diff --git a/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/mesh_study/TP-R-layered_soil_with_inner_patch-realistic-same-intrinsic.py b/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/mesh_study/TP-R-layered_soil_with_inner_patch-realistic-same-intrinsic.py
new file mode 100644
index 0000000000000000000000000000000000000000..cb6372a665985099e1e0b064bbbc38be26984370
--- /dev/null
+++ b/Two-phase-Richards/multi-patch/layered_soil_with_inner_patch/mesh_study/TP-R-layered_soil_with_inner_patch-realistic-same-intrinsic.py
@@ -0,0 +1,481 @@
+#!/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 functions as fts
+import LDDsimulation as ldd
+import helpers as hlp
+import datetime
+import os
+import multiprocessing as mp
+import domainSubstructuring as dss
+
+# init sympy session
+sym.init_printing()
+
+# PREREQUISITS ###############################################################
+# check if output directory "./output" exists. This will be used in
+# the generation of the output string.
+if not os.path.exists('./output'):
+ os.mkdir('./output')
+ print("Directory ", './output', " created ")
+else:
+ print("Directory ", './output', " already exists. Will use as output \
+ directory")
+
+date = datetime.datetime.now()
+datestr = date.strftime("%Y-%m-%d")
+
+# Name of the usecase that will be printed during simulation.
+use_case = "TP-R-layered-soil-with-inner-patch-realistic-same-intrinsic"
+# The name of this very file. Needed for creating log output.
+thisfile = "TP-R-layered_soil_with_inner_patch-realistic-same-intrinsic.py"
+
+# GENERAL SOLVER CONFIG ######################################################
+# maximal iteration per timestep
+max_iter_num = 1000
+FEM_Lagrange_degree = 1
+
+# GRID AND MESH STUDY SPECIFICATIONS #########################################
+mesh_study = True
+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: 1e-6, # h=0.1412
+ 32: 1e-6,
+ 64: 5e-7,
+ 128: 5e-7
+ }
+
+# starttimes gives a list of starttimes to run the simulation from.
+# The list is looped over and a simulation is run with t_0 as initial time
+# for each element t_0 in starttimes.
+starttimes = {0: 0.0}
+# starttimes = {0: 0.0, 1:0.3, 2:0.6, 3:0.9}
+timestep_size = 0.001
+number_of_timesteps = 1000
+
+# LDD scheme parameters ######################################################
+
+Lw1 = 0.01 # /timestep_size
+Lnw1 = Lw1
+
+Lw2 = 0.01 # /timestep_size
+Lnw2 = Lw2
+
+Lw3 = 0.01 # /timestep_size
+Lnw3 = 0.003
+
+Lw4 = 0.01 # /timestep_size
+Lnw4 = 0.003
+
+Lw5 = 0.01 # /timestep_size
+Lnw5 = 0.003
+
+Lw6 = 0.01 # /timestep_size
+Lnw6 = 0.003
+
+lambda12_w = 0.5
+lambda12_nw = 0.5
+
+lambda23_w = 0.5
+lambda23_nw = 0.5
+
+lambda24_w = 0.5
+lambda24_nw= 0.5
+
+lambda25_w= 0.5
+lambda25_nw= 0.5
+
+lambda34_w = 0.5
+lambda34_nw = 0.5
+
+lambda36_w = 0.5
+lambda36_nw = 0.5
+
+lambda45_w = 0.5
+lambda45_nw = 0.5
+
+lambda46_w = 0.5
+lambda46_nw = 0.5
+
+lambda56_w = 0.5
+lambda56_nw = 0.5
+
+include_gravity = False
+debugflag = False
+analyse_condition = False
+
+# I/O CONFIG #################################################################
+# when number_of_timesteps is high, it might take a long time to write all
+# timesteps to disk. Therefore, you can choose to only write data of every
+# plot_timestep_every timestep to disk.
+plot_timestep_every = 3
+# Decide how many timesteps you want analysed. Analysed means, that
+# subsequent errors of the L-iteration within the timestep are written out.
+number_of_timesteps_to_analyse = 5
+
+# fine grained control over data to be written to disk in the mesh study case
+# as well as for a regular simuation for a fixed grid.
+if mesh_study:
+ write_to_file = {
+ # output the relative errornorm (integration in space) w.r.t. an exact
+ # solution for each timestep into a csv file.
+ 'space_errornorms': True,
+ # save the mesh and marker functions to disk
+ 'meshes_and_markers': True,
+ # save xdmf/h5 data for each LDD iteration for timesteps determined by
+ # number_of_timesteps_to_analyse. I/O intensive!
+ 'L_iterations_per_timestep': False,
+ # save solution to xdmf/h5.
+ 'solutions': True,
+ # save absolute differences w.r.t an exact solution to xdmf/h5 file
+ # to monitor where on the domains errors happen
+ 'absolute_differences': True,
+ # analyise condition numbers for timesteps determined by
+ # number_of_timesteps_to_analyse and save them over time to csv.
+ 'condition_numbers': analyse_condition,
+ # output subsequent iteration errors measured in L^2 to csv for
+ # timesteps determined by number_of_timesteps_to_analyse.
+ # Usefull to monitor convergence of the acutal LDD solver.
+ '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
+ }
+
+# OUTPUT FILE STRING #########################################################
+output_string = "./output/{}-{}_timesteps{}_P{}".format(
+ datestr, use_case, number_of_timesteps, FEM_Lagrange_degree
+ )
+
+# DOMAIN AND INTERFACES #######################################################
+substructuring = dss.layeredSoilInnerPatch()
+interface_def_points = substructuring.interface_def_points
+adjacent_subdomains = substructuring.adjacent_subdomains
+subdomain_def_points = substructuring.subdomain_def_points
+outer_boundary_def_points = substructuring.outer_boundary_def_points
+
+# MODEL CONFIGURATION #########################################################
+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': 997.0, #997
+ 'nonwetting': 1.225}, #1}, #1.225},
+ 2: {'wetting': 997.0, #997
+ 'nonwetting': 1.225}, #1.225},
+ 3: {'wetting': 997.0, #997
+ 'nonwetting': 1.225}, #1.225},
+ 4: {'wetting': 997.0, #997
+ 'nonwetting': 1.225}, #1.225}
+ 5: {'wetting': 997.0, #997
+ 'nonwetting': 1.225}, #1.225},
+ 6: {'wetting': 997.0, #997
+ 'nonwetting': 1.225} #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: 0.2, #0.2, # Clayey gravels, clayey sandy gravels
+ 2: 0.2, #0.22, # Silty gravels, silty sandy gravels
+ 3: 0.2, #0.37, # Clayey sands
+ 4: 0.2, #0.2 # Silty or sandy clay
+ 5: 0.2, #
+ 6: 0.2, #
+}
+
+# subdom_num : subdomain L for L-scheme
+L = {
+ 1: {'wetting' :Lw1,
+ 'nonwetting': Lnw1},
+ 2: {'wetting' :Lw2,
+ 'nonwetting': Lnw2},
+ 3: {'wetting' :Lw3,
+ 'nonwetting': Lnw3},
+ 4: {'wetting' :Lw4,
+ 'nonwetting': Lnw4},
+ 5: {'wetting' :Lw5,
+ 'nonwetting': Lnw5},
+ 6: {'wetting' :Lw6,
+ 'nonwetting': Lnw6}
+}
+
+
+# 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_a,
+# interface45_vertices_b,
+# 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': lambda45_w,
+ 'nonwetting': lambda45_nw},
+ 8: {'wetting': lambda46_w,
+ 'nonwetting': lambda46_nw},
+ 9: {'wetting': lambda56_w,
+ 'nonwetting': lambda56_nw},
+}
+
+
+# after Lewis, see pdf file
+intrinsic_permeability = {
+ 1: 0.01, # sand
+ 2: 0.01, # sand, there is a range
+ 3: 0.01, #10e-2, # clay has a range
+ 4: 0.01, #10e-3
+ 5: 0.01, #10e-2, # clay has a range
+ 6: 0.01, #10e-3
+}
+
+# relative permeabilties
+rel_perm_definition = {
+ 1: {"wetting": "Spow2",
+ "nonwetting": "oneMinusSpow2"},
+ 2: {"wetting": "Spow2",
+ "nonwetting": "oneMinusSpow2"},
+ 3: {"wetting": "Spow3",
+ "nonwetting": "oneMinusSpow3"},
+ 4: {"wetting": "Spow3",
+ "nonwetting": "oneMinusSpow3"},
+ 5: {"wetting": "Spow3",
+ "nonwetting": "oneMinusSpow3"},
+ 6: {"wetting": "Spow3",
+ "nonwetting": "oneMinusSpow3"},
+}
+
+rel_perm_dict = fts.generate_relative_permeability_dicts(rel_perm_definition)
+relative_permeability = rel_perm_dict["ka"]
+ka_prime = rel_perm_dict["ka_prime"]
+
+# S-pc relation
+Spc_on_subdomains = {
+ 1: {"testSpc": {"index": 1}},
+ 2: {"testSpc": {"index": 1}},
+ 3: {"testSpc": {"index": 2}},
+ 4: {"testSpc": {"index": 2}},
+ 5: {"testSpc": {"index": 2}},
+ 6: {"testSpc": {"index": 2}},
+}
+
+Spc = fts.generate_Spc_dicts(Spc_on_subdomains)
+S_pc_sym = Spc["symbolic"]
+S_pc_sym_prime = Spc["prime_symbolic"]
+sat_pressure_relationship = Spc["dolfin"]
+
+###############################################################################
+# 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*t },
+ 2: {'wetting': -7.0 - (1.0 + t*t)*(1.0 + x*x + y*y),
+ 'nonwetting': 0*t },
+ 3: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1.0 -t*(1.0 + x**2) - sym.sqrt(2+t**2)**2)*y**2 },
+ 4: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1.0 -t*(1.0 + x**2) - sym.sqrt(2+t**2)**2)*y**2 },
+ 5: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1.0 -t*(1.0 + x**2) - sym.sqrt(2+t**2)**2)*y**2 },
+ 6: {'wetting': (-7.0 - (1.0 + t*t)*(1.0 + x*x)),
+ 'nonwetting': (-1.0 -t*(1.0 + x**2) - sym.sqrt(2+t**2)**2)*y**2 },
+}
+
+pc_e_sym = hlp.generate_exact_symbolic_pc(
+ isRichards=isRichards,
+ symbolic_pressure=p_e_sym
+ )
+
+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,
+ intrinsic_permeability=intrinsic_permeability,
+ 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']
+
+# BOUNDARY CONDITIONS #########################################################
+# Dictionary of dirichlet boundary conditions. If an exact solution case is
+# used, use the hlp.generate_exact_DirichletBC() method to generate the
+# Dirichlet Boundary conditions from the exact solution.
+dirichletBC = hlp.generate_exact_DirichletBC(
+ isRichards=isRichards,
+ outer_boundary_def_points=outer_boundary_def_points,
+ exact_solution=exact_solution
+ )
+# If no exact solution is provided you need to provide a dictionary of boundary
+# conditions. See the definiton of hlp.generate_exact_DirichletBC() to see
+# the structure.
+
+# LOG FILE OUTPUT #############################################################
+# 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()
+
+# MAIN ########################################################################
+if __name__ == '__main__':
+ # dictionary of simualation parameters to pass to the run function.
+ # mesh_resolution and starttime are excluded, as they get passed explicitly
+ # to achieve parallelisation in these parameters in these parameters for
+ # mesh studies etc.
+ simulation_parameter = {
+ "tol": 1E-14,
+ "debugflag": debugflag,
+ "max_iter_num": max_iter_num,
+ "FEM_Lagrange_degree": FEM_Lagrange_degree,
+ "mesh_study": mesh_study,
+ "use_case": use_case,
+ "output_string": 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,
+ "intrinsic_permeability": intrinsic_permeability,
+ "sat_pressure_relationship": 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,
+ "source_expression": source_expression,
+ "initial_condition": initial_condition,
+ "dirichletBC": dirichletBC,
+ "exact_solution": exact_solution,
+ "densities": densities,
+ "include_gravity": include_gravity,
+ "gravity_acceleration": gravity_acceleration,
+ "write_to_file": write_to_file,
+ "analyse_condition": analyse_condition
+ }
+ for number_shift, starttime in starttimes.items():
+ simulation_parameter.update(
+ {"starttime_timestep_number_shift": number_shift}
+ )
+ for mesh_resolution, solver_tol in resolutions.items():
+ simulation_parameter.update({"solver_tol": solver_tol})
+ hlp.info(simulation_parameter["use_case"])
+ processQueue = mp.Queue()
+ LDDsim = mp.Process(
+ target=hlp.run_simulation,
+ args=(
+ simulation_parameter,
+ processQueue,
+ starttime,
+ mesh_resolution
+ )
+ )
+ LDDsim.start()
+ # LDDsim.join()
+ # hlp.run_simulation(
+ # mesh_resolution=mesh_resolution,
+ # starttime=starttime,
+ # parameter=simulation_parameter
+ # )
+
+ LDDsim.join()
+ if mesh_study:
+ simulation_output_dir = processQueue.get()
+ hlp.merge_spacetime_errornorms(isRichards=isRichards,
+ resolutions=resolutions,
+ output_dir=simulation_output_dir)