Commit 76e0ea47 authored by Johannes Hommel's avatar Johannes Hommel

DUMUX pub for the Dissertation of Johannes Hommel

parents
cmake_minimum_required(VERSION 2.8.12)
project(Hommel2016a CXX)
if(NOT (dune-common_DIR OR dune-common_ROOT OR
"${CMAKE_PREFIX_PATH}" MATCHES ".*dune-common.*"))
string(REPLACE ${CMAKE_PROJECT_NAME} dune-common dune-common_DIR
${PROJECT_BINARY_DIR})
endif()
#find dune-common and set the module path
find_package(dune-common REQUIRED)
list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake/modules"
${dune-common_MODULE_PATH})
#include the dune macros
include(DuneMacros)
# start a dune project with information from dune.module
dune_project()
dune_enable_all_packages()
add_subdirectory("m4")
add_subdirectory("dumux")
add_subdirectory("appl")
add_subdirectory("doc")
add_subdirectory("cmake/modules")
add_subdirectory("test")
# finalize the dune project, e.g. generating config.h etc.
finalize_dune_project(GENERATE_CONFIG_H_CMAKE)
prefix=@prefix@
exec_prefix=@exec_prefix@
libdir=@libdir@
includedir=@includedir@
CXX=@CXX@
CC=@CC@
DEPENDENCIES=@REQUIRES@
Name: @PACKAGE_NAME@
Version: @VERSION@
Description: Hommel2016a module
URL: http://dune-project.org/
Requires: dune-common dune-geometry dune-grid dune-istl dune-localfunctions dumux
Libs: -L${libdir}
Cflags: -I${includedir}
# we need the module file to be able to build via dunecontrol
EXTRA_DIST = dune.module \
CMakeLists.txt \
config.h.cmake
SUBDIRS = m4 appl dumux doc cmake
if BUILD_DOCS
# TODO: set up documentation tree automatically
#SUBDIRS += doc
endif
# don't follow the full GNU-standard
# we need automake 1.9 or newer
AUTOMAKE_OPTIONS = foreign 1.9
# pass most important options when "make distcheck" is used
DISTCHECK_CONFIGURE_FLAGS = --with-dune-common=$(DUNE_COMMON_ROOT) --with-dune-geometry=$(DUNE_GEOMETRY_ROOT) --with-dune-grid=$(DUNE_GRID_ROOT) --with-dune-istl=$(DUNE_ISTL_ROOT) --with-dune-localfunctions=$(DUNE_LOCALFUNCTIONS_ROOT) --with-dumux=$(DUMUX_ROOT) CXX="$(CXX)" CC="$(CC)"
include $(top_srcdir)/am/top-rules
include $(top_srcdir)/am/global-rules
# Generate package configuration files for finding
# installed modules with CMake
include $(top_srcdir)/am/cmake-pkg-config
This file has been created automatically. Please adapt it to your needs.
===============================
The content of this DUNE module was extracted from the module dumux-devel.
In particular, the following subfolders of dumux-devel have been extracted:
appl/co2/biomin,
test/modelcoupling/ncchem2pnctransp/,
Additionally, all headers in dumux-devel that are required to build the
executables from the sources
appl/co2/biomin/biomin.cc,
appl/co2/biomin/test_biomin.cc,
test/modelcoupling/ncchem2pnctransp/test_ncchem2ptransp.cc,
test/modelcoupling/ncchem2pnctransp/test_sequential_biomin.cc,
have been extracted. You can build the module just like any other DUNE
module. For building and running the executables, please go to the folders
containing the sources listed above.
===============================
When this module was created, the original module dumux-devel was using
the following list of DUNE modules and third-party libraries.
- DUNE 2.4 (common, grid, istl, geometry, localfunctions)
- dumux-stable 2.8
- external/ug 3.12.1
BEWARE: This does not necessarily mean that the applications in this
extracted module actually depend on all these components.
##########################################################################
# Parameter file for biomin
# Everything behind a '#' is a comment
# Groups can be ordered e.g. : [BoundaryConditions]
# Parameters in groups have to be accessed hierarchically e.g.: FluidSystem.pressureLow
##########################################################################
####################################################################
# Mandatory arguments
####################################################################
[Newton]
NewtonTolerance = 1e-3 #
####################################################################
[Model]
PlausibilityTolerance = 1e-2 #
pHMin = 0 #
pHMax = 15 #
####################################################################
[Problem]
Name = Gorgas # name passed to the output routines
MaxCouplingError = 1e-5 #
---------------------------------------------------------------------
# the TimeIntegrationIdx specifies which time integration scheme will be used. Choose with care!
---------------------------------------------------------------------
#TimeIntegrationIdx = 1 # sequential iterative:
# --->transport problem gets an average chemical reaction rate from the chemistry model, a new reaction rate is calculated from previous solution and half of the transport only changes. iterated on
#TimeIntegrationIdx = 2 # sequential non iterative:
# --->transport problem gets an average chemical reaction rate from the chemistry model, solutions are exchanged at the end of each main time step.
#TimeIntegrationIdx = 2012 # sequential non iterative:
# --->transport problem gets an average chemical reaction rate from the chemistry model, solutions are exchanged at the end of each main time step.
#TimeIntegrationIdx = 212 # sequential non iterative, chemistry is calculated first, transport second:
# --->main Timestep is set to the chemistry timestep, chemistry is calculated first, after that transport is calculated.
#######################
TimeIntegrationIdx = 221 # sequential non iterative, transport is calculated first, chemistry second:
# --->main Timestep is set to the transport timestep, transport is calculated first, after that chemistry is calculated.
#######################
#TimeIntegrationIdx = 99 # plain decoupled:
# --->subproblems run in parallel, solutions are exchanged at the end of each main time step.
numOutputSteps = 500 #
####################################################################
[Initial]
initDensityW = 1087 # [kg/m³]
initPressure = 1.79e6 # [Pa] #Gorgas
initxlTC = 2.341e-7 # [mol/mol]
initxlNa = 0.007 # [mol/mol]
initxlCl = 0.007 # [mol/mol]
initxlCa = 0.0 # [mol/mol]
initxlUrea = 0.0 # [mol/mol]
initxlTNH = 0.0 # [mol/mol]
initxlO2 = 0.0 # [mol/mol]
initxlSubstrate = 0.0 # [mol/mol]
initxlBiosusp = 0.0 # [mol/mol]
initBiofilm = 0.0 # [-]
initCalcite = 0.0 # [-]
xlNaCorr = 1.95e-7 # [mol/mol] //NaCorr to get the pH to 6.2 calculated as molefraction
xlClCorr = 0.0 # [mol/mol]
####################################################################
[Injection]
injVolumeflux = 1.0515e-5 # //[m³/s] // = 10 gallons/h
angle = 0.3925 # = pi/8 //section of the radial system modelled.
Height = 0.05 # [m] 10*10grid
#Height = 0.1 # [m] 100*100grid
injTC = 5.8e-7 # [kg/kg] //equilibrium with atmospheric CO2 at atmospheric pressure
injNa = 9.441 # [kg/m³] //computed from 24 g/l NaCl
injCa = 13.575 # [kg/m³] //computed from 49 g/l CaCl2*2H2O (molar mass = 147.02g/mol --> 0.33molCa/l, )
injUrea = 24 # [kg/m³]
injTNH = 0.3184 # [kg/m³] //computed from 1 g/l NH4Cl
injO2 = 0.008 # [kg/m³]
injSub = 4 # [kg/m³] //1 g/l Yeast extract + 3 g/l molasses
injBiosusp = 0.0125 # [kg/m³] #Gorgas //0.5e8 cfu/ml (40e8cfu/ml~1g/l)
injNaCorr= 0.00379 # [kg/m³] //NaCorr to get the pH to 6.2
numInjections = 91 #
InjectionParamFile = injections/Gorgas2Inj.dat #
####################################################################
[TimeManager]
DtInitial = 10 #0.01# [s]
TEnd = 336300 # [s] # Gorgas1
#DtMax = 200 # [s]
DtMax = 400 # [s]
DtMaxChem = 20 # [s]
DtInitialSubProblem1 = 5 # [s]
DtInitialSubProblem2 = 1 # [s]
####################################################################
[Grid]
#File = grid/hp_core.dgf # relative path to the grid file
#File = grid/VanoGrid.dgf # relative path to the grid file
#File = grid/40newFCM.dgf #VanoGrid.dgf # relative path to the grid file
#File = grid/simpleCake.dgf
#File = grid/unitcube.dgf
#File = grid/unitplane.dgf
#File = grid/tube.dgf
#File = grid/pieceofcake10_10.dgf
#File = grid/refined_frac_1slice.dgf
#File = grid/refined_frac_1slice_fine_r.dgf
File = grid/elenagrid.dgf
#File = grid/1slice2.4x2.4_refined.dgf
#File = grid/1slice2.4x2.4_refined_more.dgf
#File = grid/recoarsed.dgf
####################################################################
[SpatialParams]
#Porosity
Porosity = 0.12 # [-]
#FracPorosity
FracPorosity = 0.12 #0.0125
CritPorosity = 0.10 # [-] # Kozeny-Carman Parameter, data from pdf: K_0 = 37mD,
# K_end = 2,4mD,
# phi_end = 0,137
# Permeabilities
RockPermeability = 1.0856e-14 # [m^2]
FracPermeability = 1.645e-12 # [m^2]
#additional params
FracWidth = 0.05 # [m] 10*10grid
#FracWidth = 0.1 # [m] 100*100grid
FracRadius = 4 # [m]
TotalHeight = 8 # [m] 10*10grid
#TotalHeight = 100 # [m] 100*100grid
#####################################################################
[BioCoefficients]
ca1 = 1.5e-5 # // [1/s]from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
ca2 = 5e-6 # // [1/s] from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
cd1 = 2.894e-8 # // [1/s] from Anozie (3)
dc0 = 3.183e-7 # // [1/s] from Anozie (37)
kmue = 4.167e-5 # // [1/s] from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
F = 0.5 # // [-] from Anozie (40)
Ke = 2e-5 # // [kg/m³] from Anozie (54)
KpHa = 6.15e-10 # //[mol²/kgH2O²] Kim et al. 2000
Ks = 7.99e-4 # // [kg/m³] from Anozie (37)
Yield = 0.5 # // [-] from Anozie (55)
rhoBiofilm = 10 # //[kg/m³] from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
#####################################################################
[CalciteCoefficients]
ac = 2000 # // [1/dm] from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
kdiss1 = 8.9e-3 # // [kgH2O/dm²s] from Anozie (17)
kdiss2 = 6.5e-9 # // [mol/dm²s] from Anozie (17)
kprec = 1.5e-12 # // [mol/dm²s] from Anozie (29)
ndiss = 1.0 # // TODO ask Anozie from where
nprec = 3.27 # // [-] from Anozie (29)
Asw0 = 500.0 # // [1/dm]estimated from Anozie A/V
###############################################################################################################################################################
[UreolysisCoefficients]
kub = 0.01 # //new value from Anozie//0.035; //[kgureas/kgbio] from Anozie () ask him from where TODO
kurease = 706.7 # //[molurea/(kgurease s)]//0.04167; //[molurea/(gurease s)] from Anozie (57)
nub = 1 # //new value from Anozie// 0.5; // from Anozie () ask him from where TODO
Keu1 = 7.57e-7 # //[mol/kgH2O] from Anozie (21)
Keu2 = 1.27e-8 # //[mol/kgH2O] from Anozie (21)
KNH4 = 10000 # //[mol/kgH2O] from Anozie (21)
Ku = 0.355 # //[mol/kgH2O] from Anozie (37)
###############################################################################################################################################################
# Simulation restart
#
# DuMux simulations can be restarted from *.drs files
# Set restart to the value of a specific file, e.g.: 'restart = 27184.1'
# for the restart file
# name_time = 27184.1_rank = 0.drs
# Please comment in the below value, if restart is desired.
####################################################################
[TimeManager]
Restart = 252136
###################################################################
This diff is collapsed.
##########################################################################
# Parameter file for biomin
# Everything behind a '#' is a comment
# Groups can be ordered e.g. : [BoundaryConditions]
# Parameters in groups have to be accessed hierarchically e.g.: FluidSystem.pressureLow
##########################################################################
####################################################################
# Mandatory arguments
####################################################################
[Newton]
NewtonTolerance = 1e-3 #
####################################################################
[Model]
PlausibilityTolerance = 1e-2 #
pHMin = 0 #
pHMax = 15 #
####################################################################
[Problem]
Name = Gorgas # name passed to the output routines
MaxCouplingError = 1e-5 #
---------------------------------------------------------------------
# the TimeIntegrationIdx specifies which time integration scheme will be used. Choose with care!
---------------------------------------------------------------------
#TimeIntegrationIdx = 1 # sequential iterative:
# --->transport problem gets an average chemical reaction rate from the chemistry model, a new reaction rate is calculated from previous solution and half of the transport only changes. iterated on
#TimeIntegrationIdx = 2 # sequential non iterative:
# --->transport problem gets an average chemical reaction rate from the chemistry model, solutions are exchanged at the end of each main time step.
#TimeIntegrationIdx = 2012 # sequential non iterative:
# --->transport problem gets an average chemical reaction rate from the chemistry model, solutions are exchanged at the end of each main time step.
#TimeIntegrationIdx = 212 # sequential non iterative, chemistry is calculated first, transport second:
# --->main Timestep is set to the chemistry timestep, chemistry is calculated first, after that transport is calculated.
#######################
TimeIntegrationIdx = 221 # sequential non iterative, transport is calculated first, chemistry second:
# --->main Timestep is set to the transport timestep, transport is calculated first, after that chemistry is calculated.
#######################
#TimeIntegrationIdx = 99 # plain decoupled:
# --->subproblems run in parallel, solutions are exchanged at the end of each main time step.
numOutputSteps = 500 #
####################################################################
[Initial]
initDensityW = 1087 # [kg/m³]
initPressure = 1.79e6 # [Pa] #Gorgas
initxlTC = 2.341e-7 # [mol/mol]
initxlNa = 0.007 # [mol/mol]
initxlCl = 0.007 # [mol/mol]
initxlCa = 0.0 # [mol/mol]
initxlUrea = 0.0 # [mol/mol]
initxlTNH = 0.0 # [mol/mol]
initxlO2 = 0.0 # [mol/mol]
initxlSubstrate = 0.0 # [mol/mol]
initxlBiosusp = 0.0 # [mol/mol]
initBiofilm = 0.0 # [-]
initCalcite = 0.0 # [-]
xlNaCorr = 1.95e-7 # [mol/mol] //NaCorr to get the pH to 6.2 calculated as molefraction
xlClCorr = 0.0 # [mol/mol]
####################################################################
[Injection]
injVolumeflux = 1.0515e-5 # //[m³/s] // = 10 gallons/h
angle = 0.3925 # = pi/8 //section of the radial system modelled.
Height = 0.04 # [m] 10*10grid
#Height = 0.1 # [m] 100*100grid
injTC = 5.8e-7 # [kg/kg] //equilibrium with atmospheric CO2 at atmospheric pressure
injNa = 9.441 # [kg/m³] //computed from 24 g/l NaCl
injCa = 13.575 # [kg/m³] //computed from 49 g/l CaCl2*2H2O (molar mass = 147.02g/mol --> 0.33molCa/l, )
injUrea = 24 # [kg/m³]
injTNH = 0.3184 # [kg/m³] //computed from 1 g/l NH4Cl
injO2 = 0.008 # [kg/m³]
injSub = 4 # [kg/m³] //1 g/l Yeast extract + 3 g/l molasses
injBiosusp = 0.0125 # [kg/m³] #Gorgas //0.5e8 cfu/ml (40e8cfu/ml~1g/l)
injNaCorr= 0.00379 # [kg/m³] //NaCorr to get the pH to 6.2
numInjections = 91 #
InjectionParamFile = injections/Gorgas2Inj.dat #
####################################################################
[TimeManager]
DtInitial = 10 #0.01# [s]
TEnd = 336300 # [s] # Gorgas1
#DtMax = 200 # [s]
DtMax = 400 # [s]
DtMaxChem = 20 # [s]
DtInitialSubProblem1 = 5 # [s]
DtInitialSubProblem2 = 1 # [s]
####################################################################
[Grid]
#File = grid/hp_core.dgf # relative path to the grid file
#File = grid/VanoGrid.dgf # relative path to the grid file
#File = grid/40newFCM.dgf #VanoGrid.dgf # relative path to the grid file
#File = grid/simpleCake.dgf
#File = grid/unitcube.dgf
#File = grid/unitplane.dgf
#File = grid/tube.dgf
#File = grid/pieceofcake10_10.dgf
#File = grid/refined_frac_1slice.dgf
#File = grid/refined_frac_1slice_fine_r.dgf
#File = grid/elenagrid.dgf
File = grid/1slice2.4x2.4_refined.dgf
#File = grid/1slice2.4x2.4_refined_more.dgf
#File = grid/recoarsed.dgf
####################################################################
[SpatialParams]
#Porosity
Porosity = 0.12 # [-]
#FracPorosity
FracPorosity = 0.12 #0.0125
CritPorosity = 0.10 # [-] # Kozeny-Carman Parameter, data from pdf: K_0 = 37mD,
# K_end = 2,4mD,
# phi_end = 0,137
# Permeabilities
RockPermeability = 1.0856e-14 # [m^2]
FracPermeability = 1.645e-12 # [m^2]
#additional params
FracWidth = 0.04 # 0.05 [m] 10*10grid
#FracWidth = 0.1 # [m] 100*100grid
FracRadius = 1.6 # [m]
TotalHeight = 2.4 # [m] 10*10grid
#TotalHeight = 100 # [m] 100*100grid
#####################################################################
[BioCoefficients]
ca1 = 1.5e-5 # // [1/s]from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
ca2 = 5e-6 # // [1/s] from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
cd1 = 2.894e-8 # // [1/s] from Anozie (3)
dc0 = 3.183e-7 # // [1/s] from Anozie (37)
kmue = 4.167e-5 # // [1/s] from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
F = 0.5 # // [-] from Anozie (40)
Ke = 2e-5 # // [kg/m³] from Anozie (54)
KpHa = 6.15e-10 # //[mol²/kgH2O²] Kim et al. 2000
Ks = 7.99e-4 # // [kg/m³] from Anozie (37)
Yield = 0.5 # // [-] from Anozie (55)
rhoBiofilm = 10 # //[kg/m³] from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
#####################################################################
[CalciteCoefficients]
ac = 2000 # // [1/dm] from Anozie Ebigbo 2011 // TODO Check for value, fittet parameter!!!!!!!!!!!!
kdiss1 = 8.9e-3 # // [kgH2O/dm²s] from Anozie (17)
kdiss2 = 6.5e-9 # // [mol/dm²s] from Anozie (17)
kprec = 1.5e-12 # // [mol/dm²s] from Anozie (29)
ndiss = 1.0 # // TODO ask Anozie from where
nprec = 3.27 # // [-] from Anozie (29)
Asw0 = 500.0 # // [1/dm]estimated from Anozie A/V
###############################################################################################################################################################
[UreolysisCoefficients]
kub = 0.01 # //new value from Anozie//0.035; //[kgureas/kgbio] from Anozie () ask him from where TODO
kurease = 706.7 # //[molurea/(kgurease s)]//0.04167; //[molurea/(gurease s)] from Anozie (57)
nub = 1 # //new value from Anozie// 0.5; // from Anozie () ask him from where TODO
Keu1 = 7.57e-7 # //[mol/kgH2O] from Anozie (21)
Keu2 = 1.27e-8 # //[mol/kgH2O] from Anozie (21)
KNH4 = 10000 # //[mol/kgH2O] from Anozie (21)
Ku = 0.355 # //[mol/kgH2O] from Anozie (37)
###############################################################################################################################################################
# Simulation restart
#
# DuMux simulations can be restarted from *.drs files
# Set restart to the value of a specific file, e.g.: 'restart = 27184.1'
# for the restart file
# name_time = 27184.1_rank = 0.drs
# Please comment in the below value, if restart is desired.
####################################################################
[TimeManager]
Restart = 206192
###################################################################
This diff is collapsed.
##########################################################################
# Parameter file for biomin
# Everything behind a '#' is a comment
# Groups can be ordered e.g. : [BoundaryConditions]
# Parameters in groups have to be accessed hierarchically e.g.: FluidSystem.pressureLow
##########################################################################