, 0, 0)
F_base = dc.v('F', range(0, jmax + 1), 0, 0, 0) - dc.v(
'F', 'diffusion_river', range(0, jmax + 1), 0, 0, 0)
# loop
self.timer.tic()
qq = 1 # counter for saving
for i, Q in enumerate(Qarray[1:]):
# quantities at old time step
Told = copy(T)
Fold = copy(F)
alpha1old = copy(alpha1)
alpha2old = copy(alpha2)
# Update transport terms and hatc2 & load new transport terms
T_riv, T_rivriv, T_difriv, F_difriv = self.update_transport(Q)
ur = self.uQ[:, -1] * Q
hatc2 = self.update_hatc2(ur)
T = T_base + T_riv + T_rivriv + T_difriv
F = F_base + F_difriv
# Make one time step and iterate over non-linearity
self.dt = t[i + 1] - t[i]
alpha1 = np.trapz(c00 + hatc2, x=-self.zarr, axis=1)
if alpha1[-1] == 0:
alpha1[-1] = alpha1[-2]
alpha2 = c04_int / alpha1 + 1e-3
X = self.timestepping(T, F, alpha1, alpha2, Told, Fold, alpha1old,
alpha2old, X, fsea, G)
# save output on output timestep
if t[i + 1] >= toutput[qq]:
toutput[qq] = t[
i +
1] # correct output time to real time if time step and output time do not correspond
d['T']['river'][:, 0, 0, qq] = T_riv
d['T']['river_river'][:, 0, 0, qq] = T_rivriv
d['T']['diffusion_river'][:, 0, 0, qq] = T_difriv
d['F']['diffusion_river'][:, 0, 0, qq] = F_difriv
f[:, 0, 0, qq] = X[:jmax + 1]
S[:, 0, 0, qq] = X[jmax + 1:]
qq += 1
qq = np.minimum(qq, len(toutput) - 1)
# display progress
if i % np.floor(len(Qarray[1:]) / 100.) == 0:
percent = float(i) / len(Qarray[1:])
hashes = '#' * int(round(percent * 10))
spaces = ' ' * (10 - len(hashes))
sys.stdout.write("\rProgress: [{0}]{1}%".format(
hashes + spaces, int(round(percent * 100))))
sys.stdout.flush()
sys.stdout.write('\n')
self.timer.toc()
self.timer.disp('time integration time')
################################################################################################################
# Prepare output
################################################################################################################
d['f'] = f
d['a'] = S
fx = np.gradient(f, self.x, axis=0, edge_order=2)
hatc0 = self.input.v('hatc0', 'a', range(0, jmax + 1),
range(0, kmax + 1), range(0, fmax + 1), [0])
hatc1 = self.input.v('hatc1', 'a', range(0, jmax + 1),
range(0, kmax + 1), range(0, fmax + 1), [0])
hatc1x = self.input.v('hatc1', 'ax', range(0, jmax + 1),
range(0, kmax + 1), range(0, fmax + 1), [0])
hatc2 = self.input.v('hatc2', 'a', range(0, jmax + 1),
range(0, kmax + 1), range(0, fmax + 1), [0])
d['c0'] = hatc0 * f
d['c1'] = hatc1 * f + hatc1x * fx
d['c2'] = hatc2 * f
d['t'] = toutput
return d
def run(self):
"""Run function to initiate the calculation of the sediment transport
Returns:
Dictionary with results. At least contains the variables listed as output in the registry
"""
self.logger.info('Running module Sediment')
# Initiate variables
self.SIGMA = self.input.v('OMEGA')
self.RHOS = self.input.v('RHOS')
self.DS = self.input.v('DS')
self.GPRIME = self.input.v('G') * (self.RHOS - self.input.v('RHO0')) / self.input.v('RHO0') #
self.ASTAR = self.input.v('astar')
self.WS = self.input.v('ws0')
self.KH = self.input.v('Kh')
self.L = self.input.v('L')
self.x = self.input.v('grid', 'axis', 'x') * self.input.v('L')
self.dx = self.x[1:]-self.x[:-1]
jmax = self.input.v('grid', 'maxIndex', 'x')
kmax = self.input.v('grid', 'maxIndex', 'z')
fmax = self.input.v('grid', 'maxIndex', 'f')
self.z = self.input.v('grid', 'axis', 'z', 0, range(0, kmax+1))
self.zarr = ny.dimensionalAxis(self.input.slice('grid'), 'z')[:, :, 0]-self.input.v('R', x=self.x/self.L).reshape((len(self.x), 1)) #YMD 22-8-17 includes reference level; note that we take a reference frame z=[-H-R, 0]
self.Av0 = self.input.v('Kv', range(0, jmax+1), 0, 0).reshape(jmax+1, 1)
self.Av0x = self.input.d('Kv', range(0, jmax+1), 0, 0, dim='x').reshape(jmax+1, 1)
self.H = (self.input.v('H', range(0, jmax+1)).reshape(jmax+1, 1) +
self.input.v('R', range(0, jmax+1)).reshape(jmax+1, 1))
self.Hx = (self.input.d('H', range(0, jmax+1), dim='x').reshape(jmax+1, 1) +
self.input.d('R', range(0, jmax+1), dim='x').reshape(jmax+1, 1))
self.B = self.input.v('B', range(0, jmax+1))
self.Bx = self.input.d('B', range(0, jmax+1), dim='x').reshape(jmax+1, 1)
self.sf = self.input.v('Roughness', range(0, jmax+1), 0, 0).reshape(jmax+1, 1)
self.sfx = self.input.d('Roughness', range(0, jmax+1), 0, 0, dim='x').reshape(jmax+1, 1)
self.submodules_hydro = self.input.data['u1'].keys()
self.submodules_sed = self.input.v('submodules')
# Extract leading order surface elevation and horizontal and vertical velocities
self.zeta0 = self.input.v('zeta0', 'tide', range(0, jmax+1), 0, 1).reshape(jmax+1, 1)
self.u0 = self.input.v('u0', 'tide', range(0, jmax+1), range(0, kmax+1), 1)
self.w0 = self.input.v('w0', 'tide', range(0, jmax+1), range(0, kmax+1), 1)
# Initiate dictionary to save results
d = {}
################################################################################################################
## Calculate leading, first and second order concentration amplitudes hatc0, hatc1 and hatc2
################################################################################################################
# Allocate space
d['hatc0'] = {}
d['hatc1'] = {'a': {}, 'ax': {}}
d['hatc2'] = {}
# Calculate leading order concentration amplitudes
d['hatc0'] = self.erosion_lead()
# Calculate first order concentration amplitudes
for sedmod in self.submodules_sed:
hatc1 = getattr(self, sedmod)()
for k in hatc1.keys():
d['hatc1'][k].update(hatc1[k])
# Calculate second order concentration amplitudes
d['hatc2'] = self.erosion_second()
################################################################################################################
## Calculate Transport function T and diffusion function F
################################################################################################################
# Allocate space
d['T'] = {}
d['F'] = {}
## Transport T #################################################################################################
# Transport terms that are a function of the first order velocity, i.e. u1*c0 terms.
for submod in self.input.getKeysOf('u1'):
u1_comp = self.input.v('u1', submod, range(0, jmax+1), range(0, kmax+1), range(0, fmax+1))
d['T'] = self.dictExpand(d['T'], submod, ['TM' + str(2 * n) for n in range(0, fmax + 1)])
# calculate residual Transport terms
for n in (0, 2):
tmp = u1_comp[:, :, n]
if n==0:
if submod == 'stokes':
tmp = np.real(np.trapz(tmp * self.c00, x=-self.zarr, axis=1))
if any(tmp) > 10**-14:
d['T'][submod] = self.dictExpand(d['T'][submod], 'TM0', ['return', 'drift'])
d['T'][submod]['TM0']['return'] += tmp
else:
tmp = np.real(np.trapz(tmp * self.c00, x=-self.zarr, axis=1))
if any(tmp) > 10**-14:
d['T'][submod]['TM' + str(2 * n)] += tmp
elif n==2:
if submod == 'stokes':
tmp = np.real(np.trapz((tmp * np.conj(self.c04) + np.conj(tmp) * self.c04) / 4., x=-self.zarr, axis=1))
if any(tmp) > 10**-14:
d['T'][submod] = self.dictExpand(d['T'][submod], 'TM4', ['return', 'drift'])
d['T'][submod]['TM4']['return'] += tmp
else:
tmp = np.real(np.trapz((tmp * np.conj(self.c04) + np.conj(tmp) * self.c04) / 4., x=-self.zarr, axis=1))
if any(tmp) > 10**-14:
d['T'][submod]['TM' + str(2 * n)] += tmp
# Transport terms that are a function of the first order concentration, i.e. u0*c1 terms.
for submod in d['hatc1']['a'].keys():
if submod == 'erosion':
for subsubmod in d['hatc1']['a'][submod].keys():
c1_comp = d['hatc1']['a'][submod][subsubmod]
d['T'] = self.dictExpand(d['T'], subsubmod, ['TM' + str(2 * n) for n in range(0, fmax + 1)])
tmp = c1_comp[:, :, 1]
tmp = np.real(np.trapz((self.u0 * np.conj(tmp) + np.conj(self.u0) * tmp) / 4., x=-self.zarr, axis=1))
if subsubmod == 'stokes':
if any(tmp) > 10**-14:
d['T'][subsubmod] = self.dictExpand(d['T'][subsubmod], 'TM2', ['return', 'drift'])
d['T'][subsubmod]['TM2']['return'] += tmp
else:
if any(tmp) > 10**-14:
d['T'][subsubmod]['TM2'] += tmp
else:
c1_comp = d['hatc1']['a'][submod]
d['T'] = self.dictExpand(d['T'], submod, ['TM' + str(2 * n) for n in range(0, fmax + 1)])
tmp = c1_comp[:, :, 1]
tmp = np.real(np.trapz((self.u0 * np.conj(tmp) + np.conj(self.u0) * tmp) / 4., x=-self.zarr, axis=1))
if any(tmp) > 10**-14:
d['T'][submod]['TM2'] += tmp
# Transport terms that are related to diffusion, i.e. K_h*c0 or K_h*c2
d['T'] = self.dictExpand(d['T'], 'diffusion_tide', ['TM' + str(2 * n) for n in range(0, fmax + 1)])
d['T']['diffusion_tide']['TM0'] = np.real(-np.trapz(self.KH * self.c00x, x=-self.zarr, axis=1))
d['T'] = self.dictExpand(d['T'], 'diffusion_river', ['TM' + str(2 * n) for n in range(0, fmax + 1)])
tmp = d['hatc2']['a']['erosion']['river_river'][:, :, 0]
tmp, __ = np.gradient(tmp, self.x[1], edge_order=2)
tmp = np.real(-np.trapz(self.KH * tmp, x=-self.zarr, axis=1))
if any(tmp) > 10**-14:
d['T']['diffusion_river']['TM0'] = tmp
# Transport terms that are related to Stokes drift, i.e. u0*c0*zeta0
if 'stokes' in self.submodules_hydro:
for n in (0, 2):
u0s = self.u0[:, 0]
tmp = d['hatc0']['a']['erosion'][:, 0, n]
if n==0:
tmp = np.real(np.conj(u0s) * tmp * self.zeta0[:, 0] + u0s * tmp * np.conj(self.zeta0[:, 0])) / 4
elif n==2:
tmp = np.real(u0s * np.conj(tmp) * self.zeta0[:, 0] + np.conj(u0s) * tmp * np.conj(self.zeta0[:, 0])) / 8
if any(tmp) > 10**-14:
d['T']['stokes']['TM' + str(2 * n)]['drift'] = tmp
# Transport term that is related to the river-river interaction u1river*c2river
d['T'] = self.dictExpand(d['T'], 'river_river', ['TM' + str(2 * n) for n in range(0, fmax + 1)])
if self.input.v('u1', 'river') is not None:
u1_comp = self.input.v('u1', 'river', range(0, jmax+1), range(0, kmax+1), 0)
tmp = d['hatc2']['a']['erosion']['river_river'][:, :, 0]
d['T']['river_river']['TM0'] = np.real(np.trapz(u1_comp * tmp, x=-self.zarr, axis=1))
## Diffusion F #################################################################################################
# Diffusive part, i.e. Kh*c00 and Kh*c20
d['F'] = self.dictExpand(d['F'], 'diffusion_tide', ['FM' + str(2 * n) for n in range(0, fmax + 1)])
d['F']['diffusion_tide']['FM0'] = np.real(-np.trapz(self.KH * self.c00, x=-self.zarr, axis=1))
d['F'] = self.dictExpand(d['F'], 'diffusion_river', ['FM' + str(2 * n) for n in range(0, fmax + 1)])
tmp = d['hatc2']['a']['erosion']['river_river'][:, :, 0]
tmp = np.real(-np.trapz(self.KH * tmp, x=-self.zarr, axis=1))
d['F']['diffusion_river']['FM0'] = tmp
# Part of F that is related to sediment advection, i.e. u0*c1sedadv
for submod in d['hatc1']['ax'].keys():
c1_comp = d['hatc1']['ax'][submod]
d['F'] = self.dictExpand(d['F'], submod, ['FM' + str(2 * n) for n in range(0, fmax + 1)])
tmp = c1_comp[:, :, 1]
tmp = np.real(np.trapz((self.u0 * np.conj(tmp) + np.conj(self.u0) * tmp) / 4., x=-self.zarr, axis=1))
if any(tmp) > 10**-14:
d['F']['sedadv']['FM2'] += tmp
################################################################################################################
# Calculate availability
################################################################################################################
# Add all mechanisms to datacontainer
dctrans = DataContainer(d)
# Calculate availability
d['a'] = {}
d['a'] = self.availability(dctrans.v('F'), dctrans.v('T')).reshape(len(self.x), 1)
ax = np.gradient(d['a'][:, 0], self.x[1], edge_order=2).reshape(len(self.x), 1)
################################################################################################################
# Calculate concentrations, i.e. a*hatc(a) + ax*hatc(ax)
################################################################################################################
d['c0'] = {}
d['c1'] = {}
d['c2'] = {}
# Calculate a*c0(a)
for submod in d['hatc0']['a'].keys():
c0_comp = d['hatc0']['a'][submod]
d['c0'][submod] = {}
tmp = d['a'][:, None] * c0_comp
d['c0'][submod] = tmp
# Calculate a*c1(a) + ax*c1(ax)
for submod in d['hatc1']['a'].keys():
if submod == 'erosion':
for subsubmod in d['hatc1']['a'][submod].keys():
c1_comp = d['hatc1']['a'][submod][subsubmod]
d['c1'] = self.dictExpand(d['c1'], submod, subsubmod)
tmp = d['a'][:, None] * c1_comp
d['c1'][submod][subsubmod] = tmp
elif submod == 'sedadv':
c1_comp_a = d['hatc1']['a'][submod]
c1_comp_ax = d['hatc1']['ax'][submod]
d['c1'][submod] = {}
tmp = d['a'][:, None] * c1_comp_a + ax[:, None] * c1_comp_ax
d['c1'][submod] = tmp
else:
c1_comp = d['hatc1']['a'][submod]
d['c1'][submod] = {}
tmp = d['a'][:, None] * c1_comp
d['c1'][submod] = tmp
# Calculate a*c2(a)
for submod in d['hatc2']['a']['erosion'].keys():
c2_comp = d['hatc2']['a']['erosion'][submod]
d['c2'] = self.dictExpand(d['c2'], 'erosion', submod)
tmp = d['a'][:, None] * c2_comp
d['c2']['erosion'][submod] = tmp
return d
class NumericalFunctionBase(FunctionBase):
#Variables
#Methods
def __init__(self, dimNames):
FunctionBase.__init__(self, dimNames)
self.dataContainer = DataContainer()
self.valueSize = 0
return
def function(self, **kwargs):
if len([
i for i in kwargs.keys()
if i in self.dataContainer.v('grid', 'dimensions')
]) == 0:
return self.__setReturnReference(kwargs.get('operation'))
# evaluate function
try:
returnval = self.__evaluateFunction(**kwargs)
except FunctionEvaluationError:
returnval = self.__setReturnReference(kwargs.get('operation'))
return returnval
def __evaluateFunction(self, **kwargs):
"""Overrides the function method of FunctionBase, but is very similar.
The difference is only that FunctionBase transfers kwargs to args before calling the actual functions
Here we keep the kwargs as the actual functions also use this.
"""
requestSize = sum(
[dim in kwargs for dim in self.dimNames]
) # count the number of dimensions in kwargs (this makes sure that other parameters or irrelevant dimensions are ignored)
operation = kwargs.get('operation')
try:
kwargs.pop('operation')
except:
pass
# direct to actual function
if operation is None:
returnval = self.value(**kwargs)
elif operation == 'd':
returnval = self.derivative(**kwargs)
elif operation == 'n':
returnval = -self.value(**kwargs)
elif operation == 'dn':
returnval = -self.derivative(**kwargs)
else:
raise FunctionEvaluationError
return returnval
def __setReturnReference(self, operation=None):
'''No difference with FunctionBase, but required here to refer to its own functions
'''
if not operation:
returnval = self.function
elif operation == 'n':
returnval = self.negfunction
elif operation == 'd':
returnval = self.derfunction
elif operation == 'dn':
returnval = self.dnfunction
else:
raise KnownError(
'Function called with unknown operation. (This error indicates an incorrectly defined function)'
)
return returnval
def negfunction(self, **kwargs):
"""No difference with FunctionBase, but required here to refer to its own functions
"""
# reset operations
if kwargs.get(
'operation'
) == 'n': # if the negative of a negfunction is called, return to function.
kwargs.pop('operation')
elif kwargs.get('operation') == 'd':
kwargs['operation'] = 'dn'
else:
kwargs['operation'] = 'n'
# evaluate
returnval = self.function(**kwargs)
return returnval
def addGrid(self, gridData, gridName='grid'):
# set own DataContainer containing grid data
data = gridData.slice(gridName, excludeKey=True)
self.dataContainer.addData(
'grid', data.data
) # improper use of the DataContainer by accessing its data directly
return
def addValue(self, value):
"""Add a variable 'value' to the numerical function
Parameters:
value (ndarray) - value to be put in the internal DataContainer
"""
self.dataContainer.addData('value', value)
self.valueSize = len(value.shape)
return
def addDerivative(self, derivative, dim):
self.dataContainer.merge({'derivative': {dim: derivative}})
return
### Depreciated v2.2 [dep01] ###
def addSecondDerivative(self, derivative, dim):
""" Depreciated v2.2
"""
self.dataContainer.merge({'secondDerivative': {dim: derivative}})
return
### End ###
def value(self, **kwargs):
"""Return the value of the variable in this numerical function.
Parameters:
kwargs (dict) - coordinates
Returns:
Array value using DataContainer interpolation.
"""
return self.dataContainer.v('value', **kwargs)
def derivative(self, **kwargs):
"""Similar to .value(). Returns the derivative uploaded to the numerical function or makes a call
to a numerical derivation method if no derivative is uploaded.
"""
# kwargs.pop('operation') # obsolete
dim = kwargs.get('dim')
v = self.dataContainer.v(
'derivative', dim,
**kwargs) # try if analytical derivative is available
if v is None:
v = self.dataContainer.d(
'value', **kwargs) # else take numerical derivative
return v
### Depreciated v2.2 [dep01] ###
def secondDerivative(self, **kwargs):
"""See .derivative(). This method does the same for the second derivative
Depreciated 2.2 [dep01]
"""
# kwargs.pop('operation') # obsolete
dim = kwargs.get('dim')
v = self.dataContainer.v('secondDerivative', dim, **kwargs)
if v is None:
v = self.dataContainer.dd('value', **kwargs)
return v
def run(self):
self.logger.info('Running module StaticAvailability')
################################################################################################################
## Init
################################################################################################################
jmax = self.input.v('grid', 'maxIndex', 'x')
kmax = self.input.v('grid', 'maxIndex', 'z')
fmax = self.input.v('grid', 'maxIndex', 'f')
c0 = self.input.v('hatc0', 'a', range(0, jmax + 1), range(0, kmax + 1),
range(0, fmax + 1))
c1_a0 = self.input.v('hatc1', 'a', range(0, jmax + 1),
range(0, kmax + 1), range(0, fmax + 1))
c1_a0x = self.input.v('hatc1', 'ax', range(0, jmax + 1),
range(0, kmax + 1), range(0, fmax + 1))
if isinstance(c1_a0x, bool):
c1_a0x = np.zeros((jmax + 1, kmax + 1, fmax + 1))
d = {}
c0_int = ny.integrate(c0, 'z', kmax, 0, self.input.slice('grid'))
B = self.input.v('B', range(0, jmax + 1), [0], [0])
u0 = self.input.v('u0', range(0, jmax + 1), range(0, kmax + 1),
range(0, fmax + 1))
zeta0 = self.input.v('zeta0', range(0, jmax + 1), [0],
range(0, fmax + 1))
Kh = self.input.v('Kh', range(0, jmax + 1), [0], [0])
################################################################################################################
## Second order closure
################################################################################################################
u1 = self.input.v('u1', range(0, jmax + 1), range(0, kmax + 1),
range(0, fmax + 1))
d['T'] = {}
d['F'] = {}
T0 = 0
F0 = 0
## Transport T ############################################################################################
## T.1. - u0*c1_a0
# Total
c1a_f0 = c1_a0
T0 += ny.integrate(ny.complexAmplitudeProduct(u0, c1a_f0, 2), 'z',
kmax, 0, self.input.slice('grid'))
# Decomposition
for submod in self.input.getKeysOf('hatc1', 'a'):
if submod == 'erosion':
for subsubmod in self.input.getKeysOf('hatc1', 'a', 'erosion'):
c1_a0_comp = self.input.v('hatc1', 'a', submod, subsubmod,
range(0, jmax + 1),
range(0, kmax + 1),
range(0, fmax + 1))
c1a_f0_comp_res = c1_a0_comp
d['T'] = self.dictExpand(
d['T'], subsubmod,
['TM' + str(2 * n) for n in range(0, fmax + 1)
]) # add submod index to dict if not already
# transport with residual availability
for n in range(0, fmax + 1):
tmp = np.zeros(c1a_f0_comp_res.shape, dtype=complex)
tmp[:, :, n] = c1a_f0_comp_res[:, :, n]
tmp = ny.integrate(
ny.complexAmplitudeProduct(u0, tmp, 2), 'z', kmax,
0, self.input.slice('grid'))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['T'][subsubmod]['TM' + str(2 * n)] += tmp
else:
c1_a0_comp = self.input.v('hatc1', 'a', submod,
range(0,
jmax + 1), range(0, kmax + 1),
range(0, fmax + 1))
c1a_f0_comp_res = c1_a0_comp
d['T'] = self.dictExpand(
d['T'], submod,
['TM' + str(2 * n) for n in range(0, fmax + 1)
]) # add submod index to dict if not already
# transport with residual availability
for n in range(0, fmax + 1):
tmp = np.zeros(c1a_f0_comp_res.shape, dtype=complex)
tmp[:, :, n] = c1a_f0_comp_res[:, :, n]
tmp = ny.integrate(ny.complexAmplitudeProduct(u0, tmp, 2),
'z', kmax, 0,
self.input.slice('grid'))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['T'][submod]['TM' + str(2 * n)] += tmp
## T.2. - u1*c0
# Total
T0 += ny.integrate(ny.complexAmplitudeProduct(u1, c0, 2), 'z', kmax, 0,
self.input.slice('grid'))
# Decomposition
for submod in self.input.getKeysOf('u1'):
u1_comp = self.input.v('u1', submod, range(0, jmax + 1),
range(0, kmax + 1), range(0, fmax + 1))
d['T'] = self.dictExpand(
d['T'], submod,
['TM' + str(2 * n) for n in range(0, fmax + 1)
]) # add submod index to dict if not already
# transport with residual availability
for n in range(0, fmax + 1):
tmp = np.zeros(u1_comp.shape, dtype=complex)
tmp[:, :, n] = u1_comp[:, :, n]
if submod == 'stokes':
tmp = ny.integrate(ny.complexAmplitudeProduct(tmp, c0, 2),
'z', kmax, 0,
self.input.slice('grid'))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['T'][submod] = self.dictExpand(
d['T'][submod], 'TM' + str(2 * n),
['return', 'drift'])
d['T'][submod]['TM0']['return'] += tmp
else:
tmp = ny.integrate(ny.complexAmplitudeProduct(tmp, c0, 2),
'z', kmax, 0,
self.input.slice('grid'))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['T'][submod]['TM' + str(2 * n)] += tmp
## T.5. - u0*c0*zeta0
# Total
T0 += ny.complexAmplitudeProduct(
ny.complexAmplitudeProduct(u0[:, [0], :], c0[:, [0], :], 2), zeta0,
2)
# Decomposition
uzeta = ny.complexAmplitudeProduct(u0[:, [0], :], zeta0, 2)
d['T'] = self.dictExpand(
d['T'], 'stokes', ['TM' + str(2 * n) for n in range(0, fmax + 1)])
# transport with residual availability
for n in range(0, fmax + 1):
tmp = np.zeros(c0[:, [0], :].shape, dtype=complex)
tmp[:, :, n] = c0[:, [0], n]
tmp = ny.complexAmplitudeProduct(uzeta, tmp, 2)[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['T']['stokes']['TM' + str(2 * n)]['drift'] += tmp
## T.6. - u1riv*c2rivriv
c2 = self.input.v('hatc2', 'a', 'erosion', 'river_river',
range(0, jmax + 1), range(0, kmax + 1),
range(0, fmax + 1))
u1riv = self.input.v('u1', 'river', range(0, jmax + 1),
range(0, kmax + 1), range(0, fmax + 1))
if u1riv is not None:
d['T'] = self.dictExpand(
d['T'], 'river_river',
'TM0') # add submod index to dict if not already
tmp = ny.integrate(ny.complexAmplitudeProduct(u1riv, c2, 2), 'z',
kmax, 0, self.input.slice('grid'))
if any(abs(tmp[:, 0, 0])) > 10**-14:
d['T']['river_river']['TM0'] = tmp[:, 0, 0]
T0 += tmp
## T.7. - diffusive part
# Total
c0x = self.input.d('hatc0',
'a',
range(0, jmax + 1),
range(0, kmax + 1),
range(0, fmax + 1),
dim='x')
T0 += -Kh * ny.integrate(c0x, 'z', kmax, 0, self.input.slice('grid'))
c2x = self.input.d('hatc2',
'a',
'erosion',
'river_river',
range(0, jmax + 1),
range(0, kmax + 1),
range(0, fmax + 1),
dim='x')
T0 += -Kh * ny.integrate(c2x, 'z', kmax, 0, self.input.slice('grid'))
# Decomposition
d['T'] = self.dictExpand(d['T'], 'diffusion_tide', ['TM0'])
d['T'] = self.dictExpand(d['T'], 'diffusion_river', ['TM0'])
# transport with residual availability
tmp = -(Kh * ny.integrate(c0x, 'z', kmax, 0,
self.input.slice('grid')))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['T']['diffusion_tide']['TM0'] = tmp
tmp = -(Kh * ny.integrate(c2x, 'z', kmax, 0,
self.input.slice('grid')))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['T']['diffusion_river']['TM0'] = tmp
## Diffusion F ############################################################################################
## F.1. - u0*C1ax*f0
# Total
F0 += ny.integrate(ny.complexAmplitudeProduct(u0, c1_a0x, 2), 'z',
kmax, 0, self.input.slice('grid'))
# Decomposition
for submod in self.input.getKeysOf('hatc1', 'ax'):
c1_ax0_comp = self.input.v('hatc1', 'ax', submod,
range(0, jmax + 1), range(0, kmax + 1),
range(0, fmax + 1))
d['F'] = self.dictExpand(
d['F'], submod,
['FM' + str(2 * n) for n in range(0, fmax + 1)
]) # add submod index to dict if not already
# transport with residual availability
for n in range(0, fmax + 1):
tmp = np.zeros(u0.shape, dtype=complex)
tmp[:, :, n] = u0[:, :, n]
tmp = ny.integrate(
ny.complexAmplitudeProduct(tmp, c1_ax0_comp, 2), 'z', kmax,
0, self.input.slice('grid'))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['F'][submod]['FM' + str(2 * n)] += tmp
## F.3. - diffusive part
# Total
F0 += -Kh * ny.integrate(c0, 'z', kmax, 0, self.input.slice('grid'))
F0 += -Kh * ny.integrate(c2, 'z', kmax, 0, self.input.slice('grid'))
# Decomposition
d['F'] = self.dictExpand(d['F'], 'diffusion_tide', ['FM0'])
d['F'] = self.dictExpand(d['F'], 'diffusion_river', ['FM0'])
# transport with residual availability
tmp = -(Kh * ny.integrate(c0, 'z', kmax, 0,
self.input.slice('grid')))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['F']['diffusion_tide']['FM0'] = tmp
tmp = -(Kh * ny.integrate(c2, 'z', kmax, 0,
self.input.slice('grid')))[:, 0, 0]
if any(abs(tmp)) > 10**-14:
d['F']['diffusion_river']['FM0'] = tmp
## Solve ################################################################################################
## Add all mechanisms & compute a0c
from src.DataContainer import DataContainer
dc = DataContainer(d)
dc.merge(self.input.slice('grid'))
T_til = np.real(dc.v('T', range(0, jmax + 1)))
F_til = np.real(dc.v('F', range(0, jmax + 1)))
# DEBUG: CHECKS IF COMPOSITE T, F == total T, F
# print np.max(abs((dc.v('T', range(0, jmax+1))-T0[:, 0, 0])/(T0[:, 0, 0]+10**-10)))
# print np.max(abs((dc.v('F', range(0, jmax+1))-F0[:, 0, 0])/(F0[:, 0, 0]+10**-10)))
integral = -ny.integrate(T_til / (F_til - 10**-6), 'x', 0,
range(0, jmax + 1), self.input.slice('grid'))
if self.input.v('Qsed') is None:
G = 0
else:
G = self.input.v('Qsed') / B[-1, 0, 0]
P = ny.integrate(G / (F_til - 10**-6) * np.exp(-integral), 'x', 0,
range(0, jmax + 1), self.input.slice('grid'))
################################################################################################################
# Boundary condition 1
################################################################################################################
if self.input.v('sedbc') == 'astar':
astar = self.input.v('astar')
k = astar * ny.integrate(B[:, 0, 0], 'x', 0, jmax,
self.input.slice('grid')) / ny.integrate(
B[:, 0, 0] * np.exp(integral), 'x', 0,
jmax, self.input.slice('grid'))
f0 = (k - P) * np.exp(integral)
f0x = (-T_til * f0 - G) / (F_til - 10**-6)
################################################################################################################
# Boundary condition 2
################################################################################################################
elif self.input.v('sedbc') == 'csea':
csea = self.input.v('csea')
c000 = np.real(c0_int[0, 0, 0])
k = csea / c000 * (self.input.v('grid', 'low', 'z', 0) -
self.input.v('grid', 'high', 'z', 0))
f0 = (k - P) * np.exp(integral)
f0x = (-T_til * f0 - G) / (F_til - 10**-6)
else:
from src.util.diagnostics.KnownError import KnownError
raise KnownError(
'sediment boundary sedbc not known: use astar or csea')
################################################################################################################
# Store in dict
################################################################################################################
d['a'] = f0
d['c0'] = c0 * f0.reshape((jmax + 1, 1, 1))
d['c1'] = c1_a0 * f0.reshape((jmax + 1, 1, 1)) + c1_a0x * f0x.reshape(
(jmax + 1, 1, 1))
d['c2'] = c2 * f0.reshape((jmax + 1, 1, 1))
return d
def run(self):
"""Run function to initiate the calculation of the sediment concentration based on dynamic erodibility. Hereby,
we solve the following three equations:
S_t = - [Flux_x + Flux * (B_x/B)] (1)
Flux = T*f + F*f_x (2)
f = f(Stilde) (3)
with:
S = sediment stock, which is the total amount of sediment in the water column and the erodible bottom
Flux = sediment transport
f = relative sediment erodibility
B = estuary width
T = transport function
F = diffusion function
Stilde = S / Chat, with Chat is the subtidal carrying capacity
Returns:
Dictionary with results. At least contains the variables listed as output in the registry
"""
self.logger.info('Running module DynamicAvailability')
## Initiate variables
# general variables
self.RHOS = self.input.v('RHOS')
self.DS = self.input.v('DS')
self.WS = self.input.v('ws0')
self.GPRIME = self.input.v('G') * (
self.RHOS - self.input.v('RHO0')) / self.input.v('RHO0')
self.Mhat = self.input.v('Mhat')
self.CSEA = self.input.v('csea')
self.FCAP = self.input.v('fcap')
self.P = self.input.v('p')
self.TOL = self.input.v('tol')
self.ASTAR = self.input.v('astar')
self.Kh = self.input.v('Kh')
self.L = self.input.v('L')
self.x = self.input.v('grid', 'axis', 'x') * self.L
self.dx = (self.x[1:] - self.x[:-1]).reshape(len(self.x) - 1, 1)
jmax = self.input.v('grid', 'maxIndex', 'x')
kmax = self.input.v('grid', 'maxIndex', 'z')
fmax = self.input.v('grid', 'maxIndex', 'f')
self.z = self.input.v('grid', 'axis', 'z', 0, range(0, kmax + 1))
self.zarr = ny.dimensionalAxis(self.input.slice('grid'), 'z')[:, :, 0]
self.H = (self.input.v('H', range(0, jmax + 1)).reshape(jmax + 1, 1) +
self.input.v('R', range(0, jmax + 1)).reshape(jmax + 1, 1))
self.Hx = (self.input.d('H', range(0, jmax + 1), dim='x').reshape(
jmax + 1, 1) + self.input.d('R', range(0, jmax + 1),
dim='x').reshape(jmax + 1, 1))
self.B = self.input.v('B', range(0, jmax + 1)).reshape(jmax + 1, 1)
self.Bx = self.input.d('B', range(0, jmax + 1),
dim='x').reshape(jmax + 1, 1)
self.sf = self.input.v('Roughness', range(0, jmax + 1), 0,
0).reshape(jmax + 1, 1)
self.Av0 = self.input.v('Av', range(0, jmax + 1), 0,
0).reshape(jmax + 1, 1)
# velocity
self.u1river = np.real(
self.input.v('u1', 'river', range(0, jmax + 1), range(0, kmax + 1),
0))
self.Q_fromhydro = -np.trapz(self.u1river[-1, :],
x=-self.zarr[-1, :]) * self.B[-1]
# c hat
self.c00 = np.real(
self.input.v('hatc0', range(0, jmax + 1), range(0, kmax + 1), 0))
self.c04 = self.input.v('hatc0', range(0, jmax + 1),
range(0, kmax + 1), 2)
## Compute transport (in superclass)
d = self.compute_transport()
dc = DataContainer(d)
self.Fc = (dc.v('F', range(0, jmax + 1)) -
dc.v('F', 'diffusion_river', range(0, jmax + 1))).reshape(
jmax + 1, 1)
self.Tc = (dc.v('T') -
(dc.v('T', 'river', range(0, jmax + 1)) +
dc.v('T', 'river_river', range(0, jmax + 1)) +
dc.v('T', 'diffusion_river', range(0, jmax + 1)))).reshape(
len(self.x), 1)
self.TQ = dc.v('T', 'river', range(0, jmax + 1)).reshape(
jmax + 1, 1) / self.Q_fromhydro
## User input
#TODO: make a consistent and effective script that handles user input of the discharge time series or any other time-dependent variable
#load time serie Q
self.dt = self.interpretValues(self.input.v('dt'))
if self.input.v('t') is not None:
self.t = self.interpretValues(self.input.v('t'))
self.Q = self.interpretValues(self.input.v('Q'))
## Run
self.logger.info('Running time-integrator')
vars = self.implicit()
## Collect output
d = {}
for key, value in vars.iteritems():
d[key] = value
return d