diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-realistic-parameters-densities-scaled.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/Archive/TP-R-2-realistic-parameters-densities-scaled.py
similarity index 100%
rename from Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-realistic-parameters-densities-scaled.py
rename to Two-phase-Richards/two-patch/TP-R-two-patch-test-case/Archive/TP-R-2-realistic-parameters-densities-scaled.py
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd-realistic.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd-realistic.py
index 9ae8b6b42002422144213fd485e605f8d890bd34..d0d78747e81577d7178e04fce5e472cf1a19b1a2 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd-realistic.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd-realistic.py
@@ -1,147 +1,138 @@
-#!/usr/bin/python3
+"""TPR 2 patch soil simulation.
+
+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 domainPatch as dp
-import LDDsimulation as ldd
 import functools as ft
+import LDDsimulation as ldd
 import helpers as hlp
 import datetime
 import os
 import pandas as pd
+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")
-#import ufl as ufl
 
-# init sympy session
-sym.init_printing()
+# Name of the usecase that will be printed during simulation.
+use_case = "TPR-2-patch-realistic-pure-dd"
+# The name of this very file. Needed for creating log output.
+thisfile = "TP-R-2-patch-pure-dd-realistic.py"
 
-use_case = "TP-R-2-patch-realistic-pure-dd"
-# solver_tol = 6E-7
-max_iter_num = 1000
+# GENERAL SOLVER CONFIG  ######################################################
+# maximal iteration per timestep
+max_iter_num = 500
 FEM_Lagrange_degree = 1
+
+# GRID AND MESH STUDY SPECIFICATIONS  #########################################
 mesh_study = False
 resolutions = {
-                # 1: 7e-7,
-                # 2: 7e-7,
-                # 4: 7e-7,
-                # 8: 7e-7,
-                # 16: 7e-7,
-                32: 1e-6,
-                # 64: 7e-7,
-                # 128: 7e-7,
-                # 256: 7e-7
+                # 1: 1e-5,
+                # 2: 1e-5,
+                # 4: 1e-5,
+                # 8: 1e-5,
+                16: 5e-6,
+                # 32: 5e-6,
+                # 64: 2e-6,
+                # 128: 2e-6,
+                # 256: 1e-6,
                 }
 
-############ GRID #######################
-timestep_size = 0.00001
-number_of_timesteps = 20
-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 = 4
+# 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]
+timestep_size = 0.00001
+number_of_timesteps = 5
 
-Lw = 0.5 #/timestep_size
-Lnw= 0.5
+# LDD scheme parameters  ######################################################
+Lw1 = 0.5 #/timestep_size
+Lnw1= 0.5
+
+Lw2 = 0.5 #/timestep_size
+Lnw2= 0.5
 
 lambda_w = 1
 lambda_nw = 1
 
 include_gravity = True
-debugflag = True
+debugflag = False
 analyse_condition = False
 
-output_string = "./output/{}-{}_timesteps{}_P{}".format(datestr, use_case, number_of_timesteps, FEM_Lagrange_degree)
+# 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 = 1
+# 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 = 1
 
-# toggle what should be written to files
+# 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,
-        'solutions': False,
-        'absolute_differences': 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,
-        'subsequent_errors': False
+        # 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': 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 Interface ####
-# global simulation domain domain
-sub_domain0_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)]
-# interface between subdomain1 and subdomain2
-interface12_vertices = [df.Point(-1.0, 0.0),
-                        df.Point(1.0, 0.0) ]
-# subdomain1.
-sub_domain1_vertices = [interface12_vertices[0],
-                        interface12_vertices[1],
-                        sub_domain0_vertices[2],
-                        sub_domain0_vertices[3]]
-
-# 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: [interface12_vertices[1], #
-        sub_domain0_vertices[2],
-        sub_domain0_vertices[3], #
-        interface12_vertices[0]]
-}
-# subdomain2
-sub_domain2_vertices = [sub_domain0_vertices[0],
-                        sub_domain0_vertices[1],
-                        interface12_vertices[1],
-                        interface12_vertices[0] ]
-
-subdomain2_outer_boundary_verts = {
-    0: [interface12_vertices[0], #
-        sub_domain0_vertices[0],
-        sub_domain0_vertices[1],
-        interface12_vertices[1]]
-}
-
-# list of subdomains given by the boundary polygon vertices.
-# Subdomains are given as a list of dolfin points forming
-# a closed polygon, such that mshr.Polygon(subdomain_def_points[i]) can be used
-# to create the subdomain. subdomain_def_points[0] contains the
-# vertices of the global simulation domain and subdomain_def_points[i] contains the
-# vertices of the subdomain i.
-subdomain_def_points = [sub_domain0_vertices,#
-                      sub_domain1_vertices,#
-                      sub_domain2_vertices]
-# in the below list, index 0 corresponds to the 12 interface which has index 1
-interface_def_points = [interface12_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
-}
+# DOMAIN AND INTERFACE  #######################################################
+substructuring = dss.twoSoilLayers()
+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
 
-# adjacent_subdomains[i] contains the indices of the subdomains sharing the
-# interface i (i.e. given by interface_def_points[i]).
-adjacent_subdomains = [[1,2]]
+# MODEL CONFIGURATION #########################################################
 isRichards = {
     1: True, #
     2: False
@@ -387,14 +378,10 @@ p_e_sym = {
         'nonwetting': (-1 -t*(1.1 + y*y) - sym.sin((x*y-0.5*t)*y**2)**2)},  #*(sym.sin((1+y)/2*sym.pi)*sym.sin((1+x)/2*sym.pi))**2},
 }
 
-pc_e_sym = dict()
-for subdomain, isR in isRichards.items():
-    if isR:
-        pc_e_sym.update({subdomain: -p_e_sym[subdomain]['wetting'].copy()})
-    else:
-        pc_e_sym.update({subdomain: p_e_sym[subdomain]['nonwetting'].copy()
-                                        - p_e_sym[subdomain]['wetting'].copy()})
-
+pc_e_sym = hlp.generate_exact_symbolic_pc(
+                isRichards=isRichards,
+                symbolic_pressure=p_e_sym
+            )
 
 symbols = {"x": x,
            "y": y,
@@ -420,34 +407,18 @@ 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]}
-                )
-
+# 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
@@ -457,88 +428,63 @@ print(f.read())
 f.close()
 
 
-# RUN #########################################################################
-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,
-            gravity_acceleration=gravity_acceleration,
-            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
+# 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,
+        "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 starttime in starttimes:
+        for mesh_resolution, solver_tol in resolutions.items():
+            simulation_parameter.update({"solver_tol": solver_tol})
+            hlp.info(simulation_parameter["use_case"])
+            LDDsim = mp.Process(
+                        target=hlp.run_simulation,
+                        args=(
+                            simulation_parameter,
+                            starttime,
+                            mesh_resolution
                             )
-                else:
-                    errors.to_csv(
-                        filename,
-                        sep='\t',
-                        encoding='utf-8',
-                        index=False
                         )
+            LDDsim.start()
+            LDDsim.join()
+            # hlp.run_simulation(
+            #     mesh_resolution=mesh_resolution,
+            #     starttime=starttime,
+            #     parameter=simulation_parameter
+            #     )
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd.py
index 2a42078bdd12a33967010e246814fd2660292fbb..7e26fbfc5c077d05f0d79255d3291cb91764a39d 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-pure-dd.py
@@ -1,73 +1,113 @@
-#!/usr/bin/python3
+"""TPR 2 patch soil simulation.
+
+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 domainPatch as dp
-import LDDsimulation as ldd
 import functools as ft
+import LDDsimulation as ldd
 import helpers as hlp
 import datetime
 import os
 import pandas as pd
+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")
-#import ufl as ufl
 
-# init sympy session
-sym.init_printing()
+# Name of the usecase that will be printed during simulation.
+use_case = "TPR-2-patch-params-one-pure-dd"
+# The name of this very file. Needed for creating log output.
+thisfile = "TP-R-2-patch-pure-dd.py"
 
-use_case = "TP-R-2-patch-pure-dd"
-# solver_tol = 6E-7
-max_iter_num = 1000
+# GENERAL SOLVER CONFIG  ######################################################
+# maximal iteration per timestep
+max_iter_num = 500
 FEM_Lagrange_degree = 1
+
+# GRID AND MESH STUDY SPECIFICATIONS  #########################################
 mesh_study = False
 resolutions = {
-                # 1: 7e-7,
-                # 2: 7e-7,
-                # 4: 7e-7,
-                # 8: 7e-7,
-                # 16: 5e-7,
-                32: 1e-7,
-                # 64: 7e-7,
-                # 128: 7e-7,
-                # 256: 7e-7
+                # 1: 1e-5,
+                # 2: 1e-5,
+                # 4: 1e-5,
+                # 8: 1e-5,
+                16: 5e-6,
+                # 32: 5e-6,
+                # 64: 2e-6,
+                # 128: 2e-6,
+                # 256: 1e-6,
                 }
 
-############ GRID #######################
-# mesh_resolution = 20
+# 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]
 timestep_size = 0.005
-number_of_timesteps = 200
+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 = 0
-starttimes = [0.0]
+# LDD scheme parameters  ######################################################
+Lw1 = 0.05 #/timestep_size
+Lnw1= 0.05
 
-Lw = 0.05 #/timestep_size
-Lnw= 0.05
+Lw2 = 0.05 #/timestep_size
+Lnw2= 0.05
 
 lambda_w = 20
 lambda_nw = 20
+
 include_gravity = True
 debugflag = False
-analyse_condition = True
+analyse_condition = False
 
-output_string = "./output/{}-{}_timesteps{}_P{}".format(datestr, use_case, number_of_timesteps, FEM_Lagrange_degree)
+# 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 = 1
+# 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 = 1
 
-# toggle what should be written to files
+# 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,
-        'solutions': False,
-        'absolute_differences': 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,
-        'subsequent_errors': False
+        # 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 = {
@@ -80,69 +120,154 @@ else:
         'subsequent_errors': True
     }
 
+# OUTPUT FILE STRING  #########################################################
+output_string = "./output/{}-{}_timesteps{}_P{}".format(
+    datestr, use_case, number_of_timesteps, FEM_Lagrange_degree
+    )
 
-##### Domain and Interface ####
-# global simulation domain domain
-sub_domain0_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)]
-# interface between subdomain1 and subdomain2
-interface12_vertices = [df.Point(-1.0, 0.0),
-                        df.Point(1.0, 0.0) ]
-# subdomain1.
-sub_domain1_vertices = [interface12_vertices[0],
-                        interface12_vertices[1],
-                        sub_domain0_vertices[2],
-                        sub_domain0_vertices[3]]
-
-# 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: [interface12_vertices[1], #
-        sub_domain0_vertices[2],
-        sub_domain0_vertices[3], #
-        interface12_vertices[0]]
-}
-# subdomain2
-sub_domain2_vertices = [sub_domain0_vertices[0],
-                        sub_domain0_vertices[1],
-                        interface12_vertices[1],
-                        interface12_vertices[0] ]
-
-subdomain2_outer_boundary_verts = {
-    0: [interface12_vertices[0], #
-        sub_domain0_vertices[0],
-        sub_domain0_vertices[1],
-        interface12_vertices[1]]
-}
+# DOMAIN AND INTERFACE  #######################################################
+substructuring = dss.twoSoilLayers()
+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
 
-# list of subdomains given by the boundary polygon vertices.
-# Subdomains are given as a list of dolfin points forming
-# a closed polygon, such that mshr.Polygon(subdomain_def_points[i]) can be used
-# to create the subdomain. subdomain_def_points[0] contains the
-# vertices of the global simulation domain and subdomain_def_points[i] contains the
-# vertices of the subdomain i.
-subdomain_def_points = [sub_domain0_vertices,#
-                      sub_domain1_vertices,#
-                      sub_domain2_vertices]
-# in the below list, index 0 corresponds to the 12 interface which has index 1
-interface_def_points = [interface12_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
-}
+# MODEL CONFIGURATION #########################################################
+"""TPR 2 patch soil simulation.
 
-# adjacent_subdomains[i] contains the indices of the subdomains sharing the
-# interface i (i.e. given by interface_def_points[i]).
-adjacent_subdomains = [[1,2]]
+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
+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 = "TPR-2-patch-realistic"
+# The name of this very file. Needed for creating log output.
+thisfile = "TP-R-2-patch-realistic.py"
+
+# GENERAL SOLVER CONFIG  ######################################################
+# maximal iteration per timestep
+max_iter_num = 500
+FEM_Lagrange_degree = 1
+
+# GRID AND MESH STUDY SPECIFICATIONS  #########################################
+mesh_study = False
+resolutions = {
+                # 1: 1e-5,
+                # 2: 1e-5,
+                # 4: 1e-5,
+                # 8: 1e-5,
+                16: 5e-6,
+                # 32: 5e-6,
+                # 64: 2e-6,
+                # 128: 2e-6,
+                # 256: 1e-6,
+                }
+
+# 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]
+timestep_size = 0.001
+number_of_timesteps = 5
+
+# LDD scheme parameters  ######################################################
+Lw1 = 0.025 #/timestep_size
+Lnw1= 0.025
+
+Lw2 = 0.025 #/timestep_size
+Lnw2= 0.025
+
+lambda_w = 4
+lambda_nw = 4
+
+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 = 1
+# 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 = 1
+
+# 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 INTERFACE  #######################################################
+substructuring = dss.twoSoilLayers()
+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: False
@@ -380,14 +505,10 @@ p_e_sym = {
         'nonwetting': -t**2*(1.1 + y*x)*y**4},#*(sym.sin((x*y-0.5*t)*y**3))**4},  #*(sym.sin((1+y)/2*sym.pi)*sym.sin((1+x)/2*sym.pi))**2},
 }
 
-pc_e_sym = dict()
-for subdomain, isR in isRichards.items():
-    if isR:
-        pc_e_sym.update({subdomain: -p_e_sym[subdomain]['wetting'].copy()})
-    else:
-        pc_e_sym.update({subdomain: p_e_sym[subdomain]['nonwetting'].copy()
-                                        - p_e_sym[subdomain]['wetting'].copy()})
-
+pc_e_sym = hlp.generate_exact_symbolic_pc(
+                isRichards=isRichards,
+                symbolic_pressure=p_e_sym
+            )
 
 symbols = {"x": x,
            "y": y,
@@ -413,34 +534,18 @@ 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]}
-                )
-
+# 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
@@ -450,88 +555,63 @@ print(f.read())
 f.close()
 
 
-# RUN #########################################################################
-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,
-            gravity_acceleration=gravity_acceleration,
-            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
+# 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,
+        "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 starttime in starttimes:
+        for mesh_resolution, solver_tol in resolutions.items():
+            simulation_parameter.update({"solver_tol": solver_tol})
+            hlp.info(simulation_parameter["use_case"])
+            LDDsim = mp.Process(
+                        target=hlp.run_simulation,
+                        args=(
+                            simulation_parameter,
+                            starttime,
+                            mesh_resolution
                             )
-                else:
-                    errors.to_csv(
-                        filename,
-                        sep='\t',
-                        encoding='utf-8',
-                        index=False
                         )
+            LDDsim.start()
+            LDDsim.join()
+            # hlp.run_simulation(
+            #     mesh_resolution=mesh_resolution,
+            #     starttime=starttime,
+            #     parameter=simulation_parameter
+            #     )
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-gravity-but-same-intrinsic-perm.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-gravity-but-same-intrinsic-perm.py
index 3f9f35aca65c43aa538f6f0431264a07905c34df..10586745f8a82d2ad21f22b857751715f9b70352 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-gravity-but-same-intrinsic-perm.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-gravity-but-same-intrinsic-perm.py
@@ -12,6 +12,9 @@ import helpers as hlp
 import datetime
 import os
 import pandas as pd
+import multiprocessing as mp
+import domainSubstructuring as dss
+
 
 # init sympy session
 sym.init_printing()
@@ -120,82 +123,16 @@ else:
     }
 
 # OUTPUT FILE STRING  #########################################################
-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
-        )
-
+output_string = "./output/{}-{}_timesteps{}_P{}".format(
+    datestr, use_case, number_of_timesteps, FEM_Lagrange_degree
+    )
 
 # DOMAIN AND INTERFACE  #######################################################
-# global simulation domain domain
-sub_domain0_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)]
-# interface between subdomain1 and subdomain2
-interface12_vertices = [df.Point(-1.0, 0.0),
-                        df.Point(1.0, 0.0)]
-# subdomain1.
-sub_domain1_vertices = [interface12_vertices[0],
-                        interface12_vertices[1],
-                        sub_domain0_vertices[2],
-                        sub_domain0_vertices[3]]
-
-# 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: [interface12_vertices[1],
-        sub_domain0_vertices[2],
-        sub_domain0_vertices[3],
-        interface12_vertices[0]]
-}
-# subdomain2
-sub_domain2_vertices = [sub_domain0_vertices[0],
-                        sub_domain0_vertices[1],
-                        interface12_vertices[1],
-                        interface12_vertices[0]]
-
-subdomain2_outer_boundary_verts = {
-    0: [interface12_vertices[0],
-        sub_domain0_vertices[0],
-        sub_domain0_vertices[1],
-        interface12_vertices[1]]
-}
-
-# list of subdomains given by the boundary polygon vertices.
-# Subdomains are given as a list of dolfin points forming
-# a closed polygon, such that mshr.Polygon(subdomain_def_points[i]) can be used
-# to create the subdomain. subdomain_def_points[0] contains the
-# vertices of the global simulation domain and subdomain_def_points[i] contains
-# the vertices of the subdomain i.
-subdomain_def_points = [
-    sub_domain0_vertices,
-    sub_domain1_vertices,
-    sub_domain2_vertices
-    ]
-# in the below list, index 0 corresponds to the 12 interface which has index 1
-interface_def_points = [interface12_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
-}
-
-# adjacent_subdomains[i] contains the indices of the subdomains sharing the
-# interface i (i.e. given by interface_def_points[i]).
-adjacent_subdomains = [[1, 2]]
+substructuring = dss.twoSoilLayers()
+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 = {
@@ -445,14 +382,10 @@ p_e_sym = {
 } #-y*y*(sym.sin(-2*t+2*x)*sym.sin(1/2*y-1.2*t)) - t*t*x*(0.5-y)*y*(1-x)
 
 
-pc_e_sym = dict()
-for subdomain, isR in isRichards.items():
-    if isR:
-        pc_e_sym.update({subdomain: -p_e_sym[subdomain]['wetting'].copy()})
-    else:
-        pc_e_sym.update({subdomain: p_e_sym[subdomain]['nonwetting'].copy()
-                        - p_e_sym[subdomain]['wetting'].copy()})
-
+pc_e_sym = hlp.generate_exact_symbolic_pc(
+                isRichards=isRichards,
+                symbolic_pressure=p_e_sym
+            )
 
 symbols = {"x": x,
            "y": y,
@@ -478,35 +411,18 @@ 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.
-
 # BOUNDARY CONDITIONS #########################################################
-# subdomain index: {outer boudary part index: {phase: expression}}
-for subdomain in isRichards.keys():
-    # subdomain can have no outer boundary
-    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]}
-                )
-
+# 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
@@ -516,88 +432,63 @@ print(f.read())
 f.close()
 
 
-# RUN #########################################################################
-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,
-            gravity_acceleration=gravity_acceleration,
-            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
+# 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,
+        "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 starttime in starttimes:
+        for mesh_resolution, solver_tol in resolutions.items():
+            simulation_parameter.update({"solver_tol": solver_tol})
+            hlp.info(simulation_parameter["use_case"])
+            LDDsim = mp.Process(
+                        target=hlp.run_simulation,
+                        args=(
+                            simulation_parameter,
+                            starttime,
+                            mesh_resolution
                             )
-                else:
-                    errors.to_csv(
-                        filename,
-                        sep='\t',
-                        encoding='utf-8',
-                        index=False
                         )
+            LDDsim.start()
+            LDDsim.join()
+            # hlp.run_simulation(
+            #     mesh_resolution=mesh_resolution,
+            #     starttime=starttime,
+            #     parameter=simulation_parameter
+            #     )
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-no-gravity-but-varying-intrinsic-perm.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-no-gravity-but-varying-intrinsic-perm.py
index d51852eb0b811ee78b3aad39c593a54f15cd1508..f2f48ffab2ff83c1f1a1cbc3c9fd1223302d289e 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-no-gravity-but-varying-intrinsic-perm.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-no-gravity-but-varying-intrinsic-perm.py
@@ -3,7 +3,6 @@
 
 This program sets up an LDD simulation
 """
-
 import dolfin as df
 import sympy as sym
 import functools as ft
@@ -12,6 +11,8 @@ import helpers as hlp
 import datetime
 import os
 import pandas as pd
+import multiprocessing as mp
+import domainSubstructuring as dss
 
 # init sympy session
 sym.init_printing()
@@ -120,82 +121,16 @@ else:
     }
 
 # OUTPUT FILE STRING  #########################################################
-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
-        )
-
+output_string = "./output/{}-{}_timesteps{}_P{}".format(
+    datestr, use_case, number_of_timesteps, FEM_Lagrange_degree
+    )
 
 # DOMAIN AND INTERFACE  #######################################################
-# global simulation domain domain
-sub_domain0_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)]
-# interface between subdomain1 and subdomain2
-interface12_vertices = [df.Point(-1.0, 0.0),
-                        df.Point(1.0, 0.0)]
-# subdomain1.
-sub_domain1_vertices = [interface12_vertices[0],
-                        interface12_vertices[1],
-                        sub_domain0_vertices[2],
-                        sub_domain0_vertices[3]]
-
-# 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: [interface12_vertices[1],
-        sub_domain0_vertices[2],
-        sub_domain0_vertices[3],
-        interface12_vertices[0]]
-}
-# subdomain2
-sub_domain2_vertices = [sub_domain0_vertices[0],
-                        sub_domain0_vertices[1],
-                        interface12_vertices[1],
-                        interface12_vertices[0]]
-
-subdomain2_outer_boundary_verts = {
-    0: [interface12_vertices[0],
-        sub_domain0_vertices[0],
-        sub_domain0_vertices[1],
-        interface12_vertices[1]]
-}
-
-# list of subdomains given by the boundary polygon vertices.
-# Subdomains are given as a list of dolfin points forming
-# a closed polygon, such that mshr.Polygon(subdomain_def_points[i]) can be used
-# to create the subdomain. subdomain_def_points[0] contains the
-# vertices of the global simulation domain and subdomain_def_points[i] contains
-# the vertices of the subdomain i.
-subdomain_def_points = [
-    sub_domain0_vertices,
-    sub_domain1_vertices,
-    sub_domain2_vertices
-    ]
-# in the below list, index 0 corresponds to the 12 interface which has index 1
-interface_def_points = [interface12_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
-}
-
-# adjacent_subdomains[i] contains the indices of the subdomains sharing the
-# interface i (i.e. given by interface_def_points[i]).
-adjacent_subdomains = [[1, 2]]
+substructuring = dss.twoSoilLayers()
+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 = {
@@ -444,15 +379,10 @@ p_e_sym = {
         'nonwetting': (-2-t*(1.1+y + x**2))*y**2}, #*(1-x)**2*(1+x)**2*(1+y)**2},
 } #-y*y*(sym.sin(-2*t+2*x)*sym.sin(1/2*y-1.2*t)) - t*t*x*(0.5-y)*y*(1-x)
 
-
-pc_e_sym = dict()
-for subdomain, isR in isRichards.items():
-    if isR:
-        pc_e_sym.update({subdomain: -p_e_sym[subdomain]['wetting'].copy()})
-    else:
-        pc_e_sym.update({subdomain: p_e_sym[subdomain]['nonwetting'].copy()
-                        - p_e_sym[subdomain]['wetting'].copy()})
-
+pc_e_sym = hlp.generate_exact_symbolic_pc(
+                isRichards=isRichards,
+                symbolic_pressure=p_e_sym
+            )
 
 symbols = {"x": x,
            "y": y,
@@ -478,35 +408,18 @@ 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.
-
 # BOUNDARY CONDITIONS #########################################################
-# subdomain index: {outer boudary part index: {phase: expression}}
-for subdomain in isRichards.keys():
-    # subdomain can have no outer boundary
-    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]}
-                )
-
+# 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
@@ -516,88 +429,63 @@ print(f.read())
 f.close()
 
 
-# RUN #########################################################################
-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,
-            gravity_acceleration=gravity_acceleration,
-            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
+# 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,
+        "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 starttime in starttimes:
+        for mesh_resolution, solver_tol in resolutions.items():
+            simulation_parameter.update({"solver_tol": solver_tol})
+            hlp.info(simulation_parameter["use_case"])
+            LDDsim = mp.Process(
+                        target=hlp.run_simulation,
+                        args=(
+                            simulation_parameter,
+                            starttime,
+                            mesh_resolution
                             )
-                else:
-                    errors.to_csv(
-                        filename,
-                        sep='\t',
-                        encoding='utf-8',
-                        index=False
                         )
+            LDDsim.start()
+            LDDsim.join()
+            # hlp.run_simulation(
+            #     mesh_resolution=mesh_resolution,
+            #     starttime=starttime,
+            #     parameter=simulation_parameter
+            #     )
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-same-intrinsic-perm.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-same-intrinsic-perm.py
index 163ff3d323e60e006beaeb4f68da10c1ace2c412..92b123ffc013ce529113510ea5c37adcf068c34d 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-same-intrinsic-perm.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic-same-intrinsic-perm.py
@@ -3,7 +3,6 @@
 
 This program sets up an LDD simulation
 """
-
 import dolfin as df
 import sympy as sym
 import functools as ft
@@ -12,6 +11,8 @@ import helpers as hlp
 import datetime
 import os
 import pandas as pd
+import multiprocessing as mp
+import domainSubstructuring as dss
 
 # init sympy session
 sym.init_printing()
@@ -125,69 +126,11 @@ output_string = "./output/{}-{}_timesteps{}_P{}".format(
     )
 
 # DOMAIN AND INTERFACE  #######################################################
-# global simulation domain domain
-sub_domain0_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)]
-# interface between subdomain1 and subdomain2
-interface12_vertices = [df.Point(-1.0, 0.0),
-                        df.Point(1.0, 0.0)]
-# subdomain1.
-sub_domain1_vertices = [interface12_vertices[0],
-                        interface12_vertices[1],
-                        sub_domain0_vertices[2],
-                        sub_domain0_vertices[3]]
-
-# 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: [interface12_vertices[1],
-        sub_domain0_vertices[2],
-        sub_domain0_vertices[3],
-        interface12_vertices[0]]
-}
-# subdomain2
-sub_domain2_vertices = [sub_domain0_vertices[0],
-                        sub_domain0_vertices[1],
-                        interface12_vertices[1],
-                        interface12_vertices[0]]
-
-subdomain2_outer_boundary_verts = {
-    0: [interface12_vertices[0],
-        sub_domain0_vertices[0],
-        sub_domain0_vertices[1],
-        interface12_vertices[1]]
-}
-
-# list of subdomains given by the boundary polygon vertices.
-# Subdomains are given as a list of dolfin points forming
-# a closed polygon, such that mshr.Polygon(subdomain_def_points[i]) can be used
-# to create the subdomain. subdomain_def_points[0] contains the
-# vertices of the global simulation domain and subdomain_def_points[i] contains
-# the vertices of the subdomain i.
-subdomain_def_points = [
-    sub_domain0_vertices,
-    sub_domain1_vertices,
-    sub_domain2_vertices
-    ]
-# in the below list, index 0 corresponds to the 12 interface which has index 1
-interface_def_points = [interface12_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
-}
-
-# adjacent_subdomains[i] contains the indices of the subdomains sharing the
-# interface i (i.e. given by interface_def_points[i]).
-adjacent_subdomains = [[1, 2]]
+substructuring = dss.twoSoilLayers()
+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 = {
@@ -436,15 +379,10 @@ p_e_sym = {
         'nonwetting': (-2-t*(1.1+y + x**2))*y**2}, #*(1-x)**2*(1+x)**2*(1+y)**2},
 } #-y*y*(sym.sin(-2*t+2*x)*sym.sin(1/2*y-1.2*t)) - t*t*x*(0.5-y)*y*(1-x)
 
-
-pc_e_sym = dict()
-for subdomain, isR in isRichards.items():
-    if isR:
-        pc_e_sym.update({subdomain: -p_e_sym[subdomain]['wetting'].copy()})
-    else:
-        pc_e_sym.update({subdomain: p_e_sym[subdomain]['nonwetting'].copy()
-                        - p_e_sym[subdomain]['wetting'].copy()})
-
+pc_e_sym = hlp.generate_exact_symbolic_pc(
+                isRichards=isRichards,
+                symbolic_pressure=p_e_sym
+            )
 
 symbols = {"x": x,
            "y": y,
@@ -470,35 +408,18 @@ 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.
-
 # BOUNDARY CONDITIONS #########################################################
-# subdomain index: {outer boudary part index: {phase: expression}}
-for subdomain in isRichards.keys():
-    # subdomain can have no outer boundary
-    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]}
-                )
-
+# 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
@@ -508,88 +429,63 @@ print(f.read())
 f.close()
 
 
-# RUN #########################################################################
-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,
-            gravity_acceleration=gravity_acceleration,
-            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
+# 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,
+        "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 starttime in starttimes:
+        for mesh_resolution, solver_tol in resolutions.items():
+            simulation_parameter.update({"solver_tol": solver_tol})
+            hlp.info(simulation_parameter["use_case"])
+            LDDsim = mp.Process(
+                        target=hlp.run_simulation,
+                        args=(
+                            simulation_parameter,
+                            starttime,
+                            mesh_resolution
                             )
-                else:
-                    errors.to_csv(
-                        filename,
-                        sep='\t',
-                        encoding='utf-8',
-                        index=False
                         )
+            LDDsim.start()
+            LDDsim.join()
+            # hlp.run_simulation(
+            #     mesh_resolution=mesh_resolution,
+            #     starttime=starttime,
+            #     parameter=simulation_parameter
+            #     )
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic.py
index 5cad90c4e21b5b79b13080d2a58663cb14736af8..c95a5d15f6709b4617b40d15fd8f8e6bd2c287ef 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-realistic.py
@@ -122,17 +122,9 @@ else:
     }
 
 # OUTPUT FILE STRING  #########################################################
-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
-        )
-
+output_string = "./output/{}-{}_timesteps{}_P{}".format(
+    datestr, use_case, number_of_timesteps, FEM_Lagrange_degree
+    )
 
 # DOMAIN AND INTERFACE  #######################################################
 substructuring = dss.twoSoilLayers()
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-test.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-test.py
index a3e6306eaa8d6fed2c84d2344d74ea4074fe7fb5..09106bdcd97cc86a865d580128ff3ae2bdc0ffd1 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-test.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/TP-R-2-patch-test.py
@@ -3,7 +3,6 @@
 
 This program sets up an LDD simulation
 """
-
 import dolfin as df
 import sympy as sym
 import functools as ft
@@ -12,6 +11,8 @@ import helpers as hlp
 import datetime
 import os
 import pandas as pd
+import multiprocessing as mp
+import domainSubstructuring as dss
 
 # init sympy session
 sym.init_printing()
@@ -124,69 +125,12 @@ output_string = "./output/{}-{}_timesteps{}_P{}".format(
     datestr, use_case, number_of_timesteps, FEM_Lagrange_degree
     )
 
-
 # DOMAIN AND INTERFACE  #######################################################
-# global simulation domain domain
-sub_domain0_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)]
-# interface between subdomain1 and subdomain2
-interface12_vertices = [df.Point(-1.0, 0.0),
-                        df.Point(1.0, 0.0) ]
-# subdomain1.
-sub_domain1_vertices = [interface12_vertices[0],
-                        interface12_vertices[1],
-                        sub_domain0_vertices[2],
-                        sub_domain0_vertices[3]]
-
-# 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: [interface12_vertices[1], #
-        sub_domain0_vertices[2],
-        sub_domain0_vertices[3], #
-        interface12_vertices[0]]
-}
-# subdomain2
-sub_domain2_vertices = [sub_domain0_vertices[0],
-                        sub_domain0_vertices[1],
-                        interface12_vertices[1],
-                        interface12_vertices[0] ]
-
-subdomain2_outer_boundary_verts = {
-    0: [interface12_vertices[0], #
-        sub_domain0_vertices[0],
-        sub_domain0_vertices[1],
-        interface12_vertices[1]]
-}
-
-# list of subdomains given by the boundary polygon vertices.
-# Subdomains are given as a list of dolfin points forming
-# a closed polygon, such that mshr.Polygon(subdomain_def_points[i]) can be used
-# to create the subdomain. subdomain_def_points[0] contains the
-# vertices of the global simulation domain and subdomain_def_points[i] contains the
-# vertices of the subdomain i.
-subdomain_def_points = [sub_domain0_vertices,#
-                      sub_domain1_vertices,#
-                      sub_domain2_vertices]
-# in the below list, index 0 corresponds to the 12 interface which has index 1
-interface_def_points = [interface12_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
-}
-
-# adjacent_subdomains[i] contains the indices of the subdomains sharing the
-# interface i (i.e. given by interface_def_points[i]).
-adjacent_subdomains = [[1,2]]
+substructuring = dss.twoSoilLayers()
+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 = {
@@ -423,15 +367,10 @@ p_e_sym = {
         'nonwetting': (-2-t*(1.1+y + x**2))*y**2}, #*(1-x)**2*(1+x)**2*(1+y)**2},
 } #-y*y*(sym.sin(-2*t+2*x)*sym.sin(1/2*y-1.2*t)) - t*t*x*(0.5-y)*y*(1-x)
 
-
-pc_e_sym = dict()
-for subdomain, isR in isRichards.items():
-    if isR:
-        pc_e_sym.update({subdomain: -p_e_sym[subdomain]['wetting'].copy()})
-    else:
-        pc_e_sym.update({subdomain: p_e_sym[subdomain]['nonwetting'].copy()
-                                        - p_e_sym[subdomain]['wetting'].copy()})
-
+pc_e_sym = hlp.generate_exact_symbolic_pc(
+                isRichards=isRichards,
+                symbolic_pressure=p_e_sym
+            )
 
 symbols = {"x": x,
            "y": y,
@@ -458,34 +397,17 @@ exact_solution = exact_solution_example['exact_solution']
 initial_condition = exact_solution_example['initial_condition']
 
 # BOUNDARY CONDITIONS #########################################################
-# 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():
-    # subdomain can have no outer boundary
-    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]}
-                )
-
+# 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
@@ -495,88 +417,63 @@ print(f.read())
 f.close()
 
 
-# RUN #########################################################################
-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,
-            gravity_acceleration=gravity_acceleration,
-            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
+# 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,
+        "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 starttime in starttimes:
+        for mesh_resolution, solver_tol in resolutions.items():
+            simulation_parameter.update({"solver_tol": solver_tol})
+            hlp.info(simulation_parameter["use_case"])
+            LDDsim = mp.Process(
+                        target=hlp.run_simulation,
+                        args=(
+                            simulation_parameter,
+                            starttime,
+                            mesh_resolution
                             )
-                else:
-                    errors.to_csv(
-                        filename,
-                        sep='\t',
-                        encoding='utf-8',
-                        index=False
                         )
+            LDDsim.start()
+            LDDsim.join()
+            # hlp.run_simulation(
+            #     mesh_resolution=mesh_resolution,
+            #     starttime=starttime,
+            #     parameter=simulation_parameter
+            #     )