diff --git a/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/TP-R-layered_soil_with_inner_patch-all-params-one.py b/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/TP-R-layered_soil_with_inner_patch-all-params-one.py
new file mode 100644
index 0000000000000000000000000000000000000000..d96b0f28ffae9d46342c958e01f7ea4498627ac0
--- /dev/null
+++ b/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/TP-R-layered_soil_with_inner_patch-all-params-one.py
@@ -0,0 +1,1000 @@
+#!/usr/bin/python3
+"""Layered soil simulation with inner patch.
+
+This program sets up an LDD simulation
+"""
+
+import dolfin as df
+import sympy as sym
+import functools as ft
+import LDDsimulation as ldd
+import helpers as hlp
+import datetime
+import os
+import pandas as pd
+
+# check if output directory exists
+if not os.path.exists('./output'):
+ os.mkdir('./output')
+ print("Directory ", './output', " created ")
+else:
+ print("Directory ", './output', " already exists. Will use as output \
+ directory")
+
+
+# init sympy session
+sym.init_printing()
+# solver_tol = 6E-7
+use_case = "TP-R-layered-soil-with-inner-patch-realistic"
+# name of this very file. Needed for log output.
+thisfile = "TP-R-layered_soil_with_inner_patch-all-params-one.py"
+
+max_iter_num = 300
+FEM_Lagrange_degree = 1
+mesh_study = False
+resolutions = {
+ # 1: 2e-6, # h=2
+ # 2: 2e-6, # h=1.1180
+ # 4: 2e-6, # h=0.5590
+ # 8: 2e-6, # h=0.2814
+ 16: 2e-6, # h=0.1412
+ # 32: 2e-6,
+ # 64: 2e-6,
+ # 128: 2e-6
+ }
+
+# GRID #######################
+# mesh_resolution = 20
+timestep_size = 0.001
+number_of_timesteps = 5
+plot_timestep_every = 1
+# decide how many timesteps you want analysed. Analysed means, that we write
+# out subsequent errors of the L-iteration within the timestep.
+number_of_timesteps_to_analyse = 5
+starttimes = [0.0]
+
+Lw1 = 0.025 # /timestep_size
+Lnw1 = Lw1
+
+Lw2 = 0.025 # /timestep_size
+Lnw2 = Lw2
+
+Lw3 = 0.025 # /timestep_size
+Lnw3 = Lw3
+
+Lw4 = 0.025 # /timestep_size
+Lnw4 = Lw4
+
+Lw5 = 0.025 # /timestep_size
+Lnw5 = Lw5
+
+Lw6 = 0.025 # /timestep_size
+Lnw6 = Lw6
+
+lambda12_w = 40
+lambda12_nw = 40
+
+lambda23_w = 40
+lambda23_nw = 40
+
+lambda24_w = 40
+lambda24_nw= 40
+
+lambda25_w= 40
+lambda25_nw= 40
+
+lambda34_w = 40
+lambda34_nw = 40
+
+lambda36_w = 40
+lambda36_nw = 40
+
+lambda45_w = 40
+lambda45_nw = 40
+
+lambda46_w = 40
+lambda46_nw = 40
+
+lambda56_w = 40
+lambda56_nw = 40
+
+include_gravity = False
+debugflag = True
+analyse_condition = True
+
+if mesh_study:
+ output_string = "./output/{}-{}_timesteps{}_P{}".format(
+ datestr, use_case, number_of_timesteps, FEM_Lagrange_degree
+ )
+else:
+ for tol in resolutions.values():
+ solver_tol = tol
+ output_string = "./output/{}-{}_timesteps{}_P{}_solver_tol{}".format(
+ datestr, use_case, number_of_timesteps, FEM_Lagrange_degree, solver_tol
+ )
+
+
+# toggle what should be written to files
+if mesh_study:
+ write_to_file = {
+ 'space_errornorms': True,
+ 'meshes_and_markers': True,
+ 'L_iterations_per_timestep': False,
+ 'solutions': True,
+ 'absolute_differences': True,
+ 'condition_numbers': analyse_condition,
+ 'subsequent_errors': True
+ }
+else:
+ write_to_file = {
+ 'space_errornorms': True,
+ 'meshes_and_markers': True,
+ 'L_iterations_per_timestep': False,
+ 'solutions': True,
+ 'absolute_differences': True,
+ 'condition_numbers': analyse_condition,
+ 'subsequent_errors': True
+ }
+
+
+# global domain
+subdomain0_vertices = [df.Point(-1.0,-1.0), #
+ df.Point(1.0,-1.0),#
+ df.Point(1.0,1.0),#
+ df.Point(-1.0,1.0)]
+
+interface12_vertices = [df.Point(-1.0, 0.8),
+ df.Point(0.3, 0.8),
+ df.Point(0.5, 0.9),
+ df.Point(0.8, 0.7),
+ df.Point(1.0, 0.65)]
+
+
+ # interface23
+interface23_vertices = [df.Point(-1.0, 0.0),
+ df.Point(-0.35, 0.0),
+ # df.Point(6.5, 4.5),
+ df.Point(0.0, 0.0)]
+
+interface24_vertices = [interface23_vertices[2],
+ df.Point(0.6, 0.0),
+ ]
+
+interface25_vertices = [interface24_vertices[1],
+ df.Point(1.0, 0.0)
+ ]
+
+
+interface32_vertices = [interface23_vertices[2],
+ interface23_vertices[1],
+ interface23_vertices[0]]
+
+
+interface36_vertices = [df.Point(-1.0, -0.6),
+ df.Point(-0.6, -0.45)]
+
+
+interface46_vertices = [interface36_vertices[1],
+ df.Point(0.3, -0.25)]
+
+interface56_vertices = [interface46_vertices[1],
+ df.Point(0.65, -0.6),
+ df.Point(1.0, -0.7)]
+
+
+
+
+interface34_vertices = [interface36_vertices[1],
+ interface23_vertices[2]]
+# interface36
+
+interface45_vertices = [interface56_vertices[0],
+ df.Point(0.7, -0.2),
+ interface25_vertices[0]
+ ]
+
+
+# interface_vertices introduces a global numbering of interfaces.
+interface_def_points = [interface12_vertices,
+ interface23_vertices,
+ interface24_vertices,
+ interface25_vertices,
+ interface34_vertices,
+ interface36_vertices,
+ interface45_vertices,
+ interface46_vertices,
+ interface56_vertices,
+ ]
+
+adjacent_subdomains = [[1,2],
+ [2,3],
+ [2,4],
+ [2,5],
+ [3,4],
+ [3,6],
+ [4,5],
+ [4,6],
+ [5,6]
+ ]
+
+# subdomain1.
+subdomain1_vertices = [interface12_vertices[0],
+ interface12_vertices[1],
+ interface12_vertices[2],
+ interface12_vertices[3],
+ interface12_vertices[4], # southern boundary, 12 interface
+ subdomain0_vertices[2], # eastern boundary, outer boundary
+ subdomain0_vertices[3]] # northern boundary, outer on_boundary
+
+# vertex coordinates of the outer boundaries. If it can not be specified as a
+# polygon, use an entry per boundary polygon.
+# This information is used for defining
+# the Dirichlet boundary conditions. If a domain is completely internal, the
+# dictionary entry should be 0: None
+subdomain1_outer_boundary_verts = {
+ 0: [subdomain1_vertices[4],
+ subdomain1_vertices[5], # eastern boundary, outer boundary
+ subdomain1_vertices[6],
+ subdomain1_vertices[0]]
+}
+
+#subdomain1
+subdomain2_vertices = [interface23_vertices[0],
+ interface23_vertices[1],
+ interface23_vertices[2],
+ interface24_vertices[1],
+ interface25_vertices[1], # southern boundary, 23 interface
+ subdomain1_vertices[4], # eastern boundary, outer boundary
+ subdomain1_vertices[3],
+ subdomain1_vertices[2],
+ subdomain1_vertices[1],
+ subdomain1_vertices[0] ] # northern boundary, 12 interface
+
+subdomain2_outer_boundary_verts = {
+ 0: [subdomain2_vertices[9],
+ subdomain2_vertices[0]],
+ 1: [subdomain2_vertices[4],
+ subdomain2_vertices[5]]
+}
+
+
+subdomain3_vertices = [interface36_vertices[0],
+ interface36_vertices[1],
+ # interface34_vertices[0],
+ interface34_vertices[1],
+ # interface32_vertices[0],
+ interface32_vertices[1],
+ interface32_vertices[2]
+ ]
+
+subdomain3_outer_boundary_verts = {
+ 0: [subdomain3_vertices[4],
+ subdomain3_vertices[0]]
+}
+
+
+# subdomain3
+subdomain4_vertices = [interface46_vertices[0],
+ interface46_vertices[1],
+ interface45_vertices[1],
+ interface24_vertices[1],
+ interface24_vertices[0],
+ interface34_vertices[1]
+ ]
+
+subdomain4_outer_boundary_verts = None
+
+subdomain5_vertices = [interface56_vertices[0],
+ interface56_vertices[1],
+ interface56_vertices[2],
+ interface25_vertices[1],
+ interface25_vertices[0],
+ interface45_vertices[1],
+ interface45_vertices[0]
+]
+
+subdomain5_outer_boundary_verts = {
+ 0: [subdomain5_vertices[2],
+ subdomain5_vertices[3]]
+}
+
+
+
+subdomain6_vertices = [subdomain0_vertices[0],
+ subdomain0_vertices[1], # southern boundary, outer boundary
+ interface56_vertices[2],
+ interface56_vertices[1],
+ interface56_vertices[0],
+ interface36_vertices[1],
+ interface36_vertices[0]
+ ]
+
+subdomain6_outer_boundary_verts = {
+ 0: [subdomain6_vertices[6],
+ subdomain6_vertices[0],
+ subdomain6_vertices[1],
+ subdomain6_vertices[2]]
+}
+
+
+subdomain_def_points = [subdomain0_vertices,#
+ subdomain1_vertices,#
+ subdomain2_vertices,#
+ subdomain3_vertices,#
+ subdomain4_vertices,
+ subdomain5_vertices,
+ subdomain6_vertices
+ ]
+
+
+# if a subdomain has no outer boundary write None instead, i.e.
+# i: None
+# if i is the index of the inner subdomain.
+outer_boundary_def_points = {
+ # subdomain number
+ 1: subdomain1_outer_boundary_verts,
+ 2: subdomain2_outer_boundary_verts,
+ 3: subdomain3_outer_boundary_verts,
+ 4: subdomain4_outer_boundary_verts,
+ 5: subdomain5_outer_boundary_verts,
+ 6: subdomain6_outer_boundary_verts
+}
+
+
+isRichards = {
+ 1: True,
+ 2: True,
+ 3: False,
+ 4: False,
+ 5: False,
+ 6: False
+ }
+
+# isRichards = {
+# 1: True,
+# 2: True,
+# 3: True,
+# 4: True,
+# 5: True,
+# 6: True
+# }
+
+# Dict of the form: { subdom_num : viscosity }
+viscosity = {
+ 1: {'wetting' :1,
+ 'nonwetting': 1},
+ 2: {'wetting' :1,
+ 'nonwetting': 1},
+ 3: {'wetting' :1,
+ 'nonwetting': 1},
+ 4: {'wetting' :1,
+ 'nonwetting': 1},
+ 5: {'wetting' :1,
+ 'nonwetting': 1},
+ 6: {'wetting' :1,
+ 'nonwetting': 1},
+}
+
+# Dict of the form: { subdom_num : density }
+densities = {
+ 1: {'wetting': 1, #997
+ 'nonwetting': 1}, #1}, #1.225},
+ 2: {'wetting': 1, #997
+ 'nonwetting': 1}, #1.225},
+ 3: {'wetting': 1, #997
+ 'nonwetting': 1}, #1.225},
+ 4: {'wetting': 1, #997
+ 'nonwetting': 1}, #1.225}
+ 5: {'wetting': 1, #997
+ 'nonwetting': 1}, #1.225},
+ 6: {'wetting': 1, #997
+ 'nonwetting': 1} #1.225}
+}
+
+gravity_acceleration = 9.81
+# porosities taken from
+# https://www.geotechdata.info/parameter/soil-porosity.html
+# Dict of the form: { subdom_num : porosity }
+porosity = {
+ 1: 1, #0.2, # Clayey gravels, clayey sandy gravels
+ 2: 1, #0.22, # Silty gravels, silty sandy gravels
+ 3: 1, #0.37, # Clayey sands
+ 4: 1, #0.2 # Silty or sandy clay
+ 5: 1, #
+ 6: 1, #
+}
+
+# subdom_num : subdomain L for L-scheme
+L = {
+ 1: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 2: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 3: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 4: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 5: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 6: {'wetting' :Lw,
+ 'nonwetting': Lnw}
+}
+
+
+# interface_num : lambda parameter for the L-scheme on that interface.
+# Note that interfaces are numbered starting from 0, because
+# adjacent_subdomains is a list and not a dict. Historic fuckup, I know
+# We have defined above as interfaces
+# # interface_vertices introduces a global numbering of interfaces.
+# interface_def_points = [interface12_vertices,
+# interface23_vertices,
+# interface24_vertices,
+# interface25_vertices,
+# interface34_vertices,
+# interface36_vertices,
+# interface45_vertices,
+# interface46_vertices,
+# interface56_vertices,
+# ]
+lambda_param = {
+ 0: {'wetting': lambda12_w,
+ 'nonwetting': lambda12_nw},#
+ 1: {'wetting': lambda23_w,
+ 'nonwetting': lambda23_nw},#
+ 2: {'wetting': lambda24_w,
+ 'nonwetting': lambda24_nw},#
+ 3: {'wetting': lambda25_w,
+ 'nonwetting': lambda25_nw},#
+ 4: {'wetting': lambda34_w,
+ 'nonwetting': lambda34_nw},#
+ 5: {'wetting': lambda36_w,
+ 'nonwetting': lambda36_nw},#
+ 6: {'wetting': lambda45_w,
+ 'nonwetting': lambda45_nw},#
+ 7: {'wetting': lambda46_w,
+ 'nonwetting': lambda46_nw},#
+ 8: {'wetting': lambda56_w,
+ 'nonwetting': lambda56_nw},#
+}
+
+
+# after Lewis, see pdf file
+intrinsic_permeability = {
+ 1: 1, # sand
+ 2: 1, # sand, there is a range
+ 3: 1, #10e-2, # clay has a range
+ 4: 1, #10e-3
+ 5: 1, #10e-2, # clay has a range
+ 6: 1, #10e-3
+}
+
+
+# relative permeabilty functions on subdomain 1
+def rel_perm1w(s):
+ # relative permeabilty wetting on subdomain1
+ return intrinsic_permeability[1]*s**2
+
+
+def rel_perm1nw(s):
+ # relative permeabilty nonwetting on subdomain1
+ return intrinsic_permeability[1]*(1-s)**2
+
+
+# relative permeabilty functions on subdomain 2
+def rel_perm2w(s):
+ # relative permeabilty wetting on subdomain2
+ return intrinsic_permeability[2]*s**2
+
+
+def rel_perm2nw(s):
+ # relative permeabilty nonwetting on subdomain2
+ return intrinsic_permeability[2]*(1-s)**2
+
+
+# relative permeabilty functions on subdomain 3
+def rel_perm3w(s):
+ # relative permeabilty wetting on subdomain3
+ return intrinsic_permeability[3]*s**3
+
+
+def rel_perm3nw(s):
+ # relative permeabilty nonwetting on subdomain3
+ return intrinsic_permeability[3]*(1-s)**3
+
+
+# relative permeabilty functions on subdomain 4
+def rel_perm4w(s):
+ # relative permeabilty wetting on subdomain4
+ return intrinsic_permeability[4]*s**3
+
+
+def rel_perm4nw(s):
+ # relative permeabilty nonwetting on subdomain4
+ return intrinsic_permeability[4]*(1-s)**3
+
+
+# relative permeabilty functions on subdomain 5
+def rel_perm5w(s):
+ # relative permeabilty wetting on subdomain5
+ return intrinsic_permeability[5]*s**3
+
+
+def rel_perm5nw(s):
+ # relative permeabilty nonwetting on subdomain5
+ return intrinsic_permeability[5]*(1-s)**3
+
+
+# relative permeabilty functions on subdomain 6
+def rel_perm6w(s):
+ # relative permeabilty wetting on subdomain6
+ return intrinsic_permeability[6]*s**3
+
+
+def rel_perm6nw(s):
+ # relative permeabilty nonwetting on subdomain6
+ return intrinsic_permeability[6]*(1-s)**3
+
+
+_rel_perm1w = ft.partial(rel_perm1w)
+_rel_perm1nw = ft.partial(rel_perm1nw)
+
+_rel_perm2w = ft.partial(rel_perm2w)
+_rel_perm2nw = ft.partial(rel_perm2nw)
+
+_rel_perm3w = ft.partial(rel_perm3w)
+_rel_perm3nw = ft.partial(rel_perm3nw)
+
+_rel_perm4w = ft.partial(rel_perm4w)
+_rel_perm4nw = ft.partial(rel_perm4nw)
+
+_rel_perm5w = ft.partial(rel_perm5w)
+_rel_perm5nw = ft.partial(rel_perm5nw)
+
+_rel_perm6w = ft.partial(rel_perm6w)
+_rel_perm6nw = ft.partial(rel_perm6nw)
+
+subdomain1_rel_perm = {
+ 'wetting': _rel_perm1w,
+ 'nonwetting': _rel_perm1nw
+}
+
+subdomain2_rel_perm = {
+ 'wetting': _rel_perm2w,
+ 'nonwetting': _rel_perm2nw
+}
+
+subdomain3_rel_perm = {
+ 'wetting': _rel_perm3w,
+ 'nonwetting': _rel_perm3nw
+}
+
+subdomain4_rel_perm = {
+ 'wetting': _rel_perm4w,
+ 'nonwetting': _rel_perm4nw
+}
+
+subdomain5_rel_perm = {
+ 'wetting': _rel_perm5w,
+ 'nonwetting': _rel_perm5nw
+}
+
+subdomain6_rel_perm = {
+ 'wetting': _rel_perm6w,
+ 'nonwetting': _rel_perm6nw
+}
+
+# dictionary of relative permeabilties on all domains.
+relative_permeability = {
+ 1: subdomain1_rel_perm,
+ 2: subdomain2_rel_perm,
+ 3: subdomain3_rel_perm,
+ 4: subdomain4_rel_perm,
+ 5: subdomain5_rel_perm,
+ 6: subdomain6_rel_perm
+}
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 1
+def rel_perm1w_prime(s):
+ # relative permeabilty on subdomain1
+ return intrinsic_permeability[1]*2*s
+
+
+def rel_perm1nw_prime(s):
+ # relative permeabilty on subdomain1
+ return -1*intrinsic_permeability[1]*2*(1-s)
+
+
+def rel_perm2w_prime(s):
+ # relative permeabilty on subdomain2
+ return intrinsic_permeability[2]*2*s
+
+
+def rel_perm2nw_prime(s):
+ # relative permeabilty on subdomain2
+ return -1*intrinsic_permeability[2]*2*(1-s)
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 3
+def rel_perm3w_prime(s):
+ # relative permeabilty on subdomain3
+ return intrinsic_permeability[3]*3*s**2
+
+
+def rel_perm3nw_prime(s):
+ # relative permeabilty on subdomain3
+ return -1*intrinsic_permeability[3]*3*(1-s)**2
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 4
+def rel_perm4w_prime(s):
+ # relative permeabilty on subdomain4
+ return intrinsic_permeability[4]*3*s**2
+
+
+def rel_perm4nw_prime(s):
+ # relative permeabilty on subdomain4
+ return -1*intrinsic_permeability[4]*3*(1-s)**2
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 5
+def rel_perm5w_prime(s):
+ # relative permeabilty on subdomain5
+ return intrinsic_permeability[5]*3*s**2
+
+
+def rel_perm5nw_prime(s):
+ # relative permeabilty on subdomain5
+ return -1*intrinsic_permeability[5]*3*(1-s)**2
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 6
+def rel_perm6w_prime(s):
+ # relative permeabilty on subdomain6
+ return intrinsic_permeability[6]*3*s**2
+
+
+def rel_perm6nw_prime(s):
+ # relative permeabilty on subdomain6
+ return -1*intrinsic_permeability[6]*3*(1-s)**2
+
+
+_rel_perm1w_prime = ft.partial(rel_perm1w_prime)
+_rel_perm1nw_prime = ft.partial(rel_perm1nw_prime)
+_rel_perm2w_prime = ft.partial(rel_perm2w_prime)
+_rel_perm2nw_prime = ft.partial(rel_perm2nw_prime)
+_rel_perm3w_prime = ft.partial(rel_perm3w_prime)
+_rel_perm3nw_prime = ft.partial(rel_perm3nw_prime)
+_rel_perm4w_prime = ft.partial(rel_perm4w_prime)
+_rel_perm4nw_prime = ft.partial(rel_perm4nw_prime)
+_rel_perm5w_prime = ft.partial(rel_perm5w_prime)
+_rel_perm5nw_prime = ft.partial(rel_perm5nw_prime)
+_rel_perm6w_prime = ft.partial(rel_perm6w_prime)
+_rel_perm6nw_prime = ft.partial(rel_perm6nw_prime)
+
+subdomain1_rel_perm_prime = {
+ 'wetting': _rel_perm1w_prime,
+ 'nonwetting': _rel_perm1nw_prime
+}
+
+
+subdomain2_rel_perm_prime = {
+ 'wetting': _rel_perm2w_prime,
+ 'nonwetting': _rel_perm2nw_prime
+}
+
+subdomain3_rel_perm_prime = {
+ 'wetting': _rel_perm3w_prime,
+ 'nonwetting': _rel_perm3nw_prime
+}
+
+
+subdomain4_rel_perm_prime = {
+ 'wetting': _rel_perm4w_prime,
+ 'nonwetting': _rel_perm4nw_prime
+}
+
+subdomain5_rel_perm_prime = {
+ 'wetting': _rel_perm5w_prime,
+ 'nonwetting': _rel_perm5nw_prime
+}
+
+subdomain6_rel_perm_prime = {
+ 'wetting': _rel_perm6w_prime,
+ 'nonwetting': _rel_perm6nw_prime
+}
+
+
+# dictionary of relative permeabilties on all domains.
+ka_prime = {
+ 1: subdomain1_rel_perm_prime,
+ 2: subdomain2_rel_perm_prime,
+ 3: subdomain3_rel_perm_prime,
+ 4: subdomain4_rel_perm_prime,
+ 5: subdomain5_rel_perm_prime,
+ 6: subdomain6_rel_perm_prime,
+}
+
+
+
+# S-pc-relation ship. We use the van Genuchten approach, i.e.
+# pc = 1/alpha*(S^{-1/m} -1)^1/n, where we set alpha = 0, assume
+# m = 1-1/n (see Helmig) and assume that residual saturation is Sw
+# this function needs to be monotonically decreasing in the capillary pressure
+# pc.
+# Since in the richards case pc=-pw, this becomes as a function of pw a mono
+# tonically INCREASING function like in our Richards-Richards paper. However
+# since we unify the treatment in the code for Richards and two-phase, we need
+# the same requierment
+# for both cases, two-phase and Richards.
+# def saturation(pc, n_index, alpha):
+# # inverse capillary pressure-saturation-relationship
+# return df.conditional(pc > 0, 1/((1 + (alpha*pc)**n_index)**((n_index - 1)/n_index)), 1)
+#
+# # S-pc-relation ship. We use the van Genuchten approach, i.e. pc = 1/alpha*(S^{-1/m} -1)^1/n, where
+# # we set alpha = 0, assume m = 1-1/n (see Helmig) and assume that residual saturation is Sw
+# def saturation_sym(pc, n_index, alpha):
+# # inverse capillary pressure-saturation-relationship
+# #df.conditional(pc > 0,
+# return 1/((1 + (alpha*pc)**n_index)**((n_index - 1)/n_index))
+#
+#
+# # derivative of S-pc relationship with respect to pc. This is needed for the
+# # construction of a analytic solution.
+# def saturation_sym_prime(pc, n_index, alpha):
+# # inverse capillary pressure-saturation-relationship
+# return -(alpha*(n_index - 1)*(alpha*pc)**(n_index - 1)) / ( (1 + (alpha*pc)**n_index)**((2*n_index - 1)/n_index) )
+##
+# # note that the conditional definition of S-pc in the nonsymbolic part will be
+# # incorporated in the construction of the exact solution below.
+# S_pc_sym = {
+# 1: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 2: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 3: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 4: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 5: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 6: ft.partial(saturation_sym, n_index=3, alpha=0.001)
+# }
+#
+# S_pc_sym_prime = {
+# 1: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 2: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 3: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 4: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 5: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 6: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001)
+# }
+#
+# sat_pressure_relationship = {
+# 1: ft.partial(saturation, n_index=3, alpha=0.001),
+# 2: ft.partial(saturation, n_index=3, alpha=0.001),
+# 3: ft.partial(saturation, n_index=3, alpha=0.001),
+# 4: ft.partial(saturation, n_index=3, alpha=0.001),
+# 5: ft.partial(saturation, n_index=3, alpha=0.001),
+# 6: ft.partial(saturation, n_index=3, alpha=0.001)
+# }
+
+def saturation(pc, n_index):
+ # inverse capillary pressure-saturation-relationship
+ return df.conditional(pc > 0, 1/((1 + pc)**(1/(n_index + 1))), 1)
+
+
+def saturation_sym(pc, n_index):
+ # inverse capillary pressure-saturation-relationship
+ return 1/((1 + pc)**(1/(n_index + 1)))
+
+
+def saturation_sym_prime(pc, n_index):
+ # inverse capillary pressure-saturation-relationship
+ return -1/((n_index+1)*(1 + pc)**((n_index+2)/(n_index+1)))
+
+
+S_pc_sym = {
+ 1: ft.partial(saturation_sym, n_index=1),
+ 2: ft.partial(saturation_sym, n_index=1),
+ 3: ft.partial(saturation_sym, n_index=2),
+ 4: ft.partial(saturation_sym, n_index=2),
+ 5: ft.partial(saturation_sym, n_index=2),
+ 6: ft.partial(saturation_sym, n_index=2)
+}
+
+S_pc_sym_prime = {
+ 1: ft.partial(saturation_sym_prime, n_index=1),
+ 2: ft.partial(saturation_sym_prime, n_index=1),
+ 3: ft.partial(saturation_sym_prime, n_index=2),
+ 4: ft.partial(saturation_sym_prime, n_index=2),
+ 5: ft.partial(saturation_sym_prime, n_index=2),
+ 6: ft.partial(saturation_sym_prime, n_index=2)
+}
+
+sat_pressure_relationship = {
+ 1: ft.partial(saturation, n_index=1),
+ 2: ft.partial(saturation, n_index=1),
+ 3: ft.partial(saturation, n_index=2),
+ 4: ft.partial(saturation, n_index=2),
+ 5: ft.partial(saturation, n_index=2),
+ 6: ft.partial(saturation, n_index=2)
+}
+
+#############################################
+# Manufacture source expressions with sympy #
+#############################################
+x, y = sym.symbols('x[0], x[1]') # needed by UFL
+t = sym.symbols('t', positive=True)
+
+
+p_e_sym = {
+ 1: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x + y*y)),
+ 'nonwetting': 0.0*t },
+ 2: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x + y*y)),
+ 'nonwetting': 0.0*t },
+ 3: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1 -t*(1 + x**2) - sym.sqrt(2+t**2)*(1+y)*y**2)*y**2 },
+ 4: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1 -t*(1 + x**2) - sym.sqrt(2+t**2)*(1+y)*y**2)*y**2 },
+ 5: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1 -t*(1 + x**2) - sym.sqrt(2+t**2)*(1+y)*y**2)*y**2 },
+ 6: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1 -t*(1 + x**2) - sym.sqrt(2+t**2)*(1+y)*y**2)*y**2 },
+}
+
+pc_e_sym = dict()
+for subdomain, isR in isRichards.items():
+ if isR:
+ pc_e_sym.update({subdomain: -p_e_sym[subdomain]['wetting']})
+ else:
+ pc_e_sym.update(
+ {subdomain: p_e_sym[subdomain]['nonwetting']
+ - p_e_sym[subdomain]['wetting']}
+ )
+
+
+symbols = {"x": x,
+ "y": y,
+ "t": t}
+# turn above symbolic code into exact solution for dolphin and
+# construct the rhs that matches the above exact solution.
+exact_solution_example = hlp.generate_exact_solution_expressions(
+ symbols=symbols,
+ isRichards=isRichards,
+ symbolic_pressure=p_e_sym,
+ symbolic_capillary_pressure=pc_e_sym,
+ saturation_pressure_relationship=S_pc_sym,
+ saturation_pressure_relationship_prime=S_pc_sym_prime,
+ viscosity=viscosity,
+ porosity=porosity,
+ relative_permeability=relative_permeability,
+ relative_permeability_prime=ka_prime,
+ densities=densities,
+ gravity_acceleration=gravity_acceleration,
+ include_gravity=include_gravity,
+ )
+source_expression = exact_solution_example['source']
+exact_solution = exact_solution_example['exact_solution']
+initial_condition = exact_solution_example['initial_condition']
+
+# Dictionary of dirichlet boundary conditions.
+dirichletBC = dict()
+# similarly to the outer boundary dictionary, if a patch has no outer boundary
+# None should be written instead of an expression.
+# This is a bit of a brainfuck:
+# dirichletBC[ind] gives a dictionary of the outer boundaries of subdomain ind.
+# Since a domain patch can have several disjoint outer boundary parts, the
+# expressions need to get an enumaration index which starts at 0.
+# So dirichletBC[ind][j] is the dictionary of outer dirichlet conditions of
+# subdomain ind and boundary part j.
+# Finally, dirichletBC[ind][j]['wetting'] and dirichletBC[ind][j]['nonwetting']
+# return the actual expression needed for the dirichlet condition for both
+# phases if present.
+
+# subdomain index: {outer boudary part index: {phase: expression}}
+for subdomain in isRichards.keys():
+ # if subdomain has no outer boundary, outer_boundary_def_points[subdomain]
+ # is None
+ if outer_boundary_def_points[subdomain] is None:
+ dirichletBC.update({subdomain: None})
+ else:
+ dirichletBC.update({subdomain: dict()})
+ # set the dirichlet conditions to be the same code as exact solution on
+ # the subdomain.
+ for outer_boundary_ind in outer_boundary_def_points[subdomain].keys():
+ dirichletBC[subdomain].update(
+ {outer_boundary_ind: exact_solution[subdomain]}
+ )
+
+
+# read this file and print it to std out. This way the simulation can produce a
+# log file with ./TP-R-layered_soil.py | tee simulation.log
+f = open(thisfile, 'r')
+print(f.read())
+f.close()
+
+
+for starttime in starttimes:
+ for mesh_resolution, solver_tol in resolutions.items():
+ # initialise LDD simulation class
+ simulation = ldd.LDDsimulation(
+ tol=1E-14,
+ LDDsolver_tol=solver_tol,
+ debug=debugflag,
+ max_iter_num=max_iter_num,
+ FEM_Lagrange_degree=FEM_Lagrange_degree,
+ mesh_study=mesh_study
+ )
+
+ simulation.set_parameters(
+ use_case=use_case,
+ output_dir=output_string,
+ subdomain_def_points=subdomain_def_points,
+ isRichards=isRichards,
+ interface_def_points=interface_def_points,
+ outer_boundary_def_points=outer_boundary_def_points,
+ adjacent_subdomains=adjacent_subdomains,
+ mesh_resolution=mesh_resolution,
+ viscosity=viscosity,
+ porosity=porosity,
+ L=L,
+ lambda_param=lambda_param,
+ relative_permeability=relative_permeability,
+ saturation=sat_pressure_relationship,
+ starttime=starttime,
+ number_of_timesteps=number_of_timesteps,
+ number_of_timesteps_to_analyse=number_of_timesteps_to_analyse,
+ plot_timestep_every=plot_timestep_every,
+ timestep_size=timestep_size,
+ sources=source_expression,
+ initial_conditions=initial_condition,
+ dirichletBC_expression_strings=dirichletBC,
+ exact_solution=exact_solution,
+ densities=densities,
+ include_gravity=include_gravity,
+ write2file=write_to_file,
+ )
+
+ simulation.initialise()
+ output_dir = simulation.output_dir
+ # simulation.write_exact_solution_to_xdmf()
+ output = simulation.run(analyse_condition=analyse_condition)
+ for subdomain_index, subdomain_output in output.items():
+ mesh_h = subdomain_output['mesh_size']
+ for phase, error_dict in subdomain_output['errornorm'].items():
+ filename = output_dir \
+ + "subdomain{}".format(subdomain_index)\
+ + "-space-time-errornorm-{}-phase.csv".format(phase)
+ # for errortype, errornorm in error_dict.items():
+
+ # eocfile = open("eoc_filename", "a")
+ # eocfile.write( str(mesh_h) + " " + str(errornorm) + "\n" )
+ # eocfile.close()
+ # if subdomain.isRichards:mesh_h
+ data_dict = {
+ 'mesh_parameter': mesh_resolution,
+ 'mesh_h': mesh_h,
+ }
+ for norm_type, errornorm in error_dict.items():
+ data_dict.update(
+ {norm_type: errornorm}
+ )
+ errors = pd.DataFrame(data_dict, index=[mesh_resolution])
+ # check if file exists
+ if os.path.isfile(filename) is True:
+ with open(filename, 'a') as f:
+ errors.to_csv(
+ f,
+ header=False,
+ sep='\t',
+ encoding='utf-8',
+ index=False
+ )
+ else:
+ errors.to_csv(
+ filename,
+ sep='\t',
+ encoding='utf-8',
+ index=False
+ )
diff --git a/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/TP-R-layered_soil_with_inner_patch-realistic.py b/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/TP-R-layered_soil_with_inner_patch-realistic.py
new file mode 100755
index 0000000000000000000000000000000000000000..370f9c7507e802582d2e3cdf1af937655aabe284
--- /dev/null
+++ b/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/TP-R-layered_soil_with_inner_patch-realistic.py
@@ -0,0 +1,1003 @@
+#!/usr/bin/python3
+"""Layered soil simulation with inner patch.
+
+This program sets up an LDD simulation
+"""
+
+import dolfin as df
+# import mshr
+# import numpy as np
+import sympy as sym
+# import typing as tp
+import functools as ft
+# import domainPatch as dp
+import LDDsimulation as ldd
+import helpers as hlp
+import datetime
+import os
+import pandas as pd
+
+# check if output directory exists
+if not os.path.exists('./output'):
+ os.mkdir('./output')
+ print("Directory ", './output', " created ")
+else:
+ print("Directory ", './output', " already exists. Will use as output \
+ directory")
+
+
+# init sympy session
+sym.init_printing()
+# solver_tol = 6E-7
+use_case = "TP-R-layered-soil-with-inner-patch-realistic"
+# name of this very file. Needed for log output.
+thisfile = "TP-R-layered_soil_with_inner_patch.py"
+max_iter_num = 300
+FEM_Lagrange_degree = 1
+mesh_study = False
+resolutions = {
+ # 1: 2e-6, # h=2
+ # 2: 2e-6, # h=1.1180
+ # 4: 2e-6, # h=0.5590
+ # 8: 2e-6, # h=0.2814
+ 16: 2e-6, # h=0.1412
+ # 32: 2e-6,
+ # 64: 2e-6,
+ # 128: 2e-6
+ }
+
+# GRID #######################
+# mesh_resolution = 20
+timestep_size = 0.001
+number_of_timesteps = 5
+plot_timestep_every = 1
+# decide how many timesteps you want analysed. Analysed means, that we write
+# out subsequent errors of the L-iteration within the timestep.
+number_of_timesteps_to_analyse = 5
+starttimes = [0.0]
+
+Lw1 = 0.025 # /timestep_size
+Lnw1 = Lw1
+
+Lw2 = 0.025 # /timestep_size
+Lnw2 = Lw2
+
+Lw3 = 0.025 # /timestep_size
+Lnw3 = Lw3
+
+Lw4 = 0.025 # /timestep_size
+Lnw4 = Lw4
+
+Lw5 = 0.025 # /timestep_size
+Lnw5 = Lw5
+
+Lw6 = 0.025 # /timestep_size
+Lnw6 = Lw6
+
+lambda12_w = 40
+lambda12_nw = 40
+
+lambda23_w = 40
+lambda23_nw = 40
+
+lambda24_w = 40
+lambda24_nw= 40
+
+lambda25_w= 40
+lambda25_nw= 40
+
+lambda34_w = 40
+lambda34_nw = 40
+
+lambda36_w = 40
+lambda36_nw = 40
+
+lambda45_w = 40
+lambda45_nw = 40
+
+lambda46_w = 40
+lambda46_nw = 40
+
+lambda56_w = 40
+lambda56_nw = 40
+
+include_gravity = False
+debugflag = True
+analyse_condition = True
+
+if mesh_study:
+ output_string = "./output/{}-{}_timesteps{}_P{}".format(
+ datestr, use_case, number_of_timesteps, FEM_Lagrange_degree
+ )
+else:
+ for tol in resolutions.values():
+ solver_tol = tol
+ output_string = "./output/{}-{}_timesteps{}_P{}_solver_tol{}".format(
+ datestr, use_case, number_of_timesteps, FEM_Lagrange_degree, solver_tol
+ )
+
+
+# toggle what should be written to files
+if mesh_study:
+ write_to_file = {
+ 'space_errornorms': True,
+ 'meshes_and_markers': True,
+ 'L_iterations_per_timestep': False,
+ 'solutions': True,
+ 'absolute_differences': True,
+ 'condition_numbers': analyse_condition,
+ 'subsequent_errors': True
+ }
+else:
+ write_to_file = {
+ 'space_errornorms': True,
+ 'meshes_and_markers': True,
+ 'L_iterations_per_timestep': False,
+ 'solutions': True,
+ 'absolute_differences': True,
+ 'condition_numbers': analyse_condition,
+ 'subsequent_errors': True
+ }
+
+
+# global domain
+subdomain0_vertices = [df.Point(-1.0,-1.0), #
+ df.Point(1.0,-1.0),#
+ df.Point(1.0,1.0),#
+ df.Point(-1.0,1.0)]
+
+interface12_vertices = [df.Point(-1.0, 0.8),
+ df.Point(0.3, 0.8),
+ df.Point(0.5, 0.9),
+ df.Point(0.8, 0.7),
+ df.Point(1.0, 0.65)]
+
+
+ # interface23
+interface23_vertices = [df.Point(-1.0, 0.0),
+ df.Point(-0.35, 0.0),
+ # df.Point(6.5, 4.5),
+ df.Point(0.0, 0.0)]
+
+interface24_vertices = [interface23_vertices[2],
+ df.Point(0.6, 0.0),
+ ]
+
+interface25_vertices = [interface24_vertices[1],
+ df.Point(1.0, 0.0)
+ ]
+
+
+interface32_vertices = [interface23_vertices[2],
+ interface23_vertices[1],
+ interface23_vertices[0]]
+
+
+interface36_vertices = [df.Point(-1.0, -0.6),
+ df.Point(-0.6, -0.45)]
+
+
+interface46_vertices = [interface36_vertices[1],
+ df.Point(0.3, -0.25)]
+
+interface56_vertices = [interface46_vertices[1],
+ df.Point(0.65, -0.6),
+ df.Point(1.0, -0.7)]
+
+
+
+
+interface34_vertices = [interface36_vertices[1],
+ interface23_vertices[2]]
+# interface36
+
+interface45_vertices = [interface56_vertices[0],
+ df.Point(0.7, -0.2),
+ interface25_vertices[0]
+ ]
+
+
+# interface_vertices introduces a global numbering of interfaces.
+interface_def_points = [interface12_vertices,
+ interface23_vertices,
+ interface24_vertices,
+ interface25_vertices,
+ interface34_vertices,
+ interface36_vertices,
+ interface45_vertices,
+ interface46_vertices,
+ interface56_vertices,
+ ]
+
+adjacent_subdomains = [[1,2],
+ [2,3],
+ [2,4],
+ [2,5],
+ [3,4],
+ [3,6],
+ [4,5],
+ [4,6],
+ [5,6]
+ ]
+
+# subdomain1.
+subdomain1_vertices = [interface12_vertices[0],
+ interface12_vertices[1],
+ interface12_vertices[2],
+ interface12_vertices[3],
+ interface12_vertices[4], # southern boundary, 12 interface
+ subdomain0_vertices[2], # eastern boundary, outer boundary
+ subdomain0_vertices[3]] # northern boundary, outer on_boundary
+
+# vertex coordinates of the outer boundaries. If it can not be specified as a
+# polygon, use an entry per boundary polygon.
+# This information is used for defining
+# the Dirichlet boundary conditions. If a domain is completely internal, the
+# dictionary entry should be 0: None
+subdomain1_outer_boundary_verts = {
+ 0: [subdomain1_vertices[4],
+ subdomain1_vertices[5], # eastern boundary, outer boundary
+ subdomain1_vertices[6],
+ subdomain1_vertices[0]]
+}
+
+#subdomain1
+subdomain2_vertices = [interface23_vertices[0],
+ interface23_vertices[1],
+ interface23_vertices[2],
+ interface24_vertices[1],
+ interface25_vertices[1], # southern boundary, 23 interface
+ subdomain1_vertices[4], # eastern boundary, outer boundary
+ subdomain1_vertices[3],
+ subdomain1_vertices[2],
+ subdomain1_vertices[1],
+ subdomain1_vertices[0] ] # northern boundary, 12 interface
+
+subdomain2_outer_boundary_verts = {
+ 0: [subdomain2_vertices[9],
+ subdomain2_vertices[0]],
+ 1: [subdomain2_vertices[4],
+ subdomain2_vertices[5]]
+}
+
+
+subdomain3_vertices = [interface36_vertices[0],
+ interface36_vertices[1],
+ # interface34_vertices[0],
+ interface34_vertices[1],
+ # interface32_vertices[0],
+ interface32_vertices[1],
+ interface32_vertices[2]
+ ]
+
+subdomain3_outer_boundary_verts = {
+ 0: [subdomain3_vertices[4],
+ subdomain3_vertices[0]]
+}
+
+
+# subdomain3
+subdomain4_vertices = [interface46_vertices[0],
+ interface46_vertices[1],
+ interface45_vertices[1],
+ interface24_vertices[1],
+ interface24_vertices[0],
+ interface34_vertices[1]
+ ]
+
+subdomain4_outer_boundary_verts = None
+
+subdomain5_vertices = [interface56_vertices[0],
+ interface56_vertices[1],
+ interface56_vertices[2],
+ interface25_vertices[1],
+ interface25_vertices[0],
+ interface45_vertices[1],
+ interface45_vertices[0]
+]
+
+subdomain5_outer_boundary_verts = {
+ 0: [subdomain5_vertices[2],
+ subdomain5_vertices[3]]
+}
+
+
+
+subdomain6_vertices = [subdomain0_vertices[0],
+ subdomain0_vertices[1], # southern boundary, outer boundary
+ interface56_vertices[2],
+ interface56_vertices[1],
+ interface56_vertices[0],
+ interface36_vertices[1],
+ interface36_vertices[0]
+ ]
+
+subdomain6_outer_boundary_verts = {
+ 0: [subdomain6_vertices[6],
+ subdomain6_vertices[0],
+ subdomain6_vertices[1],
+ subdomain6_vertices[2]]
+}
+
+
+subdomain_def_points = [subdomain0_vertices,#
+ subdomain1_vertices,#
+ subdomain2_vertices,#
+ subdomain3_vertices,#
+ subdomain4_vertices,
+ subdomain5_vertices,
+ subdomain6_vertices
+ ]
+
+
+# if a subdomain has no outer boundary write None instead, i.e.
+# i: None
+# if i is the index of the inner subdomain.
+outer_boundary_def_points = {
+ # subdomain number
+ 1: subdomain1_outer_boundary_verts,
+ 2: subdomain2_outer_boundary_verts,
+ 3: subdomain3_outer_boundary_verts,
+ 4: subdomain4_outer_boundary_verts,
+ 5: subdomain5_outer_boundary_verts,
+ 6: subdomain6_outer_boundary_verts
+}
+
+
+isRichards = {
+ 1: True,
+ 2: True,
+ 3: False,
+ 4: False,
+ 5: False,
+ 6: False
+ }
+
+# isRichards = {
+# 1: True,
+# 2: True,
+# 3: True,
+# 4: True,
+# 5: True,
+# 6: True
+# }
+
+# Dict of the form: { subdom_num : viscosity }
+viscosity = {
+ 1: {'wetting' :1,
+ 'nonwetting': 1/50},
+ 2: {'wetting' :1,
+ 'nonwetting': 1/50},
+ 3: {'wetting' :1,
+ 'nonwetting': 1/50},
+ 4: {'wetting' :1,
+ 'nonwetting': 1/50},
+ 5: {'wetting' :1,
+ 'nonwetting': 1/50},
+ 6: {'wetting' :1,
+ 'nonwetting': 1/50},
+}
+
+# Dict of the form: { subdom_num : density }
+densities = {
+ 1: {'wetting': 1, #997
+ 'nonwetting': 1}, #1}, #1.225},
+ 2: {'wetting': 1, #997
+ 'nonwetting': 1}, #1.225},
+ 3: {'wetting': 1, #997
+ 'nonwetting': 1}, #1.225},
+ 4: {'wetting': 1, #997
+ 'nonwetting': 1}, #1.225}
+ 5: {'wetting': 1, #997
+ 'nonwetting': 1}, #1.225},
+ 6: {'wetting': 1, #997
+ 'nonwetting': 1} #1.225}
+}
+
+gravity_acceleration = 9.81
+# porosities taken from
+# https://www.geotechdata.info/parameter/soil-porosity.html
+# Dict of the form: { subdom_num : porosity }
+porosity = {
+ 1: 1, #0.2, # Clayey gravels, clayey sandy gravels
+ 2: 1, #0.22, # Silty gravels, silty sandy gravels
+ 3: 1, #0.37, # Clayey sands
+ 4: 1, #0.2 # Silty or sandy clay
+ 5: 1, #
+ 6: 1, #
+}
+
+# subdom_num : subdomain L for L-scheme
+L = {
+ 1: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 2: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 3: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 4: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 5: {'wetting' :Lw,
+ 'nonwetting': Lnw},
+ 6: {'wetting' :Lw,
+ 'nonwetting': Lnw}
+}
+
+
+# interface_num : lambda parameter for the L-scheme on that interface.
+# Note that interfaces are numbered starting from 0, because
+# adjacent_subdomains is a list and not a dict. Historic fuckup, I know
+# We have defined above as interfaces
+# # interface_vertices introduces a global numbering of interfaces.
+# interface_def_points = [interface12_vertices,
+# interface23_vertices,
+# interface24_vertices,
+# interface25_vertices,
+# interface34_vertices,
+# interface36_vertices,
+# interface45_vertices,
+# interface46_vertices,
+# interface56_vertices,
+# ]
+lambda_param = {
+ 0: {'wetting': lambda12_w,
+ 'nonwetting': lambda12_nw},#
+ 1: {'wetting': lambda23_w,
+ 'nonwetting': lambda23_nw},#
+ 2: {'wetting': lambda24_w,
+ 'nonwetting': lambda24_nw},#
+ 3: {'wetting': lambda25_w,
+ 'nonwetting': lambda25_nw},#
+ 4: {'wetting': lambda34_w,
+ 'nonwetting': lambda34_nw},#
+ 5: {'wetting': lambda36_w,
+ 'nonwetting': lambda36_nw},#
+ 6: {'wetting': lambda45_w,
+ 'nonwetting': lambda45_nw},#
+ 7: {'wetting': lambda46_w,
+ 'nonwetting': lambda46_nw},#
+ 8: {'wetting': lambda56_w,
+ 'nonwetting': lambda56_nw},#
+}
+
+
+# after Lewis, see pdf file
+intrinsic_permeability = {
+ 1: 0.1, # sand
+ 2: 0.1, # sand, there is a range
+ 3: 0.001, #10e-2, # clay has a range
+ 4: 0.001, #10e-3
+ 5: 0.001, #10e-2, # clay has a range
+ 6: 0.001, #10e-3
+}
+
+
+# relative permeabilty functions on subdomain 1
+def rel_perm1w(s):
+ # relative permeabilty wetting on subdomain1
+ return intrinsic_permeability[1]*s**2
+
+
+def rel_perm1nw(s):
+ # relative permeabilty nonwetting on subdomain1
+ return intrinsic_permeability[1]*(1-s)**2
+
+
+# relative permeabilty functions on subdomain 2
+def rel_perm2w(s):
+ # relative permeabilty wetting on subdomain2
+ return intrinsic_permeability[2]*s**2
+
+
+def rel_perm2nw(s):
+ # relative permeabilty nonwetting on subdomain2
+ return intrinsic_permeability[2]*(1-s)**2
+
+
+# relative permeabilty functions on subdomain 3
+def rel_perm3w(s):
+ # relative permeabilty wetting on subdomain3
+ return intrinsic_permeability[3]*s**3
+
+
+def rel_perm3nw(s):
+ # relative permeabilty nonwetting on subdomain3
+ return intrinsic_permeability[3]*(1-s)**3
+
+
+# relative permeabilty functions on subdomain 4
+def rel_perm4w(s):
+ # relative permeabilty wetting on subdomain4
+ return intrinsic_permeability[4]*s**3
+
+
+def rel_perm4nw(s):
+ # relative permeabilty nonwetting on subdomain4
+ return intrinsic_permeability[4]*(1-s)**3
+
+
+# relative permeabilty functions on subdomain 5
+def rel_perm5w(s):
+ # relative permeabilty wetting on subdomain5
+ return intrinsic_permeability[5]*s**3
+
+
+def rel_perm5nw(s):
+ # relative permeabilty nonwetting on subdomain5
+ return intrinsic_permeability[5]*(1-s)**3
+
+
+# relative permeabilty functions on subdomain 6
+def rel_perm6w(s):
+ # relative permeabilty wetting on subdomain6
+ return intrinsic_permeability[6]*s**3
+
+
+def rel_perm6nw(s):
+ # relative permeabilty nonwetting on subdomain6
+ return intrinsic_permeability[6]*(1-s)**3
+
+
+_rel_perm1w = ft.partial(rel_perm1w)
+_rel_perm1nw = ft.partial(rel_perm1nw)
+
+_rel_perm2w = ft.partial(rel_perm2w)
+_rel_perm2nw = ft.partial(rel_perm2nw)
+
+_rel_perm3w = ft.partial(rel_perm3w)
+_rel_perm3nw = ft.partial(rel_perm3nw)
+
+_rel_perm4w = ft.partial(rel_perm4w)
+_rel_perm4nw = ft.partial(rel_perm4nw)
+
+_rel_perm5w = ft.partial(rel_perm5w)
+_rel_perm5nw = ft.partial(rel_perm5nw)
+
+_rel_perm6w = ft.partial(rel_perm6w)
+_rel_perm6nw = ft.partial(rel_perm6nw)
+
+subdomain1_rel_perm = {
+ 'wetting': _rel_perm1w,
+ 'nonwetting': _rel_perm1nw
+}
+
+subdomain2_rel_perm = {
+ 'wetting': _rel_perm2w,
+ 'nonwetting': _rel_perm2nw
+}
+
+subdomain3_rel_perm = {
+ 'wetting': _rel_perm3w,
+ 'nonwetting': _rel_perm3nw
+}
+
+subdomain4_rel_perm = {
+ 'wetting': _rel_perm4w,
+ 'nonwetting': _rel_perm4nw
+}
+
+subdomain5_rel_perm = {
+ 'wetting': _rel_perm5w,
+ 'nonwetting': _rel_perm5nw
+}
+
+subdomain6_rel_perm = {
+ 'wetting': _rel_perm6w,
+ 'nonwetting': _rel_perm6nw
+}
+
+# dictionary of relative permeabilties on all domains.
+relative_permeability = {
+ 1: subdomain1_rel_perm,
+ 2: subdomain2_rel_perm,
+ 3: subdomain3_rel_perm,
+ 4: subdomain4_rel_perm,
+ 5: subdomain5_rel_perm,
+ 6: subdomain6_rel_perm
+}
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 1
+def rel_perm1w_prime(s):
+ # relative permeabilty on subdomain1
+ return intrinsic_permeability[1]*2*s
+
+
+def rel_perm1nw_prime(s):
+ # relative permeabilty on subdomain1
+ return -1*intrinsic_permeability[1]*2*(1-s)
+
+
+def rel_perm2w_prime(s):
+ # relative permeabilty on subdomain2
+ return intrinsic_permeability[2]*2*s
+
+
+def rel_perm2nw_prime(s):
+ # relative permeabilty on subdomain2
+ return -1*intrinsic_permeability[2]*2*(1-s)
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 3
+def rel_perm3w_prime(s):
+ # relative permeabilty on subdomain3
+ return intrinsic_permeability[3]*3*s**2
+
+
+def rel_perm3nw_prime(s):
+ # relative permeabilty on subdomain3
+ return -1*intrinsic_permeability[3]*3*(1-s)**2
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 4
+def rel_perm4w_prime(s):
+ # relative permeabilty on subdomain4
+ return intrinsic_permeability[4]*3*s**2
+
+
+def rel_perm4nw_prime(s):
+ # relative permeabilty on subdomain4
+ return -1*intrinsic_permeability[4]*3*(1-s)**2
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 5
+def rel_perm5w_prime(s):
+ # relative permeabilty on subdomain5
+ return intrinsic_permeability[5]*3*s**2
+
+
+def rel_perm5nw_prime(s):
+ # relative permeabilty on subdomain5
+ return -1*intrinsic_permeability[5]*3*(1-s)**2
+
+
+# definition of the derivatives of the relative permeabilities
+# relative permeabilty functions on subdomain 6
+def rel_perm6w_prime(s):
+ # relative permeabilty on subdomain6
+ return intrinsic_permeability[6]*3*s**2
+
+
+def rel_perm6nw_prime(s):
+ # relative permeabilty on subdomain6
+ return -1*intrinsic_permeability[6]*3*(1-s)**2
+
+
+_rel_perm1w_prime = ft.partial(rel_perm1w_prime)
+_rel_perm1nw_prime = ft.partial(rel_perm1nw_prime)
+_rel_perm2w_prime = ft.partial(rel_perm2w_prime)
+_rel_perm2nw_prime = ft.partial(rel_perm2nw_prime)
+_rel_perm3w_prime = ft.partial(rel_perm3w_prime)
+_rel_perm3nw_prime = ft.partial(rel_perm3nw_prime)
+_rel_perm4w_prime = ft.partial(rel_perm4w_prime)
+_rel_perm4nw_prime = ft.partial(rel_perm4nw_prime)
+_rel_perm5w_prime = ft.partial(rel_perm5w_prime)
+_rel_perm5nw_prime = ft.partial(rel_perm5nw_prime)
+_rel_perm6w_prime = ft.partial(rel_perm6w_prime)
+_rel_perm6nw_prime = ft.partial(rel_perm6nw_prime)
+
+subdomain1_rel_perm_prime = {
+ 'wetting': _rel_perm1w_prime,
+ 'nonwetting': _rel_perm1nw_prime
+}
+
+
+subdomain2_rel_perm_prime = {
+ 'wetting': _rel_perm2w_prime,
+ 'nonwetting': _rel_perm2nw_prime
+}
+
+subdomain3_rel_perm_prime = {
+ 'wetting': _rel_perm3w_prime,
+ 'nonwetting': _rel_perm3nw_prime
+}
+
+
+subdomain4_rel_perm_prime = {
+ 'wetting': _rel_perm4w_prime,
+ 'nonwetting': _rel_perm4nw_prime
+}
+
+subdomain5_rel_perm_prime = {
+ 'wetting': _rel_perm5w_prime,
+ 'nonwetting': _rel_perm5nw_prime
+}
+
+subdomain6_rel_perm_prime = {
+ 'wetting': _rel_perm6w_prime,
+ 'nonwetting': _rel_perm6nw_prime
+}
+
+
+# dictionary of relative permeabilties on all domains.
+ka_prime = {
+ 1: subdomain1_rel_perm_prime,
+ 2: subdomain2_rel_perm_prime,
+ 3: subdomain3_rel_perm_prime,
+ 4: subdomain4_rel_perm_prime,
+ 5: subdomain5_rel_perm_prime,
+ 6: subdomain6_rel_perm_prime,
+}
+
+
+
+# S-pc-relation ship. We use the van Genuchten approach, i.e.
+# pc = 1/alpha*(S^{-1/m} -1)^1/n, where we set alpha = 0, assume
+# m = 1-1/n (see Helmig) and assume that residual saturation is Sw
+# this function needs to be monotonically decreasing in the capillary pressure
+# pc.
+# Since in the richards case pc=-pw, this becomes as a function of pw a mono
+# tonically INCREASING function like in our Richards-Richards paper. However
+# since we unify the treatment in the code for Richards and two-phase, we need
+# the same requierment
+# for both cases, two-phase and Richards.
+# def saturation(pc, n_index, alpha):
+# # inverse capillary pressure-saturation-relationship
+# return df.conditional(pc > 0, 1/((1 + (alpha*pc)**n_index)**((n_index - 1)/n_index)), 1)
+#
+# # S-pc-relation ship. We use the van Genuchten approach, i.e. pc = 1/alpha*(S^{-1/m} -1)^1/n, where
+# # we set alpha = 0, assume m = 1-1/n (see Helmig) and assume that residual saturation is Sw
+# def saturation_sym(pc, n_index, alpha):
+# # inverse capillary pressure-saturation-relationship
+# #df.conditional(pc > 0,
+# return 1/((1 + (alpha*pc)**n_index)**((n_index - 1)/n_index))
+#
+#
+# # derivative of S-pc relationship with respect to pc. This is needed for the
+# # construction of a analytic solution.
+# def saturation_sym_prime(pc, n_index, alpha):
+# # inverse capillary pressure-saturation-relationship
+# return -(alpha*(n_index - 1)*(alpha*pc)**(n_index - 1)) / ( (1 + (alpha*pc)**n_index)**((2*n_index - 1)/n_index) )
+##
+# # note that the conditional definition of S-pc in the nonsymbolic part will be
+# # incorporated in the construction of the exact solution below.
+# S_pc_sym = {
+# 1: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 2: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 3: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 4: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 5: ft.partial(saturation_sym, n_index=3, alpha=0.001),
+# 6: ft.partial(saturation_sym, n_index=3, alpha=0.001)
+# }
+#
+# S_pc_sym_prime = {
+# 1: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 2: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 3: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 4: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 5: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001),
+# 6: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001)
+# }
+#
+# sat_pressure_relationship = {
+# 1: ft.partial(saturation, n_index=3, alpha=0.001),
+# 2: ft.partial(saturation, n_index=3, alpha=0.001),
+# 3: ft.partial(saturation, n_index=3, alpha=0.001),
+# 4: ft.partial(saturation, n_index=3, alpha=0.001),
+# 5: ft.partial(saturation, n_index=3, alpha=0.001),
+# 6: ft.partial(saturation, n_index=3, alpha=0.001)
+# }
+
+def saturation(pc, n_index):
+ # inverse capillary pressure-saturation-relationship
+ return df.conditional(pc > 0, 1/((1 + pc)**(1/(n_index + 1))), 1)
+
+
+def saturation_sym(pc, n_index):
+ # inverse capillary pressure-saturation-relationship
+ return 1/((1 + pc)**(1/(n_index + 1)))
+
+
+def saturation_sym_prime(pc, n_index):
+ # inverse capillary pressure-saturation-relationship
+ return -1/((n_index+1)*(1 + pc)**((n_index+2)/(n_index+1)))
+
+
+S_pc_sym = {
+ 1: ft.partial(saturation_sym, n_index=1),
+ 2: ft.partial(saturation_sym, n_index=1),
+ 3: ft.partial(saturation_sym, n_index=2),
+ 4: ft.partial(saturation_sym, n_index=2),
+ 5: ft.partial(saturation_sym, n_index=2),
+ 6: ft.partial(saturation_sym, n_index=2)
+}
+
+S_pc_sym_prime = {
+ 1: ft.partial(saturation_sym_prime, n_index=1),
+ 2: ft.partial(saturation_sym_prime, n_index=1),
+ 3: ft.partial(saturation_sym_prime, n_index=2),
+ 4: ft.partial(saturation_sym_prime, n_index=2),
+ 5: ft.partial(saturation_sym_prime, n_index=2),
+ 6: ft.partial(saturation_sym_prime, n_index=2)
+}
+
+sat_pressure_relationship = {
+ 1: ft.partial(saturation, n_index=1),
+ 2: ft.partial(saturation, n_index=1),
+ 3: ft.partial(saturation, n_index=2),
+ 4: ft.partial(saturation, n_index=2),
+ 5: ft.partial(saturation, n_index=2),
+ 6: ft.partial(saturation, n_index=2)
+}
+
+#############################################
+# Manufacture source expressions with sympy #
+#############################################
+x, y = sym.symbols('x[0], x[1]') # needed by UFL
+t = sym.symbols('t', positive=True)
+
+
+p_e_sym = {
+ 1: {'wetting': -5.0 - (1.0 + t*t)*(1.0 + x*x + y*y),
+ 'nonwetting': (-1 -t*(1.1 + y + x**2)) },
+ 2: {'wetting': -5.0 - (1.0 + t*t)*(1.0 + x*x + y*y),
+ 'nonwetting': (-1 -t*(1.1 + y + x**2)) },
+ 3: {'wetting': (-5.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1 -t*(1 + x**2) - sym.sqrt(2+t**2)*(1+y)*y**2) },
+ 4: {'wetting': (-5.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1 -t*(1 + x**2) - sym.sqrt(2+t**2)*(1+y)*y**2) },
+ 5: {'wetting': (-5.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1 -t*(1 + x**2) - sym.sqrt(2+t**2)*(1+y)*y**2) },
+ 6: {'wetting': (-5.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1 -t*(1 + x**2) - sym.sqrt(2+t**2)*(1+y)*y**2) },
+}
+
+pc_e_sym = dict()
+for subdomain, isR in isRichards.items():
+ if isR:
+ pc_e_sym.update({subdomain: -p_e_sym[subdomain]['wetting']})
+ else:
+ pc_e_sym.update(
+ {subdomain: p_e_sym[subdomain]['nonwetting']
+ - p_e_sym[subdomain]['wetting']}
+ )
+
+
+symbols = {"x": x,
+ "y": y,
+ "t": t}
+# turn above symbolic code into exact solution for dolphin and
+# construct the rhs that matches the above exact solution.
+exact_solution_example = hlp.generate_exact_solution_expressions(
+ symbols=symbols,
+ isRichards=isRichards,
+ symbolic_pressure=p_e_sym,
+ symbolic_capillary_pressure=pc_e_sym,
+ saturation_pressure_relationship=S_pc_sym,
+ saturation_pressure_relationship_prime=S_pc_sym_prime,
+ viscosity=viscosity,
+ porosity=porosity,
+ relative_permeability=relative_permeability,
+ relative_permeability_prime=ka_prime,
+ densities=densities,
+ gravity_acceleration=gravity_acceleration,
+ include_gravity=include_gravity,
+ )
+source_expression = exact_solution_example['source']
+exact_solution = exact_solution_example['exact_solution']
+initial_condition = exact_solution_example['initial_condition']
+
+# Dictionary of dirichlet boundary conditions.
+dirichletBC = dict()
+# similarly to the outer boundary dictionary, if a patch has no outer boundary
+# None should be written instead of an expression.
+# This is a bit of a brainfuck:
+# dirichletBC[ind] gives a dictionary of the outer boundaries of subdomain ind.
+# Since a domain patch can have several disjoint outer boundary parts, the
+# expressions need to get an enumaration index which starts at 0.
+# So dirichletBC[ind][j] is the dictionary of outer dirichlet conditions of
+# subdomain ind and boundary part j.
+# Finally, dirichletBC[ind][j]['wetting'] and dirichletBC[ind][j]['nonwetting']
+# return the actual expression needed for the dirichlet condition for both
+# phases if present.
+
+# subdomain index: {outer boudary part index: {phase: expression}}
+for subdomain in isRichards.keys():
+ # if subdomain has no outer boundary, outer_boundary_def_points[subdomain]
+ # is None
+ if outer_boundary_def_points[subdomain] is None:
+ dirichletBC.update({subdomain: None})
+ else:
+ dirichletBC.update({subdomain: dict()})
+ # set the dirichlet conditions to be the same code as exact solution on
+ # the subdomain.
+ for outer_boundary_ind in outer_boundary_def_points[subdomain].keys():
+ dirichletBC[subdomain].update(
+ {outer_boundary_ind: exact_solution[subdomain]}
+ )
+
+
+# read this file and print it to std out. This way the simulation can produce a
+# log file with ./TP-R-layered_soil.py | tee simulation.log
+f = open(thisfile, 'r')
+print(f.read())
+f.close()
+
+
+for starttime in starttimes:
+ for mesh_resolution, solver_tol in resolutions.items():
+ # initialise LDD simulation class
+ simulation = ldd.LDDsimulation(
+ tol=1E-14,
+ LDDsolver_tol=solver_tol,
+ debug=debugflag,
+ max_iter_num=max_iter_num,
+ FEM_Lagrange_degree=FEM_Lagrange_degree,
+ mesh_study=mesh_study
+ )
+
+ simulation.set_parameters(
+ use_case=use_case,
+ output_dir=output_string,
+ subdomain_def_points=subdomain_def_points,
+ isRichards=isRichards,
+ interface_def_points=interface_def_points,
+ outer_boundary_def_points=outer_boundary_def_points,
+ adjacent_subdomains=adjacent_subdomains,
+ mesh_resolution=mesh_resolution,
+ viscosity=viscosity,
+ porosity=porosity,
+ L=L,
+ lambda_param=lambda_param,
+ relative_permeability=relative_permeability,
+ saturation=sat_pressure_relationship,
+ starttime=starttime,
+ number_of_timesteps=number_of_timesteps,
+ number_of_timesteps_to_analyse=number_of_timesteps_to_analyse,
+ plot_timestep_every=plot_timestep_every,
+ timestep_size=timestep_size,
+ sources=source_expression,
+ initial_conditions=initial_condition,
+ dirichletBC_expression_strings=dirichletBC,
+ exact_solution=exact_solution,
+ densities=densities,
+ include_gravity=include_gravity,
+ write2file=write_to_file,
+ )
+
+ simulation.initialise()
+ output_dir = simulation.output_dir
+ # simulation.write_exact_solution_to_xdmf()
+ output = simulation.run(analyse_condition=analyse_condition)
+ for subdomain_index, subdomain_output in output.items():
+ mesh_h = subdomain_output['mesh_size']
+ for phase, error_dict in subdomain_output['errornorm'].items():
+ filename = output_dir \
+ + "subdomain{}".format(subdomain_index)\
+ + "-space-time-errornorm-{}-phase.csv".format(phase)
+ # for errortype, errornorm in error_dict.items():
+
+ # eocfile = open("eoc_filename", "a")
+ # eocfile.write( str(mesh_h) + " " + str(errornorm) + "\n" )
+ # eocfile.close()
+ # if subdomain.isRichards:mesh_h
+ data_dict = {
+ 'mesh_parameter': mesh_resolution,
+ 'mesh_h': mesh_h,
+ }
+ for norm_type, errornorm in error_dict.items():
+ data_dict.update(
+ {norm_type: errornorm}
+ )
+ errors = pd.DataFrame(data_dict, index=[mesh_resolution])
+ # check if file exists
+ if os.path.isfile(filename) is True:
+ with open(filename, 'a') as f:
+ errors.to_csv(
+ f,
+ header=False,
+ sep='\t',
+ encoding='utf-8',
+ index=False
+ )
+ else:
+ errors.to_csv(
+ filename,
+ sep='\t',
+ encoding='utf-8',
+ index=False
+ )
diff --git a/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/run-simulation b/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/run-simulation
new file mode 100755
index 0000000000000000000000000000000000000000..0eb497502a082a0fec07a5449b1fe946d59c8cc7
--- /dev/null
+++ b/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/run-simulation
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+[ $# -eq 0 ] && { echo "Usage: $0 simulation_file [logfile_name]"; exit 1; }
+
+SIMULATION_FILE=$1
+SIMULATION=${SIMULATION_FILE%.py}
+LOGFILE_DEFAULT="$SIMULATION.log"
+
+DATE=$(date -I)
+LOGFILE=${2:-$DATE-$LOGFILE_DEFAULT}
+
+GREETING="Simulation $SIMULATION is run on $DATE by $USER"
+
+echo $GREETING
+echo "running $SIMULATION_FILE | tee $LOGFILE"
+./$SIMULATION_FILE | tee $LOGFILE