From 7a7dbd883fcba26c43a16e80a5172acc8f7f3197 Mon Sep 17 00:00:00 2001
From: David <forenkram@gmx.de>
Date: Wed, 10 Jun 2020 13:17:28 +0200
Subject: [PATCH] setup two mesh studies for TPR with parameter set to one
---
...-patch-mesh-study-all-params-one-but-g.py} | 322 ++++++-----
.../TP-R-2-patch-mesh-study-all-params-one.py | 298 +++++-----
.../TP-R-2-patch-mesh-study-new-gli-bak.py | 512 ------------------
.../mesh_studies/TP-R-2-patch-mesh-study.py | 10 +-
4 files changed, 380 insertions(+), 762 deletions(-)
rename Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/{TP-R-2-patch-mesh-study-with-intrinsic-permeability.py => TP-R-2-patch-mesh-study-all-params-one-but-g.py} (62%)
delete mode 100755 Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-new-gli-bak.py
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-with-intrinsic-permeability.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-all-params-one-but-g.py
similarity index 62%
rename from Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-with-intrinsic-permeability.py
rename to Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-all-params-one-but-g.py
index a253874..f1d9073 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-with-intrinsic-permeability.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-all-params-one-but-g.py
@@ -1,71 +1,111 @@
#!/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
+# 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-all-params-one-but-g"
+# The name of this very file. Needed for creating log output.
+thisfile = "TP-R-2-patch-mesh-study-all-params-one-but-g.py"
-use_case = "TPR-2-patch-realistic-with-intrinsic"
-# solver_tol = 6E-7
+# GENERAL SOLVER CONFIG ######################################################
+# maximal iteration per timestep
max_iter_num = 500
FEM_Lagrange_degree = 1
+
+# GRID AND MESH STUDY SPECIFICATIONS #########################################
mesh_study = True
-resolutions = { 1: 7e-7,
- 2: 7e-7,
- 4: 7e-7,
- 8: 7e-7,
- 16: 7e-7,
- 32: 7e-7,
- 64: 7e-7,
- 128: 7e-7,
- #256: 7e-7,
+resolutions = {
+ 1: 1e-5,
+ 2: 1e-5,
+ 4: 1e-5,
+ 8: 1e-5,
+ 16: 1e-5,
+ 32: 1e-5,
+ 64: 1e-5,
+ 128: 1e-5,
+ # 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 = 0.001
number_of_timesteps = 800
-plot_timestep_every = 2
-# 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 = [0.0, 0.7]
-Lw = 0.025 #/timestep_size
-Lnw=Lw
+# LDD scheme parameters ######################################################
+Lw1 = 0.25 #/timestep_size
+Lnw1= 0.25
-lambda_w = 40
-lambda_nw = 40
+Lw2 = 0.25 #/timestep_size
+Lnw2= 0.25
-include_gravity = False
-debugflag = False
-analyse_condition = True
+lambda_w = 4.0
+lambda_nw = 4.0
-output_string = "./output/{}-{}_timesteps{}_P{}".format(datestr, use_case, number_of_timesteps, FEM_Lagrange_degree)
+include_gravity = True
+debugflag = False
+analyse_condition = False
+
+# I/O CONFIG #################################################################
+# when number_of_timesteps is high, it might take a long time to write all
+# timesteps to disk. Therefore, you can choose to only write data of every
+# plot_timestep_every timestep to disk.
+plot_timestep_every = 3
+# Decide how many timesteps you want analysed. Analysed means, that
+# subsequent errors of the L-iteration within the timestep are written out.
+number_of_timesteps_to_analyse = 4
-# 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,
- 'L_iterations_per_timestep': 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:
@@ -79,9 +119,20 @@ else:
'subsequent_errors': True
}
+# 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
+ )
-##### Domain and Interface ####
+# DOMAIN AND INTERFACE #######################################################
# global simulation domain domain
sub_domain0_vertices = [df.Point(-1.0, -1.0),
df.Point(1.0, -1.0),
@@ -143,6 +194,8 @@ 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
@@ -151,47 +204,46 @@ isRichards = {
viscosity = {#
# subdom_num : viscosity
- 1 : {'wetting' :1},
- #'nonwetting': 1}, #
- 2 : {'wetting' :1,
- 'nonwetting': 1/50}
+ 1: {'wetting' :1.0,
+ 'nonwetting': 1.0}, #
+ 2: {'wetting' :1.0,
+ 'nonwetting': 1.0}
}
porosity = {#
# subdom_num : porosity
- 1 : 0.22,#
- 2 : 0.0022
+ 1: 1.0,
+ 2: 1.0
}
# Dict of the form: { subdom_num : density }
densities = {
- 1: {'wetting': 997},
- 2: {'wetting': 997,
- 'nonwetting': 1.225},
-}
-
-intrinsic_permeability = {
- 1: 10e-11, #laut wikipedia in der range of sand
- 2: 10e-14, # layered clay achtung: auf wikipedia in cm^2 angegeb. hier m^2
+ 1: {'wetting': 1.0,
+ 'nonwetting': 1.0},
+ 2: {'wetting': 1.0,
+ 'nonwetting': 1.0}
}
gravity_acceleration = 9.81
L = {#
# subdom_num : subdomain L for L-scheme
- 1 : {'wetting' :Lw},
- # 'nonwetting': 0.25},#
- 2 : {'wetting' :Lw,
- 'nonwetting': Lnw}
+ 1 : {'wetting' :Lw1,
+ 'nonwetting': Lnw1},#
+ 2 : {'wetting' :Lw2,
+ 'nonwetting': Lnw2}
}
lambda_param = {#
# subdom_num : lambda parameter for the L-scheme
- 1 : {'wetting' :lambda_w,
+ 0 : {'wetting' :lambda_w,
'nonwetting': lambda_nw},#
- 2 : {'wetting' :lambda_w,
- 'nonwetting': lambda_nw}
+}
+
+intrinsic_permeability = {
+ 1: 1.0,
+ 2: 1.0,
}
## relative permeabilty functions on subdomain 1
@@ -199,23 +251,24 @@ def rel_perm1w(s):
# relative permeabilty wetting on subdomain1
return intrinsic_permeability[1]*s**2
-# def rel_perm1nw(s):
-# # relative permeabilty nonwetting on subdomain1
-# return (1-s)**2
+def rel_perm1nw(s):
+ # relative permeabilty nonwetting on subdomain1
+ return intrinsic_permeability[1]*(1-s)**2
_rel_perm1w = ft.partial(rel_perm1w)
-# _rel_perm1nw = ft.partial(rel_perm1nw)
+_rel_perm1nw = ft.partial(rel_perm1nw)
+
subdomain1_rel_perm = {
'wetting': _rel_perm1w,#
- # 'nonwetting': _rel_perm1nw
+ 'nonwetting': _rel_perm1nw
}
## relative permeabilty functions on subdomain 2
def rel_perm2w(s):
# relative permeabilty wetting on subdomain2
return intrinsic_permeability[2]*s**3
def rel_perm2nw(s):
- # relative permeabilty nonwetting on subdosym.cos(0.8*t - (0.8*x + 1/7*y))main2
- return intrinsic_permeability[1]*(1-s)**3
+ # relative permeabilty nonwetting on subdomain2
+ return intrinsic_permeability[2]*(1-s)**3
_rel_perm2w = ft.partial(rel_perm2w)
_rel_perm2nw = ft.partial(rel_perm2nw)
@@ -236,30 +289,30 @@ relative_permeability = {#
# relative permeabilty functions on subdomain 1
def rel_perm1w_prime(s):
# relative permeabilty on subdomain1
- return 2*s
+ return intrinsic_permeability[1]*2*s
-# def rel_perm1nw_prime(s):
-# # relative permeabilty on subdomain1
-# return 2*(1-s)
+def rel_perm1nw_prime(s):
+ # relative permeabilty on subdomain1
+ return -1*intrinsic_permeability[1]*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
+ # relative permeabilty on subdomain2
+ return intrinsic_permeability[2]*3*s**2
def rel_perm2nw_prime(s):
- # relative permeabilty on subdomain1
- return -3*(1-s)**2
+ # relative permeabilty on subdomain2
+ return -3*intrinsic_permeability[2]*(1-s)**2
_rel_perm1w_prime = ft.partial(rel_perm1w_prime)
-# _rel_perm1nw_prime = ft.partial(rel_perm1nw_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
+ 'wetting': _rel_perm1w_prime,
+ 'nonwetting': _rel_perm1nw_prime
}
@@ -365,16 +418,16 @@ sat_pressure_relationship = {
}
-#############################################
+###############################################################################
# Manufacture source expressions with sympy #
-#############################################
+###############################################################################
x, y = sym.symbols('x[0], x[1]') # needed by UFL
t = sym.symbols('t', positive=True)
p_e_sym = {
1: {'wetting': (-6.0 - (1.0 + t*t)*(1.0 + x*x + y*y))}, #*(1-x)**2*(1+x)**2*(1-y)**2},
2: {'wetting': (-6.0 - (1.0 + t*t)*(1.0 + x*x)), #*(1-x)**2*(1+x)**2*(1+y)**2,
- 'nonwetting': (-1-t*(1.1+y + x**2))*y**2}, #*(1-x)**2*(1+x)**2*(1+y)**2},
+ 'nonwetting': (-1.0-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)
@@ -425,9 +478,11 @@ dirichletBC = dict()
# 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():
- # if subdomain has no outer boundary, outer_boundary_def_points[subdomain] is None
+ # subdomain can have no outer boundary
if outer_boundary_def_points[subdomain] is None:
dirichletBC.update({subdomain: None})
else:
@@ -440,12 +495,15 @@ for subdomain in isRichards.keys():
)
-# def saturation(pressure, subdomain_index):
-# # inverse capillary pressure-saturation-relationship
-# return df.conditional(pressure < 0, 1/((1 - pressure)**(1/(subdomain_index + 1))), 1)
-#
-# sa
+# LOG FILE OUTPUT #############################################################
+# read this file and print it to std out. This way the simulation can produce a
+# log file with ./TP-R-layered_soil.py | tee simulation.log
+f = open(thisfile, 'r')
+print(f.read())
+f.close()
+
+# RUN #########################################################################
for starttime in starttimes:
for mesh_resolution, solver_tol in resolutions.items():
# initialise LDD simulation class
@@ -458,33 +516,34 @@ for starttime in starttimes:
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.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
@@ -492,26 +551,39 @@ for starttime in starttimes:
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
+ 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 error_type, errornorms in different_errornorms.items():
+ for norm_type, errornorm in error_dict.items():
data_dict.update(
- {error_type: errornorms}
+ {norm_type: errornorm}
)
errors = pd.DataFrame(data_dict, index=[mesh_resolution])
# check if file exists
- if os.path.isfile(filename) == True:
+ 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)
+ 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)
+ errors.to_csv(
+ filename,
+ sep='\t',
+ encoding='utf-8',
+ index=False
+ )
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-all-params-one.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-all-params-one.py
index 62d507c..64512a6 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-all-params-one.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-all-params-one.py
@@ -1,77 +1,111 @@
#!/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
+# 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-all-params-one"
+# The name of this very file. Needed for creating log output.
+thisfile = "TP-R-2-patch-mesh-study-all-params-one.py"
-use_case = "TPR-2-desities-scaled-down"
-# solver_tol = 6E-7
-max_iter_num = 500
+# GENERAL SOLVER CONFIG ######################################################
+# maximal iteration per timestep
+max_iter_num = 250
FEM_Lagrange_degree = 1
-mesh_study = False
+
+# GRID AND MESH STUDY SPECIFICATIONS #########################################
+mesh_study = True
resolutions = {
- # 1: 1e-6,
- # 2: 1e-6,
- # 4: 1e-6,
- # 8: 1e-6,
- # 16: 1e-6,
- 32: 1e-6,
- # 64: 1e-6,
- # 128: 1e-6,
+ 1: 5e-6,
+ 2: 5e-6,
+ 4: 5e-6,
+ 8: 5e-6,
+ 16: 5e-6,
+ 32: 5e-6,
+ 64: 5e-6,
+ 128: 5e-6,
# 256: 1e-6,
}
-############ GRID #######################
-# mesh_resolution = 20
-timestep_size = 0.001
-number_of_timesteps = 1000
-plot_timestep_every = 4
-# decide how many timesteps you want analysed. Analysed means, that we write out
-# subsequent errors of the L-iteration within the timestep.
-number_of_timesteps_to_analyse = 5
+# starttimes 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 = 800
-Lw = 0.025 #/timestep_size
-Lnw= 0.025
+# LDD scheme parameters ######################################################
+Lw1 = 0.25 #/timestep_size
+Lnw1= 0.25
-lambda_w = 40
-lambda_nw = 40
+Lw2 = 0.25 #/timestep_size
+Lnw2= 0.25
+
+lambda_w = 4.0
+lambda_nw = 4.0
include_gravity = True
debugflag = False
-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
+analyse_condition = False
+
+# I/O CONFIG #################################################################
+# when number_of_timesteps is high, it might take a long time to write all
+# timesteps to disk. Therefore, you can choose to only write data of every
+# plot_timestep_every timestep to disk.
+plot_timestep_every = 3
+# Decide how many timesteps you want analysed. Analysed means, that
+# subsequent errors of the L-iteration within the timestep are written out.
+number_of_timesteps_to_analyse = 4
+
+# 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,
- 'L_iterations_per_timestep': 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:
@@ -85,9 +119,20 @@ else:
'subsequent_errors': True
}
+# 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
+ )
-##### Domain and Interface ####
+# DOMAIN AND INTERFACE #######################################################
# global simulation domain domain
sub_domain0_vertices = [df.Point(-1.0, -1.0),
df.Point(1.0, -1.0),
@@ -149,6 +194,8 @@ 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
@@ -157,55 +204,46 @@ isRichards = {
viscosity = {#
# subdom_num : viscosity
- 1: {'wetting' :1,
- 'nonwetting': 1/50}, #
- 2: {'wetting' :1,
- 'nonwetting': 1/50}
+ 1: {'wetting' :1.0,
+ 'nonwetting': 1.0}, #
+ 2: {'wetting' :1.0,
+ 'nonwetting': 1.0}
}
porosity = {#
# subdom_num : porosity
- 1: 0.22,#
- 2: 0.0022
+ 1: 1.0,
+ 2: 1.0
}
# Dict of the form: { subdom_num : density }
densities = {
- 1: {'wetting': 9.97,
- 'nonwetting': 00.12041},
- 2: {'wetting': 9.97,
- 'nonwetting': 00.12041}
+ 1: {'wetting': 1.0,
+ 'nonwetting': 1.0},
+ 2: {'wetting': 1.0,
+ 'nonwetting': 1.0}
}
-gravity_acceleration = 9.81
+gravity_acceleration = 1.0
L = {#
# subdom_num : subdomain L for L-scheme
- 1 : {'wetting' :Lw,
- 'nonwetting': Lnw},#
- 2 : {'wetting' :Lw,
- 'nonwetting': Lnw}
+ 1 : {'wetting' :Lw1,
+ 'nonwetting': Lnw1},#
+ 2 : {'wetting' :Lw2,
+ 'nonwetting': Lnw2}
}
lambda_param = {#
# subdom_num : lambda parameter for the L-scheme
- 1 : {'wetting' :lambda_w,
+ 0 : {'wetting' :lambda_w,
'nonwetting': lambda_nw},#
- 2 : {'wetting' :lambda_w,
- 'nonwetting': lambda_nw}
}
-# intrinsic_permeability = {
-# 1: {"wetting": 1,
-# "nonwetting": 1},
-# 2: {"wetting": 1,
-# "nonwetting": 1},
-# }
-
intrinsic_permeability = {
- 1: 1,
- 2: 1,
+ 1: 1.0,
+ 2: 1.0,
}
## relative permeabilty functions on subdomain 1
@@ -229,7 +267,7 @@ def rel_perm2w(s):
# relative permeabilty wetting on subdomain2
return intrinsic_permeability[2]*s**3
def rel_perm2nw(s):
- # relative permeabilty nonwetting on subdosym.cos(0.8*t - (0.8*x + 1/7*y))main2
+ # relative permeabilty nonwetting on subdomain2
return intrinsic_permeability[2]*(1-s)**3
_rel_perm2w = ft.partial(rel_perm2w)
@@ -380,16 +418,16 @@ sat_pressure_relationship = {
}
-#############################################
+###############################################################################
# Manufacture source expressions with sympy #
-#############################################
+###############################################################################
x, y = sym.symbols('x[0], x[1]') # needed by UFL
t = sym.symbols('t', positive=True)
p_e_sym = {
1: {'wetting': (-6.0 - (1.0 + t*t)*(1.0 + x*x + y*y))}, #*(1-x)**2*(1+x)**2*(1-y)**2},
2: {'wetting': (-6.0 - (1.0 + t*t)*(1.0 + x*x)), #*(1-x)**2*(1+x)**2*(1+y)**2,
- 'nonwetting': (-1-t*(1.1+y + x**2))*y**2}, #*(1-x)**2*(1+x)**2*(1+y)**2},
+ 'nonwetting': (-1.0-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)
@@ -440,9 +478,11 @@ dirichletBC = dict()
# 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():
- # if subdomain has no outer boundary, outer_boundary_def_points[subdomain] is None
+ # subdomain can have no outer boundary
if outer_boundary_def_points[subdomain] is None:
dirichletBC.update({subdomain: None})
else:
@@ -455,17 +495,15 @@ for subdomain in isRichards.keys():
)
-# def saturation(pressure, subdomain_index):
-# # inverse capillary pressure-saturation-relationship
-# return df.conditional(pressure < 0, 1/((1 - pressure)**(1/(subdomain_index + 1))), 1)
-#
-# sa
-
-f = open('TP-R-2-patch-mesh-study.py', 'r')
+# LOG FILE OUTPUT #############################################################
+# read this file and print it to std out. This way the simulation can produce a
+# log file with ./TP-R-layered_soil.py | tee simulation.log
+f = open(thisfile, 'r')
print(f.read())
f.close()
+# RUN #########################################################################
for starttime in starttimes:
for mesh_resolution, solver_tol in resolutions.items():
# initialise LDD simulation class
@@ -478,33 +516,34 @@ for starttime in starttimes:
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.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
@@ -512,26 +551,39 @@ for starttime in starttimes:
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
+ 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 error_type, errornorms in different_errornorms.items():
+ for norm_type, errornorm in error_dict.items():
data_dict.update(
- {error_type: errornorms}
+ {norm_type: errornorm}
)
errors = pd.DataFrame(data_dict, index=[mesh_resolution])
# check if file exists
- if os.path.isfile(filename) == True:
+ 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)
+ 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)
+ errors.to_csv(
+ filename,
+ sep='\t',
+ encoding='utf-8',
+ index=False
+ )
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-new-gli-bak.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-new-gli-bak.py
deleted file mode 100755
index 23463c3..0000000
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study-new-gli-bak.py
+++ /dev/null
@@ -1,512 +0,0 @@
-#!/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-R-2-patch-realistic-new-nw-gli"
-# solver_tol = 6E-7
-max_iter_num = 1000
-FEM_Lagrange_degree = 1
-mesh_study = True
-resolutions = { 1: 7e-7,
- 2: 7e-7,
- 4: 7e-7,
- 8: 7e-7,
- 16: 7e-7,
- 32: 7e-7,
- 64: 7e-7,
- 128: 7e-7,
- #256: 7e-7,
- }
-
-############ GRID #######################
-# mesh_resolution = 20
-timestep_size = 0.001
-number_of_timesteps = 800
-plot_timestep_every = 2
-# 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 = [0.0, 0.7]
-
-Lw = 0.025 #/timestep_size
-Lnw=Lw
-
-lambda_w = 40
-lambda_nw = 40
-
-include_gravity = False
-debugflag = False
-analyse_condition = False
-
-output_string = "./output/{}-{}_timesteps{}_P{}".format(datestr, use_case, number_of_timesteps, FEM_Lagrange_degree)
-
-# 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, 0.0),
- 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]]
-isRichards = {
- 1: True, #
- 2: False
- }
-
-
-viscosity = {#
-# subdom_num : viscosity
- 1 : {'wetting' :1},
- #'nonwetting': 1}, #
- 2 : {'wetting' :1,
- 'nonwetting': 1/50}
-}
-
-porosity = {#
-# subdom_num : porosity
- 1 : 0.22,#
- 2 : 0.0022
-}
-
-# Dict of the form: { subdom_num : density }
-densities = {
- 1: {'wetting': 997},
- 2: {'wetting': 997,
- 'nonwetting': 1.225},
-}
-
-gravity_acceleration = 9.81
-
-L = {#
-# subdom_num : subdomain L for L-scheme
- 1 : {'wetting' :Lw},
- # 'nonwetting': 0.25},#
- 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 saturation1(pc, subdomain_index):
-# # inverse capillary pressure-saturation-relationship
-# return df.conditional(pc > 0, 1/((1 + pc)**(1/(subdomain_index + 1))), 1)
-#
-# def saturation2(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 saturation1_sym(pc, subdomain_index):
-# # inverse capillary pressure-saturation-relationship
-# return 1/((1 + pc)**(1/(subdomain_index + 1)))
-#
-#
-# def saturation2_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 saturation1_sym_prime(pc, subdomain_index):
-# # inverse capillary pressure-saturation-relationship
-# return -(1/(subdomain_index + 1))*(1 + pc)**((-subdomain_index - 2)/(subdomain_index + 1))
-#
-#
-# def saturation2_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(saturation1_sym, subdomain_index = 1),
-# 2: ft.partial(saturation2_sym, n_index=3, alpha=0.001),
-# }
-#
-# S_pc_sym_prime = {
-# 1: ft.partial(saturation1_sym_prime, subdomain_index = 1),
-# 2: ft.partial(saturation2_sym_prime, n_index=3, alpha=0.001),
-# }
-#
-# sat_pressure_relationship = {
-# 1: ft.partial(saturation1, subdomain_index = 1),#,
-# 2: ft.partial(saturation2, n_index=3, alpha=0.001),
-# }
-
-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=1),
- 2: ft.partial(saturation_sym, index=2),
- # 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=1),
- 2: ft.partial(saturation_sym_prime, index=2),
- # 3: ft.partial(saturation_sym_prime, index=2),
- # 4: ft.partial(saturation_sym_prime, index=1)
-}
-
-sat_pressure_relationship = {
- 1: ft.partial(saturation, index=1),
- 2: ft.partial(saturation, index=2),
- # 3: ft.partial(saturation, index=2),
- # 4: ft.partial(saturation, index=1)
-}
-
-
-#############################################
-# Manufacture source expressions with sympy #
-#############################################
-x, y = sym.symbols('x[0], x[1]') # needed by UFL
-t = sym.symbols('t', positive=True)
-
-p_e_sym = {
- 1: {'wetting': (-5.0 - (1.0 + t*t)*(1.0 + x*x + y*y))}, #*(1-x)**2*(1+x)**2*(1-y)**2},
- 2: {'wetting': (-5.0 - (1.0 + t*t)*(1.0 + x*x)), #*(1-x)**2*(1+x)**2*(1+y)**2,
- 'nonwetting': (-1-t*(1.1+y + x**2))*y**3}, #*(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()})
-
-
-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]}
- )
-
-
-# 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 starttime in starttimes:
- for mesh_resolution, solver_tol in resolutions.items():
- # initialise LDD simulation class
- simulation = ldd.LDDsimulation(
- tol=1E-14,
- LDDsolver_tol=solver_tol,
- debug=debugflag,
- max_iter_num=max_iter_num,
- FEM_Lagrange_degree=FEM_Lagrange_degree,
- mesh_study=mesh_study
- )
-
- simulation.set_parameters(use_case=use_case,
- output_dir=output_string,
- subdomain_def_points=subdomain_def_points,
- isRichards=isRichards,
- interface_def_points=interface_def_points,
- outer_boundary_def_points=outer_boundary_def_points,
- adjacent_subdomains=adjacent_subdomains,
- mesh_resolution=mesh_resolution,
- viscosity=viscosity,
- porosity=porosity,
- L=L,
- lambda_param=lambda_param,
- relative_permeability=relative_permeability,
- saturation=sat_pressure_relationship,
- starttime=starttime,
- number_of_timesteps=number_of_timesteps,
- number_of_timesteps_to_analyse=number_of_timesteps_to_analyse,
- plot_timestep_every=plot_timestep_every,
- timestep_size=timestep_size,
- sources=source_expression,
- initial_conditions=initial_condition,
- dirichletBC_expression_strings=dirichletBC,
- exact_solution=exact_solution,
- densities=densities,
- include_gravity=include_gravity,
- write2file=write_to_file,
- )
-
- simulation.initialise()
- output_dir = simulation.output_dir
- # simulation.write_exact_solution_to_xdmf()
- output = simulation.run(analyse_condition=analyse_condition)
- for subdomain_index, subdomain_output in output.items():
- mesh_h = subdomain_output['mesh_size']
- for phase, 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)
diff --git a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study.py b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study.py
index 6afe2dc..fd1b6c0 100755
--- a/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study.py
+++ b/Two-phase-Richards/two-patch/TP-R-two-patch-test-case/mesh_studies/TP-R-2-patch-mesh-study.py
@@ -194,6 +194,8 @@ 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
@@ -416,9 +418,9 @@ sat_pressure_relationship = {
}
-#############################################
+###############################################################################
# Manufacture source expressions with sympy #
-#############################################
+###############################################################################
x, y = sym.symbols('x[0], x[1]') # needed by UFL
t = sym.symbols('t', positive=True)
@@ -476,6 +478,8 @@ dirichletBC = dict()
# 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
@@ -491,6 +495,7 @@ for subdomain in isRichards.keys():
)
+# LOG FILE OUTPUT #############################################################
# read this file and print it to std out. This way the simulation can produce a
# log file with ./TP-R-layered_soil.py | tee simulation.log
f = open(thisfile, 'r')
@@ -498,6 +503,7 @@ print(f.read())
f.close()
+# RUN #########################################################################
for starttime in starttimes:
for mesh_resolution, solver_tol in resolutions.items():
# initialise LDD simulation class
--
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