diff --git a/Two-phase-Two-phase/two-patch/injection/TP-TP-2-patch-injection.py b/Two-phase-Two-phase/two-patch/injection/TP-TP-2-patch-injection.py new file mode 100755 index 0000000000000000000000000000000000000000..6206cd934a9cc9d2930cc7c73069686509c99fe4 --- /dev/null +++ b/Two-phase-Two-phase/two-patch/injection/TP-TP-2-patch-injection.py @@ -0,0 +1,608 @@ +#!/usr/bin/python3 +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 helpers as hlp +import datetime +import os +import pandas as pd + +date = datetime.datetime.now() +datestr = date.strftime("%Y-%m-%d") +#import ufl as ufl + +# init sympy session +sym.init_printing() + +use_case = "TP-TP-2-patch-injection" +# solver_tol = 5E-7 +max_iter_num = 1000 +FEM_Lagrange_degree = 1 +mesh_study = False +resolutions = { + # 1: 1e-7, # h=2 + # 2: 2e-5, # h=1.1180 + # 4: 1e-6, # h=0.5590 + # 8: 1e-6, # h=0.2814 + # 16: 5e-7, # h=0.1412 + 32: 2e-6, + # 64: 5e-7, + # 128: 5e-7 + } + + +############ GRID ####################### +# mesh_resolution = 20 +timestep_size = 0.000001 +number_of_timesteps = 13 +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 +starttime = 0.0 + +Lw = 0.5 #/timestep_size +Lnw=Lw + +lambda_w = 4000 +lambda_nw = 4000 + +include_gravity = False +debugflag = True +analyse_condition = True + +if mesh_study: + output_string = "./output/{}-{}_timesteps{}_P{}".format(datestr, use_case, number_of_timesteps, FEM_Lagrange_degree) +else: + for tol in resolutions.values(): + solver_tol = tol + output_string = "./output/{}-{}_timesteps{}_P{}_solver_tol{}".format(datestr, use_case, number_of_timesteps, FEM_Lagrange_degree, solver_tol) + + +# toggle what should be written to files +if mesh_study: + write_to_file = { + 'space_errornorms': True, + 'meshes_and_markers': True, + 'L_iterations_per_timestep': False, + 'solutions': False, + 'absolute_differences': False, + 'condition_numbers': analyse_condition, + 'subsequent_errors': False + } +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 + } + +##### 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, 0.9), + df.Point(1.0, 0.4) ] + # interface equation: y = -1/4*x + 13/20 +# 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]] +isRichards = { + 1: False, # + 2: False + } + + +viscosity = {# +# subdom_num : viscosity + 1 : {'wetting' :1, + 'nonwetting': 1/50}, # + 2 : {'wetting' :1, + 'nonwetting': 1/50} +} + +porosity = {# +# subdom_num : porosity + 1 : 0.2,# + 2 : 0.002 +} + +# Dict of the form: { subdom_num : density } +densities = { + 1: {'wetting': 997, #997, + 'nonwetting': 1225}, #1225}, + 2: {'wetting': 997, #997, + 'nonwetting': 1225}, #1225}, +} + +gravity_acceleration = 9.81 + +L = {# +# subdom_num : subdomain L for L-scheme + 1 : {'wetting' :Lw, + 'nonwetting': Lnw},# + 2 : {'wetting' :Lw, + 'nonwetting': Lnw} +} + + +lambda_param = {# +# subdom_num : lambda parameter for the L-scheme + 1 : {'wetting' :lambda_w, + 'nonwetting': lambda_nw},# + 2 : {'wetting' :lambda_w, + 'nonwetting': lambda_nw} +} + +## relative permeabilty functions on subdomain 1 +def rel_perm1w(s): + # relative permeabilty wetting on subdomain1 + return s**2 + +def rel_perm1nw(s): + # relative permeabilty nonwetting on subdomain1 + return (1-s)**2 + +_rel_perm1w = ft.partial(rel_perm1w) +_rel_perm1nw = ft.partial(rel_perm1nw) + +subdomain1_rel_perm = { + 'wetting': _rel_perm1w,# + 'nonwetting': _rel_perm1nw +} +## relative permeabilty functions on subdomain 2 +def rel_perm2w(s): + # relative permeabilty wetting on subdomain2 + return s**3 +def rel_perm2nw(s): + # relative permeabilty nonwetting on subdosym.cos(0.8*t - (0.8*x + 1/7*y))main2 + return (1-s)**3 + +_rel_perm2w = ft.partial(rel_perm2w) +_rel_perm2nw = ft.partial(rel_perm2nw) + +subdomain2_rel_perm = { + 'wetting': _rel_perm2w,# + 'nonwetting': _rel_perm2nw +} + +## dictionary of relative permeabilties on all domains. +relative_permeability = {# + 1: subdomain1_rel_perm, + 2: subdomain2_rel_perm +} + + +# definition of the derivatives of the relative permeabilities +# relative permeabilty functions on subdomain 1 +def rel_perm1w_prime(s): + # relative permeabilty on subdomain1 + return 2*s + +def rel_perm1nw_prime(s): + # relative permeabilty on subdomain1 + return -2*(1-s) + +# # definition of the derivatives of the relative permeabilities +# # relative permeabilty functions on subdomain 1 +def rel_perm2w_prime(s): + # relative permeabilty on subdomain1 + return 3*s**2 + +def rel_perm2nw_prime(s): + # relative permeabilty on subdomain1 + return -3*(1-s)**2 + +_rel_perm1w_prime = ft.partial(rel_perm1w_prime) +_rel_perm1nw_prime = ft.partial(rel_perm1nw_prime) +_rel_perm2w_prime = ft.partial(rel_perm2w_prime) +_rel_perm2nw_prime = ft.partial(rel_perm2nw_prime) + +subdomain1_rel_perm_prime = { + 'wetting': _rel_perm1w_prime, + 'nonwetting': _rel_perm1nw_prime +} + + +subdomain2_rel_perm_prime = { + 'wetting': _rel_perm2w_prime, + 'nonwetting': _rel_perm2nw_prime +} + +# dictionary of relative permeabilties on all domains. +ka_prime = { + 1: subdomain1_rel_perm_prime, + 2: subdomain2_rel_perm_prime, +} + + + +def saturation(pc, index): + # inverse capillary pressure-saturation-relationship + return df.conditional(pc > 0, 1/((1 + pc)**(1/(index + 1))), 1) + + +def saturation_sym(pc, index): + # inverse capillary pressure-saturation-relationship + return 1/((1 + pc)**(1/(index + 1))) + + +# derivative of S-pc relationship with respect to pc. This is needed for the +# construction of a analytic solution. +def saturation_sym_prime(pc, index): + # inverse capillary pressure-saturation-relationship + return -1/((index+1)*(1 + pc)**((index+2)/(index+1))) + + +# note that the conditional definition of S-pc in the nonsymbolic part will be +# incorporated in the construction of the exact solution below. +S_pc_sym = { + 1: ft.partial(saturation_sym, index=3), + 2: ft.partial(saturation_sym, index=4), + # 3: ft.partial(saturation_sym, index=2), + # 4: ft.partial(saturation_sym, index=1) +} + +S_pc_sym_prime = { + 1: ft.partial(saturation_sym_prime, index=3), + 2: ft.partial(saturation_sym_prime, index=4), + # 3: ft.partial(saturation_sym_prime, index=2), + # 4: ft.partial(saturation_sym_prime, index=1) +} + +sat_pressure_relationship = { + 1: ft.partial(saturation, index=3), + 2: ft.partial(saturation, index=4), + # 3: ft.partial(saturation, index=2), + # 4: ft.partial(saturation, index=1) +} + +# +# def saturation(pc, n_index, alpha): +# # inverse capillary pressure-saturation-relationship +# return df.conditional(pc > 0, 1/((1 + (alpha*pc)**n_index)**((n_index - 1)/n_index)), 1) +# +# # S-pc-relation ship. We use the van Genuchten approach, i.e. pc = 1/alpha*(S^{-1/m} -1)^1/n, where +# # we set alpha = 0, assume m = 1-1/n (see Helmig) and assume that residual saturation is Sw +# def saturation_sym(pc, n_index, alpha): +# # inverse capillary pressure-saturation-relationship +# #df.conditional(pc > 0, +# return 1/((1 + (alpha*pc)**n_index)**((n_index - 1)/n_index)) +# +# +# # derivative of S-pc relationship with respect to pc. This is needed for the +# # construction of a analytic solution. +# def saturation_sym_prime(pc, n_index, alpha): +# # inverse capillary pressure-saturation-relationship +# return -(alpha*(n_index - 1)*(alpha*pc)**(n_index - 1)) / ( (1 + (alpha*pc)**n_index)**((2*n_index - 1)/n_index) ) +# +# # note that the conditional definition of S-pc in the nonsymbolic part will be +# # incorporated in the construction of the exact solution below. +# S_pc_sym = { +# 1: ft.partial(saturation_sym, n_index=3, alpha=0.001), +# 2: ft.partial(saturation_sym, n_index=6, alpha=0.001), +# # 3: ft.partial(saturation_sym, n_index=3, alpha=0.001), +# # 4: ft.partial(saturation_sym, n_index=3, alpha=0.001), +# # 5: ft.partial(saturation_sym, n_index=3, alpha=0.001), +# # 6: ft.partial(saturation_sym, n_index=3, alpha=0.001) +# } +# +# S_pc_sym_prime = { +# 1: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001), +# 2: ft.partial(saturation_sym_prime, n_index=6, alpha=0.001), +# # 3: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001), +# # 4: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001), +# # 5: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001), +# # 6: ft.partial(saturation_sym_prime, n_index=3, alpha=0.001) +# } +# +# sat_pressure_relationship = { +# 1: ft.partial(saturation, n_index=3, alpha=0.001), +# 2: ft.partial(saturation, n_index=6, alpha=0.001), +# # 3: ft.partial(saturation, n_index=3, alpha=0.001), +# # 4: ft.partial(saturation, n_index=3, alpha=0.001), +# # 5: ft.partial(saturation, n_index=3, alpha=0.001), +# # 6: ft.partial(saturation, n_index=3, alpha=0.001) +# } +# + + +############################################# +# Manufacture source expressions with sympy # +############################################# +x, y = sym.symbols('x[0], x[1]') # needed by UFL +t = sym.symbols('t', positive=True) + +initial_condition = { + 1: {'wetting': sym.printing.ccode(-6 - (1+t*t)*(1 + x*x + y*y)), #*cutoff, + 'nonwetting': sym.printing.ccode(-1 -t*(1.1+ y*y))}, #*(sym.sin((1+y)/2*sym.pi)*sym.sin((1+x)/2*sym.pi))**2}, + 2: {'wetting': sym.printing.ccode(-6.0 - (1.0 + t*t)*(1.0 + x*x)), #*(sym.sin((1+y)/2*sym.pi)*sym.sin((1+x)/2*sym.pi))**2, + 'nonwetting': sym.printing.ccode(-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}, +} + +### constructing source experessions. +injection_coord = [-0.85, -0.8] +extraction_coord = [0.75, 0.7] +injection_radius = 0.075 +extraction_radius = 0.075 +# epsilon_y_inner = epsilon_x_inner +# epsilon_y_outer = epsilon_x_outer +# +# def mollifier(x, epsilon): +# """ one d mollifier """ +# out_expr = sym.exp(-1/(1-(x/epsilon)**2) + 1) +# return out_expr +# +# mollifier_handle = ft.partial(mollifier, epsilon=epsilon_x_inner) +# +# pw_sym_x = sym.Piecewise( +# (mollifier_handle(x), x**2 < epsilon_x_outer**2), +# (0, True) +# ) +# pw_sym_y = sym.Piecewise( +# (mollifier_handle(y), y**2 < epsilon_y_outer**2), +# (0, True) +# ) +# +def mollifier2d(x, y, epsilon): + """ one d mollifier """ + out_expr = sym.exp(-1/(1-(x**2 + y**2)/epsilon**2)) + return out_expr + +mollifier2d_handle_i = ft.partial(mollifier2d, epsilon=injection_radius) + +source_in = sym.Piecewise( + (0*t + mollifier2d_handle_i(x, y), (x-injection_coord[0])**2 + (y-injection_coord[1])**2 < injection_radius**2), + (0*t, True) +) + +mollifier2d_handle_e = ft.partial(mollifier2d, epsilon=extraction_radius) + +source_ext = sym.Piecewise( + (0*t + mollifier2d_handle_e(x, y), (x-extraction_coord[0])**2 + (y-extraction_coord[1])**2 < extraction_radius**2), + (0*t, True) +) + +extraction_water_ratio = 0.7 +injection_water_ratio = 0.7 + +source_expression = { + 1: {"wetting": sym.printing.ccode(extraction_water_ratio*source_ext), + "nonwetting": sym.printing.ccode((1-extraction_water_ratio)*source_ext)}, + 2: {"wetting": sym.printing.ccode(injection_water_ratio*source_in), + "nonwetting": sym.printing.ccode((1-injection_water_ratio)*source_in)} +} + +exact_solution = None +# +# zero_on_epsilon_shrinking_of_subdomain = sym.Piecewise( +# (mollifier_handle(sym.sqrt(x**2 + y**2)+2*epsilon_x_inner), ((-2*epsilon_x_inner<sym.sqrt(x**2 + y**2)) & (sym.sqrt(x**2 + y**2)<-epsilon_x_inner))), +# (0, ((-epsilon_x_inner<=sym.sqrt(x**2 + y**2)) & (sym.sqrt(x**2 + y**2)<=epsilon_x_inner))), +# (mollifier_handle(sym.sqrt(x**2 + y**2)-2*epsilon_x_inner), ((epsilon_x_inner<sym.sqrt(x**2 + y**2)) & (sym.sqrt(x**2 + y**2)<2*epsilon_x_inner))), +# (1, True), +# ) +# +# zero_on_epsilon_shrinking_of_subdomain_x = sym.Piecewise( +# (mollifier_handle(x+2*epsilon_x_inner), ((-2*epsilon_x_inner<x) & (x<-epsilon_x_inner))), +# (0, ((-epsilon_x_inner<=x) & (x<=epsilon_x_inner))), +# (mollifier_handle(x-2*epsilon_x_inner), ((epsilon_x_inner<x) & (x<2*epsilon_x_inner))), +# (1, True), +# ) +# +# zero_on_epsilon_shrinking_of_subdomain_y = sym.Piecewise( +# (1, y<=-2*epsilon_x_inner), +# (mollifier_handle(y+2*epsilon_x_inner), ((-2*epsilon_x_inner<y) & (y<-epsilon_x_inner))), +# (0, ((-epsilon_x_inner<=y) & (y<=epsilon_x_inner))), +# (mollifier_handle(y-2*epsilon_x_inner), ((epsilon_x_inner<y) & (y<2*epsilon_x_inner))), +# (1, True), +# ) +# +# zero_on_shrinking = zero_on_epsilon_shrinking_of_subdomain #zero_on_epsilon_shrinking_of_subdomain_x + zero_on_epsilon_shrinking_of_subdomain_y +# gaussian = pw_sym2d_x# pw_sym_y*pw_sym_x +# cutoff = gaussian/(gaussian + zero_on_shrinking) + + +# 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()}) + + +symbols = {"x": x, + "y": y, + "t": t} +# # turn above symbolic code into exact solution for dolphin and +# # construct the rhs that matches the above exact solution. +# exact_solution_example = hlp.generate_exact_solution_expressions( +# symbols=symbols, +# isRichards=isRichards, +# symbolic_pressure=p_e_sym, +# symbolic_capillary_pressure=pc_e_sym, +# saturation_pressure_relationship=S_pc_sym, +# saturation_pressure_relationship_prime=S_pc_sym_prime, +# viscosity=viscosity, +# porosity=porosity, +# relative_permeability=relative_permeability, +# relative_permeability_prime=ka_prime, +# densities=densities, +# gravity_acceleration=gravity_acceleration, +# include_gravity=include_gravity, +# ) +# source_expression = exact_solution_example['source'] +# exact_solution = exact_solution_example['exact_solution'] +# initial_condition = exact_solution_example['initial_condition'] + +# Dictionary of dirichlet boundary conditions. +dirichletBC = dict() +# similarly to the outer boundary dictionary, if a patch has no outer boundary +# None should be written instead of an expression. +# This is a bit of a brainfuck: +# dirichletBC[ind] gives a dictionary of the outer boundaries of subdomain ind. +# Since a domain patch can have several disjoint outer boundary parts, the +# expressions need to get an enumaration index which starts at 0. +# So dirichletBC[ind][j] is the dictionary of outer dirichlet conditions of +# subdomain ind and boundary part j. +# Finally, dirichletBC[ind][j]['wetting'] and dirichletBC[ind][j]['nonwetting'] +# return the actual expression needed for the dirichlet condition for both +# phases if present. + +# subdomain index: {outer boudary part index: {phase: expression}} +for subdomain in isRichards.keys(): + # if subdomain has no outer boundary, outer_boundary_def_points[subdomain] is None + if outer_boundary_def_points[subdomain] is None: + dirichletBC.update({subdomain: None}) + else: + dirichletBC.update({subdomain: dict()}) + # set the dirichlet conditions to be the same code as exact solution on + # the subdomain. + for outer_boundary_ind in outer_boundary_def_points[subdomain].keys(): + dirichletBC[subdomain].update( + # {outer_boundary_ind: exact_solution[subdomain]} + { + outer_boundary_ind: { + "wetting": sym.printing.ccode(0*t), + "nonwetting": sym.printing.ccode(0*t) + } + } + ) + + +# def saturation(pressure, subdomain_index): +# # inverse capillary pressure-saturation-relationship +# return df.conditional(pressure < 0, 1/((1 - pressure)**(1/(subdomain_index + 1))), 1) +# +# sa + +for mesh_resolution, solver_tol in resolutions.items(): + # initialise LDD simulation class + simulation = ldd.LDDsimulation( + tol=1E-14, + LDDsolver_tol=solver_tol, + debug=debugflag, + max_iter_num=max_iter_num, + FEM_Lagrange_degree=FEM_Lagrange_degree, + mesh_study=mesh_study + ) + + simulation.set_parameters(use_case=use_case, + output_dir=output_string, + subdomain_def_points=subdomain_def_points, + isRichards=isRichards, + interface_def_points=interface_def_points, + outer_boundary_def_points=outer_boundary_def_points, + adjacent_subdomains=adjacent_subdomains, + mesh_resolution=mesh_resolution, + viscosity=viscosity, + porosity=porosity, + L=L, + lambda_param=lambda_param, + relative_permeability=relative_permeability, + saturation=sat_pressure_relationship, + starttime=starttime, + number_of_timesteps=number_of_timesteps, + number_of_timesteps_to_analyse=number_of_timesteps_to_analyse, + plot_timestep_every=plot_timestep_every, + timestep_size=timestep_size, + sources=source_expression, + initial_conditions=initial_condition, + dirichletBC_expression_strings=dirichletBC, + exact_solution=exact_solution, + densities=densities, + include_gravity=include_gravity, + write2file=write_to_file, + ) + + simulation.initialise() + output_dir = simulation.output_dir + # simulation.write_exact_solution_to_xdmf() + output = simulation.run(analyse_condition=analyse_condition) + for subdomain_index, subdomain_output in output.items(): + mesh_h = subdomain_output['mesh_size'] + for phase, different_errornorms in subdomain_output['errornorm'].items(): + filename = output_dir + "subdomain{}-space-time-errornorm-{}-phase.csv".format(subdomain_index, phase) + # for errortype, errornorm in different_errornorms.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 error_type, errornorms in different_errornorms.items(): + data_dict.update( + {error_type: errornorms} + ) + errors = pd.DataFrame(data_dict, index=[mesh_resolution]) + # check if file exists + if os.path.isfile(filename) == True: + with open(filename, 'a') as f: + errors.to_csv(f, header=False, sep='\t', encoding='utf-8', index=False) + else: + errors.to_csv(filename, sep='\t', encoding='utf-8', index=False)