From 541dab677ad57c97c3af058901f60a755246fbc2 Mon Sep 17 00:00:00 2001
From: hommel <johannes.hommel@iws.uni-stuttgart.de>
Date: Wed, 31 Jul 2019 14:14:27 +0200
Subject: [PATCH] [examples][biomin] added new biomineralization example
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
with contributions by Felix Weinhardt
and some proof reading by Timo Koch and Dennis Gläser
---
examples/CMakeLists.txt | 1 +
examples/README.md | 21 +
examples/biomineralization/.doc_config | 53 +
examples/biomineralization/CMakeLists.txt | 11 +
examples/biomineralization/README.md | 190 ++++
examples/biomineralization/doc/_intro.md | 159 +++
.../biomineralization/doc/fluidmaterial.md | 784 ++++++++++++++
.../doc/fluidmaterial_intro.md | 42 +
examples/biomineralization/doc/mainfile.md | 330 ++++++
.../biomineralization/doc/mainfile_intro.md | 14 +
examples/biomineralization/doc/material.md | 990 ++++++++++++++++++
.../biomineralization/doc/modelconcept.md | 271 +++++
.../doc/modelconcept_intro.md | 261 +++++
examples/biomineralization/doc/setup.md | 938 +++++++++++++++++
examples/biomineralization/doc/setup_intro.md | 17 +
.../biomineralization/doc/solidmaterial.md | 258 +++++
.../doc/solidmaterial_intro.md | 38 +
.../img/pore_scale_w_processes_named.png | Bin 0 -> 154841 bytes
.../results_volfracs_over_length_100000s.png | Bin 0 -> 17950 bytes
.../injection_checkpoints.dat | 212 ++++
examples/biomineralization/injection_type.dat | 212 ++++
examples/biomineralization/main.cc | 278 +++++
.../material/co2tableslaboratory.hh | 38 +
.../material/co2valueslaboratory.inc | 424 ++++++++
.../material/components/biofilm.hh | 74 ++
.../material/components/suspendedbiomass.hh | 65 ++
.../material/fluidsystems/CMakeLists.txt | 5 +
.../fluidsystems/biominsimplechemistry.hh | 582 ++++++++++
.../fluidsystems/icpcomplexsalinitybrine.hh | 391 +++++++
.../material/solidsystems/biominsolids.hh | 197 ++++
examples/biomineralization/params.input | 63 ++
examples/biomineralization/problem.hh | 590 +++++++++++
examples/biomineralization/properties.hh | 125 +++
examples/biomineralization/spatialparams.hh | 149 +++
.../example_biomineralization-reference.vtp | 296 ++++++
35 files changed, 8079 insertions(+)
create mode 100644 examples/biomineralization/.doc_config
create mode 100644 examples/biomineralization/CMakeLists.txt
create mode 100644 examples/biomineralization/README.md
create mode 100644 examples/biomineralization/doc/_intro.md
create mode 100644 examples/biomineralization/doc/fluidmaterial.md
create mode 100644 examples/biomineralization/doc/fluidmaterial_intro.md
create mode 100644 examples/biomineralization/doc/mainfile.md
create mode 100644 examples/biomineralization/doc/mainfile_intro.md
create mode 100644 examples/biomineralization/doc/material.md
create mode 100644 examples/biomineralization/doc/modelconcept.md
create mode 100644 examples/biomineralization/doc/modelconcept_intro.md
create mode 100644 examples/biomineralization/doc/setup.md
create mode 100644 examples/biomineralization/doc/setup_intro.md
create mode 100644 examples/biomineralization/doc/solidmaterial.md
create mode 100644 examples/biomineralization/doc/solidmaterial_intro.md
create mode 100644 examples/biomineralization/img/pore_scale_w_processes_named.png
create mode 100644 examples/biomineralization/img/results_volfracs_over_length_100000s.png
create mode 100644 examples/biomineralization/injection_checkpoints.dat
create mode 100644 examples/biomineralization/injection_type.dat
create mode 100644 examples/biomineralization/main.cc
create mode 100644 examples/biomineralization/material/co2tableslaboratory.hh
create mode 100644 examples/biomineralization/material/co2valueslaboratory.inc
create mode 100644 examples/biomineralization/material/components/biofilm.hh
create mode 100644 examples/biomineralization/material/components/suspendedbiomass.hh
create mode 100644 examples/biomineralization/material/fluidsystems/CMakeLists.txt
create mode 100644 examples/biomineralization/material/fluidsystems/biominsimplechemistry.hh
create mode 100644 examples/biomineralization/material/fluidsystems/icpcomplexsalinitybrine.hh
create mode 100644 examples/biomineralization/material/solidsystems/biominsolids.hh
create mode 100644 examples/biomineralization/params.input
create mode 100644 examples/biomineralization/problem.hh
create mode 100644 examples/biomineralization/properties.hh
create mode 100644 examples/biomineralization/spatialparams.hh
create mode 100644 test/references/example_biomineralization-reference.vtp
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index 058cc9e278..d839bb9070 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -1,5 +1,6 @@
add_subdirectory(2pinfiltration)
add_subdirectory(1ptracer)
+add_subdirectory(biomineralization)
add_subdirectory(shallowwaterfriction)
add_subdirectory(freeflowchannel)
add_subdirectory(1protationsymmetry)
diff --git a/examples/README.md b/examples/README.md
index e4e0e646c5..8f3fc62a4f 100644
--- a/examples/README.md
+++ b/examples/README.md
@@ -91,3 +91,24 @@ You learn how to
<figure><img src="1protationsymmetry/img/setup.svg" alt="Rotation-symmetric setup"/></figure></td>
</a></td>
</tr></table>
+
+### [:open_file_folder: Example 6: Biomineralization](biomineralization/README.md)
+
+<table><tr><td>
+
+In this example, we simulate microbially-induced calcite precipitation
+You learn how to
+
+* solve a reactive transport model including
+ * biofilm growth
+ * mineral precipitation and dissolution
+ * changing porosity and permeability
+* use complex fluid and solid systems
+* set a complex time loop with checkpoints, reading the check points from a file
+* set complex injection boundary conditions, reading the injection types from a file
+
+</td>
+<td width="20%"><a href="biomineralization/README.md">
+<figure><img src="biomineralization/img/pore_scale_w_processes_named.png" alt="biomin result"/></figure></td>
+</a></td>
+</tr></table>
diff --git a/examples/biomineralization/.doc_config b/examples/biomineralization/.doc_config
new file mode 100644
index 0000000000..4481d351ff
--- /dev/null
+++ b/examples/biomineralization/.doc_config
@@ -0,0 +1,53 @@
+{
+ "README.md" : [
+ "doc/_intro.md"
+ ],
+
+ "doc/modelconcept.md" : [
+ "doc/modelconcept_intro.md"
+ ],
+
+ "doc/mainfile.md" : [
+ "doc/mainfile_intro.md",
+ "main.cc"
+ ],
+
+ "doc/setup.md" : [
+ "doc/setup_intro.md",
+ "problem.hh",
+ "spatialparams.hh",
+ "properties.hh"
+ ],
+
+ "doc/fluidmaterial.md" : [
+ "doc/fluidmaterial_intro.md",
+ "material/co2tableslaboratory.hh",
+ "material/components/suspendedbiomass.hh",
+ "material/fluidsystems/biominsimplechemistry.hh",
+ "material/fluidsystems/icpcomplexsalinitybrine.hh"
+ ],
+
+ "doc/solidmaterial.md" : [
+ "doc/solidmaterial_intro.md",
+ "material/components/biofilm.hh",
+ "material/solidsystems/biominsolids.hh"
+ ],
+
+ "navigation" : {
+ "mainpage" : "README.md",
+ "subpages" : [
+ "doc/modelconcept.md",
+ "doc/mainfile.md",
+ "doc/setup.md",
+ "doc/fluidmaterial.md",
+ "doc/solidmaterial.md"
+ ],
+ "subtitles" : [
+ "Model concept",
+ "Main file",
+ "Simulation setup",
+ "Specific fluid material files",
+ "Specific solid material files"
+ ]
+ }
+}
diff --git a/examples/biomineralization/CMakeLists.txt b/examples/biomineralization/CMakeLists.txt
new file mode 100644
index 0000000000..9820938673
--- /dev/null
+++ b/examples/biomineralization/CMakeLists.txt
@@ -0,0 +1,11 @@
+dune_symlink_to_source_files(FILES injection_checkpoints.dat injection_type.dat params.input)
+
+# compile MICP simplified chemistry column setup
+dumux_add_test(NAME example_biomineralization
+ LABELS porousmediumflow
+ SOURCES main.cc
+ COMMAND ${CMAKE_SOURCE_DIR}/bin/testing/runtest.py
+ CMD_ARGS --script fuzzy
+ --files ${CMAKE_SOURCE_DIR}/test/references/example_biomineralization-reference.vtp
+ ${CMAKE_CURRENT_BINARY_DIR}/example_biomineralization-00018.vtp
+ --command "${CMAKE_CURRENT_BINARY_DIR}/example_biomineralization params.input -Problem.Name example_biomineralization")
diff --git a/examples/biomineralization/README.md b/examples/biomineralization/README.md
new file mode 100644
index 0000000000..42529a0986
--- /dev/null
+++ b/examples/biomineralization/README.md
@@ -0,0 +1,190 @@
+<!-- Important: This file has been automatically generated by generate_example_docs.py. Do not edit this file directly! -->
+
+# Biomineralization
+
+We simulate microbially-induced calcite precipitation in a vertical sand-column.
+The problem is considered radially-symmetric so that a one-dimensional problem can be simulated.
+
+__The main points illustrated in this example are__
+* solving a reactive transport model including
+ * biofilm growth
+ * mineral precipitation and dissolution
+ * changing porosity and permeability
+* using complex fluid and solid systems
+* setting a complex time loop with checkpoints, reading the check points from a file
+* set complex injection boundary conditions, reading the injection types from a file
+
+__Table of contents__. This description is structured as follows:
+
+[[_TOC_]]
+
+__Result__. The result will look like below.
+You see the volume fractions of the solid components after 100000s over the column.
+
+<figure>
+ <center>
+ <img src="img/results_volfracs_over_length_100000s.png" alt="Biofilm and calcite volume fractions" width="50%"/>
+ <figcaption> <b> Fig.1 </b> - Biofilm and calcite volume fractions.</figcaption>
+ </center>
+</figure>
+
+## Problem set-up
+A vertical, sand-filled column is biomineralized by repeated injections of various aqueous solutions
+from its bottom end. The setup will be explained in more detail in [Part 3: Example Setup](doc/setup.md).
+For more information, see the description of _column experiment D1_ in Section 4.2 of [@Hommel2016].
+
+## What is microbially-induced calcite precipitation?
+Microbially-induced calcite precipitation (MICP) is an engineering technology for targeted biomineralization.
+It can be used in the context of sealing possible leakage pathways of subsurface gas or oil reservoirs as well as other applications.
+The governing processes are two-phase multi-component reactive transport including precipitation and dissolution
+of calcite, as well as biomass-related processes:
+* attachment of biomass to surfaces,
+* detachment of biomass from a biofilm,
+* growth and decay of biomass.
+
+Additionally, the reduction in porosity and permeability has to be considered.
+This results from the presence of the solid phases biofilm and calcite in the pore space.
+
+In subsurface applications, MICP is typically
+associated with a reduction of porosity, which, even more importantly, corresponds to a
+reduction of permeability.
+MICP can be used to alter hydraulic flow conditions, for example, by filling highly permeable pathways such as
+fractures, faults, or behind-casing defects in boreholes within a geological
+formation, e.g. [@Phillips2013a].
+
+The bacterium _Sporosarcina pasteurii_
+expresses the enzyme urease that catalyzes the hydrolysis reaction of
+urea (CO(NH<sub>2</sub>)<sub>2</sub>) into ammonia (NH<sub>3</sub>) and carbon
+dioxide (CO<sub>2</sub>):
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} \xrightarrow{urease}
+2\mathrm{NH_{3}} + \mathrm{H_2CO_{3}}.
+\tag{1}
+```
+
+Aqueous solutions of ammonia become alkaline until the equilibrium of ammonium and ammonia is reached.
+Thus, the ureolysis reaction leads to an increase in pH until the pH is equal to the pKa of ammonia.
+This shifts the
+carbonate balance in an aqueous solution toward higher concentrations of
+dissolved carbonate.
+Adding calcium to the system results then in the precipitation of calcium carbonate:
+
+```math
+\mathrm{CO_{3}^{2-}} + \mathrm{Ca^{2+}} \longrightarrow \mathrm{CaCO_3 \downarrow}.
+```
+
+The resulting overall MICP reaction equation is:
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} + \mathrm{Ca^{2+}} \xrightarrow{urease}
+2\mathrm{NH_{4}^{+}} + \mathrm{CaCO_{3}} \downarrow.
+```
+
+In a porous medium, biofilm growth, fluid dynamics,
+and reaction rates are strongly interacting.
+A pore-scale sketch of the most important processes of MICP is shown
+in Fig.2.
+
+<figure>
+ <center>
+ <img src="img/pore_scale_w_processes_named.png" alt="Schematic pore-scale sketch of the processes during biomineralization." width="50%"/>
+ <figcaption> <b> Fig.2 </b> - Schematic pore-scale sketch of the processes during biomineralization.</figcaption>
+ </center>
+</figure>
+
+A major difficulty for practical engineering applications of MICP is the predictive planning of a scenario and its impact.
+While the basic chemistry and the flow processes are known, it is mainly the quantitative description
+of the influence of the biofilm and the developing precipitates on hydraulic parameters that poses challenges to achieving predictability.
+More details on modeling biomineralization are given in [Part 1: Model Concept](doc/modelconcept.md).
+
+# The code documentation
+
+In the following, we take a closer look at the source files for this example.
+The setup is rather complex in comparison to the other examples.
+We will discuss the different parts of the code in detail subsequently.
+
+```
+└── biomineralization/
+ ├── CMakeLists.txt -> build system file
+ ├── main.cc -> main program flow
+ ├── params.input -> runtime parameters
+ ├── injections.dat -> runtime injection strategy input file
+ ├── properties.hh -> compile time settings for the simulation
+ ├── problem.hh -> boundary & initial conditions for the simulation
+ ├── spatialparams.hh -> parameter distributions for the simulation
+ └── material/ -> components, fluid- and solidsystems
+ ├── components/
+ │ ├── biofilm.hh
+ │ └── suspendedbiomass.hh
+ ├── fluidsystems/
+ │ ├── biominsimplechemistry.hh
+ │ └── icpcomplexsalinitybrine.hh
+ ├── solidsystems/
+ │ └── biominsolids.hh
+ └── co2tableslaboratory.hh
+```
+
+In order to define a simulation setup in DuMu<sup>x</sup>, you need to implement compile-time settings,
+where you specify the classes and compile-time options that DuMu<sup>x</sup> should use for the simulation.
+Moreover, a `Problem` class needs to be implemented, in which the initial and boundary conditions
+are specified. Finally, spatially-distributed values for the parameters required by the used model
+are implemented in a `SpatialParams` class.
+
+__Part 1__ discusses the mathematical model in more detail.
+
+__Part 2__ takes a close look at the main file.
+`main.cc` controlling the simulation, and containing the time loop management,
+A special feature of this example, which might be interesting also for non-biomineralization modelers,
+is that it uses the class `CheckPointTimeLoop` extensively to set the injections of the various consecutive
+biomineralization solution injections based on a separate input file `injections_checkpoints.dat`.
+Similar strategies might be useful when simulating experimental setups with boundary conditions changing over time.
+
+__Part 3__ takes a close look at the problem set-up.
+`problem.hh` featuring the reactive source and sink terms discussed in the model concept and the time-dependent injection boundary conditions, and
+`spatialparams.hh` with the spatially distributed parameters, most importantly the porosity and permeability changing due to the reactions.
+A special feature of this example, which might be interesting also for non-biomineralization modelers,
+is that `problem.hh`, determines the Neumann boundary condition, more specifically which type of solution is currently injected, (the `injectionType_`) based on a separate input file `injections_type.dat`.
+Similar strategies might be useful when simulating experimental setups with boundary conditions changing over time.
+
+__Part 4__ discusses the code concerned with the fluid (files in the folder `material/`),
+especially the multi-component fluidsystems.
+The CO<sub>2</sub> properties are stored in the CO<sub>2</sub> tables in the subfolder `material` (`co2tableslaboratory.hh`,`co2valueslaboratory.inc`).
+
+__Part 5__ discusses the code concerned with the solid properties (files in the folder `material/`),
+especially the multi-component solidsystems and variable solid volume fractions.
+
+
+[@Ebigbo2012]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2011WR011714 "Darcy-scale modeling of microbially induced carbonate mineral precipitation in sand columns"
+[@Hommel2015]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2014WR016503 "A revised model for microbially induced calcite precipitation: Improvements and new insights based on recent experiments"
+[@Hommel2016]: https://elib.uni-stuttgart.de/handle/11682/8787 "Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation"
+[@Phillips2013a]: https://pubs.acs.org/doi/abs/10.1021/es301294q "Potential CO<sub>2</sub> leakage reduction through biofilm-induced calcium carbonate precipitation"
+
+## Part 1: Model concept
+
+| [:arrow_right: Click to continue with part 1 of the documentation](doc/modelconcept.md) |
+|---:|
+
+
+## Part 2: Main file
+
+| [:arrow_right: Click to continue with part 2 of the documentation](doc/mainfile.md) |
+|---:|
+
+
+## Part 3: Simulation setup
+
+| [:arrow_right: Click to continue with part 3 of the documentation](doc/setup.md) |
+|---:|
+
+
+## Part 4: Specific fluid material files
+
+| [:arrow_right: Click to continue with part 4 of the documentation](doc/fluidmaterial.md) |
+|---:|
+
+
+## Part 5: Specific solid material files
+
+| [:arrow_right: Click to continue with part 5 of the documentation](doc/solidmaterial.md) |
+|---:|
\ No newline at end of file
diff --git a/examples/biomineralization/doc/_intro.md b/examples/biomineralization/doc/_intro.md
new file mode 100644
index 0000000000..34d532bb0a
--- /dev/null
+++ b/examples/biomineralization/doc/_intro.md
@@ -0,0 +1,159 @@
+# Biomineralization
+
+We simulate microbially-induced calcite precipitation in a vertical sand-column.
+The problem is considered radially-symmetric so that a one-dimensional problem can be simulated.
+
+__The main points illustrated in this example are__
+* solving a reactive transport model including
+ * biofilm growth
+ * mineral precipitation and dissolution
+ * changing porosity and permeability
+* using complex fluid and solid systems
+* setting a complex time loop with checkpoints, reading the check points from a file
+* set complex injection boundary conditions, reading the injection types from a file
+
+__Table of contents__. This description is structured as follows:
+
+[[_TOC_]]
+
+__Result__. The result will look like below.
+You see the volume fractions of the solid components after 100000s over the column.
+
+<figure>
+ <center>
+ <img src="img/results_volfracs_over_length_100000s.png" alt="Biofilm and calcite volume fractions" width="50%"/>
+ <figcaption> <b> Fig.1 </b> - Biofilm and calcite volume fractions.</figcaption>
+ </center>
+</figure>
+
+## Problem set-up
+A vertical, sand-filled column is biomineralized by repeated injections of various aqueous solutions
+from its bottom end. The setup will be explained in more detail in [Part 3: Example Setup](doc/setup.md).
+For more information, see the description of _column experiment D1_ in Section 4.2 of [@Hommel2016].
+
+## What is microbially-induced calcite precipitation?
+Microbially-induced calcite precipitation (MICP) is an engineering technology for targeted biomineralization.
+It can be used in the context of sealing possible leakage pathways of subsurface gas or oil reservoirs as well as other applications.
+The governing processes are two-phase multi-component reactive transport including precipitation and dissolution
+of calcite, as well as biomass-related processes:
+* attachment of biomass to surfaces,
+* detachment of biomass from a biofilm,
+* growth and decay of biomass.
+
+Additionally, the reduction in porosity and permeability has to be considered.
+This results from the presence of the solid phases biofilm and calcite in the pore space.
+
+In subsurface applications, MICP is typically
+associated with a reduction of porosity, which, even more importantly, corresponds to a
+reduction of permeability.
+MICP can be used to alter hydraulic flow conditions, for example, by filling highly permeable pathways such as
+fractures, faults, or behind-casing defects in boreholes within a geological
+formation, e.g. [@Phillips2013a].
+
+The bacterium _Sporosarcina pasteurii_
+expresses the enzyme urease that catalyzes the hydrolysis reaction of
+urea (CO(NH<sub>2</sub>)<sub>2</sub>) into ammonia (NH<sub>3</sub>) and carbon
+dioxide (CO<sub>2</sub>):
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} \xrightarrow{urease}
+2\mathrm{NH_{3}} + \mathrm{H_2CO_{3}}.
+\tag{1}
+```
+
+Aqueous solutions of ammonia become alkaline until the equilibrium of ammonium and ammonia is reached.
+Thus, the ureolysis reaction leads to an increase in pH until the pH is equal to the pKa of ammonia.
+This shifts the
+carbonate balance in an aqueous solution toward higher concentrations of
+dissolved carbonate.
+Adding calcium to the system results then in the precipitation of calcium carbonate:
+
+```math
+\mathrm{CO_{3}^{2-}} + \mathrm{Ca^{2+}} \longrightarrow \mathrm{CaCO_3 \downarrow}.
+```
+
+The resulting overall MICP reaction equation is:
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} + \mathrm{Ca^{2+}} \xrightarrow{urease}
+2\mathrm{NH_{4}^{+}} + \mathrm{CaCO_{3}} \downarrow.
+```
+
+In a porous medium, biofilm growth, fluid dynamics,
+and reaction rates are strongly interacting.
+A pore-scale sketch of the most important processes of MICP is shown
+in Fig.2.
+
+<figure>
+ <center>
+ <img src="img/pore_scale_w_processes_named.png" alt="Schematic pore-scale sketch of the processes during biomineralization." width="50%"/>
+ <figcaption> <b> Fig.2 </b> - Schematic pore-scale sketch of the processes during biomineralization.</figcaption>
+ </center>
+</figure>
+
+A major difficulty for practical engineering applications of MICP is the predictive planning of a scenario and its impact.
+While the basic chemistry and the flow processes are known, it is mainly the quantitative description
+of the influence of the biofilm and the developing precipitates on hydraulic parameters that poses challenges to achieving predictability.
+More details on modeling biomineralization are given in [Part 1: Model Concept](doc/modelconcept.md).
+
+# The code documentation
+
+In the following, we take a closer look at the source files for this example.
+The setup is rather complex in comparison to the other examples.
+We will discuss the different parts of the code in detail subsequently.
+
+```
+└── biomineralization/
+ ├── CMakeLists.txt -> build system file
+ ├── main.cc -> main program flow
+ ├── params.input -> runtime parameters
+ ├── injections.dat -> runtime injection strategy input file
+ ├── properties.hh -> compile time settings for the simulation
+ ├── problem.hh -> boundary & initial conditions for the simulation
+ ├── spatialparams.hh -> parameter distributions for the simulation
+ └── material/ -> components, fluid- and solidsystems
+ ├── components/
+ │ ├── biofilm.hh
+ │ └── suspendedbiomass.hh
+ ├── fluidsystems/
+ │ ├── biominsimplechemistry.hh
+ │ └── icpcomplexsalinitybrine.hh
+ ├── solidsystems/
+ │ └── biominsolids.hh
+ └── co2tableslaboratory.hh
+```
+
+In order to define a simulation setup in DuMu<sup>x</sup>, you need to implement compile-time settings,
+where you specify the classes and compile-time options that DuMu<sup>x</sup> should use for the simulation.
+Moreover, a `Problem` class needs to be implemented, in which the initial and boundary conditions
+are specified. Finally, spatially-distributed values for the parameters required by the used model
+are implemented in a `SpatialParams` class.
+
+__Part 1__ discusses the mathematical model in more detail.
+
+__Part 2__ takes a close look at the main file.
+`main.cc` controlling the simulation, and containing the time loop management,
+A special feature of this example, which might be interesting also for non-biomineralization modelers,
+is that it uses the class `CheckPointTimeLoop` extensively to set the injections of the various consecutive
+biomineralization solution injections based on a separate input file `injections_checkpoints.dat`.
+Similar strategies might be useful when simulating experimental setups with boundary conditions changing over time.
+
+__Part 3__ takes a close look at the problem set-up.
+`problem.hh` featuring the reactive source and sink terms discussed in the model concept and the time-dependent injection boundary conditions, and
+`spatialparams.hh` with the spatially distributed parameters, most importantly the porosity and permeability changing due to the reactions.
+A special feature of this example, which might be interesting also for non-biomineralization modelers,
+is that `problem.hh`, determines the Neumann boundary condition, more specifically which type of solution is currently injected, (the `injectionType_`) based on a separate input file `injections_type.dat`.
+Similar strategies might be useful when simulating experimental setups with boundary conditions changing over time.
+
+__Part 4__ discusses the code concerned with the fluid (files in the folder `material/`),
+especially the multi-component fluidsystems.
+The CO<sub>2</sub> properties are stored in the CO<sub>2</sub> tables in the subfolder `material` (`co2tableslaboratory.hh`,`co2valueslaboratory.inc`).
+
+__Part 5__ discusses the code concerned with the solid properties (files in the folder `material/`),
+especially the multi-component solidsystems and variable solid volume fractions.
+
+
+[@Ebigbo2012]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2011WR011714 "Darcy-scale modeling of microbially induced carbonate mineral precipitation in sand columns"
+[@Hommel2015]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2014WR016503 "A revised model for microbially induced calcite precipitation: Improvements and new insights based on recent experiments"
+[@Hommel2016]: https://elib.uni-stuttgart.de/handle/11682/8787 "Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation"
+[@Phillips2013a]: https://pubs.acs.org/doi/abs/10.1021/es301294q "Potential CO<sub>2</sub> leakage reduction through biofilm-induced calcium carbonate precipitation"
diff --git a/examples/biomineralization/doc/fluidmaterial.md b/examples/biomineralization/doc/fluidmaterial.md
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+<!-- Important: This file has been automatically generated by generate_example_docs.py. Do not edit this file directly! -->
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 3](setup.md) | [:arrow_right: Continue with part 5](solidmaterial.md) |
+|---|---|---:|
+
+# Biomineralization - Fluids
+
+The main idea of biomineralization revolves around
+biologically-induced mineral precipitation.
+I our example, it is about precipitation of calcite
+due to urea hydrolysis.
+The resulting overall reaction equation is:
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} + \mathrm{Ca^{2+}} \xrightarrow{urease}
+2\mathrm{NH_{4}^{+}} + \mathrm{CaCO_{3}} \downarrow.
+```
+
+To describe the processes, the minimum set of components is:
+water (w), dissolved inorganic carbon (C<sub>tot</sub>),
+sodium (Na), chloride (Cl), calcium (Ca), urea (u), glucose as a substrate (s), oxygen (O<sub>2</sub>), and suspended biomass (b),
+as well as the solid components biofilm and calcite.
+Thus, there are many components involved and keeping track of the components and their interactions,
+necessitates a sophisticated handling.
+This is why the material folder in this example is both separated from the regular material folder in dumux/dumux/material
+and also documented separately.
+For further specialization, the overview over the material subfolder is split into solid and fluid, this description considering the fluids.
+
+## Fluids in the folder `material`
+
+As this example is about biomineralization involving many components with complex inteactions, some specific fluid material files are necessary.
+A CO_2-Table file provides tabulated CO_2 properties according to @Span1996 in `material/co2tableslaboratory.hh`
+In the component subfolder, `material/components/suspendedbiomass.hh` defines the component suspended biomass, which is the mobile form of biomass being transported suspended in the aqueous fluid phase.
+In the fluidsystem subfolder, the biomineralization fluidsystem `material/fluidsystems/biominsimplechemistry.hh` as well as
+the complex salinity brine adapter `material/fluidsystems/icpcomplexsalinitybrine.hh` can be found.
+The biomineralization fluidsystem `material/fluidsystems/biominsimplechemistry.hh`
+contains the fluid related properties and the interactions of the components in the fluids.
+The complex salinity brine adapter `material/fluidsystems/icpcomplexsalinitybrine.hh`
+adapts the brine fluidsystem (dumux/dumux/material/fluidsystems/brine.hh) expecting a single non-aqueous component defining salinity to be reused for biomineralization with three ions (calcium, sodium, chloride) being assumed to contribute to salinity.
+
+
+The subsequent documentation is structured as follows:
+
+[[_TOC_]]
+
+
+[@Span1996]: https://aip.scitation.org/doi/abs/10.1063/1.555991 "A new equation of state for carbon dioxide covering the fluid region from the triple-point temperature to 1100 K at pressures up to 800 MPa"
+
+
+## The CO2 tables (`co2tableslaboratory.hh`)
+
+This file contains the __co2table class__ which forwards to tabulated properties of CO2 according to Span and Wagner 1996.
+The real work (creating the tables) is done by some external program by Span and Wagner 1996 which provides the ready-to-use tables.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/co2tableslaboratory.hh))</summary>
+
+
+
+```cpp
+
+#include <assert.h>
+namespace Dumux::ICP {
+#include "co2valueslaboratory.inc"
+}// end namespace Dumux::ICP
+```
+
+
+</details>
+
+
+
+## The suspended biomass component (`suspendedbiomass.hh`)
+
+This file contains the __ component class__ which defines the name and molar mass of suspended biomass
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/components/suspendedbiomass.hh))</summary>
+
+
+### Include files
+
+```cpp
+// including the base component
+#include <dumux/material/components/base.hh>
+```
+
+### The suspended biomass component
+
+```cpp
+namespace Dumux::Components {
+
+// In SuspendedBiomass, we define the properties of the component suspended biomass
+template <class Scalar>
+class SuspendedBiomass
+: public Components::Base<Scalar, SuspendedBiomass<Scalar> >
+{
+public:
+ // the name
+ static std::string name()
+ { return "Suspended_Biomass"; }
+```
+
+### The suspended biomass component's properties
+
+```cpp
+ // The molar mass, which is not really defined for suspended biomass. Thus, we read it from params.input or use a default of 1.
+ // Based on a cell mass of 2.5e-16, the molar mass of cells would be 1.5e8 kg/mol, but such high molar masses would lead to numerical problems.
+ static Scalar molarMass()
+ {
+ Scalar molarMass = getParam<Scalar>("BioCoefficients.SuspendedBiomassMolarMass", 1);
+ return molarMass;
+ }
+};
+
+
+} // end namespace Dumux::Components
+```
+
+
+</details>
+
+
+
+## The fluid system (`biominsimplechemistry.hh`)
+
+This file contains the __fluidsystem class__ which defines all functions needed to describe the fluids and their properties,
+which are needed to model biomineralization.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/fluidsystems/biominsimplechemistry.hh))</summary>
+
+
+### Include files
+<details><summary> Click to show </summary>
+
+```cpp
+#include <dumux/material/idealgas.hh>
+
+// we include the base fluid system
+#include <dumux/material/fluidsystems/base.hh>
+// we include the brine adapter adapting component indices to use the brine fluidsystem
+#include "icpcomplexsalinitybrine.hh"
+
+// we include all necessary fluid components
+#include <dumux/material/fluidstates/adapter.hh>
+#include <dumux/material/components/co2.hh>
+#include <dumux/material/components/h2o.hh>
+#include <dumux/material/components/tabulatedcomponent.hh>
+#include <dumux/material/components/co2tablereader.hh>
+#include <dumux/material/components/sodiumion.hh>
+#include <dumux/material/components/chlorideion.hh>
+#include <dumux/material/components/calciumion.hh>
+#include <dumux/material/components/urea.hh>
+#include <dumux/material/components/o2.hh>
+#include <dumux/material/components/glucose.hh>
+#include <examples/biomineralization/material/components/suspendedbiomass.hh>
+
+// we include brine-co2 and h2o-co2 binary coefficients
+#include <dumux/material/binarycoefficients/brine_co2.hh>
+#include <dumux/material/binarycoefficients/h2o_o2.hh>
+```
+
+
+```cpp
+
+#include <dumux/material/fluidsystems/nullparametercache.hh>
+#include <dumux/common/valgrind.hh>
+#include <dumux/common/exceptions.hh>
+
+#include <assert.h>
+```
+
+</details>
+
+### The fluidsystem class
+In the BioMinSimpleChemistryFluid fluid system, we define all functions needed to describe the fluids and their properties accounted for in our simulation.
+The simplified biogeochemistry biomineralization fluid system requires the CO2 tables and the H2OType as template parameters.
+We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+
+```cpp
+namespace Dumux::FluidSystems {
+
+template <class Scalar,
+ class CO2Table,
+ class H2OType = Components::TabulatedComponent<Components::H2O<Scalar>> >
+class BioMinSimpleChemistryFluid
+: public Base<Scalar, BioMinSimpleChemistryFluid<Scalar, CO2Table, H2OType> >
+{
+ using ThisType = BioMinSimpleChemistryFluid<Scalar, CO2Table, H2OType>;
+ using Base = Dumux::FluidSystems::Base<Scalar, ThisType>;
+ using IdealGas = Dumux::IdealGas<Scalar>;
+```
+
+
+#### Component and phase definitions
+With the following function we define what phases and components will be used by the fluid system and define the indices used to distinguish phases and components in the course of the simulation.
+
+```cpp
+public:
+ // We use convenient declarations that we derive from the property system
+ typedef Components::CO2<Scalar, CO2Table> CO2;
+ using H2O = H2OType;
+ // export the underlying brine fluid system for the liquid phase, as brine is used as a "pseudo component"
+ using Brine = Dumux::FluidSystems::ICPComplexSalinityBrine<Scalar, H2OType>;
+ using Na = Components::SodiumIon<Scalar>;
+ using Cl = Components::ChlorideIon<Scalar>;
+ using Ca = Components::CalciumIon<Scalar>;
+ using Urea = Components::Urea<Scalar>;
+ using O2 = Components::O2<Scalar>;
+ using Glucose = Components::Glucose<Scalar>;
+ using SuspendedBiomass = Components::SuspendedBiomass<Scalar>;
+
+ // We define the binary coefficents file, which accounts for the interactions of the main fluids in our setup, water/brine and CO2
+ using Brine_CO2 = BinaryCoeff::Brine_CO2<Scalar, CO2Table, true>;
+
+ // the type of parameter cache objects. this fluid system does not
+ // cache anything, so it uses Dumux::NullParameterCache
+ typedef Dumux::NullParameterCache ParameterCache;
+
+ // We define phase-related indices and properties
+ static constexpr int numPhases = 2; // liquid and gas phases
+ static constexpr int wPhaseIdx = 0; // index of the liquid phase
+ static constexpr int nPhaseIdx = 1; // index of the gas phase
+ static constexpr int phase0Idx = wPhaseIdx;
+ static constexpr int phase1Idx = nPhaseIdx;
+
+ // the phase names
+ static std::string phaseName(int phaseIdx)
+ {
+ static std::string name[] = {
+ "w",
+ "n"
+ };
+
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ return name[phaseIdx];
+ }
+
+ // We define component-related indices and properties
+ static constexpr int numComponents = 9; // H2O, TotalC, Na, Cl, Ca,...
+ static constexpr int numSecComponents = 6;
+
+ static constexpr int H2OIdx = 0;
+ static constexpr int BrineIdx = 0;
+ static constexpr int TCIdx = 1;
+ static constexpr int wCompIdx = BrineIdx;
+ static constexpr int nCompIdx = TCIdx;
+ static constexpr int comp0Idx = wCompIdx;
+ static constexpr int comp1Idx = nCompIdx;
+
+ static constexpr int NaIdx = 2;
+ static constexpr int ClIdx = 3;
+ static constexpr int CaIdx = 4;
+ static constexpr int UreaIdx = 5;
+ static constexpr int O2Idx = 6;
+ static constexpr int GlucoseIdx = 7;
+ static constexpr int SuspendedBiomassIdx = 8;
+```
+
+
+#### The Brine Adapter
+With the brine adapter, we link water and the components sodium, chloride, and calcium to form brine, to be able to use the "brine.hh" fluidsystem expecting only water and a single salt.
+Here, we define that the components water, sodium, chloride, and calcium contribute to brine.
+The real work is done by the adapter "icpcomplexsalinitybrine.hh".
+
+```cpp
+private:
+ struct BrineAdapterPolicy
+ {
+ using FluidSystem = Brine;
+
+ static constexpr int phaseIdx(int brinePhaseIdx) { return wPhaseIdx; }
+ static constexpr int compIdx(int brineCompIdx)
+ {
+ switch (brineCompIdx)
+ {
+ assert(brineCompIdx == Brine::H2OIdx
+ || brineCompIdx == Brine::NaIdx
+ || brineCompIdx == Brine::ClIdx
+ || brineCompIdx == Brine::CaIdx
+ );
+ case Brine::H2OIdx: return H2OIdx;
+ case Brine::NaIdx: return NaIdx;
+ case Brine::ClIdx: return ClIdx;
+ case Brine::CaIdx: return CaIdx;
+ default: return 0; // this will never be reached, only needed to suppress compiler warning
+ }
+ }
+ };
+
+ template<class FluidState>
+ using BrineAdapter = FluidStateAdapter<FluidState, BrineAdapterPolicy>;
+```
+
+#### Initializing the fluid system
+
+```cpp
+public:
+ static void init()
+ {
+ init(/*startTemp=*/275.15, /*endTemp=*/455.15, /*tempSteps=*/30,
+ /*startPressure=*/1e4, /*endPressure=*/99e6, /*pressureSteps=*/500);
+ }
+ static void init(Scalar startTemp, Scalar endTemp, int tempSteps,
+ Scalar startPressure, Scalar endPressure, int pressureSteps)
+ {
+ std::cout << "Initializing tables for the pure-water properties.\n";
+ H2O::init(startTemp, endTemp, tempSteps,
+ startPressure, endPressure, pressureSteps);
+ }
+```
+
+#### The Component-Phase Interactions
+In the following, we define the component-phase interactions such as // each component's fugacity coefficient in each phase
+and each component's and the phases' main components binary diffusion coefficient in the respective phase.
+
+```cpp
+ // The component fugacity coefficients
+ template <class FluidState>
+ static Scalar fugacityCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIdx && compIdx < numComponents);
+
+ if (phaseIdx == nPhaseIdx)
+ // use the fugacity coefficients of an ideal gas. the
+ // actual value of the fugacity is not relevant, as long
+ // as the relative fluid compositions are observed,
+ return 1.0;
+
+ Scalar temperature = fluidState.temperature(phaseIdx);
+ Scalar pressure = fluidState.pressure(phaseIdx);
+ if (pressure<0)
+ {
+ typedef Dune::FieldVector<Scalar, numComponents> ComponentVector;
+ ComponentVector moleFractionsw;
+ ComponentVector massFractionsw;
+
+ for (int compIdx = 0; compIdx<numComponents;++compIdx)
+ {
+ moleFractionsw[compIdx] = fluidState.moleFraction(wPhaseIdx,compIdx);
+ massFractionsw[compIdx] = fluidState.massFraction(wPhaseIdx,compIdx);
+ }
+ }
+
+ assert(temperature > 0);
+ assert(pressure > 0);
+
+ // calulate the equilibrium composition for the given
+ // temperature and pressure.
+ Scalar xgH2O, xlH2O;
+ Scalar xlCO2, xgCO2;
+ Scalar Xl_Sal = fluidState.massFraction(wPhaseIdx, NaIdx) //Salinity= XNa+XCl+XCa
+ + fluidState.massFraction(wPhaseIdx, ClIdx)
+ + fluidState.massFraction(wPhaseIdx, CaIdx);
+ Brine_CO2::calculateMoleFractions(temperature,
+ pressure,
+ Xl_Sal,
+ /*knownPhaseIdx=*/ -1,
+ xlCO2,
+ xgH2O);
+
+ xlCO2 = std::max(0.0, std::min(1.0, xlCO2));
+ xgH2O = std::max(0.0, std::min(1.0, xgH2O));
+ xlH2O = 1.0 - xlCO2;
+ xgCO2 = 1.0 - xgH2O;
+
+ // Only H2O, CO2, and O2 in the gas phase
+ if (compIdx == BrineIdx) {
+ Scalar phigH2O = 1.0;
+ return phigH2O * xgH2O / xlH2O;
+ }
+ else if (compIdx == TCIdx)
+ {
+ Scalar phigCO2 = 1.0;
+ return phigCO2 * xgCO2 / xlCO2;
+ }
+ else if (compIdx == O2Idx)
+ {
+ return Dumux::BinaryCoeff::H2O_O2::henry(temperature)/pressure;
+ }
+ // All other components are assumed not be present in the gas phase
+ else
+ {
+ return 1e-20;
+ }
+ }
+
+ template <class FluidState>
+ static Scalar diffusionCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIdx)
+ {
+ DUNE_THROW(Dune::NotImplemented, "Diffusion coefficients");
+ };
+
+ // The binary diffusion coefficients of the components and the phases main component
+ template <class FluidState>
+ static Scalar binaryDiffusionCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIIdx,
+ int compJIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIIdx && compIIdx < numComponents);
+ assert(0 <= compJIdx && compJIdx < numComponents);
+
+ Scalar temperature = fluidState.temperature(phaseIdx);
+ Scalar pressure = fluidState.pressure(phaseIdx);
+
+ if (phaseIdx == wPhaseIdx) {
+ assert(compIIdx == H2OIdx);
+ Scalar result = 0.0;
+ if(compJIdx == TCIdx)
+ result = Brine_CO2::liquidDiffCoeff(temperature, pressure);
+ else if(compJIdx == O2Idx)
+ result = Dumux::BinaryCoeff::H2O_O2::liquidDiffCoeff(temperature, pressure);
+ else //all other components
+ result = 1.587e-9; //[m²/s] //J. Phys. D: Appl. Phys. 40 (2007) 2769-2776 //old Value from Anozie 1e-9
+
+ Valgrind::CheckDefined(result);
+ return result;
+ }
+ else {
+ assert(phaseIdx == nPhaseIdx);
+ assert(compIIdx == TCIdx);
+ Scalar result = 0.0;
+ if(compJIdx == H2OIdx)
+ result = Brine_CO2::gasDiffCoeff(temperature, pressure);
+ else if(compJIdx == O2Idx)
+ result = Dumux::BinaryCoeff::H2O_O2::gasDiffCoeff(temperature, pressure);
+ else //all other components
+ result = 0.0;
+
+ Valgrind::CheckDefined(result);
+ return result;
+ }
+ };
+```
+
+#### The Fluid Properties
+In the following, all functions defining the phase properties are given:
+the density, viscosity, enthalpy, thermal conductivities, and heat capacities
+of each phase depending on temperature, pressure, and phase composition
+
+```cpp
+ // The phase density of the liquid phase is calculated accounting for the impact of solutes in the brine as well as the contribution of CO2.
+ // For the gas phase, a mixture of water and CO2 is considered, as solutes do not partition into the gas phase.
+ template <class FluidState>
+ static Scalar density(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ const Scalar T = fluidState.temperature(phaseIdx);
+
+ if (phaseIdx == wPhaseIdx)
+ {
+ const Scalar pl = fluidState.pressure(phaseIdx);
+ const Scalar xlCO2 = fluidState.moleFraction(wPhaseIdx, TCIdx);
+ const Scalar xlH2O = fluidState.moleFraction(wPhaseIdx, H2OIdx);
+ if(T < 273.15) {
+ DUNE_THROW(NumericalProblem,
+ "Liquid density for Brine and CO2 is only "
+ "defined above 273.15K (is" << T << ")");
+ }
+ if(pl >= 2.5e8) {
+ DUNE_THROW(NumericalProblem,
+ "Liquid density for Brine and CO2 is only "
+ "defined below 250MPa (is" << pl << ")");
+ }
+
+ // calling the brine adapter for brine density
+ Scalar rho_brine = Brine::molarDensity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx)
+ *(H2O::molarMass()*fluidState.moleFraction(wPhaseIdx, H2OIdx)
+ + Na::molarMass()*fluidState.moleFraction(wPhaseIdx, NaIdx)
+ + Cl::molarMass()*fluidState.moleFraction(wPhaseIdx, ClIdx)
+ + Ca::molarMass()*fluidState.moleFraction(wPhaseIdx, CaIdx)
+ );
+ // the density of pure water
+ Scalar rho_pure = H2O::liquidDensity(T, pl);
+ //we also use a private helper function to calculate the liquid density of the same amount of CO2 in pure water
+ Scalar rho_lCO2 = liquidDensityWaterCO2_(T, pl, xlH2O, xlCO2);
+ // calculating the density contribution of CO2 in pure water
+ Scalar contribCO2 = rho_lCO2 - rho_pure;
+ // assuming CO2 increases the density for brine by the same amount as for pure water
+ return rho_brine + contribCO2;
+ }
+
+ else if (phaseIdx == nPhaseIdx)
+ return H2O::gasDensity(T, fluidState.partialPressure(nPhaseIdx, H2OIdx))
+ + CO2::gasDensity(T, fluidState.partialPressure(nPhaseIdx, TCIdx));
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+
+ // The phase molar density of the liquid phase is assumed to not change significantly from the molar density of the pure brine.
+ // For the gas phase, a mixture of water and CO2 is considered, as solutes do not partition into the gas phase.
+ using Base::molarDensity;
+ template <class FluidState>
+ static Scalar molarDensity(const FluidState& fluidState, int phaseIdx)
+ {
+ if (phaseIdx == wPhaseIdx)
+ return Brine::molarDensity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+ else if (phaseIdx == nPhaseIdx)
+ return H2O::gasMolarDensity(fluidState.temperature(phaseIdx),
+ fluidState.partialPressure(phaseIdx, H2OIdx))
+ + CO2::gasMolarDensity(fluidState.temperature(phaseIdx),
+ fluidState.partialPressure(phaseIdx, TCIdx));
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+
+ // The phase viscosities are assumed to not change significantly from those of the pure brine for the liquid and pure CO2 for the gas phase
+ using Base::viscosity;
+ template <class FluidState>
+ static Scalar viscosity(const FluidState& fluidState, int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ if (phaseIdx == wPhaseIdx)
+ return Brine::viscosity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+ else if (phaseIdx == nPhaseIdx)
+ {
+ return CO2::gasViscosity(fluidState.temperature(phaseIdx), fluidState.pressure(phaseIdx));
+ }
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+
+ }
+```
+
+
+</details>
+
+
+
+## The brine adapter (`icpcomplexsalinitybrine.hh`)
+
+This file contains the brineadapter class__ which defines
+how to adapt values for communication between
+the "full" fluidsystem accounting for 4 components influencing the brine properties
+and the "brine" fluidsystem assuming water and a single salt determining the brine properties.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/fluidsystems/icpcomplexsalinitybrine.hh))</summary>
+
+
+### Include files
+<details><summary> Click to show includes</summary>
+we include all necessary components
+
+```cpp
+#include <dumux/material/fluidsystems/base.hh>
+#include <dumux/material/constants.hh>
+#include <dumux/material/components/h2o.hh>
+#include <dumux/material/components/sodiumion.hh>
+#include <dumux/material/components/chlorideion.hh>
+#include <dumux/material/components/calciumion.hh>
+#include <dumux/material/components/tabulatedcomponent.hh>
+
+#include <dumux/common/exceptions.hh>
+
+#include <dumux/io/name.hh>
+```
+
+</details>
+
+### The brine adapter class
+In ICPComplexSalinityBrine we make the transition from 3 components additional to water contributing to salinity to the single component that is assumed in the brine fluid system.
+We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+
+```cpp
+namespace Dumux::FluidSystems {
+
+template< class Scalar, class H2OType = Components::TabulatedComponent<Dumux::Components::H2O<Scalar>> >
+class ICPComplexSalinityBrine : public Base< Scalar, ICPComplexSalinityBrine<Scalar, H2OType>>
+{
+ using ThisType = ICPComplexSalinityBrine<Scalar, H2OType>;
+ using Base = Dumux::FluidSystems::Base<Scalar, ThisType>;
+
+public:
+ //! export the involved components
+ using H2O = H2OType;
+ using Na = Components::SodiumIon<Scalar>;
+ using Cl = Components::ChlorideIon<Scalar>;
+ using Ca = Components::CalciumIon<Scalar>;
+```
+
+
+#### Component and phase definitions
+With the following function we define what phases and components will be used by the fluid system and define the indices used to distinguish phases and components in the course of the simulation.
+
+```cpp
+ // We use convenient declarations that we derive from the property system.
+ static constexpr int numPhases = 1; //!< Number of phases in the fluid system
+ static constexpr int numComponents = 4; //!< Number of components in the fluid system (H2O, Na, Cl, Ca)
+
+ static constexpr int phase0Idx = 0; //!< Index of the first (and only) phase
+ static constexpr int liquidPhaseIdx = phase0Idx; //!< The one considered phase is liquid
+
+ static constexpr int H2OIdx = 0; //!< index of the water component
+ static constexpr int NaIdx = 1; //!< index of the Na component
+ static constexpr int ClIdx = 2; //!< index of the Cl component
+ static constexpr int CaIdx = 3; //!< index of the Ca component
+ static constexpr int comp0Idx = H2OIdx; //!< index of the first component
+ static constexpr int comp1Idx = NaIdx; //!< index of the second component
+ static constexpr int comp2Idx = ClIdx; //!< index of the third component
+ static constexpr int comp3Idx = CaIdx; //!< index of the fourth component
+
+ // the fluid phase index
+ static std::string phaseName(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return IOName::liquidPhase();
+ }
+
+ // the miscibility
+ static constexpr bool isMiscible()
+ {
+ return false;
+ }
+
+ // we do not have a gas phase
+ static constexpr bool isGas(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return false;
+ }
+
+ // We need a ideal mixture
+ static constexpr bool isIdealMixture(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return true;
+ }
+
+ // phase compressibility
+ static constexpr bool isCompressible(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return H2O::liquidIsCompressible();
+ }
+
+ // no gas, thus no ideal gas
+ static constexpr bool isIdealGas(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return false; /*we're a liquid!*/
+ }
+```
+
+
+#### The Component-Phase Interactions
+In the following, we define the component-phase interactions such as // each component's fugacity coefficient in brine
+and each component's binary diffusion coefficient with water in brine
+
+```cpp
+ // The component fugacity coefficients
+ template <class FluidState>
+ static Scalar fugacityCoefficient(const FluidState &fluidState,
+ int phaseIdx,
+ int compIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIdx && compIdx < numComponents);
+
+ if (phaseIdx == compIdx)
+ // We could calculate the real fugacity coefficient of
+ // the component in the fluid. Probably that's not worth
+ // the effort, since the fugacity coefficient of the other
+ // component is infinite anyway...
+ return 1.0;
+ return std::numeric_limits<Scalar>::infinity();
+ }
+
+ // The binary diffusion coefficients of the components and the phases main component
+ template <class FluidState>
+ static Scalar binaryDiffusionCoefficient(const FluidState& fluidState,
+ int phaseIdx,
+ int compIIdx,
+ int compJIdx)
+ {
+ if (phaseIdx == liquidPhaseIdx)
+ {
+ if (compIIdx > compJIdx)
+ {
+ using std::swap;
+ swap(compIIdx, compJIdx);
+ }
+ if (compJIdx == NaIdx || compJIdx == ClIdx || compJIdx == CaIdx)
+ return 1.587e-9; //[m²/s] //J. Phys. D: Appl. Phys. 40 (2007) 2769-2776
+ else
+ DUNE_THROW(Dune::NotImplemented, "Binary diffusion coefficient of components "
+ << compIIdx << " and " << compJIdx
+ << " in phase " << phaseIdx);
+ }
+
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index: " << phaseIdx);
+ }
+```
+
+
+#### The Fluid (Brine) Properties
+In the following, all functions defining the phase properties are given:
+the density, viscosity, enthalpy, thermal conductivities, and heat capacities
+of each phase depending on temperature, pressure, and phase composition
+
+```cpp
+ // The phase density
+ template <class FluidState>
+ static Scalar density(const FluidState& fluidState, int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ const Scalar temperature = fluidState.temperature(phaseIdx);
+ const Scalar pressure = fluidState.pressure(phaseIdx);
+ const Scalar xNaCl = fluidState.massFraction(phaseIdx, NaIdx)
+ + fluidState.massFraction(phaseIdx, ClIdx)
+ + fluidState.massFraction(phaseIdx, CaIdx);
+
+ using std::max;
+ const Scalar TempC = temperature - 273.15;
+ const Scalar pMPa = pressure/1.0E6;
+ const Scalar salinity = max(0.0, xNaCl);
+
+ const Scalar rhow = H2O::liquidDensity(temperature, pressure);
+ const Scalar density = rhow + 1000*salinity*(0.668 +
+ 0.44*salinity +
+ 1.0E-6*(300*pMPa -
+ 2400*pMPa*salinity +
+ TempC*(80.0 +
+ 3*TempC -
+ 3300*salinity -
+ 13*pMPa +
+ 47*pMPa*salinity)));
+ assert(density > 0.0);
+ return density;
+ }
+
+
+
+ // The phase viscosity
+ template <class FluidState>
+ static Scalar viscosity(const FluidState& fluidState, int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ const Scalar temperature = fluidState.temperature(phaseIdx);
+ const Scalar xNaCl = fluidState.massFraction(phaseIdx, NaIdx)
+ + fluidState.massFraction(phaseIdx, ClIdx)
+ + fluidState.massFraction(phaseIdx, CaIdx);
+
+ using std::pow;
+ using std::exp;
+ using std::max;
+ const Scalar T = max(temperature, 275.0);
+ const Scalar salinity = max(0.0, xNaCl);
+
+ const Scalar T_C = T - 273.15;
+ const Scalar A = ((0.42*pow((pow(salinity, 0.8)-0.17), 2)) + 0.045)*pow(T_C, 0.8);
+ const Scalar mu_brine = 0.1 + (0.333*salinity) + (1.65+(91.9*salinity*salinity*salinity))*exp(-A); // [cP]
+ assert(mu_brine > 0.0);
+ return mu_brine/1000.0; // [Pa·s]
+ }
+```
+
+
+</details>
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 3](setup.md) | [:arrow_right: Continue with part 5](solidmaterial.md) |
+|---|---|---:|
+
diff --git a/examples/biomineralization/doc/fluidmaterial_intro.md b/examples/biomineralization/doc/fluidmaterial_intro.md
new file mode 100644
index 0000000000..84c360cd39
--- /dev/null
+++ b/examples/biomineralization/doc/fluidmaterial_intro.md
@@ -0,0 +1,42 @@
+# Biomineralization - Fluids
+
+The main idea of biomineralization revolves around
+biologically-induced mineral precipitation.
+I our example, it is about precipitation of calcite
+due to urea hydrolysis.
+The resulting overall reaction equation is:
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} + \mathrm{Ca^{2+}} \xrightarrow{urease}
+2\mathrm{NH_{4}^{+}} + \mathrm{CaCO_{3}} \downarrow.
+```
+
+To describe the processes, the minimum set of components is:
+water (w), dissolved inorganic carbon (C<sub>tot</sub>),
+sodium (Na), chloride (Cl), calcium (Ca), urea (u), glucose as a substrate (s), oxygen (O<sub>2</sub>), and suspended biomass (b),
+as well as the solid components biofilm and calcite.
+Thus, there are many components involved and keeping track of the components and their interactions,
+necessitates a sophisticated handling.
+This is why the material folder in this example is both separated from the regular material folder in dumux/dumux/material
+and also documented separately.
+For further specialization, the overview over the material subfolder is split into solid and fluid, this description considering the fluids.
+
+## Fluids in the folder `material`
+
+As this example is about biomineralization involving many components with complex inteactions, some specific fluid material files are necessary.
+A CO_2-Table file provides tabulated CO_2 properties according to @Span1996 in `material/co2tableslaboratory.hh`
+In the component subfolder, `material/components/suspendedbiomass.hh` defines the component suspended biomass, which is the mobile form of biomass being transported suspended in the aqueous fluid phase.
+In the fluidsystem subfolder, the biomineralization fluidsystem `material/fluidsystems/biominsimplechemistry.hh` as well as
+the complex salinity brine adapter `material/fluidsystems/icpcomplexsalinitybrine.hh` can be found.
+The biomineralization fluidsystem `material/fluidsystems/biominsimplechemistry.hh`
+contains the fluid related properties and the interactions of the components in the fluids.
+The complex salinity brine adapter `material/fluidsystems/icpcomplexsalinitybrine.hh`
+adapts the brine fluidsystem (dumux/dumux/material/fluidsystems/brine.hh) expecting a single non-aqueous component defining salinity to be reused for biomineralization with three ions (calcium, sodium, chloride) being assumed to contribute to salinity.
+
+
+The subsequent documentation is structured as follows:
+
+[[_TOC_]]
+
+
+[@Span1996]: https://aip.scitation.org/doi/abs/10.1063/1.555991 "A new equation of state for carbon dioxide covering the fluid region from the triple-point temperature to 1100 K at pressures up to 800 MPa"
diff --git a/examples/biomineralization/doc/mainfile.md b/examples/biomineralization/doc/mainfile.md
new file mode 100644
index 0000000000..3fbcc53d68
--- /dev/null
+++ b/examples/biomineralization/doc/mainfile.md
@@ -0,0 +1,330 @@
+<!-- Important: This file has been automatically generated by generate_example_docs.py. Do not edit this file directly! -->
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 1](modelconcept.md) | [:arrow_right: Continue with part 3](setup.md) |
+|---|---|---:|
+
+# Main file
+
+The main file features a time loo with check points to assure the correct timing of the injections matching an experimental setup (see [@Hommel2016], Section 4.2 under the name _column experiment D1_)
+The timing of the injections is stored in an additional input file `injections_checkpoints.dat`,
+which is read by `main.cc` to set the check points in the time loop.
+The number of check points reached is counted and passed on to `problem.hh`, so that `problem.hh` can determine the appropriate injection type.
+
+Additionally, there is an output of the porosity-dependent permeability.
+
+The subsequent file documentation is structured as follows:
+
+[[_TOC_]]
+
+[@Hommel2016]: https://elib.uni-stuttgart.de/handle/11682/8787 "Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation"
+
+
+## The main file
+This files contains the main program flow for the biomineralization example. Here we can see the programme sequence and how the system is solved using newton's method.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../main.cc))</summary>
+
+
+### Included header files
+<details>
+These are DUNE helper classes related to parallel computations
+
+```cpp
+#include <dune/common/parallel/mpihelper.hh>
+```
+
+The following headers include functionality related to property definition or retrieval, as well as
+the retrieval of input parameters specified in the input file or via the command line.
+
+```cpp
+#include <dumux/common/properties.hh>
+#include <dumux/common/parameters.hh>
+```
+
+The follwoing files contain the nonlinear Newtown method, the linear solver and the assembler
+
+```cpp
+#include <dumux/nonlinear/newtonsolver.hh>
+#include <dumux/linear/amgbackend.hh>
+#include <dumux/assembly/fvassembler.hh>
+#include <dumux/assembly/diffmethod.hh>
+```
+
+The following class provides a convenient way of writing of dumux simulation results to VTK format.
+
+```cpp
+#include <dumux/io/vtkoutputmodule.hh>
+```
+
+The gridmanager constructs a grid from the information in the input or grid file. There is a specification for the different supported grid managers.
+Many different Dune grid implementations are supported, of which a list can be found
+in `gridmanager.hh`.
+
+```cpp
+#include <dumux/io/grid/gridmanager_yasp.hh>
+```
+
+We include the problem file which defines initial and boundary conditions to describe our example problem
+remove #include "problem.hh"
+
+```cpp
+#include "properties.hh"
+```
+
+</details>
+
+### The main function
+We will now discuss the main program flow implemented within the `main` function.
+At the beginning of each program using Dune, an instance `Dune::MPIHelper` has to
+be created. Moreover, we parse the run-time arguments from the command line and the
+input file:
+
+```cpp
+int main(int argc, char** argv) try
+{
+ using namespace Dumux;
+
+ // initialize MPI, finalize is done automatically on exit
+ const auto& mpiHelper = Dune::MPIHelper::instance(argc, argv);
+
+ // parse command line arguments and input file
+ Parameters::init(argc, argv);
+```
+
+For convenience we define the type tag for this problem.
+The type tags contain all the properties that are needed to run the simulations.
+
+```cpp
+ using TypeTag = Properties::TTag::MICPColumnSimpleChemistry;
+```
+
+### Step 1: Create the grid
+The `GridManager` class creates the grid from information given in the input file.
+This can either be a grid file, or in the case of structured grids, one can specify the coordinates
+of the corners of the grid and the number of cells to be used to discretize each spatial direction. The latter is the case for this example.
+
+```cpp
+ GridManager<GetPropType<TypeTag, Properties::Grid>> gridManager;
+ gridManager.init();
+
+ // we compute on the leaf grid view
+ const auto& leafGridView = gridManager.grid().leafGridView();
+```
+
+### Step 2: Setting up the problem
+We create and initialize the finite volume grid geometry, the problem, the linear system, including the jacobian matrix, the residual and the solution vector and the gridvariables.
+We need the finite volume geometry to build up the subcontrolvolumes (scv) and subcontrolvolume faces (scvf) for each element of the grid partition.
+
+```cpp
+ using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>;
+ auto gridGeometry = std::make_shared<GridGeometry>(leafGridView);
+ gridGeometry->update();
+```
+
+We now instantiate the problem, in which we define the boundary and initial conditions.
+
+```cpp
+ using Problem = GetPropType<TypeTag, Properties::Problem>;
+ auto problem = std::make_shared<Problem>(gridGeometry);
+```
+
+get some time loop parameters
+
+```cpp
+ using Scalar = GetPropType<TypeTag, Properties::Scalar>;
+ const auto tEnd = getParam<Scalar>("TimeLoop.TEnd");
+ const auto maxDt = getParam<Scalar>("TimeLoop.MaxTimeStepSize");
+ const auto dt = getParam<Scalar>("TimeLoop.DtInitial");
+```
+
+We initialize the solution vector
+
+```cpp
+ using SolutionVector = GetPropType<TypeTag, Properties::SolutionVector>;
+ SolutionVector x;
+ problem->applyInitialSolution(x);
+ auto xOld = x;
+```
+
+on the basis of this solution, we initialize the grid variables
+
+```cpp
+ using GridVariables = GetPropType<TypeTag, Properties::GridVariables>;
+ auto gridVariables = std::make_shared<GridVariables>(problem, gridGeometry);
+ gridVariables->init(x);
+```
+
+We intialize the vtk output module. Each model has a predefined model specific output with relevant parameters for that model.
+
+```cpp
+ VtkOutputModule<GridVariables, SolutionVector> vtkWriter(*gridVariables, x, problem->name());
+ using VelocityOutput = GetPropType<TypeTag, Properties::VelocityOutput>;
+ vtkWriter.addVelocityOutput(std::make_shared<VelocityOutput>(*gridVariables));
+ GetPropType<TypeTag, Properties::IOFields>::initOutputModule(vtkWriter); //!< Add model specific output fields
+ //we add permeability as a specific output
+ vtkWriter.addField(problem->getPermeability(), "Permeability");
+ //We update the output fields before write
+ problem->updateVtkOutput(x);
+ vtkWriter.write(0.0);
+```
+
+We instantiate the time loop and define an episode index to keep track of the the actual episode number
+
+```cpp
+ int episodeIdx = 0;
+ //We set the initial episodeIdx in the problem to zero
+ problem->setEpisodeIdx(episodeIdx);
+ //We set the time loop with episodes (check points)
+ auto timeLoop = std::make_shared<CheckPointTimeLoop<Scalar>>(0.0, dt, tEnd);
+ timeLoop->setMaxTimeStepSize(maxDt);
+```
+
+### Step 3 Setting episodes specified from file
+In this example we want to specify the injected reactant solutions at certain times.
+This is specified in an external file injections_checkpoints.dat.
+Within the following code block, the parameter file read and the time for the injection are extracted.
+Based on that, the checkpoints for the simulation are set.
+
+```cpp
+ //We use a time loop with episodes if an injection parameter file is specified in the input
+ if (hasParam("Injection.NumInjections"))
+ {
+ //We first read the times of the checkpoints from the injection file
+ const auto injectionCheckPoints = readFileToContainer<std::vector<double>>("injection_checkpoints.dat");
+
+ // We set the time loop with episodes of various lengths as specified in the injection file
+ // set the episode ends /check points:
+ timeLoop->setCheckPoint(injectionCheckPoints);
+
+ // We also set the initial episodeIdx in the problem to zero, as in the problem the boundary conditions depend on the episode.
+ problem->setEpisodeIdx(episodeIdx);
+ }
+
+ // If nothing specified, we do not need to use episodes
+ else
+ {
+ // In this case, we set the time loop with one big episodes
+ timeLoop->setCheckPoint(tEnd);
+ }
+```
+
+### Step 4 solving the instationary problem
+We create and initialize the assembler with a time loop for the transient problem.
+Within the time loop, we will use this assembler in each time step to assemble the linear system.
+Additionally the linear and non-linear solvers are set
+
+```cpp
+ using Assembler = FVAssembler<TypeTag, DiffMethod::numeric>;
+ auto assembler = std::make_shared<Assembler>(problem, gridGeometry, gridVariables, timeLoop, xOld);
+
+ //We set the linear solver
+ using LinearSolver = Dumux::ILU0BiCGSTABBackend;
+ auto linearSolver = std::make_shared<LinearSolver>();
+
+ //We set the non-linear solver
+ using NewtonSolver = NewtonSolver<Assembler, LinearSolver>;
+ NewtonSolver nonLinearSolver(assembler, linearSolver);
+```
+
+#### The time loop
+We start the time loop and solve a new time step as long as `tEnd` is not reached. In every time step,
+the problem is assembled and solved, the solution is updated, and when a checkpoint is reached the solution
+is written to a new vtk file. In addition, statistics related to CPU time, the current simulation time
+and the time step sizes used is printed to the terminal.
+
+```cpp
+ timeLoop->start(); do
+ {
+ // We set the time and time step size to be used in the problem
+ problem->setTime( timeLoop->time() + timeLoop->timeStepSize() );
+ problem->setTimeStepSize( timeLoop->timeStepSize() );
+
+ // Solve the linear system with time step control
+ nonLinearSolver.solve(x, *timeLoop);
+
+ // Update the old solution with the one computed in this time step and move to the next one
+ xOld = x;
+ gridVariables->advanceTimeStep();
+ timeLoop->advanceTimeStep();
+
+ // We update the output fields before write
+ problem->updateVtkOutput(x);
+
+ // We write vtk output on checkpoints or every 20th timestep
+ if (timeLoop->timeStepIndex() % 20 == 0 || timeLoop->isCheckPoint())
+ {
+ // update the output fields before write
+ problem->updateVtkOutput(x);
+
+ // write vtk output
+ vtkWriter.write(timeLoop->time());
+ }
+ // We report statistics of this time step
+ timeLoop->reportTimeStep();
+
+ //If episodes/check points are used, we count episodes and update the episode indices in the main file and the problem.
+ if (hasParam("Injection.NumInjections") || hasParam("TimeLoop.EpisodeLength"))
+ {
+ if (timeLoop->isCheckPoint())
+ {
+ episodeIdx++;
+ problem->setEpisodeIdx(episodeIdx);
+ }
+ }
+
+ // set the new time step size that is suggested by the newton solver
+ timeLoop->setTimeStepSize(nonLinearSolver.suggestTimeStepSize(timeLoop->timeStepSize()));
+
+ } while (!timeLoop->finished());
+ timeLoop->finalize(leafGridView.comm());
+```
+
+
+```cpp
+
+ if (mpiHelper.rank() == 0)
+ Parameters::print();
+
+ return 0;
+}
+```
+
+### Exception handling
+In this part of the main file we catch and print possible exceptions that could
+occur during the simulation.
+<details><summary> Click to show error handler</summary>
+
+```cpp
+// errors related to run-time parameters
+catch (const Dumux::ParameterException &e)
+{
+ std::cerr << std::endl << e << " ---> Abort!" << std::endl;
+ return 1;
+}
+catch (const Dune::DGFException & e)
+{
+ std::cerr << "DGF exception thrown (" << e <<
+ "). Most likely, the DGF file name is wrong "
+ "or the DGF file is corrupted, "
+ "e.g. missing hash at end of file or wrong number (dimensions) of entries."
+ << " ---> Abort!" << std::endl;
+ return 2;
+}
+catch (const Dune::Exception &e)
+{
+ std::cerr << "Dune reported error: " << e << " ---> Abort!" << std::endl;
+ return 3;
+}
+```
+
+</details>
+
+</details>
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 1](modelconcept.md) | [:arrow_right: Continue with part 3](setup.md) |
+|---|---|---:|
+
diff --git a/examples/biomineralization/doc/mainfile_intro.md b/examples/biomineralization/doc/mainfile_intro.md
new file mode 100644
index 0000000000..c1435eb899
--- /dev/null
+++ b/examples/biomineralization/doc/mainfile_intro.md
@@ -0,0 +1,14 @@
+# Main file
+
+The main file features a time loo with check points to assure the correct timing of the injections matching an experimental setup (see [@Hommel2016], Section 4.2 under the name _column experiment D1_)
+The timing of the injections is stored in an additional input file `injections_checkpoints.dat`,
+which is read by `main.cc` to set the check points in the time loop.
+The number of check points reached is counted and passed on to `problem.hh`, so that `problem.hh` can determine the appropriate injection type.
+
+Additionally, there is an output of the porosity-dependent permeability.
+
+The subsequent file documentation is structured as follows:
+
+[[_TOC_]]
+
+[@Hommel2016]: https://elib.uni-stuttgart.de/handle/11682/8787 "Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation"
diff --git a/examples/biomineralization/doc/material.md b/examples/biomineralization/doc/material.md
new file mode 100644
index 0000000000..cf9a24e811
--- /dev/null
+++ b/examples/biomineralization/doc/material.md
@@ -0,0 +1,990 @@
+<!-- Important: This file has been automatically generated by generate_example_docs.py. Do not edit this file directly! -->
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 2](setup.md) |
+|---|---:|
+
+# Biomineralization
+
+The main idea of biomineralization revolves around
+biologically-induced mineral precipitation.
+I our example, it is about precipitation of calcite
+due to urea hydrolysis.
+The resulting overall reaction equation is:
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} + \mathrm{Ca^{2+}} \xrightarrow{urease}
+2\mathrm{NH_{4}^{+}} + \mathrm{CaCO_{3}} \downarrow.
+```
+
+To describe the processes, the minimum set of components is:
+water (w), dissolved inorganic carbon (C<sub>tot</sub>),
+sodium (Na), chloride (Cl), calcium (Ca), urea (u), glucose as a substrate (s), oxygen (O<sub>2</sub>), and suspended biomass (b),
+as well as the solid components biofilm and calcite.
+Thus, there are many components involved and keeping track of the components and their interactions,
+necessitates a sophisticated handling.
+This is why the material folder in this example is both separated from the regular material folder in dumux/dumux/material
+and also documented separately.
+
+## The folder `material` (fluid- and solidsystems)
+
+This material folder of the biomineralization example contains:
+A CO<sub>2</sub>-Tables file providing tabulated CO<sub>2</sub> properties according to [@Span1996] `material/co2tableslaboratory.hh`;
+a component subfolder, containing the special components biofilm `material/components/biofilm.hh` and suspended biomass `material/components/suspendedbiomass.hh`;
+a fluidsystems subfolder, containing the (simplified) biomineralization fluidsystem `material/fluidsystems/biominsimplechemistry.hh` and a brine adapter to be able to use the generic brine fluidsystem with several salts while it assumes a single salt `material/fluidsystems/icpcomplexsalinitybrine.hh`;
+a solidsystem subfolder, containing the biomineralization solid system `material/solidsystems/biominsolids.hh`.
+
+The subsequent documentation is structured as follows:
+
+[[_TOC_]]
+
+
+[@Span1996]: https://aip.scitation.org/doi/abs/10.1063/1.555991 "A new equation of state for carbon dioxide covering the fluid region from the triple-point temperature to 1100 K at pressures up to 800 MPa"
+
+
+## The CO2 tables (`co2tableslaboratory.hh`)
+
+This file contains the __ co2table class__ which forwards to tabulated properties of CO2 according to Span and Wagner 1996.
+The real work (creating the tables) is done by some external program by Span and Wagner 1996 which provides the ready-to-use tables.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/co2tableslaboratory.hh))</summary>
+
+
+
+```cpp
+
+#include <assert.h>
+namespace Dumux::ICP {
+#include "co2valueslaboratory.inc"
+}// end namespace Dumux::ICP
+```
+
+
+</details>
+
+
+
+## The biofilm component (`biofilm.hh`)
+
+This file contains the __solid component class__ which defines the name, molar mass and density of biofilm
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/components/biofilm.hh))</summary>
+
+
+### Include files
+
+```cpp
+// including the base and the generic solid component
+#include <dumux/material/components/base.hh>
+#include <dumux/material/components/solid.hh>
+```
+
+### The biofilm component
+
+```cpp
+namespace Dumux::Components {
+
+// In Biofilm, we define the properties of the solid component biofilm
+template <class Scalar>
+class Biofilm
+: public Components::Base<Scalar, Biofilm<Scalar> >
+, public Components::Solid<Scalar, Biofilm<Scalar> >
+{
+public:
+ // the name
+ static std::string name()
+ { return "Biofilm"; }
+```
+
+### The biofilm component's properties
+
+```cpp
+ // The molar mass, which is not really defined for biofilm. Thus, we read it from params.input or use a default of 1.
+ // Based on a cell mass of 2.5e-16, the molar mass of cells would be 1.5e8 kg/mol, but biofilms are more than just cells and such high molar masses would lead to numerical problems.
+ static Scalar molarMass()
+ {
+ Scalar molarMass = getParam<Scalar>("BioCoefficients.BiofilmMolarMass", 1);
+ return molarMass;
+ }
+
+ // The density, or rather the dry density (dry biomass/wet volume), most of biofilm is water.
+ // It is typically highly variable for different biofilms, thus we read it from params.input or use the default value of 10 kg/m^3
+ static Scalar solidDensity(Scalar temperature)
+ {
+ Scalar rho = getParam<Scalar>("BioCoefficients.BiofilmDensity", 10);
+ return rho;
+ }
+};
+
+} // end namespace Dumux::Components
+```
+
+
+</details>
+
+
+
+## The suspended biomass component (`suspendedbiomass.hh`)
+
+This file contains the __ component class__ which defines the name and molar mass of suspended biomass
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/components/suspendedbiomass.hh))</summary>
+
+
+### Include files
+
+```cpp
+// including the base component
+#include <dumux/material/components/base.hh>
+```
+
+### The suspended biomass component
+
+```cpp
+namespace Dumux::Components {
+
+// In SuspendedBiomass, we define the properties of the component suspended biomass
+template <class Scalar>
+class SuspendedBiomass
+: public Components::Base<Scalar, SuspendedBiomass<Scalar> >
+{
+public:
+ // the name
+ static std::string name()
+ { return "Suspended_Biomass"; }
+```
+
+### The suspended biomass component's properties
+
+```cpp
+ // The molar mass, which is not really defined for suspended biomass. Thus, we read it from params.input or use a default of 1.
+ // Based on a cell mass of 2.5e-16, the molar mass of cells would be 1.5e8 kg/mol, but such high molar masses would lead to numerical problems.
+ static Scalar molarMass()
+ {
+ Scalar molarMass = getParam<Scalar>("BioCoefficients.SuspendedBiomassMolarMass", 1);
+ return molarMass;
+ }
+};
+
+
+} // end namespace Dumux::Components
+```
+
+
+</details>
+
+
+
+## The fluid system (`biominsimplechemistry.hh`)
+
+This file contains the __fluidsystem class__ which defines all functions needed to describe the fluids and their properties,
+which are needed to model biomineralization.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/fluidsystems/biominsimplechemistry.hh))</summary>
+
+
+### Include files
+<details><summary> Click to show </summary>
+
+```cpp
+#include <dumux/material/idealgas.hh>
+
+// we include the base fluid system
+#include <dumux/material/fluidsystems/base.hh>
+// we include the brine adapter adapting component indices to use the brine fluidsystem
+#include "icpcomplexsalinitybrine.hh"
+
+// we include all necessary fluid components
+#include <dumux/material/fluidstates/adapter.hh>
+#include <dumux/material/components/co2.hh>
+#include <dumux/material/components/h2o.hh>
+#include <dumux/material/components/tabulatedcomponent.hh>
+#include <dumux/material/components/co2tablereader.hh>
+#include <dumux/material/components/sodiumion.hh>
+#include <dumux/material/components/chlorideion.hh>
+#include <dumux/material/components/calciumion.hh>
+#include <dumux/material/components/urea.hh>
+#include <dumux/material/components/o2.hh>
+#include <dumux/material/components/glucose.hh>
+#include <examples/biomineralization/material/components/suspendedbiomass.hh>
+
+// we include brine-co2 and h2o-co2 binary coefficients
+#include <dumux/material/binarycoefficients/brine_co2.hh>
+#include <dumux/material/binarycoefficients/h2o_o2.hh>
+```
+
+
+```cpp
+
+#include <dumux/material/fluidsystems/nullparametercache.hh>
+#include <dumux/common/valgrind.hh>
+#include <dumux/common/exceptions.hh>
+
+#include <assert.h>
+```
+
+</details>
+
+### The fluidsystem class
+In the BioMinSimpleChemistryFluid fluid system, we define all functions needed to describe the fluids and their properties accounted for in our simulation.
+The simplified biogeochemistry biomineralization fluid system requires the CO2 tables and the H2OType as template parameters.
+We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+
+```cpp
+namespace Dumux::FluidSystems {
+
+template <class Scalar,
+ class CO2Table,
+ class H2OType = Components::TabulatedComponent<Components::H2O<Scalar>> >
+class BioMinSimpleChemistryFluid
+: public Base<Scalar, BioMinSimpleChemistryFluid<Scalar, CO2Table, H2OType> >
+{
+ using ThisType = BioMinSimpleChemistryFluid<Scalar, CO2Table, H2OType>;
+ using Base = Dumux::FluidSystems::Base<Scalar, ThisType>;
+ using IdealGas = Dumux::IdealGas<Scalar>;
+```
+
+
+#### Component and phase definitions
+With the following function we define what phases and components will be used by the fluid system and define the indices used to distinguish phases and components in the course of the simulation.
+
+```cpp
+public:
+ // We use convenient declarations that we derive from the property system
+ typedef Components::CO2<Scalar, CO2Table> CO2;
+ using H2O = H2OType;
+ // export the underlying brine fluid system for the liquid phase, as brine is used as a "pseudo component"
+ using Brine = Dumux::FluidSystems::ICPComplexSalinityBrine<Scalar, H2OType>;
+ using Na = Components::SodiumIon<Scalar>;
+ using Cl = Components::ChlorideIon<Scalar>;
+ using Ca = Components::CalciumIon<Scalar>;
+ using Urea = Components::Urea<Scalar>;
+ using O2 = Components::O2<Scalar>;
+ using Glucose = Components::Glucose<Scalar>;
+ using SuspendedBiomass = Components::SuspendedBiomass<Scalar>;
+
+ // We define the binary coefficents file, which accounts for the interactions of the main fluids in our setup, water/brine and CO2
+ using Brine_CO2 = BinaryCoeff::Brine_CO2<Scalar, CO2Table, true>;
+
+ // the type of parameter cache objects. this fluid system does not
+ // cache anything, so it uses Dumux::NullParameterCache
+ typedef Dumux::NullParameterCache ParameterCache;
+
+ // We define phase-related indices and properties
+ static constexpr int numPhases = 2; // liquid and gas phases
+ static constexpr int wPhaseIdx = 0; // index of the liquid phase
+ static constexpr int nPhaseIdx = 1; // index of the gas phase
+ static constexpr int phase0Idx = wPhaseIdx;
+ static constexpr int phase1Idx = nPhaseIdx;
+
+ // the phase names
+ static std::string phaseName(int phaseIdx)
+ {
+ static std::string name[] = {
+ "w",
+ "n"
+ };
+
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ return name[phaseIdx];
+ }
+
+ // We define component-related indices and properties
+ static constexpr int numComponents = 9; // H2O, TotalC, Na, Cl, Ca,...
+ static constexpr int numSecComponents = 6;
+
+ static constexpr int H2OIdx = 0;
+ static constexpr int BrineIdx = 0;
+ static constexpr int TCIdx = 1;
+ static constexpr int wCompIdx = BrineIdx;
+ static constexpr int nCompIdx = TCIdx;
+ static constexpr int comp0Idx = wCompIdx;
+ static constexpr int comp1Idx = nCompIdx;
+
+ static constexpr int NaIdx = 2;
+ static constexpr int ClIdx = 3;
+ static constexpr int CaIdx = 4;
+ static constexpr int UreaIdx = 5;
+ static constexpr int O2Idx = 6;
+ static constexpr int GlucoseIdx = 7;
+ static constexpr int SuspendedBiomassIdx = 8;
+```
+
+
+#### The Brine Adapter
+With the brine adapter, we link water and the components sodium, chloride, and calcium to form brine, to be able to use the "brine.hh" fluidsystem expecting only water and a single salt.
+Here, we define that the components water, sodium, chloride, and calcium contribute to brine.
+The real work is done by the adapter "icpcomplexsalinitybrine.hh".
+
+```cpp
+private:
+ struct BrineAdapterPolicy
+ {
+ using FluidSystem = Brine;
+
+ static constexpr int phaseIdx(int brinePhaseIdx) { return wPhaseIdx; }
+ static constexpr int compIdx(int brineCompIdx)
+ {
+ switch (brineCompIdx)
+ {
+ assert(brineCompIdx == Brine::H2OIdx
+ || brineCompIdx == Brine::NaIdx
+ || brineCompIdx == Brine::ClIdx
+ || brineCompIdx == Brine::CaIdx
+ );
+ case Brine::H2OIdx: return H2OIdx;
+ case Brine::NaIdx: return NaIdx;
+ case Brine::ClIdx: return ClIdx;
+ case Brine::CaIdx: return CaIdx;
+ default: return 0; // this will never be reached, only needed to suppress compiler warning
+ }
+ }
+ };
+
+ template<class FluidState>
+ using BrineAdapter = FluidStateAdapter<FluidState, BrineAdapterPolicy>;
+```
+
+#### Initializing the fluid system
+
+```cpp
+public:
+ static void init()
+ {
+ init(/*startTemp=*/275.15, /*endTemp=*/455.15, /*tempSteps=*/30,
+ /*startPressure=*/1e4, /*endPressure=*/99e6, /*pressureSteps=*/500);
+ }
+ static void init(Scalar startTemp, Scalar endTemp, int tempSteps,
+ Scalar startPressure, Scalar endPressure, int pressureSteps)
+ {
+ std::cout << "Initializing tables for the pure-water properties.\n";
+ H2O::init(startTemp, endTemp, tempSteps,
+ startPressure, endPressure, pressureSteps);
+ }
+```
+
+#### The Component-Phase Interactions
+In the following, we define the component-phase interactions such as // each component's fugacity coefficient in each phase
+and each component's and the phases' main components binary diffusion coefficient in the respective phase.
+
+```cpp
+ // The component fugacity coefficients
+ template <class FluidState>
+ static Scalar fugacityCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIdx && compIdx < numComponents);
+
+ if (phaseIdx == nPhaseIdx)
+ // use the fugacity coefficients of an ideal gas. the
+ // actual value of the fugacity is not relevant, as long
+ // as the relative fluid compositions are observed,
+ return 1.0;
+
+ Scalar temperature = fluidState.temperature(phaseIdx);
+ Scalar pressure = fluidState.pressure(phaseIdx);
+ if (pressure<0)
+ {
+ typedef Dune::FieldVector<Scalar, numComponents> ComponentVector;
+ ComponentVector moleFractionsw;
+ ComponentVector massFractionsw;
+
+ for (int compIdx = 0; compIdx<numComponents;++compIdx)
+ {
+ moleFractionsw[compIdx] = fluidState.moleFraction(wPhaseIdx,compIdx);
+ massFractionsw[compIdx] = fluidState.massFraction(wPhaseIdx,compIdx);
+ }
+ }
+
+ assert(temperature > 0);
+ assert(pressure > 0);
+
+ // calulate the equilibrium composition for the given
+ // temperature and pressure. TODO: calculateMoleFractions()
+ // could use some cleanup.
+ Scalar xgH2O, xlH2O;
+ Scalar xlCO2, xgCO2;
+ Scalar Xl_Sal = fluidState.massFraction(wPhaseIdx, NaIdx) //Salinity= XNa+XCl+XCa
+ + fluidState.massFraction(wPhaseIdx, ClIdx)
+ + fluidState.massFraction(wPhaseIdx, CaIdx);
+ Brine_CO2::calculateMoleFractions(temperature,
+ pressure,
+ Xl_Sal,
+ /*knownPhaseIdx=*/ -1,
+ xlCO2,
+ xgH2O);
+
+ xlCO2 = std::max(0.0, std::min(1.0, xlCO2));
+ xgH2O = std::max(0.0, std::min(1.0, xgH2O));
+ xlH2O = 1.0 - xlCO2;
+ xgCO2 = 1.0 - xgH2O;
+
+ // Only H2O, CO2, and O2 in the gas phase
+ if (compIdx == BrineIdx) {
+ Scalar phigH2O = 1.0;
+ return phigH2O * xgH2O / xlH2O;
+ }
+ else if (compIdx == TCIdx)
+ {
+ Scalar phigCO2 = 1.0;
+ return phigCO2 * xgCO2 / xlCO2;
+ }
+ else if (compIdx == O2Idx)
+ {
+ return Dumux::BinaryCoeff::H2O_O2::henry(temperature)/pressure;
+ }
+ // All other components are assumed not be present in the gas phase
+ else
+ {
+ return 1e-20;
+ }
+ }
+
+ template <class FluidState>
+ static Scalar diffusionCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIdx)
+ {
+ DUNE_THROW(Dune::NotImplemented, "Diffusion coefficients");
+ };
+
+ // The binary diffusion coefficients of the components and the phases main component
+ template <class FluidState>
+ static Scalar binaryDiffusionCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIIdx,
+ int compJIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIIdx && compIIdx < numComponents);
+ assert(0 <= compJIdx && compJIdx < numComponents);
+
+ Scalar temperature = fluidState.temperature(phaseIdx);
+ Scalar pressure = fluidState.pressure(phaseIdx);
+
+ if (phaseIdx == wPhaseIdx) {
+ assert(compIIdx == H2OIdx);
+ Scalar result = 0.0;
+ if(compJIdx == TCIdx)
+ result = Brine_CO2::liquidDiffCoeff(temperature, pressure);
+ else if(compJIdx == O2Idx) //TODO Test O2 diffusion coeff from binarycoeff.
+ result = Dumux::BinaryCoeff::H2O_O2::liquidDiffCoeff(temperature, pressure);
+ else //all other components
+ result = 1.587e-9; //[m²/s] //J. Phys. D: Appl. Phys. 40 (2007) 2769-2776 //old Value from Anozie 1e-9
+
+ Valgrind::CheckDefined(result);
+ return result;
+ }
+ else {
+ assert(phaseIdx == nPhaseIdx);
+ assert(compIIdx == TCIdx);
+ Scalar result = 0.0;
+ if(compJIdx == H2OIdx) //TODO Test H2O diffusion coeff from binarycoeff.
+ result = Brine_CO2::gasDiffCoeff(temperature, pressure);
+// result = 1e-5;
+ else if(compJIdx == O2Idx) //TODO Test O2 diffusion coeff from binarycoeff.
+ result = Dumux::BinaryCoeff::H2O_O2::gasDiffCoeff(temperature, pressure);
+ else //all other components
+ result = 0.0;
+
+ Valgrind::CheckDefined(result);
+ return result;
+ }
+ };
+```
+
+#### The Fluid Properties
+In the following, all functions defining the phase properties are given:
+the density, viscosity, enthalpy, thermal conductivities, and heat capacities
+of each phase depending on temperature, pressure, and phase composition
+
+```cpp
+ // The phase density of the liquid phase is calculated accounting for the impact of solutes in the brine as well as the contribution of CO2.
+ // For the gas phase, a mixture of water and CO2 is considered, as solutes do not partition into the gas phase.
+ template <class FluidState>
+ static Scalar density(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ const Scalar T = fluidState.temperature(phaseIdx);
+
+ if (phaseIdx == wPhaseIdx)
+ {
+ const Scalar pl = fluidState.pressure(phaseIdx);
+ const Scalar xlCO2 = fluidState.moleFraction(wPhaseIdx, TCIdx);
+ const Scalar xlH2O = fluidState.moleFraction(wPhaseIdx, H2OIdx);
+ if(T < 273.15) {
+ DUNE_THROW(NumericalProblem,
+ "Liquid density for Brine and CO2 is only "
+ "defined above 273.15K (is" << T << ")");
+ }
+ if(pl >= 2.5e8) {
+ DUNE_THROW(NumericalProblem,
+ "Liquid density for Brine and CO2 is only "
+ "defined below 250MPa (is" << pl << ")");
+ }
+
+ // calling the brine adapter for brine density
+ Scalar rho_brine = Brine::molarDensity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx)
+ *(H2O::molarMass()*fluidState.moleFraction(wPhaseIdx, H2OIdx)
+ + Na::molarMass()*fluidState.moleFraction(wPhaseIdx, NaIdx)
+ + Cl::molarMass()*fluidState.moleFraction(wPhaseIdx, ClIdx)
+ + Ca::molarMass()*fluidState.moleFraction(wPhaseIdx, CaIdx)
+ );
+ // the density of pure water
+ Scalar rho_pure = H2O::liquidDensity(T, pl);
+ //we also use a private helper function to calculate the liquid density of the same amount of CO2 in pure water
+ Scalar rho_lCO2 = liquidDensityWaterCO2_(T, pl, xlH2O, xlCO2);
+ // calculating the density contribution of CO2 in pure water
+ Scalar contribCO2 = rho_lCO2 - rho_pure;
+ // assuming CO2 increases the density for brine by the same amount as for pure water
+ return rho_brine + contribCO2;
+ }
+
+ else if (phaseIdx == nPhaseIdx)
+ return H2O::gasDensity(T, fluidState.partialPressure(nPhaseIdx, H2OIdx))
+ + CO2::gasDensity(T, fluidState.partialPressure(nPhaseIdx, TCIdx));
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+
+ // The phase molar density of the liquid phase is assumed to not change significantly from the molar density of the pure brine.
+ // For the gas phase, a mixture of water and CO2 is considered, as solutes do not partition into the gas phase.
+ using Base::molarDensity;
+ template <class FluidState>
+ static Scalar molarDensity(const FluidState& fluidState, int phaseIdx)
+ {
+ if (phaseIdx == wPhaseIdx)
+ return Brine::molarDensity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+ else if (phaseIdx == nPhaseIdx)
+ return H2O::gasMolarDensity(fluidState.temperature(phaseIdx),
+ fluidState.partialPressure(phaseIdx, H2OIdx))
+ + CO2::gasMolarDensity(fluidState.temperature(phaseIdx),
+ fluidState.partialPressure(phaseIdx, TCIdx));
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+
+ // The phase viscosities are assumed to not change significantly from those of the pure brine for the liquid and pure CO2 for the gas phase
+ using Base::viscosity;
+ template <class FluidState>
+ static Scalar viscosity(const FluidState& fluidState, int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ if (phaseIdx == wPhaseIdx)
+ return Brine::viscosity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+ else if (phaseIdx == nPhaseIdx)
+ {
+ return CO2::gasViscosity(fluidState.temperature(phaseIdx), fluidState.pressure(phaseIdx));
+ }
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+
+ }
+```
+
+
+</details>
+
+
+
+## The brine adapter (`icpcomplexsalinitybrine.hh`)
+
+This file contains the brineadapter class__ which defines
+how to adapt values for communication between
+the "full" fluidsystem accounting for 4 components influencing the brine properties
+and the "brine" fluidsystem assuming water and a single salt determining the brine properties.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/fluidsystems/icpcomplexsalinitybrine.hh))</summary>
+
+
+### Include files
+<details><summary> Click to show includes</summary>
+we include all necessary components
+
+```cpp
+#include <dumux/material/fluidsystems/base.hh>
+#include <dumux/material/constants.hh>
+#include <dumux/material/components/h2o.hh>
+#include <dumux/material/components/sodiumion.hh>
+#include <dumux/material/components/chlorideion.hh>
+#include <dumux/material/components/calciumion.hh>
+#include <dumux/material/components/tabulatedcomponent.hh>
+
+#include <dumux/common/exceptions.hh>
+
+#include <dumux/io/name.hh>
+```
+
+</details>
+
+### The brine adapter class
+In ICPComplexSalinityBrine we make the transition from 3 components additional to water contributing to salinity to the single component that is assumed in the brine fluid system.
+We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+
+```cpp
+namespace Dumux::FluidSystems {
+
+template< class Scalar, class H2OType = Components::TabulatedComponent<Dumux::Components::H2O<Scalar>> >
+class ICPComplexSalinityBrine : public Base< Scalar, ICPComplexSalinityBrine<Scalar, H2OType>>
+{
+ using ThisType = ICPComplexSalinityBrine<Scalar, H2OType>;
+ using Base = Dumux::FluidSystems::Base<Scalar, ThisType>;
+
+public:
+ //! export the involved components
+ using H2O = H2OType;
+ using Na = Components::SodiumIon<Scalar>;
+ using Cl = Components::ChlorideIon<Scalar>;
+ using Ca = Components::CalciumIon<Scalar>;
+```
+
+
+#### Component and phase definitions
+With the following function we define what phases and components will be used by the fluid system and define the indices used to distinguish phases and components in the course of the simulation.
+
+```cpp
+ // We use convenient declarations that we derive from the property system.
+ static constexpr int numPhases = 1; //!< Number of phases in the fluid system
+ static constexpr int numComponents = 4; //!< Number of components in the fluid system (H2O, Na, Cl, Ca)
+
+ static constexpr int phase0Idx = 0; //!< Index of the first (and only) phase
+ static constexpr int liquidPhaseIdx = phase0Idx; //!< The one considered phase is liquid
+
+ static constexpr int H2OIdx = 0; //!< index of the water component
+ static constexpr int NaIdx = 1; //!< index of the Na component
+ static constexpr int ClIdx = 2; //!< index of the Cl component
+ static constexpr int CaIdx = 3; //!< index of the Ca component
+ static constexpr int comp0Idx = H2OIdx; //!< index of the first component
+ static constexpr int comp1Idx = NaIdx; //!< index of the second component
+ static constexpr int comp2Idx = ClIdx; //!< index of the third component
+ static constexpr int comp3Idx = CaIdx; //!< index of the fourth component
+
+ // the fluid phase index
+ static std::string phaseName(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return IOName::liquidPhase();
+ }
+
+ // the miscibility
+ static constexpr bool isMiscible()
+ {
+ return false;
+ }
+
+ // we do not have a gas phase
+ static constexpr bool isGas(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return false;
+ }
+
+ // We need a ideal mixture
+ static constexpr bool isIdealMixture(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return true;
+ }
+
+ // phase compressibility
+ static constexpr bool isCompressible(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return H2O::liquidIsCompressible();
+ }
+
+ // no gas, thus no ideal gas
+ static constexpr bool isIdealGas(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return false; /*we're a liquid!*/
+ }
+```
+
+
+#### The Component-Phase Interactions
+In the following, we define the component-phase interactions such as // each component's fugacity coefficient in brine
+and each component's binary diffusion coefficient with water in brine
+
+```cpp
+ // The component fugacity coefficients
+ template <class FluidState>
+ static Scalar fugacityCoefficient(const FluidState &fluidState,
+ int phaseIdx,
+ int compIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIdx && compIdx < numComponents);
+
+ if (phaseIdx == compIdx)
+ // We could calculate the real fugacity coefficient of
+ // the component in the fluid. Probably that's not worth
+ // the effort, since the fugacity coefficient of the other
+ // component is infinite anyway...
+ return 1.0;
+ return std::numeric_limits<Scalar>::infinity();
+ }
+
+ // The binary diffusion coefficients of the components and the phases main component
+ template <class FluidState>
+ static Scalar binaryDiffusionCoefficient(const FluidState& fluidState,
+ int phaseIdx,
+ int compIIdx,
+ int compJIdx)
+ {
+ if (phaseIdx == liquidPhaseIdx)
+ {
+ if (compIIdx > compJIdx)
+ {
+ using std::swap;
+ swap(compIIdx, compJIdx);
+ }
+ if (compJIdx == NaIdx || compJIdx == ClIdx || compJIdx == CaIdx)
+ return 1.587e-9; //[m²/s] //J. Phys. D: Appl. Phys. 40 (2007) 2769-2776
+ else
+ DUNE_THROW(Dune::NotImplemented, "Binary diffusion coefficient of components "
+ << compIIdx << " and " << compJIdx
+ << " in phase " << phaseIdx);
+ }
+
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index: " << phaseIdx);
+ }
+```
+
+
+#### The Fluid (Brine) Properties
+In the following, all functions defining the phase properties are given:
+the density, viscosity, enthalpy, thermal conductivities, and heat capacities
+of each phase depending on temperature, pressure, and phase composition
+
+```cpp
+ // The phase density
+ template <class FluidState>
+ static Scalar density(const FluidState& fluidState, int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ const Scalar temperature = fluidState.temperature(phaseIdx);
+ const Scalar pressure = fluidState.pressure(phaseIdx);
+ const Scalar xNaCl = fluidState.massFraction(phaseIdx, NaIdx)
+ + fluidState.massFraction(phaseIdx, ClIdx)
+ + fluidState.massFraction(phaseIdx, CaIdx);
+
+ using std::max;
+ const Scalar TempC = temperature - 273.15;
+ const Scalar pMPa = pressure/1.0E6;
+ const Scalar salinity = max(0.0, xNaCl);
+
+ const Scalar rhow = H2O::liquidDensity(temperature, pressure);
+ const Scalar density = rhow + 1000*salinity*(0.668 +
+ 0.44*salinity +
+ 1.0E-6*(300*pMPa -
+ 2400*pMPa*salinity +
+ TempC*(80.0 +
+ 3*TempC -
+ 3300*salinity -
+ 13*pMPa +
+ 47*pMPa*salinity)));
+ assert(density > 0.0);
+ return density;
+ }
+
+
+
+ // The phase viscosity
+ template <class FluidState>
+ static Scalar viscosity(const FluidState& fluidState, int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ const Scalar temperature = fluidState.temperature(phaseIdx);
+ const Scalar xNaCl = fluidState.massFraction(phaseIdx, NaIdx)
+ + fluidState.massFraction(phaseIdx, ClIdx)
+ + fluidState.massFraction(phaseIdx, CaIdx);
+
+ using std::pow;
+ using std::exp;
+ using std::max;
+ const Scalar T = max(temperature, 275.0);
+ const Scalar salinity = max(0.0, xNaCl);
+
+ const Scalar T_C = T - 273.15;
+ const Scalar A = ((0.42*pow((pow(salinity, 0.8)-0.17), 2)) + 0.045)*pow(T_C, 0.8);
+ const Scalar mu_brine = 0.1 + (0.333*salinity) + (1.65+(91.9*salinity*salinity*salinity))*exp(-A); // [cP]
+ assert(mu_brine > 0.0);
+ return mu_brine/1000.0; // [Pa·s]
+ }
+```
+
+
+</details>
+
+
+
+## The solid system (`biominsolids.hh`)
+
+This file contains the __solidystem class__ which defines all functions needed to describe the solid and their properties,
+which are needed to model biomineralization.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/solidsystems/biominsolids.hh))</summary>
+
+
+### Include files
+
+```cpp
+#include <string>
+#include <dune/common/exceptions.hh>
+
+// we include all necessary solid components
+#include <examples/biomineralization/material/components/biofilm.hh>
+#include <dumux/material/components/calcite.hh>
+#include <dumux/material/components/granite.hh>
+```
+
+### The solidsystem class
+In the BioMinSolidPhase solid system, we define all functions needed to describe the solids and their properties accounted for in our simulation.
+We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+
+```cpp
+namespace Dumux::SolidSystems {
+
+template <class Scalar>
+class BioMinSolidPhase
+{
+public:
+```
+
+#### Component definitions
+With the following function we define what solid components will be used by the solid system and define the indices used to distinguish solid components in the course of the simulation.
+
+```cpp
+ // We use convenient declarations that we derive from the property system.
+ using Biofilm = Components::Biofilm<Scalar>;
+ using Calcite = Components::Calcite<Scalar>;
+ using Granite = Components::Granite<Scalar>;
+
+ /****************************************
+ * Solid phase related static parameters
+ ****************************************/
+ static constexpr int numComponents = 3;
+ static constexpr int numInertComponents = 1;
+ static constexpr int BiofilmIdx = 0;
+ static constexpr int CalciteIdx = 1;
+ static constexpr int GraniteIdx = 2;
+
+ // The component names
+ const static std::string componentName(int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::name();
+ case CalciteIdx: return Calcite::name();
+ case GraniteIdx: return Granite::name();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The solid system's name
+ static std::string name()
+ { return "BiomineralizationMinSolidPhase"; }
+
+ // We assume incompressible solids
+ static constexpr bool isCompressible(int compIdx)
+ { return false; }
+
+ // we have one inert component, the others may change
+ static constexpr bool isInert()
+ { return (numComponents == numInertComponents); }
+```
+
+#### Component properties
+This simply forwards the component properties (name, molar mass, density).
+
+```cpp
+ // The component molar masses
+ static Scalar molarMass(int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::molarMass();
+ case CalciteIdx: return Calcite::molarMass();
+ case GraniteIdx: return Granite::molarMass();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The component densities
+ template <class SolidState>
+ static Scalar density(const SolidState& solidState, const int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::solidDensity(solidState.temperature());
+ case CalciteIdx: return Calcite::solidDensity(solidState.temperature());
+ case GraniteIdx: return Granite::solidDensity(solidState.temperature());
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The component molar densities
+ template <class SolidState>
+ static Scalar molarDensity(const SolidState& solidState, const int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::solidDensity(solidState.temperature())/Biofilm::molarMass();
+ case CalciteIdx: return Calcite::solidDensity(solidState.temperature())/Calcite::molarMass();
+ case GraniteIdx: return Granite::solidDensity(solidState.temperature())/Calcite::molarMass();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+```
+
+#### Averaged solid properties
+The overall solid properties are calculated by a volume-weigthed average of the pure component's properties.
+
+```cpp
+ // The average density
+ template <class SolidState>
+ static Scalar density(const SolidState& solidState)
+ {
+ const Scalar rho1 = Biofilm::solidDensity(solidState.temperature());
+ const Scalar rho2 = Calcite::solidDensity(solidState.temperature());
+ const Scalar rho3 = Granite::solidDensity(solidState.temperature());
+ const Scalar volFrac1 = solidState.volumeFraction(BiofilmIdx);
+ const Scalar volFrac2 = solidState.volumeFraction(CalciteIdx);
+ const Scalar volFrac3 = solidState.volumeFraction(GraniteIdx);
+
+ return (rho1*volFrac1+
+ rho2*volFrac2+
+ rho3*volFrac3)
+ /(volFrac1+volFrac2+volFrac3);
+ }
+```
+
+
+</details>
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 2](setup.md) |
+|---|---:|
+
diff --git a/examples/biomineralization/doc/modelconcept.md b/examples/biomineralization/doc/modelconcept.md
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+<!-- Important: This file has been automatically generated by generate_example_docs.py. Do not edit this file directly! -->
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_right: Continue with part 2](mainfile.md) |
+|---|---:|
+
+# Model Concept for Biomineralization
+
+The conceptual model for biomineralization follows the one presented by [@Ebigbo2012] and [@Hommel2015].
+It accounts for two-phase multi-component reactive transport on the continuum scale, including biofilm and calcite as solid phases.
+The reactions considered are pH-dependent dissociation reactions, microbial growth, and decay as well as microbially-catalyzed ureolysis and mass-transfer reactions between the different phases.
+A mass transfer may occur between both fluid phases by the mutual dissolution of water and CO<sub>2</sub> in the gas or the aqueous phase. It may also occur between
+the aqueous phase and the two *solid* phases, biofilm and calcite, denoted by subscripts (f) and (c) respectively, by attachment or
+detachment of biomass and precipitation or dissolution of calcite.
+
+The mobile components, denoted by superscripts k, are water (w), dissolved inorganic carbon (C<sub>tot</sub>),
+sodium (Na), chloride (Cl), calcium (Ca), urea (u), substrate (s), oxygen (O<sub>2</sub>), and suspended biomass (b).
+A substrate is the carbon and energy source of the bacteria and O<sub>2</sub> is the electron acceptor.
+
+Contrary to [@Ebigbo2012] and [@Hommel2015], for the sake of simplicity,
+the dissociation processes are not modeled in this example.
+It is assumed that the system has reached a steady state were the calcite precipitation rate is equal to the rate of ureolysis.
+Thus, in this example, we consider only the "simplified chemistry case" in which it is assumed that the precipitation rate is equal to the ureolysis rate to simplify the chemical processes considered ($`r_\mathrm{prec} = r_\mathrm{urea}`$),
+described in detail in Chapter 6 of [@Hommel2016].
+
+The documentation provided for the model concept is structured as follows:
+
+[[_TOC_]]
+
+
+## Primary variables and mass balance equations
+
+The primary variables of this system of equations are chosen as the aqueous-phase pressure, mole fractions of the components in the water phase, and
+for the solid phases biofilm and calcite, volume fractions.
+However, the CO<sub>2</sub>-phase saturation is used as the primary variable instead of the mole fraction of total inorganic carbon in water
+whenever both fluid phases are present within the same control volume ([@Class2002]).
+All reactive and mass-transfer processes are incorporated in the mass balance equations for the components by component-specific source and sink terms:
+
+```math
+\sum\limits_{\alpha} \left[\frac{\partial}{\partial t}\left(\phi \rho_\mathrm{\alpha,\,mol} x^\kappa_\alpha S_\alpha \right) + \nabla\cdotp \left(\rho_\mathrm{\alpha,\,mol} x^\kappa_\alpha \mathbf{v}_\alpha \right) - \nabla\cdotp \left(\rho_\mathrm{\alpha,\,mol} \mathbf{D}^\kappa_\mathrm{pm,\alpha} \nabla x^\kappa_\alpha \right) \right] = q^\kappa,\:\alpha\in \mathrm{\{n;w\}} .
+\tag{2}
+```
+
+However, all components except water, CO<sub>2</sub> , and O<sub>2</sub> are assumed to be restricted to the water phase.
+
+The mass balances for the solid phases calcite and biofilm contain
+only a storage and source term since they are immobile:
+
+```math
+\frac{\partial}{\partial t} \left(\phi_\lambda \rho_\lambda \right) = q^\lambda,\:\lambda\in \mathrm{\{c;f\}}.
+\tag{3}
+```
+
+Here, $`\phi_\lambda`$ and $`\rho_\lambda`$ are volume fraction and mass density of
+the solid phase $`\lambda`$, and $`q^\lambda`$ is the source term of phase $`\lambda`$ due to biochemical reactions.
+The sources and sinks due to reactions $`q^\kappa$ and $q^\lambda`$ are specific to the components and are discussed in details in the subsequent section.
+
+## Component-specific reactive source and sink terms
+
+The source and sink terms account for the biogeochemical reactions occurring during MICP and the presence of CO<sub>2</sub>:
+ureolysis, calcite precipitation, and dissolution, biomass growth under consumption of oxygen and substrate, biomass decay, as well as attachment and detachment of biomass.
+
+## Water, sodium and chloride
+Sodium and chloride do not participate in the reactions and water is the solvent and, thus, abundant, which is why its consumption by the hydrolysis of urea (Eq. [1](#mjx-eqn-eq:q_w_na_cl)) is considered negligible.
+Thus, the reactive source terms for water, sodium, and chloride are zero.
+
+## Urea and total nitrogen
+The source term for ammonia/ammonium, $`q^\mathrm{N_{tot}}`$, and the sink term for urea $`q^\mathrm{u}`$ result from ureolysis (Eq. [1](#mjx-eqn-eq:q_ntot)).
+For each mole of urea hydrolyzed, 2 moles of ammonia/ammonium are generated. The source terms are thus:
+
+```math
+q^\mathrm{u}=-r_\mathrm{urea}; \\
+q^\mathrm{N_{tot}}=2r_\mathrm{urea},
+```
+
+where $`r_\mathrm{urea}`$ is the ureolysis rate calculated according to [@Lauchnor2015],
+who investigated the influences of urea,
+NH<sup>4+</sup>, and cell concentration, and pH of the medium on the ureolysis of whole cells of _S. pasteurii_:
+
+```math
+r_\mathrm{urea} = k_\mathrm{urease}
+\:k_\mathrm{ub}\:\rho_\mathrm{f}\:\phi_\mathrm{f}
+\:\frac{m^\mathrm{u}}{m^\mathrm{u}+K_\mathrm{u}}.
+```
+
+$`r_\mathrm{urea}`$ represents the revised rate of ureolysis according to [@Lauchnor2015],
+$`k_\mathrm{urease}`$ the revised maximum activity of urease adapted from [@Lauchnor2015],
+$`\rho_\mathrm{f}`$ and $`\phi_\mathrm{f}`$ the density and volume fraction of biofilm respectively,
+$`k_\mathrm{ub}`$ the mass ratio of urease to biofilm,
+$`m^\mathrm{u}`$ the molality of urea calculated from the water phase composition,
+and $`K_\mathrm{u}`$ is the half saturation constant for urea adapted from [@Lauchnor2015].
+
+## Calcium and calcite
+The source terms of calcium $`q^\mathrm{Ca}`$ and calcite $`q^\mathrm{c}`$
+are determined by the rates of precipitation and dissolution.
+When the aqueous phase is oversaturated with respect to calcite, it precipitates.
+In the opposite case, calcite dissolves until the solution is saturated or all calcite is already dissolved:
+
+```math
+q^\mathrm{Ca} = r_\mathrm{diss} - r_\mathrm{prec}; \\
+q^\mathrm{c} = - r_\mathrm{diss} + r_\mathrm{prec}.
+```
+
+In the presented simplified chemistry system, dissolution is neglected
+and instead of calculating the complex geochemistry, e.g. dissociation of inorganic carbon into carbonate and bicarbonate,
+it is assumed that the system has reached a steady state, were the precipitation rate is equal to the ureolysis rate and, thus, it yields:
+
+```math
+r_\mathrm{prec} = r_\mathrm{urea},
+```
+as long as there is calcium to form calcite.
+Note: The "simplified chemistry case" ($`r_\mathrm{prec} = r_\mathrm{urea}`$),
+is a simplifying assumption, its effects and validity are discussed in more detail in Chapter 6 of [@Hommel2016].
+
+## Dissolved inorganic carbon
+Dissolved inorganic carbon is generated by the hydrolysis of urea
+as well as by the dissolution of calcite while it is consumed by the precipitation of calcite.
+Thus, the source term of dissolved inorganic carbon $`q^\mathrm{C_{tot}}`$ results in:
+
+```math
+q^\mathrm{C_{tot}} = r_\mathrm{urea} + r_\mathrm{diss} - r_\mathrm{prec},
+```
+
+
+## Suspended and attached biomass
+
+The source and sink terms of suspended and attached biomass (biofilm), $`q^\mathrm{b}`$ and $`q^\mathrm{f}`$,
+include four reaction rates each, corresponding to the biomass-related processes the model accounts for.
+These processes are growth and decay increasing and decreasing the suspended or attached biomass as well as
+attachment and detachment describing the transfer of biomass from the suspended to the attached state and vice versa:
+
+```math
+q^\mathrm{b} = \frac{r^\mathrm{b}_\mathrm{g} - r^\mathrm{b}_\mathrm{b} - r_\mathrm{a} + r_\mathrm{d}}{M^\mathrm{b}}; \\
+q^\mathrm{f} = \frac{r^\mathrm{f}_\mathrm{g} - r^\mathrm{f}_\mathrm{b} + r_\mathrm{a} - r_\mathrm{d}}{M^\mathrm{f}}
+```
+
+where $`r^\mathrm{b}_\mathrm{g}`$ is the growth rate and $`r^\mathrm{b}_\mathrm{b}`$ the decay rate of suspended biomass, $`r_\mathrm{a}`$ the attachment rate, $`r_\mathrm{d}`$ the detachment rate.
+Accordingly, $`r^\mathrm{f}_\mathrm{g}`$ and $`r^\mathrm{f}_\mathrm{b}`$ are the growth and decay of biofilm.
+All rates influencing both attached and suspended biomass are assumed to be of a first-order type.
+
+The growth rates of suspended and attached biomass are as given below,
+with the specific growth rate calculated using double Monod kinetics to reproduce the dependence of
+the microbial growth on both substrate and oxygen.
+
+```math
+r_\mathrm{g}^\mathrm{b} = \mu_\mathrm{g} C_\mathrm{w}^\mathrm{b}S_\mathrm{w}\phi; \\
+ r_\mathrm{g}^\mathrm{f} = \mu_\mathrm{g} \phi_\mathrm{f}\rho_\mathrm{f}; \\
+ \mu_\mathrm{g} = k_\mathrm{\mu}
+ \frac{C_\mathrm{w}^\mathrm{s}}{K_\mathrm{s} + C_\mathrm{w}^\mathrm{s}}
+ \frac{C_\mathrm{w}^\mathrm{O_2}}{K_\mathrm{O_2} + C_\mathrm{w}^\mathrm{O_2}}.
+```
+
+Here, $`k_\mathrm{\mu}`$ is the maximum specific growth rate, according to [@Connolly2014],
+$`C_\mathrm{w}^\mathrm{s}`$ and $`C_\mathrm{w}^\mathrm{O_2}`$ are the mass concentrations of substrate and oxygen in the water phase and
+K<sub>s</sub> and K<sub>O<sub>2</sub></sub> are the half-saturation coefficients for substrate and oxygen respectively.
+
+The decay rates are calculated similarly to the growth rates,
+except that the specific decay rates of suspended and attached biomass
+take different processes into account, increasing inactivation.
+For suspended biomass, non-optimal acidic pH is assumed to increase inactivation.
+As calcite precipitates mainly in or close to the biofilm, cells may be covered with calcite precipitates
+or disrupted by crystals inactivating the affected cells ([@Dupraz2009a] and [@Whiffin2007]).
+Consequently, the precipitation rate is assumed to increase the specific decay rate of attached biomass.
+
+
+```math
+r_\mathrm{b}^\mathrm{b} = k_\mathrm{b}^\mathrm{b} C_\mathrm{w}^\mathrm{b}S_\mathrm{w}\phi; \\
+ r_\mathrm{b}^\mathrm{f} = k_\mathrm{b}^\mathrm{f}\phi_\mathrm{f}\rho_\mathrm{f}; \\
+k_\mathrm{b}^\mathrm{b}=b_0\left(1+\frac{K_\mathrm{pH}}{m_\mathrm{H^{+}}^2}\right); \\
+ k_\mathrm{b}^\mathrm{f} = b_0 + \frac{r_\mathrm{prec} M^\mathrm{c}}{\rho_\mathrm{c}\left(\phi_0 - \phi_\mathrm{c}\right)}
+```
+
+The attachment rate quantifies the biomass transfer from
+the suspended to the attached state.
+As attachment is modeled assuming a first-order kinetic rather than a
+sorption-type behavior, with preferential attachment to previously attached biomass:
+
+```math
+r_\mathrm{a}= k_\mathrm{a} C^\mathrm{b}_\mathrm{w} \phi S_\mathrm{w};\\
+k_\mathrm{a}=c_\mathrm{a,1} \phi_\mathrm{f} + c_\mathrm{a,2},
+```
+
+Detachment of biomass from biofilm is assumed to be proportional to the shear stress.
+Additionally, the growth contributes to the detachment rate, as vigorously growing
+biofilm is typically weaker and as such more susceptible to detachment.
+As the model of [@Ebigbo2012] is defined on the Darcy scale but the shear stress is a micro-scale property,
+it is approximated using the absolute value of the water-phase potential gradient:
+
+```math
+r_\mathrm{d}=k_\mathrm{d} \phi_\mathrm{f} \rho_\mathrm{f};\\
+k_\mathrm{d}=c_\mathrm{d}
+\left( \phi S_\mathrm{w} \left|\nabla p_\mathrm{w} - \rho_\mathrm{w} \mathbf{g} \right| \right)^{0.58}
++ \frac{\phi_\mathrm{f}}{\phi_0-\phi_\mathrm{c}} \mu_\mathrm{g}.
+```
+
+Here, $`c_\mathrm{d}`$ is a coefficient for the shear-stress-dependent detachment,
+$`\left|\nabla p_\mathrm{w} - \rho_\mathrm{w} \mathbf{g} \right|`$ the absolute value of
+the water-phase potential gradient, and $`\phi_0`$ the initial porosity.
+
+
+## Substrate and oxygen
+The consumption of substrate and oxygen is linked to the growth of both suspended and attached biomass
+by the yield coefficient Y of substrate. In the case of oxygen, the coefficient F, which is the ration of oxygen consumed per substrate consumed,
+is used to express the biomass yield per oxygen consumed:
+
+```math
+q^\mathrm{s} = - \frac{r^\mathrm{b}_\mathrm{g} + r^\mathrm{f}_\mathrm{g}}{M^\mathrm{s}Y}; \\
+ q^\mathrm{O_2} = F q^\mathrm{s} = - F \frac{ r^\mathrm{b}_\mathrm{g} + r^\mathrm{f}_\mathrm{g}} {M^\mathrm{O_2}Y}.
+```
+
+## Supplementary equations
+\subsubsection{Permeability and porosity}\label{sec:perm_poro_pw}
+The permeability decreases due to biofilm growth and calcite precipitation.
+In the model, the reduction of permeability is calculated based on the
+reduction of porosity using a Kozenzy-Carman-type relationship:
+
+```math
+\frac{K}{K_\mathrm{0}}=\left(\frac{\phi}{\phi_\mathrm{0}}\right)^3 \left(\frac{1-\phi_0}{1-\phi}\right)^2.
+```
+
+Here, $`K_\mathrm{0}`$ is the initial permeability,
+and $`\phi_0`$ is the initial porosity. The porosity decreases as
+the volume fractions of biofilm and calcite increase:
+
+```math
+\phi=\phi_\mathrm{0}-\phi_\mathrm{c}-\phi_\mathrm{f}.
+```
+
+
+## Fluid properties
+The density and the viscosity of the CO<sub>2</sub> phase are calculated using
+the relation given by [@Span1996] and [@Fenghour1998] respectively.
+In these calculations, the effects of the small amounts of water and oxygen are neglected.
+The density and the viscosity of the aqueous phase are calculated
+according to [@Batzle1992] as a function of salinity.
+Sodium, chloride and calcium are considered to contribute to the salinity.
+
+
+## Phase partitioning of components
+The dissolution of CO<sub>2</sub> in the aqueous phase is calculated according
+to [@Duan2003] as a function of temperature, pressure and salinity.
+In the two-phase case, the concentration of carbonic acid is assumed to be
+equal to the solubility while, in the case of the exclusive presence of the aqueous phase,
+the concentration of inorganic carbon
+is exclusively dependent on the precipitation, dissolution and ureolysis reactions.
+In this case, the solubility represents the maximum possible concentration.
+For the solubility of oxygen in the aqueous phase, Henry's law is used.
+
+
+
+
+
+[@Batzle1992]: https://library.seg.org/doi/10.1190/1.1443207 "Seismic Properties of Pore Fluids"
+[@Class2002]: https://www.sciencedirect.com/science/article/pii/S0309170802000155 "Numerical simulation of non-isothermal multiphase multicomponent processes in porous media. 2. Applications for the injection of steam and air"
+[@Connolly2014]: http://www.ncbi.nlm.nih.gov/pubmed/23835134 "Construction of two ureolytic model organisms for the study of microbially induced calcium carbonate precipitation"
+[@Duan2003]: https://www.sciencedirect.com/science/article/pii/S0009254102002632 "An improved model calculating CO<sub>2</sub> solubility in pure water and aqueous NaCl solutions from 273 to 533 K and from 0 to 2000 bar"
+[@Chou1989]: https://www.sciencedirect.com/science/article/pii/0009254189900636 "Comparative study of the kinetics and mechanisms of dissolution of carbonate minerals"
+[@Compton1989]: https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.1989.tb01101.x "The dissolution of calcite in acid waters: Mass transport versus surface control"
+[@Dupraz2009a]: http://linkinghub.elsevier.com/retrieve/pii/S0009254109002265 "Experimental and numerical modeling of bacterially induced pH increase and calcite precipitation in saline aquifers"
+[@Whiffin2007]: https://www.tandfonline.com/doi/full/10.1080/01490450701436505 "Microbial Carbonate Precipitation as a Soil Improvement Technique"
+[@Ebigbo2012]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2011WR011714 "Darcy-scale modeling of microbially induced carbonate mineral precipitation in sand columns"
+[@Fenghour1998]: https://aip.scitation.org/doi/10.1063/1.556013 "The Viscosity of Carbon Dioxide"
+[@Hommel2015]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2014WR016503 "A revised model for microbially induced calcite precipitation: Improvements and new insights based on recent experiments"
+[@Hommel2016]: https://elib.uni-stuttgart.de/handle/11682/8787 "Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation"
+[@Lauchnor2015]: http://dx.doi.org/10.1111/jam.12804 "Whole cell kinetics of ureolysis by Sporosarcina pasteurii"
+[@Mitchell2008]: https://www.sciencedirect.com/science/article/pii/S0896844608002040 "Resilience of planktonic and biofilm cultures to supercritical CO<sub>2</sub>"
+[@Span1996]: https://aip.scitation.org/doi/abs/10.1063/1.555991 "A new equation of state for carbon dioxide covering the fluid region from the triple-point temperature to 1100 K at pressures up to 800 MPa"
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_right: Continue with part 2](mainfile.md) |
+|---|---:|
+
diff --git a/examples/biomineralization/doc/modelconcept_intro.md b/examples/biomineralization/doc/modelconcept_intro.md
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+# Model Concept for Biomineralization
+
+The conceptual model for biomineralization follows the one presented by [@Ebigbo2012] and [@Hommel2015].
+It accounts for two-phase multi-component reactive transport on the continuum scale, including biofilm and calcite as solid phases.
+The reactions considered are pH-dependent dissociation reactions, microbial growth, and decay as well as microbially-catalyzed ureolysis and mass-transfer reactions between the different phases.
+A mass transfer may occur between both fluid phases by the mutual dissolution of water and CO<sub>2</sub> in the gas or the aqueous phase. It may also occur between
+the aqueous phase and the two *solid* phases, biofilm and calcite, denoted by subscripts (f) and (c) respectively, by attachment or
+detachment of biomass and precipitation or dissolution of calcite.
+
+The mobile components, denoted by superscripts k, are water (w), dissolved inorganic carbon (C<sub>tot</sub>),
+sodium (Na), chloride (Cl), calcium (Ca), urea (u), substrate (s), oxygen (O<sub>2</sub>), and suspended biomass (b).
+A substrate is the carbon and energy source of the bacteria and O<sub>2</sub> is the electron acceptor.
+
+Contrary to [@Ebigbo2012] and [@Hommel2015], for the sake of simplicity,
+the dissociation processes are not modeled in this example.
+It is assumed that the system has reached a steady state were the calcite precipitation rate is equal to the rate of ureolysis.
+Thus, in this example, we consider only the "simplified chemistry case" in which it is assumed that the precipitation rate is equal to the ureolysis rate to simplify the chemical processes considered ($`r_\mathrm{prec} = r_\mathrm{urea}`$),
+described in detail in Chapter 6 of [@Hommel2016].
+
+The documentation provided for the model concept is structured as follows:
+
+[[_TOC_]]
+
+
+## Primary variables and mass balance equations
+
+The primary variables of this system of equations are chosen as the aqueous-phase pressure, mole fractions of the components in the water phase, and
+for the solid phases biofilm and calcite, volume fractions.
+However, the CO<sub>2</sub>-phase saturation is used as the primary variable instead of the mole fraction of total inorganic carbon in water
+whenever both fluid phases are present within the same control volume ([@Class2002]).
+All reactive and mass-transfer processes are incorporated in the mass balance equations for the components by component-specific source and sink terms:
+
+```math
+\sum\limits_{\alpha} \left[\frac{\partial}{\partial t}\left(\phi \rho_\mathrm{\alpha,\,mol} x^\kappa_\alpha S_\alpha \right) + \nabla\cdotp \left(\rho_\mathrm{\alpha,\,mol} x^\kappa_\alpha \mathbf{v}_\alpha \right) - \nabla\cdotp \left(\rho_\mathrm{\alpha,\,mol} \mathbf{D}^\kappa_\mathrm{pm,\alpha} \nabla x^\kappa_\alpha \right) \right] = q^\kappa,\:\alpha\in \mathrm{\{n;w\}} .
+\tag{2}
+```
+
+However, all components except water, CO<sub>2</sub> , and O<sub>2</sub> are assumed to be restricted to the water phase.
+
+The mass balances for the solid phases calcite and biofilm contain
+only a storage and source term since they are immobile:
+
+```math
+\frac{\partial}{\partial t} \left(\phi_\lambda \rho_\lambda \right) = q^\lambda,\:\lambda\in \mathrm{\{c;f\}}.
+\tag{3}
+```
+
+Here, $`\phi_\lambda`$ and $`\rho_\lambda`$ are volume fraction and mass density of
+the solid phase $`\lambda`$, and $`q^\lambda`$ is the source term of phase $`\lambda`$ due to biochemical reactions.
+The sources and sinks due to reactions $`q^\kappa$ and $q^\lambda`$ are specific to the components and are discussed in details in the subsequent section.
+
+## Component-specific reactive source and sink terms
+
+The source and sink terms account for the biogeochemical reactions occurring during MICP and the presence of CO<sub>2</sub>:
+ureolysis, calcite precipitation, and dissolution, biomass growth under consumption of oxygen and substrate, biomass decay, as well as attachment and detachment of biomass.
+
+## Water, sodium and chloride
+Sodium and chloride do not participate in the reactions and water is the solvent and, thus, abundant, which is why its consumption by the hydrolysis of urea (Eq. [1](#mjx-eqn-eq:q_w_na_cl)) is considered negligible.
+Thus, the reactive source terms for water, sodium, and chloride are zero.
+
+## Urea and total nitrogen
+The source term for ammonia/ammonium, $`q^\mathrm{N_{tot}}`$, and the sink term for urea $`q^\mathrm{u}`$ result from ureolysis (Eq. [1](#mjx-eqn-eq:q_ntot)).
+For each mole of urea hydrolyzed, 2 moles of ammonia/ammonium are generated. The source terms are thus:
+
+```math
+q^\mathrm{u}=-r_\mathrm{urea}; \\
+q^\mathrm{N_{tot}}=2r_\mathrm{urea},
+```
+
+where $`r_\mathrm{urea}`$ is the ureolysis rate calculated according to [@Lauchnor2015],
+who investigated the influences of urea,
+NH<sup>4+</sup>, and cell concentration, and pH of the medium on the ureolysis of whole cells of _S. pasteurii_:
+
+```math
+r_\mathrm{urea} = k_\mathrm{urease}
+\:k_\mathrm{ub}\:\rho_\mathrm{f}\:\phi_\mathrm{f}
+\:\frac{m^\mathrm{u}}{m^\mathrm{u}+K_\mathrm{u}}.
+```
+
+$`r_\mathrm{urea}`$ represents the revised rate of ureolysis according to [@Lauchnor2015],
+$`k_\mathrm{urease}`$ the revised maximum activity of urease adapted from [@Lauchnor2015],
+$`\rho_\mathrm{f}`$ and $`\phi_\mathrm{f}`$ the density and volume fraction of biofilm respectively,
+$`k_\mathrm{ub}`$ the mass ratio of urease to biofilm,
+$`m^\mathrm{u}`$ the molality of urea calculated from the water phase composition,
+and $`K_\mathrm{u}`$ is the half saturation constant for urea adapted from [@Lauchnor2015].
+
+## Calcium and calcite
+The source terms of calcium $`q^\mathrm{Ca}`$ and calcite $`q^\mathrm{c}`$
+are determined by the rates of precipitation and dissolution.
+When the aqueous phase is oversaturated with respect to calcite, it precipitates.
+In the opposite case, calcite dissolves until the solution is saturated or all calcite is already dissolved:
+
+```math
+q^\mathrm{Ca} = r_\mathrm{diss} - r_\mathrm{prec}; \\
+q^\mathrm{c} = - r_\mathrm{diss} + r_\mathrm{prec}.
+```
+
+In the presented simplified chemistry system, dissolution is neglected
+and instead of calculating the complex geochemistry, e.g. dissociation of inorganic carbon into carbonate and bicarbonate,
+it is assumed that the system has reached a steady state, were the precipitation rate is equal to the ureolysis rate and, thus, it yields:
+
+```math
+r_\mathrm{prec} = r_\mathrm{urea},
+```
+as long as there is calcium to form calcite.
+Note: The "simplified chemistry case" ($`r_\mathrm{prec} = r_\mathrm{urea}`$),
+is a simplifying assumption, its effects and validity are discussed in more detail in Chapter 6 of [@Hommel2016].
+
+## Dissolved inorganic carbon
+Dissolved inorganic carbon is generated by the hydrolysis of urea
+as well as by the dissolution of calcite while it is consumed by the precipitation of calcite.
+Thus, the source term of dissolved inorganic carbon $`q^\mathrm{C_{tot}}`$ results in:
+
+```math
+q^\mathrm{C_{tot}} = r_\mathrm{urea} + r_\mathrm{diss} - r_\mathrm{prec},
+```
+
+
+## Suspended and attached biomass
+
+The source and sink terms of suspended and attached biomass (biofilm), $`q^\mathrm{b}`$ and $`q^\mathrm{f}`$,
+include four reaction rates each, corresponding to the biomass-related processes the model accounts for.
+These processes are growth and decay increasing and decreasing the suspended or attached biomass as well as
+attachment and detachment describing the transfer of biomass from the suspended to the attached state and vice versa:
+
+```math
+q^\mathrm{b} = \frac{r^\mathrm{b}_\mathrm{g} - r^\mathrm{b}_\mathrm{b} - r_\mathrm{a} + r_\mathrm{d}}{M^\mathrm{b}}; \\
+q^\mathrm{f} = \frac{r^\mathrm{f}_\mathrm{g} - r^\mathrm{f}_\mathrm{b} + r_\mathrm{a} - r_\mathrm{d}}{M^\mathrm{f}}
+```
+
+where $`r^\mathrm{b}_\mathrm{g}`$ is the growth rate and $`r^\mathrm{b}_\mathrm{b}`$ the decay rate of suspended biomass, $`r_\mathrm{a}`$ the attachment rate, $`r_\mathrm{d}`$ the detachment rate.
+Accordingly, $`r^\mathrm{f}_\mathrm{g}`$ and $`r^\mathrm{f}_\mathrm{b}`$ are the growth and decay of biofilm.
+All rates influencing both attached and suspended biomass are assumed to be of a first-order type.
+
+The growth rates of suspended and attached biomass are as given below,
+with the specific growth rate calculated using double Monod kinetics to reproduce the dependence of
+the microbial growth on both substrate and oxygen.
+
+```math
+r_\mathrm{g}^\mathrm{b} = \mu_\mathrm{g} C_\mathrm{w}^\mathrm{b}S_\mathrm{w}\phi; \\
+ r_\mathrm{g}^\mathrm{f} = \mu_\mathrm{g} \phi_\mathrm{f}\rho_\mathrm{f}; \\
+ \mu_\mathrm{g} = k_\mathrm{\mu}
+ \frac{C_\mathrm{w}^\mathrm{s}}{K_\mathrm{s} + C_\mathrm{w}^\mathrm{s}}
+ \frac{C_\mathrm{w}^\mathrm{O_2}}{K_\mathrm{O_2} + C_\mathrm{w}^\mathrm{O_2}}.
+```
+
+Here, $`k_\mathrm{\mu}`$ is the maximum specific growth rate, according to [@Connolly2014],
+$`C_\mathrm{w}^\mathrm{s}`$ and $`C_\mathrm{w}^\mathrm{O_2}`$ are the mass concentrations of substrate and oxygen in the water phase and
+K<sub>s</sub> and K<sub>O<sub>2</sub></sub> are the half-saturation coefficients for substrate and oxygen respectively.
+
+The decay rates are calculated similarly to the growth rates,
+except that the specific decay rates of suspended and attached biomass
+take different processes into account, increasing inactivation.
+For suspended biomass, non-optimal acidic pH is assumed to increase inactivation.
+As calcite precipitates mainly in or close to the biofilm, cells may be covered with calcite precipitates
+or disrupted by crystals inactivating the affected cells ([@Dupraz2009a] and [@Whiffin2007]).
+Consequently, the precipitation rate is assumed to increase the specific decay rate of attached biomass.
+
+
+```math
+r_\mathrm{b}^\mathrm{b} = k_\mathrm{b}^\mathrm{b} C_\mathrm{w}^\mathrm{b}S_\mathrm{w}\phi; \\
+ r_\mathrm{b}^\mathrm{f} = k_\mathrm{b}^\mathrm{f}\phi_\mathrm{f}\rho_\mathrm{f}; \\
+k_\mathrm{b}^\mathrm{b}=b_0\left(1+\frac{K_\mathrm{pH}}{m_\mathrm{H^{+}}^2}\right); \\
+ k_\mathrm{b}^\mathrm{f} = b_0 + \frac{r_\mathrm{prec} M^\mathrm{c}}{\rho_\mathrm{c}\left(\phi_0 - \phi_\mathrm{c}\right)}
+```
+
+The attachment rate quantifies the biomass transfer from
+the suspended to the attached state.
+As attachment is modeled assuming a first-order kinetic rather than a
+sorption-type behavior, with preferential attachment to previously attached biomass:
+
+```math
+r_\mathrm{a}= k_\mathrm{a} C^\mathrm{b}_\mathrm{w} \phi S_\mathrm{w};\\
+k_\mathrm{a}=c_\mathrm{a,1} \phi_\mathrm{f} + c_\mathrm{a,2},
+```
+
+Detachment of biomass from biofilm is assumed to be proportional to the shear stress.
+Additionally, the growth contributes to the detachment rate, as vigorously growing
+biofilm is typically weaker and as such more susceptible to detachment.
+As the model of [@Ebigbo2012] is defined on the Darcy scale but the shear stress is a micro-scale property,
+it is approximated using the absolute value of the water-phase potential gradient:
+
+```math
+r_\mathrm{d}=k_\mathrm{d} \phi_\mathrm{f} \rho_\mathrm{f};\\
+k_\mathrm{d}=c_\mathrm{d}
+\left( \phi S_\mathrm{w} \left|\nabla p_\mathrm{w} - \rho_\mathrm{w} \mathbf{g} \right| \right)^{0.58}
++ \frac{\phi_\mathrm{f}}{\phi_0-\phi_\mathrm{c}} \mu_\mathrm{g}.
+```
+
+Here, $`c_\mathrm{d}`$ is a coefficient for the shear-stress-dependent detachment,
+$`\left|\nabla p_\mathrm{w} - \rho_\mathrm{w} \mathbf{g} \right|`$ the absolute value of
+the water-phase potential gradient, and $`\phi_0`$ the initial porosity.
+
+
+## Substrate and oxygen
+The consumption of substrate and oxygen is linked to the growth of both suspended and attached biomass
+by the yield coefficient Y of substrate. In the case of oxygen, the coefficient F, which is the ration of oxygen consumed per substrate consumed,
+is used to express the biomass yield per oxygen consumed:
+
+```math
+q^\mathrm{s} = - \frac{r^\mathrm{b}_\mathrm{g} + r^\mathrm{f}_\mathrm{g}}{M^\mathrm{s}Y}; \\
+ q^\mathrm{O_2} = F q^\mathrm{s} = - F \frac{ r^\mathrm{b}_\mathrm{g} + r^\mathrm{f}_\mathrm{g}} {M^\mathrm{O_2}Y}.
+```
+
+## Supplementary equations
+\subsubsection{Permeability and porosity}\label{sec:perm_poro_pw}
+The permeability decreases due to biofilm growth and calcite precipitation.
+In the model, the reduction of permeability is calculated based on the
+reduction of porosity using a Kozenzy-Carman-type relationship:
+
+```math
+\frac{K}{K_\mathrm{0}}=\left(\frac{\phi}{\phi_\mathrm{0}}\right)^3 \left(\frac{1-\phi_0}{1-\phi}\right)^2.
+```
+
+Here, $`K_\mathrm{0}`$ is the initial permeability,
+and $`\phi_0`$ is the initial porosity. The porosity decreases as
+the volume fractions of biofilm and calcite increase:
+
+```math
+\phi=\phi_\mathrm{0}-\phi_\mathrm{c}-\phi_\mathrm{f}.
+```
+
+
+## Fluid properties
+The density and the viscosity of the CO<sub>2</sub> phase are calculated using
+the relation given by [@Span1996] and [@Fenghour1998] respectively.
+In these calculations, the effects of the small amounts of water and oxygen are neglected.
+The density and the viscosity of the aqueous phase are calculated
+according to [@Batzle1992] as a function of salinity.
+Sodium, chloride and calcium are considered to contribute to the salinity.
+
+
+## Phase partitioning of components
+The dissolution of CO<sub>2</sub> in the aqueous phase is calculated according
+to [@Duan2003] as a function of temperature, pressure and salinity.
+In the two-phase case, the concentration of carbonic acid is assumed to be
+equal to the solubility while, in the case of the exclusive presence of the aqueous phase,
+the concentration of inorganic carbon
+is exclusively dependent on the precipitation, dissolution and ureolysis reactions.
+In this case, the solubility represents the maximum possible concentration.
+For the solubility of oxygen in the aqueous phase, Henry's law is used.
+
+
+
+
+
+[@Batzle1992]: https://library.seg.org/doi/10.1190/1.1443207 "Seismic Properties of Pore Fluids"
+[@Class2002]: https://www.sciencedirect.com/science/article/pii/S0309170802000155 "Numerical simulation of non-isothermal multiphase multicomponent processes in porous media. 2. Applications for the injection of steam and air"
+[@Connolly2014]: http://www.ncbi.nlm.nih.gov/pubmed/23835134 "Construction of two ureolytic model organisms for the study of microbially induced calcium carbonate precipitation"
+[@Duan2003]: https://www.sciencedirect.com/science/article/pii/S0009254102002632 "An improved model calculating CO<sub>2</sub> solubility in pure water and aqueous NaCl solutions from 273 to 533 K and from 0 to 2000 bar"
+[@Chou1989]: https://www.sciencedirect.com/science/article/pii/0009254189900636 "Comparative study of the kinetics and mechanisms of dissolution of carbonate minerals"
+[@Compton1989]: https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2427.1989.tb01101.x "The dissolution of calcite in acid waters: Mass transport versus surface control"
+[@Dupraz2009a]: http://linkinghub.elsevier.com/retrieve/pii/S0009254109002265 "Experimental and numerical modeling of bacterially induced pH increase and calcite precipitation in saline aquifers"
+[@Whiffin2007]: https://www.tandfonline.com/doi/full/10.1080/01490450701436505 "Microbial Carbonate Precipitation as a Soil Improvement Technique"
+[@Ebigbo2012]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2011WR011714 "Darcy-scale modeling of microbially induced carbonate mineral precipitation in sand columns"
+[@Fenghour1998]: https://aip.scitation.org/doi/10.1063/1.556013 "The Viscosity of Carbon Dioxide"
+[@Hommel2015]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2014WR016503 "A revised model for microbially induced calcite precipitation: Improvements and new insights based on recent experiments"
+[@Hommel2016]: https://elib.uni-stuttgart.de/handle/11682/8787 "Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation"
+[@Lauchnor2015]: http://dx.doi.org/10.1111/jam.12804 "Whole cell kinetics of ureolysis by Sporosarcina pasteurii"
+[@Mitchell2008]: https://www.sciencedirect.com/science/article/pii/S0896844608002040 "Resilience of planktonic and biofilm cultures to supercritical CO<sub>2</sub>"
+[@Span1996]: https://aip.scitation.org/doi/abs/10.1063/1.555991 "A new equation of state for carbon dioxide covering the fluid region from the triple-point temperature to 1100 K at pressures up to 800 MPa"
diff --git a/examples/biomineralization/doc/setup.md b/examples/biomineralization/doc/setup.md
new file mode 100644
index 0000000000..8debae39a9
--- /dev/null
+++ b/examples/biomineralization/doc/setup.md
@@ -0,0 +1,938 @@
+<!-- Important: This file has been automatically generated by generate_example_docs.py. Do not edit this file directly! -->
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 2](mainfile.md) | [:arrow_right: Continue with part 4](fluidmaterial.md) |
+|---|---|---:|
+
+# Simulation Setup
+
+The setup for this example is based on the initial 100000s of the _column experiment D1_ described in [@Hommel2015] and can also be found in Section 4.2 of [@Hommel2016] under the name _column experiment D1_.
+We here only consider the "simplified chemistry case" in which it is assumed that the precipitation rate is equal to the ureolysis rate to simplify the chemical processes considered ($`r_\mathrm{prec} = r_\mathrm{urea}`$) (see Chapter 6 [@Hommel2016]).
+
+The column is considered as a 1D domain with injections of various aqueous solutions at the bottom (Neumann boundary condition)
+and a fixed pressure at the top (Dirichlet boundary condition).
+The various types of injected fluid compositions are read from an additional input file `injections_type.dat`.
+Depending on the injection type, the `problem.hh` adapts the composition of the injected aqueous solution for the bottom Neumann boundary condition.
+Further, `spatialparams.hh` is an example for spatial parameters dealing with changing porosity and permeability.
+
+The subsequent file documentation is structured as follows:
+
+[[_TOC_]]
+
+[@Hommel2015]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2014WR016503 "A revised model for microbially induced calcite precipitation: Improvements and new insights based on recent experiments"
+[@Hommel2016]: https://elib.uni-stuttgart.de/handle/11682/8787 "Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation"
+
+
+## Initial and boundary conditions (`problem.hh`)
+
+This file contains the __problem class__ which defines the initial and boundary
+conditions for the biominearalization example.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../problem.hh))</summary>
+
+
+### Include files
+
+```cpp
+// This header contains the PorousMediumFlowProblem class
+#include <dumux/porousmediumflow/problem.hh>
+#include <dumux/common/properties.hh> // GetPropType
+#include <dumux/material/components/ammonia.hh>
+#include <dumux/discretization/evalgradients.hh>
+#include <dumux/io/container.hh>
+#include <algorithm> // for std::transform
+```
+
+### The problem class
+The problem class defines the boundary and initial conditions.
+As this is a biomineralization problem in porous media, we inherit from the porous-media-flow problem
+
+```cpp
+namespace Dumux {
+
+template <class TypeTag>
+class MICPColumnProblemSimpleChemistry : public PorousMediumFlowProblem<TypeTag>
+{
+ using ParentType = PorousMediumFlowProblem<TypeTag>;
+ using Scalar = GetPropType<TypeTag, Properties::Scalar>;
+ using NH3 = Components::Ammonia<Scalar>; // for molar mass of Ammonia
+ using FluidSystem = GetPropType<TypeTag, Properties::FluidSystem>;
+ using SolidSystem = GetPropType<TypeTag, Properties::SolidSystem>;
+ using VolumeVariables = GetPropType<TypeTag, Properties::VolumeVariables>;
+ using FluxVariables = GetPropType<TypeTag, Properties::FluxVariables>;
+ using Indices = typename GetPropType<TypeTag, Properties::ModelTraits>::Indices;
+
+ // We define some indices for convenience to be used later when defining the initial and boundary conditions
+ enum {
+ numComponents = FluidSystem::numComponents,
+
+ pressureIdx = Indices::pressureIdx,
+ switchIdx = Indices::switchIdx, //Saturation
+ xwNaIdx = FluidSystem::NaIdx,
+ xwClIdx = FluidSystem::ClIdx,
+ xwCaIdx = FluidSystem::CaIdx,
+ xwUreaIdx = FluidSystem::UreaIdx,
+ xwO2Idx = FluidSystem::O2Idx,
+ xwBiosubIdx = FluidSystem::GlucoseIdx,
+ xwSuspendedBiomassIdx = FluidSystem::SuspendedBiomassIdx,
+ phiBiofilmIdx = numComponents,
+ phiCalciteIdx = numComponents + 1,
+
+ //Indices of the components
+ wCompIdx = FluidSystem::wCompIdx,
+ nCompIdx = FluidSystem::nCompIdx,
+ NaIdx = FluidSystem::NaIdx,
+ ClIdx = FluidSystem::ClIdx,
+ CaIdx = FluidSystem::CaIdx,
+ UreaIdx = FluidSystem::UreaIdx,
+ O2Idx = FluidSystem::O2Idx,
+ BiosubIdx = FluidSystem::GlucoseIdx,
+ SuspendedBiomassIdx = FluidSystem::SuspendedBiomassIdx,
+
+ wPhaseIdx = FluidSystem::wPhaseIdx,
+ conti0EqIdx = Indices::conti0EqIdx,
+
+ // Phase State
+ wPhaseOnly = Indices::firstPhaseOnly,
+ bothPhases = Indices::bothPhases
+ };
+
+ using PrimaryVariables = GetPropType<TypeTag, Properties::PrimaryVariables>;
+ using NumEqVector = GetPropType<TypeTag, Properties::NumEqVector>;
+ using BoundaryTypes = GetPropType<TypeTag, Properties::BoundaryTypes>;
+ using ElementVolumeVariables = typename GetPropType<TypeTag, Properties::GridVolumeVariables>::LocalView;
+ using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>;
+ using GridView = typename GridGeometry::GridView;
+ using Element = typename GridView::template Codim<0>::Entity;
+ using FVElementGeometry = typename GridGeometry::LocalView;
+ using SubControlVolume = typename GridGeometry::SubControlVolume;
+ using GlobalPosition = typename Element::Geometry::GlobalCoordinate;
+ static constexpr int dim = GridView::dimension;
+```
+
+
+We define an enum class to distinguish between different injection processes.
+We will use these later in the definition of the Neumann boundary conditions.
+
+```cpp
+ enum class InjectionProcess : int
+ {
+ noInjection = -99,
+ noFlow = -9,
+ rinse = -1,
+ resuscitation = 3,
+ inoculation = 2,
+ mineralization = 1
+ };
+```
+
+
+### Reading of parameters specified in the params.input file
+<details><summary> Click to show parameters</summary>
+
+```cpp
+public:
+ // This is the constructor of our problem class.
+ MICPColumnProblemSimpleChemistry(std::shared_ptr<const GridGeometry> gridGeometry)
+ : ParentType(gridGeometry)
+ {
+ // We read the parameters from the params.input file.
+ name_ = getParam<std::string>("Problem.Name");
+ temperature_ = getParam<Scalar>("Problem.Temperature");
+
+ // biomass parameters
+ ca1_ = getParam<Scalar>("BioCoefficients.Ca1");
+ ca2_ = getParam<Scalar>("BioCoefficients.Ca2");
+ cd1_ = getParam<Scalar>("BioCoefficients.Cd1");
+ dc0_ = getParam<Scalar>("BioCoefficients.Dc0");
+ kmue_ = getParam<Scalar>("BioCoefficients.Kmue");
+ f_ = getParam<Scalar>("BioCoefficients.F");
+ ke_ = getParam<Scalar>("BioCoefficients.Ke");
+ ks_ = getParam<Scalar>("BioCoefficients.Ks");
+ yield_ = getParam<Scalar>("BioCoefficients.Yield");
+
+ // ureolysis kinetic parameters
+ kub_ = getParam<Scalar>("UreolysisCoefficients.Kub");
+ kurease_ = getParam<Scalar>("UreolysisCoefficients.Kurease");
+ ku_ = getParam<Scalar>("UreolysisCoefficients.Ku");
+
+ // initial values
+ densityW_ = getParam<Scalar>("Initial.DensityW");
+ initPressure_ = getParam<Scalar>("Initial.Pressure");
+
+ initxwTC_ = getParam<Scalar>("Initial.XwTC");
+ initxwNa_ = getParam<Scalar>("Initial.XwNa");
+ initxwCl_ = getParam<Scalar>("Initial.XwCl");
+ initxwCa_ = getParam<Scalar>("Initial.XwCa");
+ initxwUrea_ = getParam<Scalar>("Initial.XwUrea");
+ initxwTNH_ = getParam<Scalar>("Initial.XwTNH");
+ initxwO2_ = getParam<Scalar>("Initial.XwO2");
+ initxwBiosub_ = getParam<Scalar>("Initial.XwSubstrate");
+ initxwBiosusp_ = getParam<Scalar>("Initial.XwSuspendedBiomass");
+ initCalcite_ = getParam<Scalar>("Initial.Calcite");
+ initBiofilm_ = getParam<Scalar>("Initial.Biofilm");
+
+ xwNaCorr_ = getParam<Scalar>("Initial.XwNaCorr");
+ xwClCorr_ = getParam<Scalar>("Initial.XwClCorr");
+
+ // injection values
+ injQ_ = getParam<Scalar>("Injection.FlowRate");
+
+ injTC_ = getParam<Scalar>("Injection.MassFracTC");
+ injNa_ = getParam<Scalar>("Injection.ConcentrationNa");
+ injCa_ = getParam<Scalar>("Injection.ConcentrationCa");
+ injUrea_ = getParam<Scalar>("Injection.ConcentrationUrea");
+ injTNH_ = getParam<Scalar>("Injection.ConcentrationTNH");
+ injO2_ = getParam<Scalar>("Injection.ConcentrationO2");
+ injSub_ = getParam<Scalar>("Injection.ConcentrationSubstrate");
+ injBiosusp_= getParam<Scalar>("Injection.ConcentrationSuspendedBiomass");
+ injNaCorr_ = getParam<Scalar>("Injection.ConcentrationNaCorr");
+```
+
+</details>
+
+### Reading of the temporal sequence of the different types of injection
+Here, the number of injections and the corresponding parameters are defined based on what is specified in the input files.
+
+```cpp
+ // We get the number of injections and the injection data file name from params.input
+ numInjections_ = getParam<int>("Injection.NumInjections");
+
+ // We resize the permeability vector contaning the permeabilities for the additional output
+ permeability_.resize(gridGeometry->numDofs());
+
+ // We read from the injection data file which injection type we have in each episode.
+ // We will use this in the Neumann boundary condition to set time dependend, changing boundary conditions.
+ // We do this similarly to the episode ends in the main file.
+ const auto injType = readFileToContainer<std::vector<int>>("injection_type.dat");
+ // translate integer to InjectionProcess type
+ std::transform(injType.begin(), injType.end(), std::back_inserter(injectionType_),
+ [](int n){ return static_cast<InjectionProcess>(n); });
+```
+
+We check the injection data against the number of injections specified in the parameter file
+and print an error message if the test fails
+
+```cpp
+ if (injectionType_.size() != numInjections_)
+ DUNE_THROW(Dune::IOError, "numInjections from the parameterfile and the number of injection types "
+ << "specified in the injection data file do not match!\n"
+ << "numInjections from parameter file: " << numInjections_ << "\n"
+ << "numInjTypes from injection data file: "<< injectionType_.size());
+
+ // Initialize the fluidsystem
+ FluidSystem::init(/*startTemp=*/temperature_ -5.0, /*endTemp=*/temperature_ +5.0, /*tempSteps=*/5,
+ /*startPressure=*/1e4, /*endPressure=*/1e6, /*pressureSteps=*/500);
+ }
+```
+
+In the follwing, functions to set the time, time step size and the index of the episode
+are declared which are used the time loop in main.cc
+
+```cpp
+ void setTime(const Scalar t)
+ { time_ = t; }
+
+ // We need the time step size to regularize the reactive source terms.
+ void setTimeStepSize(const Scalar dt)
+ { timeStepSize_ = dt; }
+
+ // We need the episode index to choose the right Neumann boundary condition for each episode based on the injection data.
+ void setEpisodeIdx(const Scalar epIdx)
+ { episodeIdx_ = epIdx; }
+```
+
+Here, functions to return the injectionType, the name of the problem and the temperature
+are defined
+
+```cpp
+ int injectionType(int episodeIdx) const
+ { return injectionType_[episodeIdx]; }
+
+ // Get the problem name. It is used as a prefix for files generated by the simulation.
+ const std::string& name() const
+ { return name_; }
+
+ // Return the temperature
+ Scalar temperature() const
+ { return temperature_; }
+```
+
+#### Boundary conditions
+With the following function we define the type of boundary conditions depending on the location. Two types of boundary conditions
+can be specified: Dirichlet or Neumann boundary condition. On a Dirichlet boundary, the values of the
+primary variables need to be fixed. On a Neumann boundary condition, values for derivatives need to be fixed.
+
+```cpp
+ BoundaryTypes boundaryTypesAtPos(const GlobalPosition &globalPos) const
+ {
+ BoundaryTypes bcTypes;
+ // We set all to Neumann, except for the top boundary, which is set to Dirichlet.
+ const Scalar zmax = this->gridGeometry().bBoxMax()[dim - 1];
+ bcTypes.setAllNeumann();
+ if (globalPos[dim - 1] > zmax - eps_)
+ bcTypes.setAllDirichlet();
+
+ return bcTypes;
+ }
+```
+
+We define the Dirichlet boundary conditions
+
+```cpp
+ PrimaryVariables dirichletAtPos(const GlobalPosition &globalPos) const
+ {
+ PrimaryVariables priVars(0.0);
+ priVars.setState(wPhaseOnly);
+ // We recycle the initial conditions, but additionally enforce that substrate and oxygen necessary for biomass growth are zero.
+ priVars = initial_(globalPos);
+ priVars[xwBiosubIdx] = 0.0;
+ priVars[xwO2Idx] = 0.0;
+ return priVars;
+ }
+```
+
+The injections can be described with a Neumann boundary condition.
+Since we have multiple injections durng the whole simulation period, the Neumann boundary conditions in this case are time or rather episode depended.
+
+```cpp
+ NumEqVector neumannAtPos(const GlobalPosition& globalPos) const
+ {
+ // We only have injection at the bottom, negative values for injection
+ if (globalPos[dim - 1] > eps_)
+ return NumEqVector(0.0);
+
+ // We calculate the injected water velocity based on the volume flux injected into a 1 inch diameter column.
+ const Scalar diameter = 0.0254;
+ const Scalar waterFlux = injQ_/(3.14*diameter*diameter/4.); //[m/s]
+ const auto injProcess = injectionType_[episodeIdx_];
+
+ // We also have no-injection, no-flow periods, which are coded for by -99 or 9.
+ // Thus, for no flow, we set the Neumann BC to zero for all components.
+ if (injProcess == InjectionProcess::noInjection || injProcess == InjectionProcess::noFlow)
+ return NumEqVector(0.0);
+
+ // We set the injection BC to the basic rinse injection and later only change the BC for those components that are different.
+ NumEqVector values(0.0);
+
+ values[conti0EqIdx + wCompIdx] = -waterFlux * 996/FluidSystem::molarMass(wCompIdx);
+ values[conti0EqIdx + nCompIdx] = -waterFlux * injTC_*996 /FluidSystem::molarMass(nCompIdx);
+ values[conti0EqIdx + xwCaIdx] = 0;
+ values[conti0EqIdx + xwSuspendedBiomassIdx] = 0;
+ values[conti0EqIdx + xwBiosubIdx] = -waterFlux * injSub_ /FluidSystem::molarMass(xwBiosubIdx);
+ values[conti0EqIdx + xwO2Idx] = -waterFlux * injO2_ /FluidSystem::molarMass(O2Idx);
+ values[conti0EqIdx + xwUreaIdx] = 0;
+ values[conti0EqIdx + phiCalciteIdx] = 0;
+ values[conti0EqIdx + phiBiofilmIdx] = 0;
+ values[conti0EqIdx + xwNaIdx] = -waterFlux * (injNa_ + injNaCorr_) /FluidSystem::molarMass(NaIdx);
+ values[conti0EqIdx + xwClIdx] = -waterFlux *injTNH_ /NH3::molarMass() //NH4Cl ---> mol Cl = mol NH4
+ -waterFlux *injNa_ /FluidSystem::molarMass(NaIdx); //NaCl ---> mol Cl = mol Na
+ // rinse, used as standard injection fluid
+ if (injProcess == InjectionProcess::rinse)
+ {
+ return values; // do not change anything.
+ }
+
+ // injProcess == 1 codes for an injection of mineralization medium containing urea and calcium chloride.
+ // Thus, we add BC terms for those components.
+ // Additionally, we need to adjust the amount of water injected due to the high concentration of other components injected.
+ // Finally, we need to adapt the injected NaCorr concentration to account fo the lower pH.
+ else if (injProcess == InjectionProcess::mineralization)
+ {
+ values[conti0EqIdx + wCompIdx] = - waterFlux * 0.8716 * densityW_ /FluidSystem::molarMass(wCompIdx); //0.8716 factor accounts for less water per volume due to relatively high solute concentrations!
+ values[conti0EqIdx + nCompIdx] = - waterFlux * injTC_ * densityW_ /FluidSystem::molarMass(nCompIdx);
+ values[conti0EqIdx + xwCaIdx] = - waterFlux * injCa_/FluidSystem::molarMass(CaIdx);
+ values[conti0EqIdx + xwUreaIdx] = - waterFlux * injUrea_ /FluidSystem::molarMass(UreaIdx);
+ values[conti0EqIdx + xwNaIdx] = - waterFlux * injNa_ /FluidSystem::molarMass(NaIdx)
+ - waterFlux * injNaCorr_ /FluidSystem::molarMass(NaIdx)* 0.032;
+ values[conti0EqIdx + xwClIdx] = - waterFlux * injTNH_ /NH3::molarMass() //NH4Cl ---> mol Cl = mol NH4
+ - waterFlux * 2 * injCa_/FluidSystem::molarMass(CaIdx) //+CaCl2 ---> mol Cl = mol Ca*2
+ -waterFlux *injNa_ /FluidSystem::molarMass(NaIdx); //NaCl ---> mol Cl = mol Na
+ return values;
+ }
+
+ // injProcess == 3 codes for a resuscitation injection to regrow biomass.
+ // It is similar to a rinse injection, but with added urea, which is what we add to the basic rinse
+ else if (injProcess == InjectionProcess::resuscitation )
+ {
+ values[conti0EqIdx + xwUreaIdx] = - waterFlux * injUrea_ /FluidSystem::molarMass(UreaIdx);
+ return values;
+ }
+
+ // injProcess == 2 codes for a inoculation or biomass injection.
+ // It is similar to a rinse injection, but with added suspended biomass, which is what we add to the basic rinse
+ else if (injProcess == InjectionProcess::inoculation)
+ {
+ values[conti0EqIdx + xwSuspendedBiomassIdx] = -waterFlux * injBiosusp_ /FluidSystem::molarMass(xwSuspendedBiomassIdx);
+ return values;
+ }
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid injection process " << static_cast<int>(injProcess));
+ }
+```
+
+#### Initial conditions
+We specify the initial conditions for the primary variable depending
+on the location. Here, we set zero model fractions everywhere in the domain except for a strip
+at the bottom of the domain where we set an initial mole fraction of $`1e-9`$.
+
+```cpp
+ PrimaryVariables initialAtPos(const GlobalPosition& globalPos) const
+ { return initial_(globalPos); }
+```
+
+#### Reactive source and sink terms
+We calculate the reactive source and sink terms.
+For the details, see the "simplified chemistry case" in the dissertation of Hommel available at https://elib.uni-stuttgart.de/handle/11682/8787
+
+```cpp
+ NumEqVector source(const Element &element,
+ const FVElementGeometry& fvGeometry,
+ const ElementVolumeVariables& elemVolVars,
+ const SubControlVolume &scv) const
+ {
+ const auto elemSol = elementSolution(element, elemVolVars, fvGeometry);
+ const auto gradPw = evalGradients(element,
+ element.geometry(),
+ this->gridGeometry(),
+ elemSol,
+ scv.center())[pressureIdx];
+ const Scalar scvPotGradNorm = gradPw.two_norm();
+
+ //define and compute some parameters for siplicity:
+ const Scalar porosity = elemVolVars[scv].porosity();
+ Scalar initialPorosity = 1.0;
+ constexpr int numActiveComps = SolidSystem::numComponents-SolidSystem::numInertComponents;
+ for (int i = numActiveComps; i<SolidSystem::numComponents; ++i)
+ initialPorosity -= elemVolVars[scv].solidVolumeFraction(i);
+
+ const Scalar Sw = elemVolVars[scv].saturation(wPhaseIdx);
+ const Scalar xlSalinity = elemVolVars[scv].moleFraction(wPhaseIdx,NaIdx)
+ + elemVolVars[scv].moleFraction(wPhaseIdx,CaIdx)
+ + elemVolVars[scv].moleFraction(wPhaseIdx,ClIdx);
+ const Scalar densityBiofilm = elemVolVars[scv].solidComponentDensity(SolidSystem::BiofilmIdx);
+ const Scalar densityCalcite = elemVolVars[scv].solidComponentDensity(SolidSystem::CalciteIdx);
+ const Scalar cBio = std::max(0.0, elemVolVars[scv].moleFraction(wPhaseIdx, SuspendedBiomassIdx)
+ * elemVolVars[scv].molarDensity(wPhaseIdx)
+ * FluidSystem::molarMass(SuspendedBiomassIdx)); //[kg_suspended_Biomass/m³_waterphase]
+ const Scalar volFracCalcite = std::max(0.0, elemVolVars[scv].solidVolumeFraction(SolidSystem::CalciteIdx));
+ const Scalar volFracBiofilm = std::max(0.0, elemVolVars[scv].solidVolumeFraction(SolidSystem::BiofilmIdx));
+ const Scalar massBiofilm = densityBiofilm * volFracBiofilm;
+ const Scalar cSubstrate = std::max(0.0, elemVolVars[scv].moleFraction(wPhaseIdx, BiosubIdx)
+ * elemVolVars[scv].molarDensity(wPhaseIdx)
+ * FluidSystem::molarMass(BiosubIdx)); //[kg_substrate/m³_waterphase]
+ const Scalar cO2 = std::max(0.0, elemVolVars[scv].moleFraction(wPhaseIdx, O2Idx)
+ * elemVolVars[scv].molarDensity(wPhaseIdx)
+ * FluidSystem::molarMass(O2Idx)); //[kg_oxygen/m³_waterphase]
+ const Scalar mUrea = std::max(0.0, moleFracToMolality(elemVolVars[scv].moleFraction(wPhaseIdx,UreaIdx),
+ xlSalinity,
+ elemVolVars[scv].moleFraction(wPhaseIdx,nCompIdx))); //[mol_urea/kg_H2O]
+ // compute rate of ureolysis:
+ const Scalar vmax = kurease_;
+ const Scalar Zub = kub_ * massBiofilm; // [kgurease/m³]
+ const Scalar rurea = vmax * Zub * mUrea / (ku_ + mUrea); //[mol/m³s]
+
+ // compute precipitation rate of calcite, no dissolution! Simplification: rprec = rurea
+ // additionally regularize the precipitation rate that we do not precipitate more calcium than available.
+ const Scalar maxPrecipitationRate = elemVolVars[scv].moleFraction(wPhaseIdx,CaIdx) * Sw * porosity
+ * elemVolVars[scv].molarDensity(wPhaseIdx) / timeStepSize_;
+ const Scalar rprec = std::min(rurea, maxPrecipitationRate);
+
+ //compute biomass growth coefficient and rate
+ const Scalar mue = kmue_ * cSubstrate / (ks_ + cSubstrate) * cO2 / (ke_ + cO2);// [1/s]
+ const Scalar rgf = mue * massBiofilm; //[kg/m³s]
+ const Scalar rgb = mue * porosity * Sw * cBio; //[kg/m³s]
+
+ // compute biomass decay coefficient and rate:
+ const Scalar dcf = dc0_ + (rprec * SolidSystem::molarMass(SolidSystem::CalciteIdx)
+ /(densityCalcite * (initialPorosity - volFracCalcite)));
+ const Scalar dcb = dc0_; //[1/s]
+ const Scalar rdcf = dcf * massBiofilm; //[kg/m³s]
+ const Scalar rdcb = dcb * porosity * Sw * cBio; //[kg/m³s]
+
+ // compute attachment coefficient and rate:
+ const Scalar ka = ca1_ * volFracBiofilm + ca2_; //[1/s]
+ const Scalar ra = ka * porosity * Sw * cBio; //[kg/m³s]
+
+ // compute detachment coefficient and rate:
+ const Scalar cd2 = volFracBiofilm / (initialPorosity - volFracCalcite); //[-]
+ const Scalar kd = cd1_ * std::pow((porosity * Sw * scvPotGradNorm),0.58) + cd2 * mue; //[1/s]
+ const Scalar rd = kd * massBiofilm; //[kg/m³s]
+
+ // rprec[mol/m³s]
+ // rurea[mol/m³s]
+ // rgb + rdcb + ra + rd [kg/m³s]
+ // source[kg/m³s]
+ NumEqVector source(0.0);
+ source[wCompIdx] += 0;
+ source[nCompIdx] += rurea - rprec;
+ source[NaIdx] += 0;
+ source[ClIdx] += 0;
+ source[CaIdx] += - rprec;
+ source[UreaIdx] += - rurea;
+ source[O2Idx] += -(rgf + rgb) *f_/yield_ / FluidSystem::molarMass(O2Idx);
+ source[BiosubIdx] += -(rgf + rgb) / yield_ / FluidSystem::molarMass(BiosubIdx);
+ source[SuspendedBiomassIdx] += (rgb - rdcb - ra + rd) / FluidSystem::molarMass(SuspendedBiomassIdx);
+ source[phiBiofilmIdx] += (rgf - rdcf + ra - rd) / SolidSystem::molarMass(SolidSystem::BiofilmIdx);
+ source[phiCalciteIdx] += + rprec;
+
+ return source;
+ }
+```
+
+The permeability is added to the vtk output
+
+```cpp
+ // Function to return the permeability for additional vtk output
+ const std::vector<Scalar>& getPermeability()
+ { return permeability_; }
+
+ // Function to update the permeability for additional vtk output
+ template<class SolutionVector>
+ void updateVtkOutput(const SolutionVector& curSol)
+ {
+ for (const auto& element : elements(this->gridGeometry().gridView()))
+ {
+ const auto elemSol = elementSolution(element, curSol, this->gridGeometry());
+ auto fvGeometry = localView(this->gridGeometry());
+ fvGeometry.bindElement(element);
+ for (const auto& scv : scvs(fvGeometry))
+ {
+ VolumeVariables volVars;
+ volVars.update(elemSol, *this, element, scv);
+ const auto dofIdxGlobal = scv.dofIndex();
+ permeability_[dofIdxGlobal] = volVars.permeability();
+ }
+ }
+ }
+```
+
+### Declaring all necessary variables and private fuctions
+The internal methods are defined here
+
+```cpp
+private:
+ // Internal method for the initial condition reused for the dirichlet conditions.
+ PrimaryVariables initial_(const GlobalPosition &globalPos) const
+ {
+ PrimaryVariables priVars(0.0);
+ priVars.setState(wPhaseOnly);
+ priVars[pressureIdx] = initPressure_ ; //70e5; // - (maxHeight - globalPos[1])*densityW_*9.81; //p_atm + rho*g*h
+ priVars[switchIdx] = initxwTC_;
+ priVars[xwNaIdx] = initxwNa_ + xwNaCorr_;
+ priVars[xwClIdx] = initxwCl_ + initxwTNH_ + 2*initxwCa_ + xwClCorr_;
+ priVars[xwCaIdx] = initxwCa_;
+ priVars[xwUreaIdx] = initxwUrea_;
+ priVars[xwO2Idx] = initxwO2_;
+ priVars[xwBiosubIdx] = initxwBiosub_;
+ priVars[xwSuspendedBiomassIdx] = initxwBiosusp_;
+ priVars[phiBiofilmIdx] = initBiofilm_; // [m^3/m^3]
+ priVars[phiCalciteIdx] = initCalcite_; // [m^3/m^3]
+ return priVars;
+ }
+
+ // Internal method to calculate the molality of a component based on its mole fraction.
+ static Scalar moleFracToMolality(Scalar moleFracX, Scalar moleFracSalinity, Scalar moleFracCTot)
+ {
+ const Scalar molalityX = moleFracX / (1 - moleFracSalinity - moleFracCTot)
+ / FluidSystem::molarMass(FluidSystem::H2OIdx);
+ return molalityX;
+ }
+```
+
+The remainder of the class contains an epsilon value used for floating point comparisons
+and parameters needed to describe the chemical processess.
+Additionally the problem name, the peremability vector as well as some time-parameters are declared
+<details><summary> Click to show private members</summary>
+eps is used as a small value for the definition of the boundary conditions
+
+```cpp
+ static constexpr Scalar eps_ = 1e-6;
+```
+
+initial condition parameters
+
+```cpp
+ Scalar initPressure_;
+ Scalar densityW_;//1087; // rhow=1087;
+ Scalar initxwTC_;//2.3864e-7; // [mol/mol]
+ Scalar initxwNa_;//0;
+ Scalar initxwCl_;//0;
+ Scalar initxwCa_;//0;
+ Scalar initxwUrea_;//0;
+ Scalar initxwTNH_;//3.341641e-3;
+ Scalar initxwO2_;//4.4686e-6;
+ Scalar initxwBiosub_;//2.97638e-4;
+ Scalar initxwBiosusp_;//0;
+ Scalar xwNaCorr_;//2.9466e-6;
+ Scalar xwClCorr_;//0;
+ Scalar initBiofilm_;
+ Scalar initCalcite_;
+ Scalar temperature_;
+```
+
+biomass parameters for source/sink calculations
+
+```cpp
+ Scalar ca1_;
+ Scalar ca2_;
+ Scalar cd1_;
+ Scalar dc0_;
+ Scalar kmue_ ;
+ Scalar f_;
+ Scalar ke_;
+ Scalar ks_;
+ Scalar yield_;
+```
+
+urease parameters for source/sink calculations
+
+```cpp
+ Scalar kub_;
+ Scalar kurease_;
+ Scalar ku_;
+```
+
+injection parameters
+
+```cpp
+ Scalar injQ_;
+ Scalar injTC_; // [kg/kg]
+ Scalar injNa_; // [kg/m³]
+ Scalar injCa_; // [kg/m³] //computed from CaCl2
+ Scalar injUrea_; // [kg/m³]
+ Scalar injTNH_; // [kg/m³] //computed from NH4Cl
+ Scalar injO2_; // [kg/m³]
+ Scalar injSub_; // [kg/m³]
+ Scalar injBiosusp_; // [kg/m³]
+ Scalar injNaCorr_; // [kg/m³]
+ int numInjections_;
+ std::vector<InjectionProcess> injectionType_;
+```
+
+the problem name
+
+```cpp
+ std::string name_;
+```
+
+the permeability for output
+
+```cpp
+ std::vector<Scalar> permeability_;
+```
+
+timing parameters
+
+```cpp
+ Scalar time_ = 0.0;
+ Scalar timeStepSize_ = 0.0;
+ int episodeIdx_ = 0;
+};
+} // end namespace Dumux
+```
+
+</details>
+
+</details>
+
+
+
+## Parameter distributions (`spatialparams_1p.hh`)
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../spatialparams.hh))</summary>
+
+
+This file contains the __spatial parameters class__ which defines the
+distributions for the porous medium parameters permeability and porosity
+over the computational grid
+
+### Include files
+<details><summary> Click to show includes</summary>
+We include the basic spatial parameters for finite volumes file from which we will inherit
+
+```cpp
+#include <dumux/material/spatialparams/fv.hh>
+```
+
+We include the files for the two-phase laws: the linear material law
+
+```cpp
+#include <dumux/material/fluidmatrixinteractions/2p/linearmaterial.hh>
+```
+
+We include the files for the two-phase laws: the regularized Brooks-Corey pc-Sw and relative permeability laws
+
+```cpp
+#include <dumux/material/fluidmatrixinteractions/2p/regularizedbrookscorey.hh>
+```
+
+We include the files for the two-phase laws: the scaling from effective to absolute saturations
+
+```cpp
+#include <dumux/material/fluidmatrixinteractions/2p/efftoabslaw.hh>
+```
+
+We include the laws for changing porosity due to precipitation
+
+```cpp
+#include <dumux/material/fluidmatrixinteractions/porosityprecipitation.hh>
+```
+
+We include the laws for changing permeability based on porosity change according to Kozeny-Carman
+
+```cpp
+#include <dumux/material/fluidmatrixinteractions/permeabilitykozenycarman.hh>
+```
+
+</details>
+
+### The spatial parameters class
+In the `ICPSpatialParams` class, we define all functions needed to describe
+the porous medium, e.g. porosity and permeability.
+We inherit from the `FVSpatialParams` class which is the base class for spatial paramters using finite volume discretization schemes.
+
+```cpp
+namespace Dumux {
+
+// In the ICPSpatialParams class we define all functions needed to describe the spatial distributed parameters.
+template<class GridGeometry, class Scalar>
+class ICPSpatialParams
+: public FVSpatialParams<GridGeometry, Scalar, ICPSpatialParams<GridGeometry, Scalar>>
+{
+ // We introduce using declarations that are derived from the property system which we need in this class
+ using ThisType = ICPSpatialParams<GridGeometry, Scalar>;
+ using ParentType = FVSpatialParams<GridGeometry, Scalar, ThisType>;
+ using GridView = typename GridGeometry::GridView;
+ using EffectiveLaw = RegularizedBrooksCorey<Scalar>;
+ using SubControlVolume = typename GridGeometry::SubControlVolume;
+ using Element = typename GridView::template Codim<0>::Entity;
+ using GlobalPosition = typename Element::Geometry::GlobalCoordinate;
+
+public:
+ // type used for the permeability (i.e. tensor or scalar)
+ using PermeabilityType = Scalar;
+ using MaterialLaw = EffToAbsLaw<EffectiveLaw>;
+ using MaterialLawParams = typename MaterialLaw::Params;
+```
+
+#### Using porosity and permeability laws to return the updated values
+Due due calcium carbonate precipitation the porosity and the permeability change with time. At first, the initial values for the porosity and permeability are defined. Moreover, the functions that return the updated values, based on the chosen laws are defined.
+
+```cpp
+ ICPSpatialParams(std::shared_ptr<const GridGeometry> gridGeometry)
+ : ParentType(gridGeometry)
+ {
+ // We read reference values for porosity and permeability from the input
+ referencePorosity_ = getParam<Scalar>("SpatialParams.ReferencePorosity", 0.4);
+ referencePermeability_ = getParam<Scalar>("SpatialParams.ReferencePermeability", 2.e-10);
+
+ // Setting residual saturations
+ materialParams_.setSwr(0.2);
+ materialParams_.setSnr(0.05);
+
+ // Setting parameters for the Brooks-Corey law
+ materialParams_.setPe(1e4);
+ materialParams_.setLambda(2.0);
+ }
+
+ // We return the reference or initial porosity.
+ //This reference porosity is the porosity, for which the permeability is know and set as reference permeability
+ Scalar referencePorosity(const Element& element, const SubControlVolume &scv) const
+ { return referencePorosity_; }
+
+ // We return the volume fraction of the inert (unreactive) component
+ template<class SolidSystem>
+ Scalar inertVolumeFractionAtPos(const GlobalPosition& globalPos, int compIdx) const
+ { return 1.0-referencePorosity_; }
+
+ // [[codeblock]]
+ // We return the updated porosity using the specified porosity law
+ template<class ElementSolution>
+ Scalar porosity(const Element& element,
+ const SubControlVolume& scv,
+ const ElementSolution& elemSol) const
+ { return poroLaw_.evaluatePorosity(element, scv, elemSol, referencePorosity_); }
+
+ // We return the updated permeability using the specified permeability law
+ template<class ElementSolution>
+ PermeabilityType permeability(const Element& element,
+ const SubControlVolume& scv,
+ const ElementSolution& elemSol) const
+ {
+ const auto poro = porosity(element, scv, elemSol);
+ return permLaw_.evaluatePermeability(referencePermeability_, referencePorosity_, poro);
+ }
+```
+
+Return the brooks-corey context depending on the position
+
+```cpp
+ const MaterialLawParams& materialLawParamsAtPos(const GlobalPosition& globalPos) const
+ { return materialParams_; }
+```
+
+Define the wetting phase
+
+```cpp
+ template<class FluidSystem>
+ int wettingPhaseAtPos(const GlobalPosition& globalPos) const
+ { return FluidSystem::H2OIdx; }
+```
+
+The remainder of this class contains the data members and defines the porosity law which describes the change of porosity due to calcium carbonate precipitation.
+Additionally the change of porosity results in a change of permeability. This relation is described in the permeability law, in this case the Kozeny-Carman porosity-permeability relation
+
+```cpp
+private:
+
+ MaterialLawParams materialParams_;
+ // Setting porosity precipitation as the porosity law
+ PorosityPrecipitation<Scalar, /*numFluidComponents*/9, /*activeComponents*/2> poroLaw_;
+ // Setting the Kozeny-Carman porosity-permeability relation as the permeability law
+ PermeabilityKozenyCarman<PermeabilityType> permLaw_;
+ //The reference porosity is the porosity, for which the permeability is know and set as reference permeability
+ Scalar referencePorosity_;
+ //The reference permeability is the known (measured) permeability, of the porous medium in the initial condition, before the solid phases change during the simulation
+ PermeabilityType referencePermeability_ = 0.0;
+};// end class definition of ICPSpatialParams
+} //end namespace Dumux
+```
+
+
+</details>
+
+
+
+## `TypeTag` and compile-time settings (`properties.hh`)
+
+This file defines the `TypeTag` used for the biomineralization example,
+for which we then specialize `properties` to the needs of this setup.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../properties.hh))</summary>
+
+
+### Include files
+<details>
+
+This type tag specializes most of the `properties` required for two phase flow with
+multiple components including mineralisation simulations (2pncmin) in DuMuX
+We will use this in the following to inherit the respective properties and
+subsequently specialize those `properties` for our `TypeTag`, which we want to
+modify or for which no meaningful default can be set.
+
+```cpp
+#include <dumux/common/properties.hh>
+#include <dumux/porousmediumflow/2pncmin/model.hh>
+```
+
+We want to use `YaspGrid`, an implementation of the dune grid interface for structured grids:
+
+```cpp
+#include <dune/grid/yaspgrid.hh>
+```
+
+In this example, we want to discretize the equations with the box scheme
+
+```cpp
+#include <dumux/discretization/box.hh>
+```
+
+We include the necessary material files
+
+```cpp
+#include <examples/biomineralization/material/fluidsystems/biominsimplechemistry.hh>
+#include <examples/biomineralization/material/solidsystems/biominsolids.hh>
+#include <examples/biomineralization/material/co2tableslaboratory.hh>
+```
+
+We include the problem and spatial parameters headers used for this simulation.
+
+```cpp
+#include "problem.hh"
+#include "spatialparams.hh"
+```
+
+</details>
+
+### Definition of the `TypeTag` used for the biomineralization problem
+
+We define a `TypeTag` for our simulation with the name `MICPColumnSimpleChemistry`
+and inherit the `properties` specialized for the type tags `TwoPNCMin` and `BoxModel` respectively.
+This way, most of the `properties` required for this simulations
+using the box scheme are conveniently specialized for our new `TypeTag`.
+However, some properties depend on user choices and no meaningful default value can be set.
+Those properties will be adressed later in this file.
+
+```cpp
+namespace Dumux::Properties {
+
+// We create new type tag for our simulation which inherits from the 2pncmin model and the box discretization
+namespace TTag {
+struct MICPColumnSimpleChemistry { using InheritsFrom = std::tuple<TwoPNCMin, BoxModel>; };
+} // end namespace TTag
+```
+
+### Property specializations
+
+In the following piece of code, mandatory `properties` for which no meaningful
+dafault can be set, are specialized for our type tag `MICPColumnSimpleChemistry`.
+
+```cpp
+// We set the grid to a 1D Yasp Grid
+template<class TypeTag>
+struct Grid<TypeTag, TTag::MICPColumnSimpleChemistry>
+{ using type = Dune::YaspGrid<1>; };
+
+// We set the problem used for our simulation, defining boundary and initial conditions (see below)
+template<class TypeTag>
+struct Problem<TypeTag, TTag::MICPColumnSimpleChemistry>
+{ using type = MICPColumnProblemSimpleChemistry<TypeTag>; };
+
+// We set the fluidSystem used for our simulation
+template<class TypeTag>
+struct FluidSystem<TypeTag, TTag::MICPColumnSimpleChemistry>
+{
+ using Scalar = GetPropType<TypeTag, Properties::Scalar>;
+ using CO2Tables = Dumux::ICP::CO2Tables;
+ using H2OTabulated = Components::TabulatedComponent<Components::H2O<Scalar>>;
+ using type = Dumux::FluidSystems::BioMinSimpleChemistryFluid<Scalar, CO2Tables, H2OTabulated>;
+};
+
+// We set the solidSystem used for our simulation
+template<class TypeTag>
+struct SolidSystem<TypeTag, TTag::MICPColumnSimpleChemistry>
+{
+ using Scalar = GetPropType<TypeTag, Properties::Scalar>;
+ using type = SolidSystems::BioMinSolidPhase<Scalar>;
+};
+
+// We define the spatial parameters for our simulation. The values are specified in the corresponding spatialparameters header file, which is included above.
+template<class TypeTag>
+struct SpatialParams<TypeTag, TTag::MICPColumnSimpleChemistry>
+{
+ using type = ICPSpatialParams<GetPropType<TypeTag, Properties::GridGeometry>,
+ GetPropType<TypeTag, Properties::Scalar>>;
+};
+
+// We set the two-phase primary variable formulation used for our simulation
+template<class TypeTag>
+struct Formulation<TypeTag, TTag::MICPColumnSimpleChemistry>
+{ static constexpr auto value = TwoPFormulation::p0s1; };
+
+}// We leave the namespace Dumux::Properties.
+```
+
+
+</details>
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 2](mainfile.md) | [:arrow_right: Continue with part 4](fluidmaterial.md) |
+|---|---|---:|
+
diff --git a/examples/biomineralization/doc/setup_intro.md b/examples/biomineralization/doc/setup_intro.md
new file mode 100644
index 0000000000..e17456cd4f
--- /dev/null
+++ b/examples/biomineralization/doc/setup_intro.md
@@ -0,0 +1,17 @@
+# Simulation Setup
+
+The setup for this example is based on the initial 100000s of the _column experiment D1_ described in [@Hommel2015] and can also be found in Section 4.2 of [@Hommel2016] under the name _column experiment D1_.
+We here only consider the "simplified chemistry case" in which it is assumed that the precipitation rate is equal to the ureolysis rate to simplify the chemical processes considered ($`r_\mathrm{prec} = r_\mathrm{urea}`$) (see Chapter 6 [@Hommel2016]).
+
+The column is considered as a 1D domain with injections of various aqueous solutions at the bottom (Neumann boundary condition)
+and a fixed pressure at the top (Dirichlet boundary condition).
+The various types of injected fluid compositions are read from an additional input file `injections_type.dat`.
+Depending on the injection type, the `problem.hh` adapts the composition of the injected aqueous solution for the bottom Neumann boundary condition.
+Further, `spatialparams.hh` is an example for spatial parameters dealing with changing porosity and permeability.
+
+The subsequent file documentation is structured as follows:
+
+[[_TOC_]]
+
+[@Hommel2015]: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2014WR016503 "A revised model for microbially induced calcite precipitation: Improvements and new insights based on recent experiments"
+[@Hommel2016]: https://elib.uni-stuttgart.de/handle/11682/8787 "Modelling biogeochemical and mass transport processes in the subsurface: investigation of microbially induced calcite precipitation"
diff --git a/examples/biomineralization/doc/solidmaterial.md b/examples/biomineralization/doc/solidmaterial.md
new file mode 100644
index 0000000000..95e72dc28d
--- /dev/null
+++ b/examples/biomineralization/doc/solidmaterial.md
@@ -0,0 +1,258 @@
+<!-- Important: This file has been automatically generated by generate_example_docs.py. Do not edit this file directly! -->
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 4](fluidmaterial.md) |
+|---|---:|
+
+# Biomineralization - Solids
+
+The main idea of biomineralization revolves around
+biologically-induced mineral precipitation.
+I our example, it is about precipitation of calcite
+due to urea hydrolysis.
+The resulting overall reaction equation is:
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} + \mathrm{Ca^{2+}} \xrightarrow{urease}
+2\mathrm{NH_{4}^{+}} + \mathrm{CaCO_{3}} \downarrow.
+```
+
+To describe the processes, the minimum set of components is:
+water (w), dissolved inorganic carbon (C<sub>tot</sub>),
+sodium (Na), chloride (Cl), calcium (Ca), urea (u), glucose as a substrate (s), oxygen (O<sub>2</sub>), and suspended biomass (b),
+as well as the solid components biofilm and calcite.
+Thus, there are many components involved and keeping track of the components and their interactions,
+necessitates a sophisticated handling.
+This is why the material folder in this example is both separated from the regular material folder in dumux/dumux/material
+and also documented separately.
+For further specialization, the overview over the material subfolder is split into solid and fluid, this description considering the solids.
+
+## Solids in the folder `material`
+
+As this example is about biomineralization involving many components with complex inteactions, some specific solid material files are necessary.
+First, `material/components/biofilm.hh` defines the solid component biofilm, which plays an essential role in biomineralization by providing the essential catalytic activity for biomineralization.
+Second, as biofilm grows or calcite precipitates, the volume fractions of those non-inert solids change, influencing the overall properties of the solids in the system.
+The specific solidsystem `material/solidsystems/biominsolids.hh` gives the relations on how to
+calculate the resulting average solid properties based on the solids volume fractions.
+
+
+The subsequent documentation is structured as follows:
+
+[[_TOC_]]
+
+
+[@Span1996]: https://aip.scitation.org/doi/abs/10.1063/1.555991 "A new equation of state for carbon dioxide covering the fluid region from the triple-point temperature to 1100 K at pressures up to 800 MPa"
+
+
+## The biofilm component (`biofilm.hh`)
+
+This file contains the __solid component class__ which defines the name, molar mass and density of biofilm
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/components/biofilm.hh))</summary>
+
+
+### Include files
+
+```cpp
+// including the base and the generic solid component
+#include <dumux/material/components/base.hh>
+#include <dumux/material/components/solid.hh>
+```
+
+### The biofilm component
+
+```cpp
+namespace Dumux::Components {
+
+// In Biofilm, we define the properties of the solid component biofilm
+template <class Scalar>
+class Biofilm
+: public Components::Base<Scalar, Biofilm<Scalar> >
+, public Components::Solid<Scalar, Biofilm<Scalar> >
+{
+public:
+ // the name
+ static std::string name()
+ { return "Biofilm"; }
+```
+
+### The biofilm component's properties
+
+```cpp
+ // The molar mass, which is not really defined for biofilm. Thus, we read it from params.input or use a default of 1.
+ // Based on a cell mass of 2.5e-16, the molar mass of cells would be 1.5e8 kg/mol, but biofilms are more than just cells and such high molar masses would lead to numerical problems.
+ static Scalar molarMass()
+ {
+ Scalar molarMass = getParam<Scalar>("BioCoefficients.BiofilmMolarMass", 1);
+ return molarMass;
+ }
+
+ // The density, or rather the dry density (dry biomass/wet volume), most of biofilm is water.
+ // It is typically highly variable for different biofilms, thus we read it from params.input or use the default value of 10 kg/m^3
+ static Scalar solidDensity(Scalar temperature)
+ {
+ Scalar rho = getParam<Scalar>("BioCoefficients.BiofilmDensity", 10);
+ return rho;
+ }
+};
+
+} // end namespace Dumux::Components
+```
+
+
+</details>
+
+
+
+## The solid system (`biominsolids.hh`)
+
+This file contains the __solidystem class__ which defines all functions needed to describe the solid and their properties,
+which are needed to model biomineralization.
+
+
+<details open>
+<summary><b>Click to hide/show the file documentation</b> (or inspect the [source code](../material/solidsystems/biominsolids.hh))</summary>
+
+
+### Include files
+
+```cpp
+#include <string>
+#include <dune/common/exceptions.hh>
+
+// we include all necessary solid components
+#include <examples/biomineralization/material/components/biofilm.hh>
+#include <dumux/material/components/calcite.hh>
+#include <dumux/material/components/granite.hh>
+```
+
+### The solidsystem class
+In the BioMinSolidPhase solid system, we define all functions needed to describe the solids and their properties accounted for in our simulation.
+We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+
+```cpp
+namespace Dumux::SolidSystems {
+
+template <class Scalar>
+class BioMinSolidPhase
+{
+public:
+```
+
+#### Component definitions
+With the following function we define what solid components will be used by the solid system and define the indices used to distinguish solid components in the course of the simulation.
+
+```cpp
+ // We use convenient declarations that we derive from the property system.
+ using Biofilm = Components::Biofilm<Scalar>;
+ using Calcite = Components::Calcite<Scalar>;
+ using Granite = Components::Granite<Scalar>;
+
+ /****************************************
+ * Solid phase related static parameters
+ ****************************************/
+ static constexpr int numComponents = 3;
+ static constexpr int numInertComponents = 1;
+ static constexpr int BiofilmIdx = 0;
+ static constexpr int CalciteIdx = 1;
+ static constexpr int GraniteIdx = 2;
+
+ // The component names
+ const static std::string componentName(int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::name();
+ case CalciteIdx: return Calcite::name();
+ case GraniteIdx: return Granite::name();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The solid system's name
+ static std::string name()
+ { return "BiomineralizationMinSolidPhase"; }
+
+ // We assume incompressible solids
+ static constexpr bool isCompressible(int compIdx)
+ { return false; }
+
+ // we have one inert component, the others may change
+ static constexpr bool isInert()
+ { return (numComponents == numInertComponents); }
+```
+
+#### Component properties
+This simply forwards the component properties (name, molar mass, density).
+
+```cpp
+ // The component molar masses
+ static Scalar molarMass(int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::molarMass();
+ case CalciteIdx: return Calcite::molarMass();
+ case GraniteIdx: return Granite::molarMass();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The component densities
+ template <class SolidState>
+ static Scalar density(const SolidState& solidState, const int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::solidDensity(solidState.temperature());
+ case CalciteIdx: return Calcite::solidDensity(solidState.temperature());
+ case GraniteIdx: return Granite::solidDensity(solidState.temperature());
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The component molar densities
+ template <class SolidState>
+ static Scalar molarDensity(const SolidState& solidState, const int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::solidDensity(solidState.temperature())/Biofilm::molarMass();
+ case CalciteIdx: return Calcite::solidDensity(solidState.temperature())/Calcite::molarMass();
+ case GraniteIdx: return Granite::solidDensity(solidState.temperature())/Calcite::molarMass();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+```
+
+#### Averaged solid properties
+The overall solid properties are calculated by a volume-weigthed average of the pure component's properties.
+
+```cpp
+ // The average density
+ template <class SolidState>
+ static Scalar density(const SolidState& solidState)
+ {
+ const Scalar rho1 = Biofilm::solidDensity(solidState.temperature());
+ const Scalar rho2 = Calcite::solidDensity(solidState.temperature());
+ const Scalar rho3 = Granite::solidDensity(solidState.temperature());
+ const Scalar volFrac1 = solidState.volumeFraction(BiofilmIdx);
+ const Scalar volFrac2 = solidState.volumeFraction(CalciteIdx);
+ const Scalar volFrac3 = solidState.volumeFraction(GraniteIdx);
+
+ return (rho1*volFrac1+
+ rho2*volFrac2+
+ rho3*volFrac3)
+ /(volFrac1+volFrac2+volFrac3);
+ }
+```
+
+
+</details>
+
+
+| [:arrow_left: Back to the main documentation](../README.md) | [:arrow_left: Go back to part 4](fluidmaterial.md) |
+|---|---:|
+
diff --git a/examples/biomineralization/doc/solidmaterial_intro.md b/examples/biomineralization/doc/solidmaterial_intro.md
new file mode 100644
index 0000000000..8e223b463d
--- /dev/null
+++ b/examples/biomineralization/doc/solidmaterial_intro.md
@@ -0,0 +1,38 @@
+# Biomineralization - Solids
+
+The main idea of biomineralization revolves around
+biologically-induced mineral precipitation.
+I our example, it is about precipitation of calcite
+due to urea hydrolysis.
+The resulting overall reaction equation is:
+
+```math
+\mathrm{CO(NH_2)_2} + 2\mathrm{H_2O} + \mathrm{Ca^{2+}} \xrightarrow{urease}
+2\mathrm{NH_{4}^{+}} + \mathrm{CaCO_{3}} \downarrow.
+```
+
+To describe the processes, the minimum set of components is:
+water (w), dissolved inorganic carbon (C<sub>tot</sub>),
+sodium (Na), chloride (Cl), calcium (Ca), urea (u), glucose as a substrate (s), oxygen (O<sub>2</sub>), and suspended biomass (b),
+as well as the solid components biofilm and calcite.
+Thus, there are many components involved and keeping track of the components and their interactions,
+necessitates a sophisticated handling.
+This is why the material folder in this example is both separated from the regular material folder in dumux/dumux/material
+and also documented separately.
+For further specialization, the overview over the material subfolder is split into solid and fluid, this description considering the solids.
+
+## Solids in the folder `material`
+
+As this example is about biomineralization involving many components with complex inteactions, some specific solid material files are necessary.
+First, `material/components/biofilm.hh` defines the solid component biofilm, which plays an essential role in biomineralization by providing the essential catalytic activity for biomineralization.
+Second, as biofilm grows or calcite precipitates, the volume fractions of those non-inert solids change, influencing the overall properties of the solids in the system.
+The specific solidsystem `material/solidsystems/biominsolids.hh` gives the relations on how to
+calculate the resulting average solid properties based on the solids volume fractions.
+
+
+The subsequent documentation is structured as follows:
+
+[[_TOC_]]
+
+
+[@Span1996]: https://aip.scitation.org/doi/abs/10.1063/1.555991 "A new equation of state for carbon dioxide covering the fluid region from the triple-point temperature to 1100 K at pressures up to 800 MPa"
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diff --git a/examples/biomineralization/injection_checkpoints.dat b/examples/biomineralization/injection_checkpoints.dat
new file mode 100644
index 0000000000..fc7638a67a
--- /dev/null
+++ b/examples/biomineralization/injection_checkpoints.dat
@@ -0,0 +1,212 @@
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diff --git a/examples/biomineralization/injection_type.dat b/examples/biomineralization/injection_type.dat
new file mode 100644
index 0000000000..b2b6b791c0
--- /dev/null
+++ b/examples/biomineralization/injection_type.dat
@@ -0,0 +1,212 @@
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+-1
+-99
+3
+-99
+-1
+1
+-1
+-99
+3
+-99
+-1
+1
+-1
+-99
+3
+-99
+-1
+1
+-1
+-99
+3
+-99
+-1
+1
+-1
+-99
+3
+-99
+-1
+1
+-1
+9
+9
+9
+9
+9
+-99
+3
+9
\ No newline at end of file
diff --git a/examples/biomineralization/main.cc b/examples/biomineralization/main.cc
new file mode 100644
index 0000000000..8ae2cc3b84
--- /dev/null
+++ b/examples/biomineralization/main.cc
@@ -0,0 +1,278 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 3 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+// ## The main file
+// This files contains the main program flow for the biomineralization example. Here we can see the programme sequence and how the system is solved using newton's method.
+//
+// [[content]]
+//
+// ### Included header files
+// <details>
+// [[exclude]]
+// Some generic includes.
+#include <config.h>
+#include <iostream>
+#include <dumux/io/container.hh>
+// [[/exclude]]
+
+// These are DUNE helper classes related to parallel computations
+#include <dune/common/parallel/mpihelper.hh>
+
+// The following headers include functionality related to property definition or retrieval, as well as
+// the retrieval of input parameters specified in the input file or via the command line.
+#include <dumux/common/properties.hh>
+#include <dumux/common/parameters.hh>
+
+// The follwoing files contain the nonlinear Newtown method, the linear solver and the assembler
+#include <dumux/nonlinear/newtonsolver.hh>
+#include <dumux/linear/amgbackend.hh>
+#include <dumux/assembly/fvassembler.hh>
+#include <dumux/assembly/diffmethod.hh>
+
+// The following class provides a convenient way of writing of dumux simulation results to VTK format.
+#include <dumux/io/vtkoutputmodule.hh>
+
+// The gridmanager constructs a grid from the information in the input or grid file. There is a specification for the different supported grid managers.
+// Many different Dune grid implementations are supported, of which a list can be found
+// in `gridmanager.hh`.
+#include <dumux/io/grid/gridmanager_yasp.hh>
+
+// We include the problem file which defines initial and boundary conditions to describe our example problem
+//remove #include "problem.hh"
+#include "properties.hh"
+// </details>
+//
+
+// ### The main function
+// We will now discuss the main program flow implemented within the `main` function.
+// At the beginning of each program using Dune, an instance `Dune::MPIHelper` has to
+// be created. Moreover, we parse the run-time arguments from the command line and the
+// input file:
+// [[codeblock]]
+int main(int argc, char** argv) try
+{
+ using namespace Dumux;
+
+ // initialize MPI, finalize is done automatically on exit
+ const auto& mpiHelper = Dune::MPIHelper::instance(argc, argv);
+
+ // parse command line arguments and input file
+ Parameters::init(argc, argv);
+ // [[/codeblock]]
+
+ // For convenience we define the type tag for this problem.
+ // The type tags contain all the properties that are needed to run the simulations.
+ using TypeTag = Properties::TTag::MICPColumnSimpleChemistry;
+
+ // ### Step 1: Create the grid
+ // The `GridManager` class creates the grid from information given in the input file.
+ // This can either be a grid file, or in the case of structured grids, one can specify the coordinates
+ // of the corners of the grid and the number of cells to be used to discretize each spatial direction. The latter is the case for this example.
+ // [[codeblock]]
+ GridManager<GetPropType<TypeTag, Properties::Grid>> gridManager;
+ gridManager.init();
+
+ // we compute on the leaf grid view
+ const auto& leafGridView = gridManager.grid().leafGridView();
+ // [[/codeblock]]
+
+ // ### Step 2: Setting up the problem
+ // We create and initialize the finite volume grid geometry, the problem, the linear system, including the jacobian matrix, the residual and the solution vector and the gridvariables.
+ // We need the finite volume geometry to build up the subcontrolvolumes (scv) and subcontrolvolume faces (scvf) for each element of the grid partition.
+ using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>;
+ auto gridGeometry = std::make_shared<GridGeometry>(leafGridView);
+ gridGeometry->update();
+
+ // We now instantiate the problem, in which we define the boundary and initial conditions.
+ using Problem = GetPropType<TypeTag, Properties::Problem>;
+ auto problem = std::make_shared<Problem>(gridGeometry);
+
+ // get some time loop parameters
+ using Scalar = GetPropType<TypeTag, Properties::Scalar>;
+ const auto tEnd = getParam<Scalar>("TimeLoop.TEnd");
+ const auto maxDt = getParam<Scalar>("TimeLoop.MaxTimeStepSize");
+ const auto dt = getParam<Scalar>("TimeLoop.DtInitial");
+
+ // We initialize the solution vector
+ using SolutionVector = GetPropType<TypeTag, Properties::SolutionVector>;
+ SolutionVector x;
+ problem->applyInitialSolution(x);
+ auto xOld = x;
+
+ // on the basis of this solution, we initialize the grid variables
+ using GridVariables = GetPropType<TypeTag, Properties::GridVariables>;
+ auto gridVariables = std::make_shared<GridVariables>(problem, gridGeometry);
+ gridVariables->init(x);
+
+ // We intialize the vtk output module. Each model has a predefined model specific output with relevant parameters for that model.
+ // [[codeblock]]
+ VtkOutputModule<GridVariables, SolutionVector> vtkWriter(*gridVariables, x, problem->name());
+ using VelocityOutput = GetPropType<TypeTag, Properties::VelocityOutput>;
+ vtkWriter.addVelocityOutput(std::make_shared<VelocityOutput>(*gridVariables));
+ GetPropType<TypeTag, Properties::IOFields>::initOutputModule(vtkWriter); //!< Add model specific output fields
+ //we add permeability as a specific output
+ vtkWriter.addField(problem->getPermeability(), "Permeability");
+ //We update the output fields before write
+ problem->updateVtkOutput(x);
+ vtkWriter.write(0.0);
+ // [[/codeblock]]
+
+ //We instantiate the time loop and define an episode index to keep track of the the actual episode number
+ // [[codeblock]]
+ int episodeIdx = 0;
+ //We set the initial episodeIdx in the problem to zero
+ problem->setEpisodeIdx(episodeIdx);
+ //We set the time loop with episodes (check points)
+ auto timeLoop = std::make_shared<CheckPointTimeLoop<Scalar>>(0.0, dt, tEnd);
+ timeLoop->setMaxTimeStepSize(maxDt);
+ // [[/codeblock]]
+
+ // ### Step 3 Setting episodes specified from file
+ // In this example we want to specify the injected reactant solutions at certain times.
+ // This is specified in an external file injections_checkpoints.dat.
+ // Within the following code block, the parameter file read and the time for the injection are extracted.
+ // Based on that, the checkpoints for the simulation are set.
+
+ // [[codeblock]]
+ //We use a time loop with episodes if an injection parameter file is specified in the input
+ if (hasParam("Injection.NumInjections"))
+ {
+ //We first read the times of the checkpoints from the injection file
+ const auto injectionCheckPoints = readFileToContainer<std::vector<double>>("injection_checkpoints.dat");
+
+ // We set the time loop with episodes of various lengths as specified in the injection file
+ // set the episode ends /check points:
+ timeLoop->setCheckPoint(injectionCheckPoints);
+
+ // We also set the initial episodeIdx in the problem to zero, as in the problem the boundary conditions depend on the episode.
+ problem->setEpisodeIdx(episodeIdx);
+ }
+
+ // If nothing specified, we do not need to use episodes
+ else
+ {
+ // In this case, we set the time loop with one big episodes
+ timeLoop->setCheckPoint(tEnd);
+ }
+ // [[/codeblock]]
+
+ // ### Step 4 solving the instationary problem
+
+ // We create and initialize the assembler with a time loop for the transient problem.
+ // Within the time loop, we will use this assembler in each time step to assemble the linear system.
+ // Additionally the linear and non-linear solvers are set
+ // [[codeblock]]
+ using Assembler = FVAssembler<TypeTag, DiffMethod::numeric>;
+ auto assembler = std::make_shared<Assembler>(problem, gridGeometry, gridVariables, timeLoop, xOld);
+
+ //We set the linear solver
+ using LinearSolver = Dumux::ILU0BiCGSTABBackend;
+ auto linearSolver = std::make_shared<LinearSolver>();
+
+ //We set the non-linear solver
+ using NewtonSolver = NewtonSolver<Assembler, LinearSolver>;
+ NewtonSolver nonLinearSolver(assembler, linearSolver);
+ // [[/codeblock]]
+
+ // #### The time loop
+ // We start the time loop and solve a new time step as long as `tEnd` is not reached. In every time step,
+ // the problem is assembled and solved, the solution is updated, and when a checkpoint is reached the solution
+ // is written to a new vtk file. In addition, statistics related to CPU time, the current simulation time
+ // and the time step sizes used is printed to the terminal.
+
+ // [[codeblock]]
+ timeLoop->start(); do
+ {
+ // We set the time and time step size to be used in the problem
+ problem->setTime( timeLoop->time() + timeLoop->timeStepSize() );
+ problem->setTimeStepSize( timeLoop->timeStepSize() );
+
+ // Solve the linear system with time step control
+ nonLinearSolver.solve(x, *timeLoop);
+
+ // Update the old solution with the one computed in this time step and move to the next one
+ xOld = x;
+ gridVariables->advanceTimeStep();
+ timeLoop->advanceTimeStep();
+
+ // We update the output fields before write
+ problem->updateVtkOutput(x);
+
+ // We write vtk output on checkpoints or every 20th timestep
+ if (timeLoop->timeStepIndex() % 20 == 0 || timeLoop->isCheckPoint())
+ {
+ // update the output fields before write
+ problem->updateVtkOutput(x);
+
+ // write vtk output
+ vtkWriter.write(timeLoop->time());
+ }
+ // We report statistics of this time step
+ timeLoop->reportTimeStep();
+
+ //If episodes/check points are used, we count episodes and update the episode indices in the main file and the problem.
+ if (hasParam("Injection.NumInjections") || hasParam("TimeLoop.EpisodeLength"))
+ {
+ if (timeLoop->isCheckPoint())
+ {
+ episodeIdx++;
+ problem->setEpisodeIdx(episodeIdx);
+ }
+ }
+
+ // set the new time step size that is suggested by the newton solver
+ timeLoop->setTimeStepSize(nonLinearSolver.suggestTimeStepSize(timeLoop->timeStepSize()));
+
+ } while (!timeLoop->finished());
+ timeLoop->finalize(leafGridView.comm());
+ // [[/codeblock]]
+
+ if (mpiHelper.rank() == 0)
+ Parameters::print();
+
+ return 0;
+}
+
+// ### Exception handling
+// In this part of the main file we catch and print possible exceptions that could
+// occur during the simulation.
+// [[details]] error handler
+// [[codeblock]]
+// errors related to run-time parameters
+catch (const Dumux::ParameterException &e)
+{
+ std::cerr << std::endl << e << " ---> Abort!" << std::endl;
+ return 1;
+}
+catch (const Dune::DGFException & e)
+{
+ std::cerr << "DGF exception thrown (" << e <<
+ "). Most likely, the DGF file name is wrong "
+ "or the DGF file is corrupted, "
+ "e.g. missing hash at end of file or wrong number (dimensions) of entries."
+ << " ---> Abort!" << std::endl;
+ return 2;
+}
+catch (const Dune::Exception &e)
+{
+ std::cerr << "Dune reported error: " << e << " ---> Abort!" << std::endl;
+ return 3;
+}
+// [[/codeblock]]
+// [[/details]]
+// [[/content]]
diff --git a/examples/biomineralization/material/co2tableslaboratory.hh b/examples/biomineralization/material/co2tableslaboratory.hh
new file mode 100644
index 0000000000..ec5f71af3c
--- /dev/null
+++ b/examples/biomineralization/material/co2tableslaboratory.hh
@@ -0,0 +1,38 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#ifndef DUMUX_ICP_CO2TABLES_LABORATORY_HH
+#define DUMUX_ICP_CO2TABLES_LABORATORY_HH
+
+// ## The CO2 tables (`co2tableslaboratory.hh`)
+//
+// This file contains the __co2table class__ which forwards to tabulated properties of CO2 according to Span and Wagner 1996.
+// The real work (creating the tables) is done by some external program by Span and Wagner 1996 which provides the ready-to-use tables.
+//
+// [[content]]
+//
+// [[codeblock]]
+
+#include <assert.h>
+namespace Dumux::ICP {
+#include "co2valueslaboratory.inc"
+}// end namespace Dumux::ICP
+// [[/codeblock]]
+// [[/content]]
+#endif
diff --git a/examples/biomineralization/material/co2valueslaboratory.inc b/examples/biomineralization/material/co2valueslaboratory.inc
new file mode 100644
index 0000000000..536074c76b
--- /dev/null
+++ b/examples/biomineralization/material/co2valueslaboratory.inc
@@ -0,0 +1,424 @@
+/* Tables for CO2 fluid properties calculated according to Span and
+ * Wagner (1996).
+ *
+ * THIS AN AUTO-GENERATED FILE! DO NOT EDIT IT!
+ *
+ * Temperature range: 288.000 K to 303.000 K, using 15 sampling points
+ * Pressure range: 0.095 MPa to 0.145 MPa, using 50 sampling points
+ *
+ * Generated using:
+ *
+ * ./extractproperties 288 303 15 95000 145000 50
+ */
+
+
+struct TabulatedDensityTraits {
+ typedef double Scalar;
+ static const char *name;
+ static const int numTempSteps = 15;
+ static constexpr Scalar minTemp = 2.880000000000000e+02;
+ static constexpr Scalar maxTemp = 3.030000000000000e+02;
+ static const int numPressSteps = 50;
+ static constexpr Scalar minPress = 9.500000000000000e+04;
+ static constexpr Scalar maxPress = 1.450000000000000e+05;
+ static const Scalar vals[numTempSteps][numPressSteps];
+};
+
+const char *TabulatedDensityTraits::name = "density";
+
+const double TabulatedDensityTraits::vals[15][50] =
+{
+ {
+ 1.755308372911512e+00, 1.774264402821289e+00, 1.793222621515086e+00, 1.812183029645950e+00, 1.831145627867246e+00,
+ 1.850110416832651e+00, 1.869077397196165e+00, 1.888046569612100e+00, 1.907017934735086e+00, 1.925991493220070e+00,
+ 1.944967245722317e+00, 1.963945192897409e+00, 1.982925335401247e+00, 2.001907673890049e+00, 2.020892209020350e+00,
+ 2.039878941449006e+00, 2.058867871833190e+00, 2.077859000830393e+00, 2.096852329098427e+00, 2.115847857295424e+00,
+ 2.134845586079831e+00, 2.153845516110419e+00, 2.172847648046278e+00, 2.191851982546817e+00, 2.210858520271766e+00,
+ 2.229867261881177e+00, 2.248878208035418e+00, 2.267891359395183e+00, 2.286906716621488e+00, 2.305924280375664e+00,
+ 2.324944051319368e+00, 2.343966030114581e+00, 2.362990217423599e+00, 2.382016613909049e+00, 2.401045220233873e+00,
+ 2.420076037061341e+00, 2.439109065055041e+00, 2.458144304878889e+00, 2.477181757197121e+00, 2.496221422674298e+00,
+ 2.515263301975305e+00, 2.534307395765349e+00, 2.553353704709964e+00, 2.572402229475007e+00, 2.591452970726658e+00,
+ 2.610505929131427e+00, 2.629561105356142e+00, 2.648618500067962e+00, 2.667678113934368e+00, 2.686739947623169e+00
+ },
+ {
+ 1.748688604734713e+00, 1.767571892229173e+00, 1.786457333061390e+00, 1.805344927864506e+00, 1.824234677271969e+00,
+ 1.843126581917526e+00, 1.862020642435228e+00, 1.880916859459429e+00, 1.899815233624782e+00, 1.918715765566246e+00,
+ 1.937618455919081e+00, 1.956523305318852e+00, 1.975430314401425e+00, 1.994339483802971e+00, 2.013250814159965e+00,
+ 2.032164306109183e+00, 2.051079960287710e+00, 2.069997777332932e+00, 2.088917757882538e+00, 2.107839902574526e+00,
+ 2.126764212047197e+00, 2.145690686939155e+00, 2.164619327889312e+00, 2.183550135536884e+00, 2.202483110521394e+00,
+ 2.221418253482670e+00, 2.240355565060845e+00, 2.259295045896362e+00, 2.278236696629965e+00, 2.297180517902710e+00,
+ 2.316126510355958e+00, 2.335074674631374e+00, 2.354025011370935e+00, 2.372977521216923e+00, 2.391932204811928e+00,
+ 2.410889062798848e+00, 2.429848095820891e+00, 2.448809304521571e+00, 2.467772689544708e+00, 2.486738251534437e+00,
+ 2.505705991135198e+00, 2.524675908991741e+00, 2.543648005749125e+00, 2.562622282052718e+00, 2.581598738548199e+00,
+ 2.600577375881557e+00, 2.619558194699090e+00, 2.638541195647405e+00, 2.657526379373425e+00, 2.676513746524379e+00
+ },
+ {
+ 1.742119513324718e+00, 1.760930634944350e+00, 1.779743875160616e+00, 1.798559234587417e+00, 1.817376713838946e+00,
+ 1.836196313529680e+00, 1.855018034274388e+00, 1.873841876688128e+00, 1.892667841386243e+00, 1.911495928984368e+00,
+ 1.930326140098427e+00, 1.949158475344631e+00, 1.967992935339483e+00, 1.986829520699775e+00, 2.005668232042588e+00,
+ 2.024509069985295e+00, 2.043352035145557e+00, 2.062197128141326e+00, 2.081044349590847e+00, 2.099893700112652e+00,
+ 2.118745180325567e+00, 2.137598790848708e+00, 2.156454532301483e+00, 2.175312405303590e+00, 2.194172410475020e+00,
+ 2.213034548436057e+00, 2.231898819807275e+00, 2.250765225209542e+00, 2.269633765264017e+00, 2.288504440592153e+00,
+ 2.307377251815696e+00, 2.326252199556683e+00, 2.345129284437447e+00, 2.364008507080612e+00, 2.382889868109099e+00,
+ 2.401773368146120e+00, 2.420659007815180e+00, 2.439546787740082e+00, 2.458436708544920e+00, 2.477328770854085e+00,
+ 2.496222975292262e+00, 2.515119322484431e+00, 2.534017813055865e+00, 2.552918447632137e+00, 2.571821226839111e+00,
+ 2.590726151302949e+00, 2.609633221650109e+00, 2.628542438507346e+00, 2.647453802501707e+00, 2.666367314260542e+00
+ },
+ {
+ 1.735600503086598e+00, 1.754340028201860e+00, 1.773081637860596e+00, 1.791825332658108e+00, 1.810571113189969e+00,
+ 1.829318980052027e+00, 1.848068933840407e+00, 1.866820975151510e+00, 1.885575104582009e+00, 1.904331322728859e+00,
+ 1.923089630189284e+00, 1.941850027560791e+00, 1.960612515441156e+00, 1.979377094428439e+00, 1.998143765120974e+00,
+ 2.016912528117368e+00, 2.035683384016511e+00, 2.054456333417567e+00, 2.073231376919978e+00, 2.092008515123465e+00,
+ 2.110787748628023e+00, 2.129569078033930e+00, 2.148352503941738e+00, 2.167138026952281e+00, 2.185925647666668e+00,
+ 2.204715366686289e+00, 2.223507184612810e+00, 2.242301102048181e+00, 2.261097119594628e+00, 2.279895237854655e+00,
+ 2.298695457431049e+00, 2.317497778926874e+00, 2.336302202945476e+00, 2.355108730090479e+00, 2.373917360965788e+00,
+ 2.392728096175590e+00, 2.411540936324352e+00, 2.430355882016820e+00, 2.449172933858022e+00, 2.467992092453268e+00,
+ 2.486813358408150e+00, 2.505636732328538e+00, 2.524462214820588e+00, 2.543289806490736e+00, 2.562119507945698e+00,
+ 2.580951319792477e+00, 2.599785242638353e+00, 2.618621277090893e+00, 2.637459423757945e+00, 2.656299683247639e+00
+ },
+ {
+ 1.729130988069413e+00, 1.747799479006408e+00, 1.766470021105015e+00, 1.785142614942543e+00, 1.803817261096561e+00,
+ 1.822493960144904e+00, 1.841172712665666e+00, 1.859853519237209e+00, 1.878536380438155e+00, 1.897221296847389e+00,
+ 1.915908269044062e+00, 1.934597297607586e+00, 1.953288383117640e+00, 1.971981526154163e+00, 1.990676727297363e+00,
+ 2.009373987127709e+00, 2.028073306225935e+00, 2.046774685173041e+00, 2.065478124550290e+00, 2.084183624939213e+00,
+ 2.102891186921603e+00, 2.121600811079520e+00, 2.140312497995291e+00, 2.159026248251505e+00, 2.177742062431020e+00,
+ 2.196459941116959e+00, 2.215179884892710e+00, 2.233901894341931e+00, 2.252625970048542e+00, 2.271352112596734e+00,
+ 2.290080322570960e+00, 2.308810600555946e+00, 2.327542947136680e+00, 2.346277362898420e+00, 2.365013848426691e+00,
+ 2.383752404307285e+00, 2.402493031126264e+00, 2.421235729469957e+00, 2.439980499924959e+00, 2.458727343078137e+00,
+ 2.477476259516623e+00, 2.496227249827822e+00, 2.514980314599402e+00, 2.533735454419308e+00, 2.552492669875746e+00,
+ 2.571251961557198e+00, 2.590013330052412e+00, 2.608776775950404e+00, 2.627542299840464e+00, 2.646309902312153e+00
+ },
+ {
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+ },
+ {
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+ 1.756991240549225e+00, 1.774987611008209e+00, 1.792985734523242e+00, 1.810985611521764e+00, 1.828987242431384e+00,
+ 1.846990627679876e+00, 1.864995767695184e+00, 1.883002662905417e+00, 1.901011313738852e+00, 1.919021720623934e+00,
+ 1.937033883989274e+00, 1.955047804263653e+00, 1.973063481876017e+00, 1.991080917255481e+00, 2.009100110831328e+00,
+ 2.027121063033010e+00, 2.045143774290143e+00, 2.063168245032518e+00, 2.081194475690086e+00, 2.099222466692973e+00,
+ 2.117252218471470e+00, 2.135283731456037e+00, 2.153317006077303e+00, 2.171352042766067e+00, 2.189388841953294e+00,
+ 2.207427404070120e+00, 2.225467729547847e+00, 2.243509818817949e+00, 2.261553672312070e+00, 2.279599290462019e+00,
+ 2.297646673699778e+00, 2.315695822457497e+00, 2.333746737167496e+00, 2.351799418262262e+00, 2.369853866174454e+00,
+ 2.387910081336903e+00, 2.405968064182606e+00, 2.424027815144730e+00, 2.442089334656615e+00, 2.460152623151768e+00,
+ 2.478217681063868e+00, 2.496284508826763e+00, 2.514353106874473e+00, 2.532423475641187e+00, 2.550495615561266e+00
+ }
+};
+
+typedef TabulatedCO2Properties< TabulatedDensityTraits > TabulatedDensity;
+
+struct TabulatedEnthalpyTraits {
+ typedef double Scalar;
+ static const char *name;
+ static const int numTempSteps = 15;
+ static constexpr Scalar minTemp = 2.880000000000000e+02;
+ static constexpr Scalar maxTemp = 3.030000000000000e+02;
+ static const int numPressSteps = 50;
+ static constexpr Scalar minPress = 9.500000000000000e+04;
+ static constexpr Scalar maxPress = 1.450000000000000e+05;
+ static const Scalar vals[numTempSteps][numPressSteps];
+};
+
+const char *TabulatedEnthalpyTraits::name = "enthalpy";
+
+const double TabulatedEnthalpyTraits::vals[15][50] =
+{
+ {
+ 1.244801188627830e+04, 1.243776118212441e+04, 1.242750944725234e+04, 1.241725668135906e+04, 1.240700288414147e+04,
+ 1.239674805529627e+04, 1.238649219452005e+04, 1.237623530150919e+04, 1.236597737596004e+04, 1.235571841756868e+04,
+ 1.234545842603116e+04, 1.233519740104331e+04, 1.232493534230083e+04, 1.231467224949931e+04, 1.230440812233415e+04,
+ 1.229414296050063e+04, 1.228387676369388e+04, 1.227360953160892e+04, 1.226334126394057e+04, 1.225307196038350e+04,
+ 1.224280162063231e+04, 1.223253024438139e+04, 1.222225783132500e+04, 1.221198438115726e+04, 1.220170989357216e+04,
+ 1.219143436826350e+04, 1.218115780492498e+04, 1.217088020325013e+04, 1.216060156293235e+04, 1.215032188366487e+04,
+ 1.214004116514082e+04, 1.212975940705310e+04, 1.211947660909460e+04, 1.210919277095791e+04, 1.209890789233557e+04,
+ 1.208862197291995e+04, 1.207833501240327e+04, 1.206804701047762e+04, 1.205775796683492e+04, 1.204746788116695e+04,
+ 1.203717675316535e+04, 1.202688458252161e+04, 1.201659136892707e+04, 1.200629711207294e+04, 1.199600181165024e+04,
+ 1.198570546734989e+04, 1.197540807886265e+04, 1.196510964587912e+04, 1.195481016808974e+04, 1.194450964518485e+04
+ },
+ {
+ 1.334921879332812e+04, 1.333905343954384e+04, 1.332888707876712e+04, 1.331871971070738e+04, 1.330855133507387e+04,
+ 1.329838195157575e+04, 1.328821155992203e+04, 1.327804015982153e+04, 1.326786775098304e+04, 1.325769433311511e+04,
+ 1.324751990592623e+04, 1.323734446912471e+04, 1.322716802241874e+04, 1.321699056551638e+04, 1.320681209812554e+04,
+ 1.319663261995399e+04, 1.318645213070940e+04, 1.317627063009926e+04, 1.316608811783093e+04, 1.315590459361167e+04,
+ 1.314572005714856e+04, 1.313553450814857e+04, 1.312534794631852e+04, 1.311516037136511e+04, 1.310497178299487e+04,
+ 1.309478218091422e+04, 1.308459156482944e+04, 1.307439993444667e+04, 1.306420728947192e+04, 1.305401362961104e+04,
+ 1.304381895456975e+04, 1.303362326405367e+04, 1.302342655776822e+04, 1.301322883541872e+04, 1.300303009671038e+04,
+ 1.299283034134818e+04, 1.298262956903707e+04, 1.297242777948177e+04, 1.296222497238694e+04, 1.295202114745705e+04,
+ 1.294181630439645e+04, 1.293161044290934e+04, 1.292140356269980e+04, 1.291119566347175e+04, 1.290098674492898e+04,
+ 1.289077680677517e+04, 1.288056584871380e+04, 1.287035387044827e+04, 1.286014087168180e+04, 1.284992685211751e+04
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+ 2.507423717630408e+04, 2.506507490686689e+04, 2.505591188639637e+04, 2.504674811472057e+04, 2.503758359166751e+04,
+ 2.502841831706510e+04, 2.501925229074121e+04, 2.501008551252365e+04, 2.500091798224013e+04, 2.499174969971836e+04,
+ 2.498258066478591e+04, 2.497341087727034e+04, 2.496424033699913e+04, 2.495506904379967e+04, 2.494589699749934e+04,
+ 2.493672419792541e+04, 2.492755064490508e+04, 2.491837633826553e+04, 2.490920127783382e+04, 2.490002546343700e+04,
+ 2.489084889490202e+04, 2.488167157205576e+04, 2.487249349472505e+04, 2.486331466273668e+04, 2.485413507591731e+04,
+ 2.484495473409360e+04, 2.483577363709210e+04, 2.482659178473931e+04, 2.481740917686167e+04, 2.480822581328557e+04,
+ 2.479904169383731e+04, 2.478985681834310e+04, 2.478067118662915e+04, 2.477148479852155e+04, 2.476229765384635e+04,
+ 2.475310975242952e+04, 2.474392109409700e+04, 2.473473167867461e+04, 2.472554150598814e+04, 2.471635057586330e+04
+ }
+};
+
+typedef TabulatedCO2Properties< TabulatedEnthalpyTraits > TabulatedEnthalpy;
+
+
+// this class collects all the tabulated quantities in one convenient place
+struct CO2Tables {
+ static const TabulatedEnthalpy tabulatedEnthalpy;
+ static const TabulatedDensity tabulatedDensity;
+};
+
+const TabulatedEnthalpy CO2Tables::tabulatedEnthalpy;
+const TabulatedDensity CO2Tables::tabulatedDensity;
+
diff --git a/examples/biomineralization/material/components/biofilm.hh b/examples/biomineralization/material/components/biofilm.hh
new file mode 100644
index 0000000000..b906b030dc
--- /dev/null
+++ b/examples/biomineralization/material/components/biofilm.hh
@@ -0,0 +1,74 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#ifndef DUMUX_MATERIAL_COMPONENTS_BIOFILM_HH
+#define DUMUX_MATERIAL_COMPONENTS_BIOFILM_HH
+
+// ## The biofilm component (`biofilm.hh`)
+//
+// This file contains the __solid component class__ which defines the name, molar mass and density of biofilm
+//
+// [[content]]
+//
+// ### Include files
+// [[codeblock]]
+// including the base and the generic solid component
+#include <dumux/material/components/base.hh>
+#include <dumux/material/components/solid.hh>
+// [[/codeblock]]
+
+// ### The biofilm component
+// [[codeblock]]
+namespace Dumux::Components {
+
+// In Biofilm, we define the properties of the solid component biofilm
+template <class Scalar>
+class Biofilm
+: public Components::Base<Scalar, Biofilm<Scalar> >
+, public Components::Solid<Scalar, Biofilm<Scalar> >
+{
+public:
+ // the name
+ static std::string name()
+ { return "Biofilm"; }
+// [[/codeblock]]
+
+// ### The biofilm component's properties
+// [[codeblock]]
+ // The molar mass, which is not really defined for biofilm. Thus, we read it from params.input or use a default of 1.
+ // Based on a cell mass of 2.5e-16, the molar mass of cells would be 1.5e8 kg/mol, but biofilms are more than just cells and such high molar masses would lead to numerical problems.
+ static Scalar molarMass()
+ {
+ Scalar molarMass = getParam<Scalar>("BioCoefficients.BiofilmMolarMass", 1);
+ return molarMass;
+ }
+
+ // The density, or rather the dry density (dry biomass/wet volume), most of biofilm is water.
+ // It is typically highly variable for different biofilms, thus we read it from params.input or use the default value of 10 kg/m^3
+ static Scalar solidDensity(Scalar temperature)
+ {
+ Scalar rho = getParam<Scalar>("BioCoefficients.BiofilmDensity", 10);
+ return rho;
+ }
+};
+
+} // end namespace Dumux::Components
+// [[/codeblock]]
+// [[/content]]
+#endif
diff --git a/examples/biomineralization/material/components/suspendedbiomass.hh b/examples/biomineralization/material/components/suspendedbiomass.hh
new file mode 100644
index 0000000000..359f79eebd
--- /dev/null
+++ b/examples/biomineralization/material/components/suspendedbiomass.hh
@@ -0,0 +1,65 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#ifndef DUMUX_MATERIAL_COMPONENTS_SUSPENDEDBIOMASS_HH
+#define DUMUX_MATERIAL_COMPONENTS_SUSPENDEDBIOMASS_HH
+
+// ## The suspended biomass component (`suspendedbiomass.hh`)
+//
+// This file contains the __ component class__ which defines the name and molar mass of suspended biomass
+//
+// [[content]]
+//
+// ### Include files
+// [[codeblock]]
+// including the base component
+#include <dumux/material/components/base.hh>
+// [[/codeblock]]
+
+// ### The suspended biomass component
+// [[codeblock]]
+namespace Dumux::Components {
+
+// In SuspendedBiomass, we define the properties of the component suspended biomass
+template <class Scalar>
+class SuspendedBiomass
+: public Components::Base<Scalar, SuspendedBiomass<Scalar> >
+{
+public:
+ // the name
+ static std::string name()
+ { return "Suspended_Biomass"; }
+// [[/codeblock]]
+
+// ### The suspended biomass component's properties
+// [[codeblock]]
+ // The molar mass, which is not really defined for suspended biomass. Thus, we read it from params.input or use a default of 1.
+ // Based on a cell mass of 2.5e-16, the molar mass of cells would be 1.5e8 kg/mol, but such high molar masses would lead to numerical problems.
+ static Scalar molarMass()
+ {
+ Scalar molarMass = getParam<Scalar>("BioCoefficients.SuspendedBiomassMolarMass", 1);
+ return molarMass;
+ }
+};
+
+
+} // end namespace Dumux::Components
+// [[/codeblock]]
+// [[/content]]
+#endif
diff --git a/examples/biomineralization/material/fluidsystems/CMakeLists.txt b/examples/biomineralization/material/fluidsystems/CMakeLists.txt
new file mode 100644
index 0000000000..5b7ccac5a7
--- /dev/null
+++ b/examples/biomineralization/material/fluidsystems/CMakeLists.txt
@@ -0,0 +1,5 @@
+#install headers
+install(FILES
+biominsimplechemistry.hh
+icpcomplexsalinitybrine.hh
+DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/dumux/material/fluidsystems)
diff --git a/examples/biomineralization/material/fluidsystems/biominsimplechemistry.hh b/examples/biomineralization/material/fluidsystems/biominsimplechemistry.hh
new file mode 100644
index 0000000000..0937c55e4a
--- /dev/null
+++ b/examples/biomineralization/material/fluidsystems/biominsimplechemistry.hh
@@ -0,0 +1,582 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#ifndef DUMUX_BIOFLUID_SIMPLE_CHEM_SYSTEM_HH
+#define DUMUX_BIOFLUID_SIMPLE_CHEM_SYSTEM_HH
+
+// ## The fluid system (`biominsimplechemistry.hh`)
+//
+// This file contains the __fluidsystem class__ which defines all functions needed to describe the fluids and their properties,
+// which are needed to model biomineralization.
+//
+// [[content]]
+//
+// ### Include files
+// [[details]]
+// [[codeblock]]
+#include <dumux/material/idealgas.hh>
+
+// we include the base fluid system
+#include <dumux/material/fluidsystems/base.hh>
+// we include the brine adapter adapting component indices to use the brine fluidsystem
+#include "icpcomplexsalinitybrine.hh"
+
+// we include all necessary fluid components
+#include <dumux/material/fluidstates/adapter.hh>
+#include <dumux/material/components/co2.hh>
+#include <dumux/material/components/h2o.hh>
+#include <dumux/material/components/tabulatedcomponent.hh>
+#include <dumux/material/components/co2tablereader.hh>
+#include <dumux/material/components/sodiumion.hh>
+#include <dumux/material/components/chlorideion.hh>
+#include <dumux/material/components/calciumion.hh>
+#include <dumux/material/components/urea.hh>
+#include <dumux/material/components/o2.hh>
+#include <dumux/material/components/glucose.hh>
+#include <examples/biomineralization/material/components/suspendedbiomass.hh>
+
+// we include brine-co2 and h2o-co2 binary coefficients
+#include <dumux/material/binarycoefficients/brine_co2.hh>
+#include <dumux/material/binarycoefficients/h2o_o2.hh>
+// [[/codeblock]]
+
+#include <dumux/material/fluidsystems/nullparametercache.hh>
+#include <dumux/common/valgrind.hh>
+#include <dumux/common/exceptions.hh>
+
+#include <assert.h>
+// [[/details]]
+//
+// ### The fluidsystem class
+// In the BioMinSimpleChemistryFluid fluid system, we define all functions needed to describe the fluids and their properties accounted for in our simulation.
+// The simplified biogeochemistry biomineralization fluid system requires the CO2 tables and the H2OType as template parameters.
+// We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+// [[codeblock]]
+namespace Dumux::FluidSystems {
+
+template <class Scalar,
+ class CO2Table,
+ class H2OType = Components::TabulatedComponent<Components::H2O<Scalar>> >
+class BioMinSimpleChemistryFluid
+: public Base<Scalar, BioMinSimpleChemistryFluid<Scalar, CO2Table, H2OType> >
+{
+ using ThisType = BioMinSimpleChemistryFluid<Scalar, CO2Table, H2OType>;
+ using Base = Dumux::FluidSystems::Base<Scalar, ThisType>;
+ using IdealGas = Dumux::IdealGas<Scalar>;
+// [[/codeblock]]
+//
+// #### Component and phase definitions
+// With the following function we define what phases and components will be used by the fluid system and define the indices used to distinguish phases and components in the course of the simulation.
+// [[codeblock]]
+public:
+ // We use convenient declarations that we derive from the property system
+ typedef Components::CO2<Scalar, CO2Table> CO2;
+ using H2O = H2OType;
+ // export the underlying brine fluid system for the liquid phase, as brine is used as a "pseudo component"
+ using Brine = Dumux::FluidSystems::ICPComplexSalinityBrine<Scalar, H2OType>;
+ using Na = Components::SodiumIon<Scalar>;
+ using Cl = Components::ChlorideIon<Scalar>;
+ using Ca = Components::CalciumIon<Scalar>;
+ using Urea = Components::Urea<Scalar>;
+ using O2 = Components::O2<Scalar>;
+ using Glucose = Components::Glucose<Scalar>;
+ using SuspendedBiomass = Components::SuspendedBiomass<Scalar>;
+
+ // We define the binary coefficents file, which accounts for the interactions of the main fluids in our setup, water/brine and CO2
+ using Brine_CO2 = BinaryCoeff::Brine_CO2<Scalar, CO2Table, true>;
+
+ // the type of parameter cache objects. this fluid system does not
+ // cache anything, so it uses Dumux::NullParameterCache
+ typedef Dumux::NullParameterCache ParameterCache;
+
+ // We define phase-related indices and properties
+ static constexpr int numPhases = 2; // liquid and gas phases
+ static constexpr int wPhaseIdx = 0; // index of the liquid phase
+ static constexpr int nPhaseIdx = 1; // index of the gas phase
+ static constexpr int phase0Idx = wPhaseIdx;
+ static constexpr int phase1Idx = nPhaseIdx;
+
+ // the phase names
+ static std::string phaseName(int phaseIdx)
+ {
+ static std::string name[] = {
+ "w",
+ "n"
+ };
+
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ return name[phaseIdx];
+ }
+
+ // We define component-related indices and properties
+ static constexpr int numComponents = 9; // H2O, TotalC, Na, Cl, Ca,...
+ static constexpr int numSecComponents = 6;
+
+ static constexpr int H2OIdx = 0;
+ static constexpr int BrineIdx = 0;
+ static constexpr int TCIdx = 1;
+ static constexpr int wCompIdx = BrineIdx;
+ static constexpr int nCompIdx = TCIdx;
+ static constexpr int comp0Idx = wCompIdx;
+ static constexpr int comp1Idx = nCompIdx;
+
+ static constexpr int NaIdx = 2;
+ static constexpr int ClIdx = 3;
+ static constexpr int CaIdx = 4;
+ static constexpr int UreaIdx = 5;
+ static constexpr int O2Idx = 6;
+ static constexpr int GlucoseIdx = 7;
+ static constexpr int SuspendedBiomassIdx = 8;
+// [[/codeblock]]
+// [[exclude]]
+
+ // We check whether a phase is liquid
+ static constexpr bool isLiquid(int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ return phaseIdx != nPhaseIdx;
+ }
+
+ // We return whether a phase is gaseous
+ static constexpr bool isGas(int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ return phaseIdx == nPhaseIdx;
+ }
+
+ // We assume ideal mixtures
+ static constexpr bool isIdealMixture(int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ return true;
+ }
+
+ // We assume compressible fluid phases
+ static constexpr bool isCompressible(int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ return true;
+ }
+
+ // The component names
+ static constexpr std::string componentName(int compIdx)
+ {
+
+ switch (compIdx) {
+ case BrineIdx: return H2O::name();
+ case TCIdx: return "TotalC";
+ case CaIdx: return Ca::name();
+ case NaIdx: return Na::name();
+ case ClIdx: return Cl::name();
+ case SuspendedBiomassIdx: return SuspendedBiomass::name();
+ case GlucoseIdx: return Glucose::name();
+ case O2Idx: return O2::name();
+ case UreaIdx: return Urea::name();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx); break;
+ };
+ }
+
+ // The component molar masses
+ static constexpr Scalar molarMass(int compIdx)
+ {
+ switch (compIdx) {
+ case H2OIdx: return H2O::molarMass();
+ // actually, the molar mass of brine is only needed for diffusion
+ // but since chloride and sodium are accounted for seperately
+ // only the molar mass of water is returned.
+ case TCIdx: return CO2::molarMass();
+ case CaIdx: return Ca::molarMass();
+ case NaIdx: return Na::molarMass();
+ case ClIdx: return Cl::molarMass();
+ case SuspendedBiomassIdx: return SuspendedBiomass::molarMass();
+ case GlucoseIdx: return Glucose::molarMass();
+ case O2Idx: return O2::molarMass();
+ case UreaIdx: return Urea::molarMass();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx); break;
+ };
+ }
+// [[/exclude]]
+//
+// #### The Brine Adapter
+// With the brine adapter, we link water and the components sodium, chloride, and calcium to form brine, to be able to use the "brine.hh" fluidsystem expecting only water and a single salt.
+// Here, we define that the components water, sodium, chloride, and calcium contribute to brine.
+// The real work is done by the adapter "icpcomplexsalinitybrine.hh".
+// [[codeblock]]
+private:
+ struct BrineAdapterPolicy
+ {
+ using FluidSystem = Brine;
+
+ static constexpr int phaseIdx(int brinePhaseIdx) { return wPhaseIdx; }
+ static constexpr int compIdx(int brineCompIdx)
+ {
+ switch (brineCompIdx)
+ {
+ assert(brineCompIdx == Brine::H2OIdx
+ || brineCompIdx == Brine::NaIdx
+ || brineCompIdx == Brine::ClIdx
+ || brineCompIdx == Brine::CaIdx
+ );
+ case Brine::H2OIdx: return H2OIdx;
+ case Brine::NaIdx: return NaIdx;
+ case Brine::ClIdx: return ClIdx;
+ case Brine::CaIdx: return CaIdx;
+ default: return 0; // this will never be reached, only needed to suppress compiler warning
+ }
+ }
+ };
+
+ template<class FluidState>
+ using BrineAdapter = FluidStateAdapter<FluidState, BrineAdapterPolicy>;
+// [[/codeblock]]
+
+ // #### Initializing the fluid system
+ // [[codeblock]]
+public:
+ static void init()
+ {
+ init(/*startTemp=*/275.15, /*endTemp=*/455.15, /*tempSteps=*/30,
+ /*startPressure=*/1e4, /*endPressure=*/99e6, /*pressureSteps=*/500);
+ }
+ static void init(Scalar startTemp, Scalar endTemp, int tempSteps,
+ Scalar startPressure, Scalar endPressure, int pressureSteps)
+ {
+ std::cout << "Initializing tables for the pure-water properties.\n";
+ H2O::init(startTemp, endTemp, tempSteps,
+ startPressure, endPressure, pressureSteps);
+ }
+// [[/codeblock]]
+
+ // #### The Component-Phase Interactions
+ // In the following, we define the component-phase interactions such as // each component's fugacity coefficient in each phase
+ // and each component's and the phases' main components binary diffusion coefficient in the respective phase.
+ // [[codeblock]]
+ // The component fugacity coefficients
+ template <class FluidState>
+ static Scalar fugacityCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIdx && compIdx < numComponents);
+
+ if (phaseIdx == nPhaseIdx)
+ // use the fugacity coefficients of an ideal gas. the
+ // actual value of the fugacity is not relevant, as long
+ // as the relative fluid compositions are observed,
+ return 1.0;
+
+ Scalar temperature = fluidState.temperature(phaseIdx);
+ Scalar pressure = fluidState.pressure(phaseIdx);
+ if (pressure<0)
+ {
+ typedef Dune::FieldVector<Scalar, numComponents> ComponentVector;
+ ComponentVector moleFractionsw;
+ ComponentVector massFractionsw;
+
+ for (int compIdx = 0; compIdx<numComponents;++compIdx)
+ {
+ moleFractionsw[compIdx] = fluidState.moleFraction(wPhaseIdx,compIdx);
+ massFractionsw[compIdx] = fluidState.massFraction(wPhaseIdx,compIdx);
+ }
+ }
+
+ assert(temperature > 0);
+ assert(pressure > 0);
+
+ // calulate the equilibrium composition for the given
+ // temperature and pressure.
+ Scalar xgH2O, xlH2O;
+ Scalar xlCO2, xgCO2;
+ Scalar Xl_Sal = fluidState.massFraction(wPhaseIdx, NaIdx) //Salinity= XNa+XCl+XCa
+ + fluidState.massFraction(wPhaseIdx, ClIdx)
+ + fluidState.massFraction(wPhaseIdx, CaIdx);
+ Brine_CO2::calculateMoleFractions(temperature,
+ pressure,
+ Xl_Sal,
+ /*knownPhaseIdx=*/ -1,
+ xlCO2,
+ xgH2O);
+
+ xlCO2 = std::max(0.0, std::min(1.0, xlCO2));
+ xgH2O = std::max(0.0, std::min(1.0, xgH2O));
+ xlH2O = 1.0 - xlCO2;
+ xgCO2 = 1.0 - xgH2O;
+
+ // Only H2O, CO2, and O2 in the gas phase
+ if (compIdx == BrineIdx) {
+ Scalar phigH2O = 1.0;
+ return phigH2O * xgH2O / xlH2O;
+ }
+ else if (compIdx == TCIdx)
+ {
+ Scalar phigCO2 = 1.0;
+ return phigCO2 * xgCO2 / xlCO2;
+ }
+ else if (compIdx == O2Idx)
+ {
+ return Dumux::BinaryCoeff::H2O_O2::henry(temperature)/pressure;
+ }
+ // All other components are assumed not be present in the gas phase
+ else
+ {
+ return 1e-20;
+ }
+ }
+
+ template <class FluidState>
+ static Scalar diffusionCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIdx)
+ {
+ DUNE_THROW(Dune::NotImplemented, "Diffusion coefficients");
+ };
+
+ // The binary diffusion coefficients of the components and the phases main component
+ template <class FluidState>
+ static Scalar binaryDiffusionCoefficient(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx,
+ int compIIdx,
+ int compJIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIIdx && compIIdx < numComponents);
+ assert(0 <= compJIdx && compJIdx < numComponents);
+
+ Scalar temperature = fluidState.temperature(phaseIdx);
+ Scalar pressure = fluidState.pressure(phaseIdx);
+
+ if (phaseIdx == wPhaseIdx) {
+ assert(compIIdx == H2OIdx);
+ Scalar result = 0.0;
+ if(compJIdx == TCIdx)
+ result = Brine_CO2::liquidDiffCoeff(temperature, pressure);
+ else if(compJIdx == O2Idx)
+ result = Dumux::BinaryCoeff::H2O_O2::liquidDiffCoeff(temperature, pressure);
+ else //all other components
+ result = 1.587e-9; //[m²/s] //J. Phys. D: Appl. Phys. 40 (2007) 2769-2776 //old Value from Anozie 1e-9
+
+ Valgrind::CheckDefined(result);
+ return result;
+ }
+ else {
+ assert(phaseIdx == nPhaseIdx);
+ assert(compIIdx == TCIdx);
+ Scalar result = 0.0;
+ if(compJIdx == H2OIdx)
+ result = Brine_CO2::gasDiffCoeff(temperature, pressure);
+ else if(compJIdx == O2Idx)
+ result = Dumux::BinaryCoeff::H2O_O2::gasDiffCoeff(temperature, pressure);
+ else //all other components
+ result = 0.0;
+
+ Valgrind::CheckDefined(result);
+ return result;
+ }
+ };
+ // [[/codeblock]]
+
+ // #### The Fluid Properties
+ // In the following, all functions defining the phase properties are given:
+ // the density, viscosity, enthalpy, thermal conductivities, and heat capacities
+ // of each phase depending on temperature, pressure, and phase composition
+ // [[codeblock]]
+ // The phase density of the liquid phase is calculated accounting for the impact of solutes in the brine as well as the contribution of CO2.
+ // For the gas phase, a mixture of water and CO2 is considered, as solutes do not partition into the gas phase.
+ template <class FluidState>
+ static Scalar density(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ const Scalar T = fluidState.temperature(phaseIdx);
+
+ if (phaseIdx == wPhaseIdx)
+ {
+ const Scalar pl = fluidState.pressure(phaseIdx);
+ const Scalar xlCO2 = fluidState.moleFraction(wPhaseIdx, TCIdx);
+ const Scalar xlH2O = fluidState.moleFraction(wPhaseIdx, H2OIdx);
+ if(T < 273.15) {
+ DUNE_THROW(NumericalProblem,
+ "Liquid density for Brine and CO2 is only "
+ "defined above 273.15K (is" << T << ")");
+ }
+ if(pl >= 2.5e8) {
+ DUNE_THROW(NumericalProblem,
+ "Liquid density for Brine and CO2 is only "
+ "defined below 250MPa (is" << pl << ")");
+ }
+
+ // calling the brine adapter for brine density
+ Scalar rho_brine = Brine::molarDensity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx)
+ *(H2O::molarMass()*fluidState.moleFraction(wPhaseIdx, H2OIdx)
+ + Na::molarMass()*fluidState.moleFraction(wPhaseIdx, NaIdx)
+ + Cl::molarMass()*fluidState.moleFraction(wPhaseIdx, ClIdx)
+ + Ca::molarMass()*fluidState.moleFraction(wPhaseIdx, CaIdx)
+ );
+ // the density of pure water
+ Scalar rho_pure = H2O::liquidDensity(T, pl);
+ //we also use a private helper function to calculate the liquid density of the same amount of CO2 in pure water
+ Scalar rho_lCO2 = liquidDensityWaterCO2_(T, pl, xlH2O, xlCO2);
+ // calculating the density contribution of CO2 in pure water
+ Scalar contribCO2 = rho_lCO2 - rho_pure;
+ // assuming CO2 increases the density for brine by the same amount as for pure water
+ return rho_brine + contribCO2;
+ }
+
+ else if (phaseIdx == nPhaseIdx)
+ return H2O::gasDensity(T, fluidState.partialPressure(nPhaseIdx, H2OIdx))
+ + CO2::gasDensity(T, fluidState.partialPressure(nPhaseIdx, TCIdx));
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+
+ // The phase molar density of the liquid phase is assumed to not change significantly from the molar density of the pure brine.
+ // For the gas phase, a mixture of water and CO2 is considered, as solutes do not partition into the gas phase.
+ using Base::molarDensity;
+ template <class FluidState>
+ static Scalar molarDensity(const FluidState& fluidState, int phaseIdx)
+ {
+ if (phaseIdx == wPhaseIdx)
+ return Brine::molarDensity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+ else if (phaseIdx == nPhaseIdx)
+ return H2O::gasMolarDensity(fluidState.temperature(phaseIdx),
+ fluidState.partialPressure(phaseIdx, H2OIdx))
+ + CO2::gasMolarDensity(fluidState.temperature(phaseIdx),
+ fluidState.partialPressure(phaseIdx, TCIdx));
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+
+ // The phase viscosities are assumed to not change significantly from those of the pure brine for the liquid and pure CO2 for the gas phase
+ using Base::viscosity;
+ template <class FluidState>
+ static Scalar viscosity(const FluidState& fluidState, int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ if (phaseIdx == wPhaseIdx)
+ return Brine::viscosity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+ else if (phaseIdx == nPhaseIdx)
+ {
+ return CO2::gasViscosity(fluidState.temperature(phaseIdx), fluidState.pressure(phaseIdx));
+ }
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+
+ }
+ // [[/codeblock]]
+
+ // [[exclude]]
+ // non-isothermal phase properties
+ // The phase enthalpies are assumed to not change significantly from those of the pure brine for the liquid and pure CO2 for the gas phase
+ template <class FluidState>
+ static Scalar enthalpy(const FluidState &fluidState,
+ const ParameterCache ¶mCache,
+ int phaseIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+
+ Scalar temperature = fluidState.temperature(phaseIdx);
+ Scalar pressure = fluidState.pressure(phaseIdx);
+
+ if (phaseIdx == wPhaseIdx)
+ {
+ return Brine::enthalpy(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+ }
+ else {
+ Scalar XCO2 = fluidState.massFraction(nPhaseIdx, TCIdx);
+ Scalar XBrine = fluidState.massFraction(nPhaseIdx, H2OIdx);
+
+ Scalar result = 0;
+ result += XBrine * Brine::gasEnthalpy(temperature, pressure);
+ result += XCO2 * CO2::gasEnthalpy(temperature, pressure);
+ Valgrind::CheckDefined(result);
+ return result;
+ }
+ };
+
+ // The phase thermal conductivities are assumed to not change significantly from those of the pure brine for the liquid and pure CO2 for the gas phase
+ template <class FluidState>
+ static Scalar thermalConductivity(const FluidState& fluidState, int phaseIdx)
+ {
+ if (phaseIdx == wPhaseIdx)
+ return Brine::thermalConductivity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+ else if (phaseIdx ==nPhaseIdx)
+ return CO2::gasThermalConductivity(fluidState.temperature(phaseIdx), fluidState.pressure(phaseIdx));
+
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+
+ // The phase heat capacitiy of the liquid phase is assumed to not change significantly from the heat capacitiy of the pure brine.
+ // For the gas phase, a mixture of water and CO2 is considered, as solutes do not partition into the gas phase.
+ template <class FluidState>
+ static Scalar heatCapacity(const FluidState &fluidState, int phaseIdx)
+ {
+ const Scalar T = fluidState.temperature(phaseIdx);
+ const Scalar p = fluidState.pressure(phaseIdx);
+
+ if (phaseIdx == wPhaseIdx)
+ return Brine::heatCapacity(BrineAdapter<FluidState>(fluidState), Brine::liquidPhaseIdx);
+
+ // We assume NaCl not to be present in the gas phase here
+ else if (phaseIdx ==nPhaseIdx)
+ return CO2::gasHeatCapacity(T, p)*fluidState.moleFraction(nPhaseIdx, TCIdx)
+ + H2O::gasHeatCapacity(T, p)*fluidState.moleFraction(nPhaseIdx, H2OIdx);
+
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+
+
+private:
+
+ //a private helper function to calculate the liquid density of the same amount of CO2 as we have in our brine in pure water
+ static Scalar liquidDensityWaterCO2_(Scalar temperature,
+ Scalar pl,
+ Scalar xlH2O,
+ Scalar xlCO2)
+ {
+ const Scalar M_CO2 = CO2::molarMass();
+ const Scalar M_H2O = H2O::molarMass();
+
+ const Scalar tempC = temperature - 273.15; /* tempC : temperature in °C */
+ const Scalar rho_pure = H2O::liquidDensity(temperature, pl);
+ xlH2O = 1.0 - xlCO2; // xlH2O is available, but in case of a pure gas phase
+ // the value of M_T for the virtual liquid phase can become very large
+ const Scalar M_T = M_H2O * xlH2O + M_CO2 * xlCO2;
+ const Scalar V_phi =
+ (37.51 +
+ tempC*(-9.585e-2 +
+ tempC*(8.74e-4 -
+ tempC*5.044e-7))) / 1.0e6;
+ return 1/ (xlCO2 * V_phi/M_T + M_H2O * xlH2O / (rho_pure * M_T));
+ }
+};
+
+} // end namespace Dumux::FluidSystems
+// [[/exclude]]
+// [[/content]]
+#endif
diff --git a/examples/biomineralization/material/fluidsystems/icpcomplexsalinitybrine.hh b/examples/biomineralization/material/fluidsystems/icpcomplexsalinitybrine.hh
new file mode 100644
index 0000000000..23df24daf5
--- /dev/null
+++ b/examples/biomineralization/material/fluidsystems/icpcomplexsalinitybrine.hh
@@ -0,0 +1,391 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 3 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#ifndef DUMUX_ICP_COMPLEX_SALINITY_BRINE_FLUID_SYSTEM_HH
+#define DUMUX_ICP_COMPLEX_SALINITY_BRINE_FLUID_SYSTEM_HH
+
+// ## The brine adapter (`icpcomplexsalinitybrine.hh`)
+//
+// This file contains the brineadapter class__ which defines
+// how to adapt values for communication between
+// the "full" fluidsystem accounting for 4 components influencing the brine properties
+// and the "brine" fluidsystem assuming water and a single salt determining the brine properties.
+//
+// [[content]]
+//
+// ### Include files
+// [[details]] includes
+// we include all necessary components
+#include <dumux/material/fluidsystems/base.hh>
+#include <dumux/material/constants.hh>
+#include <dumux/material/components/h2o.hh>
+#include <dumux/material/components/sodiumion.hh>
+#include <dumux/material/components/chlorideion.hh>
+#include <dumux/material/components/calciumion.hh>
+#include <dumux/material/components/tabulatedcomponent.hh>
+
+#include <dumux/common/exceptions.hh>
+
+#include <dumux/io/name.hh>
+// [[/details]]
+//
+// ### The brine adapter class
+// In ICPComplexSalinityBrine we make the transition from 3 components additional to water contributing to salinity to the single component that is assumed in the brine fluid system.
+// We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+// [[codeblock]]
+namespace Dumux::FluidSystems {
+
+template< class Scalar, class H2OType = Components::TabulatedComponent<Dumux::Components::H2O<Scalar>> >
+class ICPComplexSalinityBrine : public Base< Scalar, ICPComplexSalinityBrine<Scalar, H2OType>>
+{
+ using ThisType = ICPComplexSalinityBrine<Scalar, H2OType>;
+ using Base = Dumux::FluidSystems::Base<Scalar, ThisType>;
+
+public:
+ //! export the involved components
+ using H2O = H2OType;
+ using Na = Components::SodiumIon<Scalar>;
+ using Cl = Components::ChlorideIon<Scalar>;
+ using Ca = Components::CalciumIon<Scalar>;
+ // [[/codeblock]]
+ //
+ // #### Component and phase definitions
+ // With the following function we define what phases and components will be used by the fluid system and define the indices used to distinguish phases and components in the course of the simulation.
+ // [[codeblock]]
+ // We use convenient declarations that we derive from the property system.
+ static constexpr int numPhases = 1; //!< Number of phases in the fluid system
+ static constexpr int numComponents = 4; //!< Number of components in the fluid system (H2O, Na, Cl, Ca)
+
+ static constexpr int phase0Idx = 0; //!< Index of the first (and only) phase
+ static constexpr int liquidPhaseIdx = phase0Idx; //!< The one considered phase is liquid
+
+ static constexpr int H2OIdx = 0; //!< index of the water component
+ static constexpr int NaIdx = 1; //!< index of the Na component
+ static constexpr int ClIdx = 2; //!< index of the Cl component
+ static constexpr int CaIdx = 3; //!< index of the Ca component
+ static constexpr int comp0Idx = H2OIdx; //!< index of the first component
+ static constexpr int comp1Idx = NaIdx; //!< index of the second component
+ static constexpr int comp2Idx = ClIdx; //!< index of the third component
+ static constexpr int comp3Idx = CaIdx; //!< index of the fourth component
+
+ // the fluid phase index
+ static std::string phaseName(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return IOName::liquidPhase();
+ }
+
+ // the miscibility
+ static constexpr bool isMiscible()
+ {
+ return false;
+ }
+
+ // we do not have a gas phase
+ static constexpr bool isGas(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return false;
+ }
+
+ // We need a ideal mixture
+ static constexpr bool isIdealMixture(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return true;
+ }
+
+ // phase compressibility
+ static constexpr bool isCompressible(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return H2O::liquidIsCompressible();
+ }
+
+ // no gas, thus no ideal gas
+ static constexpr bool isIdealGas(int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ return false; /*we're a liquid!*/
+ }
+// [[/codeblock]]
+// [[exclude]]
+ // The component names
+ static constexpr std::string componentName(int compIdx)
+ {
+ switch (compIdx)
+ {
+ case H2OIdx: return H2O::name();
+ case CaIdx: return Ca::name();
+ case NaIdx: return Na::name();
+ case ClIdx: return Cl::name();
+ };
+ DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+
+ // The component molar masses
+ static constexpr Scalar molarMass(int compIdx)
+ {
+ switch (compIdx)
+ {
+ case H2OIdx: return H2O::molarMass();
+ case CaIdx: return Ca::molarMass();
+ case NaIdx: return Na::molarMass();
+ case ClIdx: return Cl::molarMass();
+ };
+ DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+
+ //initializing
+ static void init()
+ {
+ init(/*tempMin=*/273.15,
+ /*tempMax=*/623.15,
+ /*numTemp=*/100,
+ /*pMin=*/-10.,
+ /*pMax=*/20e6,
+ /*numP=*/200);
+ }
+ static void init(Scalar tempMin, Scalar tempMax, unsigned nTemp,
+ Scalar pressMin, Scalar pressMax, unsigned nPress)
+ {
+
+ if (H2O::isTabulated)
+ {
+ std::cout << "Initializing tables for the H2O fluid properties ("
+ << nTemp*nPress
+ << " entries).\n";
+
+ H2O::init(tempMin, tempMax, nTemp, pressMin, pressMax, nPress);
+ }
+ }
+// [[/exclude]]
+ //
+ // #### The Component-Phase Interactions
+ // In the following, we define the component-phase interactions such as // each component's fugacity coefficient in brine
+ // and each component's binary diffusion coefficient with water in brine
+ // [[codeblock]]
+ // The component fugacity coefficients
+ template <class FluidState>
+ static Scalar fugacityCoefficient(const FluidState &fluidState,
+ int phaseIdx,
+ int compIdx)
+ {
+ assert(0 <= phaseIdx && phaseIdx < numPhases);
+ assert(0 <= compIdx && compIdx < numComponents);
+
+ if (phaseIdx == compIdx)
+ // We could calculate the real fugacity coefficient of
+ // the component in the fluid. Probably that's not worth
+ // the effort, since the fugacity coefficient of the other
+ // component is infinite anyway...
+ return 1.0;
+ return std::numeric_limits<Scalar>::infinity();
+ }
+
+ // The binary diffusion coefficients of the components and the phases main component
+ template <class FluidState>
+ static Scalar binaryDiffusionCoefficient(const FluidState& fluidState,
+ int phaseIdx,
+ int compIIdx,
+ int compJIdx)
+ {
+ if (phaseIdx == liquidPhaseIdx)
+ {
+ if (compIIdx > compJIdx)
+ {
+ using std::swap;
+ swap(compIIdx, compJIdx);
+ }
+ if (compJIdx == NaIdx || compJIdx == ClIdx || compJIdx == CaIdx)
+ return 1.587e-9; //[m²/s] //J. Phys. D: Appl. Phys. 40 (2007) 2769-2776
+ else
+ DUNE_THROW(Dune::NotImplemented, "Binary diffusion coefficient of components "
+ << compIIdx << " and " << compJIdx
+ << " in phase " << phaseIdx);
+ }
+
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index: " << phaseIdx);
+ }
+ // [[/codeblock]]
+ //
+ // #### The Fluid (Brine) Properties
+ // In the following, all functions defining the phase properties are given:
+ // the density, viscosity, enthalpy, thermal conductivities, and heat capacities
+ // of each phase depending on temperature, pressure, and phase composition
+ // [[codeblock]]
+ // The phase density
+ template <class FluidState>
+ static Scalar density(const FluidState& fluidState, int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ const Scalar temperature = fluidState.temperature(phaseIdx);
+ const Scalar pressure = fluidState.pressure(phaseIdx);
+ const Scalar xNaCl = fluidState.massFraction(phaseIdx, NaIdx)
+ + fluidState.massFraction(phaseIdx, ClIdx)
+ + fluidState.massFraction(phaseIdx, CaIdx);
+
+ using std::max;
+ const Scalar TempC = temperature - 273.15;
+ const Scalar pMPa = pressure/1.0E6;
+ const Scalar salinity = max(0.0, xNaCl);
+
+ const Scalar rhow = H2O::liquidDensity(temperature, pressure);
+ const Scalar density = rhow + 1000*salinity*(0.668 +
+ 0.44*salinity +
+ 1.0E-6*(300*pMPa -
+ 2400*pMPa*salinity +
+ TempC*(80.0 +
+ 3*TempC -
+ 3300*salinity -
+ 13*pMPa +
+ 47*pMPa*salinity)));
+ assert(density > 0.0);
+ return density;
+ }
+
+
+
+ // The phase viscosity
+ template <class FluidState>
+ static Scalar viscosity(const FluidState& fluidState, int phaseIdx = liquidPhaseIdx)
+ {
+ assert(phaseIdx == liquidPhaseIdx);
+ const Scalar temperature = fluidState.temperature(phaseIdx);
+ const Scalar xNaCl = fluidState.massFraction(phaseIdx, NaIdx)
+ + fluidState.massFraction(phaseIdx, ClIdx)
+ + fluidState.massFraction(phaseIdx, CaIdx);
+
+ using std::pow;
+ using std::exp;
+ using std::max;
+ const Scalar T = max(temperature, 275.0);
+ const Scalar salinity = max(0.0, xNaCl);
+
+ const Scalar T_C = T - 273.15;
+ const Scalar A = ((0.42*pow((pow(salinity, 0.8)-0.17), 2)) + 0.045)*pow(T_C, 0.8);
+ const Scalar mu_brine = 0.1 + (0.333*salinity) + (1.65+(91.9*salinity*salinity*salinity))*exp(-A); // [cP]
+ assert(mu_brine > 0.0);
+ return mu_brine/1000.0; // [Pa·s]
+ }
+// [[/codeblock]]
+// [[exclude]]
+ // The vapor pressure
+ template <class FluidState>
+ static Scalar vaporPressure(const FluidState& fluidState, int compIdx)
+ {
+ if (compIdx == H2OIdx)
+ {
+ // simplified version of Eq 2.29 in Vishal Jambhekar's Promo
+ const Scalar temperature = fluidState.temperature(H2OIdx);
+ return H2O::vaporPressure(temperature)/fluidState.massFraction(phase0Idx, H2OIdx);
+ }
+ else if (compIdx == NaIdx)
+ DUNE_THROW(Dune::NotImplemented, "Na::vaporPressure(t)");
+ else if (compIdx == ClIdx)
+ DUNE_THROW(Dune::NotImplemented, "Cl::vaporPressure(t)");
+ else if (compIdx == CaIdx)
+ DUNE_THROW(Dune::NotImplemented, "Ca::vaporPressure(t)");
+ else
+ DUNE_THROW(Dune::NotImplemented, "Invalid component index " << compIdx);
+ }
+
+ // The phase enthalpies
+ template <class FluidState>
+ static Scalar enthalpy(const FluidState& fluidState, int phaseIdx)
+ {
+ /*Numerical coefficients from PALLISER*/
+ static constexpr Scalar f[] = { 2.63500E-1, 7.48368E-6, 1.44611E-6, -3.80860E-10 };
+
+ /*Numerical coefficients from MICHAELIDES for the enthalpy of brine*/
+ static constexpr Scalar a[4][3] = { { +9633.6, -4080.0, +286.49 },
+ { +166.58, +68.577, -4.6856 },
+ { -0.90963, -0.36524, +0.249667E-1 },
+ { +0.17965E-2, +0.71924E-3, -0.4900E-4 } };
+
+ const Scalar p = fluidState.pressure(phaseIdx);
+ const Scalar T = fluidState.temperature(phaseIdx);
+ const Scalar theta = T - 273.15;
+ const Scalar salSat = f[0] + f[1]*theta + f[2]*theta*theta + f[3]*theta*theta*theta;
+
+ /*Regularization*/
+ using std::min;
+ using std::max;
+ const Scalar xNaCl = fluidState.massFraction(phaseIdx, NaIdx)
+ + fluidState.massFraction(phaseIdx, ClIdx)
+ + fluidState.massFraction(phaseIdx, CaIdx);
+ const Scalar salinity = min(max(xNaCl,0.0), salSat);
+
+ const Scalar hw = H2O::liquidEnthalpy(T, p)/1E3; /* kJ/kg */
+
+ /*DAUBERT and DANNER*/
+ const Scalar h_NaCl = (3.6710E4*T + 0.5*(6.2770E1)*T*T - ((6.6670E-2)/3)*T*T*T
+ + ((2.8000E-5)/4)*(T*T*T*T))/(58.44E3)- 2.045698e+02; /* U [kJ/kg] */
+
+ const Scalar m = (1E3/58.44)*(salinity/(1-salinity));
+
+ using std::pow;
+ Scalar d_h = 0;
+ for (int i = 0; i<=3; i++)
+ for (int j=0; j<=2; j++)
+ d_h = d_h + a[i][j] * pow(theta, i) * pow(m, j);
+
+ /* heat of dissolution for halite according to Michaelides 1971 */
+ const Scalar delta_h = (4.184/(1E3 + (58.44 * m)))*d_h;
+
+ /* Enthalpy of brine without any dissolved gas */
+ const Scalar h_ls1 =(1-salinity)*hw + salinity*h_NaCl + salinity*delta_h; /* kJ/kg */
+ return h_ls1*1E3; /*J/kg*/
+ }
+ // The molar density
+ template <class FluidState>
+ static Scalar molarDensity(const FluidState& fluidState, int phaseIdx = liquidPhaseIdx)
+ {
+ return density(fluidState, phaseIdx)/fluidState.averageMolarMass(phaseIdx);
+ }
+
+ template <class FluidState>
+ static Scalar diffusionCoefficient(const FluidState& fluidState, int phaseIdx, int compIdx)
+ {
+ DUNE_THROW(Dune::NotImplemented, "FluidSystems::ICPComplexSalinityBrine::diffusionCoefficient()");
+ }
+
+ // The thermal conductivity
+ template <class FluidState>
+ static Scalar thermalConductivity(const FluidState& fluidState, int phaseIdx)
+ {
+ if (phaseIdx == liquidPhaseIdx)
+ return H2O::liquidThermalConductivity(fluidState.temperature(phaseIdx), fluidState.pressure(phaseIdx));
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index: " << phaseIdx);
+ }
+
+ // The phase heat capacity
+ template <class FluidState>
+ static Scalar heatCapacity(const FluidState &fluidState, int phaseIdx)
+ {
+ if (phaseIdx == liquidPhaseIdx)
+ return H2O::liquidHeatCapacity(fluidState.temperature(phaseIdx), fluidState.pressure(phaseIdx));
+ DUNE_THROW(Dune::InvalidStateException, "Invalid phase index " << phaseIdx);
+ }
+};
+
+} // end namespace Dumux::FluidSystems
+// [[/exclude]]
+// [[/content]]
+#endif
diff --git a/examples/biomineralization/material/solidsystems/biominsolids.hh b/examples/biomineralization/material/solidsystems/biominsolids.hh
new file mode 100644
index 0000000000..852ca636dc
--- /dev/null
+++ b/examples/biomineralization/material/solidsystems/biominsolids.hh
@@ -0,0 +1,197 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#ifndef DUMUX_SOLIDSYSTEMS_MICP_SOLID_PHASE_HH
+#define DUMUX_SOLIDSYSTEMS_MICP_SOLID_PHASE_HH
+
+// ## The solid system (`biominsolids.hh`)
+//
+// This file contains the __solidystem class__ which defines all functions needed to describe the solid and their properties,
+// which are needed to model biomineralization.
+//
+// [[content]]
+//
+// ### Include files
+// [[codeblock]]
+#include <string>
+#include <dune/common/exceptions.hh>
+
+// we include all necessary solid components
+#include <examples/biomineralization/material/components/biofilm.hh>
+#include <dumux/material/components/calcite.hh>
+#include <dumux/material/components/granite.hh>
+// [[/codeblock]]
+
+// ### The solidsystem class
+// In the BioMinSolidPhase solid system, we define all functions needed to describe the solids and their properties accounted for in our simulation.
+// We enter the namespace Dumux. All Dumux functions and classes are in a namespace Dumux, to make sure they don`t clash with symbols from other libraries you may want to use in conjunction with Dumux.
+// [[codeblock]]
+namespace Dumux::SolidSystems {
+
+template <class Scalar>
+class BioMinSolidPhase
+{
+public:
+// [[/codeblock]]
+
+ // #### Component definitions
+ // With the following function we define what solid components will be used by the solid system and define the indices used to distinguish solid components in the course of the simulation.
+ // [[codeblock]]
+ // We use convenient declarations that we derive from the property system.
+ using Biofilm = Components::Biofilm<Scalar>;
+ using Calcite = Components::Calcite<Scalar>;
+ using Granite = Components::Granite<Scalar>;
+
+ /****************************************
+ * Solid phase related static parameters
+ ****************************************/
+ static constexpr int numComponents = 3;
+ static constexpr int numInertComponents = 1;
+ static constexpr int BiofilmIdx = 0;
+ static constexpr int CalciteIdx = 1;
+ static constexpr int GraniteIdx = 2;
+
+ // The component names
+ const static std::string componentName(int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::name();
+ case CalciteIdx: return Calcite::name();
+ case GraniteIdx: return Granite::name();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The solid system's name
+ static std::string name()
+ { return "BiomineralizationMinSolidPhase"; }
+
+ // We assume incompressible solids
+ static constexpr bool isCompressible(int compIdx)
+ { return false; }
+
+ // we have one inert component, the others may change
+ static constexpr bool isInert()
+ { return (numComponents == numInertComponents); }
+ // [[/codeblock]]
+
+ // #### Component properties
+ // This simply forwards the component properties (name, molar mass, density).
+ // [[codeblock]]
+ // The component molar masses
+ static Scalar molarMass(int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::molarMass();
+ case CalciteIdx: return Calcite::molarMass();
+ case GraniteIdx: return Granite::molarMass();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The component densities
+ template <class SolidState>
+ static Scalar density(const SolidState& solidState, const int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::solidDensity(solidState.temperature());
+ case CalciteIdx: return Calcite::solidDensity(solidState.temperature());
+ case GraniteIdx: return Granite::solidDensity(solidState.temperature());
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+
+ // The component molar densities
+ template <class SolidState>
+ static Scalar molarDensity(const SolidState& solidState, const int compIdx)
+ {
+ switch (compIdx)
+ {
+ case BiofilmIdx: return Biofilm::solidDensity(solidState.temperature())/Biofilm::molarMass();
+ case CalciteIdx: return Calcite::solidDensity(solidState.temperature())/Calcite::molarMass();
+ case GraniteIdx: return Granite::solidDensity(solidState.temperature())/Calcite::molarMass();
+ default: DUNE_THROW(Dune::InvalidStateException, "Invalid component index " << compIdx);
+ }
+ }
+ // [[/codeblock]]
+
+ // #### Averaged solid properties
+ // The overall solid properties are calculated by a volume-weigthed average of the pure component's properties.
+// [[codeblock]]
+ // The average density
+ template <class SolidState>
+ static Scalar density(const SolidState& solidState)
+ {
+ const Scalar rho1 = Biofilm::solidDensity(solidState.temperature());
+ const Scalar rho2 = Calcite::solidDensity(solidState.temperature());
+ const Scalar rho3 = Granite::solidDensity(solidState.temperature());
+ const Scalar volFrac1 = solidState.volumeFraction(BiofilmIdx);
+ const Scalar volFrac2 = solidState.volumeFraction(CalciteIdx);
+ const Scalar volFrac3 = solidState.volumeFraction(GraniteIdx);
+
+ return (rho1*volFrac1+
+ rho2*volFrac2+
+ rho3*volFrac3)
+ /(volFrac1+volFrac2+volFrac3);
+ }
+// [[/codeblock]]
+// [[exclude]]
+ // The average thermal conductivity
+ template <class SolidState>
+ static Scalar thermalConductivity(const SolidState &solidState)
+ {
+ const Scalar lambda1 = Biofilm::solidThermalConductivity(solidState.temperature());
+ const Scalar lambda2 = Calcite::solidThermalConductivity(solidState.temperature());
+ const Scalar lambda3 = Granite::solidThermalConductivity(solidState.temperature());
+ const Scalar volFrac1 = solidState.volumeFraction(BiofilmIdx);
+ const Scalar volFrac2 = solidState.volumeFraction(CalciteIdx);
+ const Scalar volFrac3 = solidState.volumeFraction(GraniteIdx);
+
+ return (lambda1*volFrac1+
+ lambda2*volFrac2+
+ lambda3*volFrac3)
+ /(volFrac1+volFrac2+volFrac3);
+ }
+
+ // The average heat capacity
+ template <class SolidState>
+ static Scalar heatCapacity(const SolidState &solidState)
+ {
+ const Scalar c1 = Biofilm::solidHeatCapacity(solidState.temperature());
+ const Scalar c2 = Calcite::solidHeatCapacity(solidState.temperature());
+ const Scalar c3 = Granite::solidHeatCapacity(solidState.temperature());
+ const Scalar volFrac1 = solidState.volumeFraction(BiofilmIdx);
+ const Scalar volFrac2 = solidState.volumeFraction(CalciteIdx);
+ const Scalar volFrac3 = solidState.volumeFraction(GraniteIdx);
+
+ return (c1*volFrac1+
+ c2*volFrac2+
+ c3*volFrac3)
+ /(volFrac1+volFrac2+volFrac3);
+ }
+
+};
+
+} // end namespace Dumux::SolidSystems
+// [[/exclude]]
+// [[/content]]
+#endif
diff --git a/examples/biomineralization/params.input b/examples/biomineralization/params.input
new file mode 100644
index 0000000000..9ec5f23397
--- /dev/null
+++ b/examples/biomineralization/params.input
@@ -0,0 +1,63 @@
+[Problem]
+Name = biomineralization #
+Temperature = 298.15 # [K] 25°C
+
+[Initial]
+DensityW = 1087 # [kg/m³] Density of the mixture
+Pressure = 1e5 # [Pa]
+XwTC = 2.3864e-7 # [mol/mol] equilibrium with atmospheric CO2 under atmospheric pressure
+XwNa = 0.0 # [mol/mol]
+XwCl = 0.0 # [mol/mol]
+XwCa = 0.0 # [mol/mol]
+XwUrea = 0.0 # [mol/mol]
+XwTNH = 3.341641e-3 # [mol/mol]
+XwO2 = 4.4686e-6 # [mol/mol]
+XwSubstrate = 2.97638e-4 # [mol/mol]
+XwSuspendedBiomass = 0.0 # [mol/mol]
+Biofilm = 0.0 # [-]
+Calcite = 0.0 # [-]
+XwNaCorr = 2.9466e-6 # [mol/mol] NaCorr to get the pH to 6.2 calculated as molefraction
+XwClCorr = 0.0 # [mol/mol]
+
+[Injection]
+FlowRate = 1.716666666667e-7 # [m³/s] The injected flow rate, see Hommel et al. 2015 =10.3/60/1e6 # = [ml/min] /[s/min] /[ml/m³]
+MassFracTC = 5.8e-7 # [kg/kg] equilibrium with atmospheric CO2 under atmospheric pressure
+ConcentrationNa = 0.0 # [kg/m³] NaCl injected
+ConcentrationCa = 13.530742 # [kg/m³] computed from 49 g/l CaCl2*2H2O (molar mass = 147.68g/mol --> 0.33molCa/l, equimolar with urea (20g/l and 60g/mol))
+ConcentrationUrea = 20 # [kg/m³]
+ConcentrationTNH = 3.183840574 # [kg/m³] computed from 10 g/l NH4Cl
+ConcentrationO2 = 0.008 # [kg/m³]
+ConcentrationSubstrate = 3 # [kg/m³]
+ConcentrationSuspendedBiomass = 0.0665 # [kg/m³] 5.6e7 cfu/ml (40e8cfu/ml~1g/l) cfu = colony forming unit = approximately equal to viable cells
+ConcentrationNaCorr= 0.00379 # [kg/m³] NaCorr to get the pH to 6.2
+NumInjections = 212 # [-] The number of injections, used to check, whether the matching injection file specified
+
+[TimeLoop]
+DtInitial = 1 # [s]
+TEnd = 100000 # [s] for the entire experiment setup described in Hommel et a. 2015 use TEnd = 3203460 #
+MaxTimeStepSize = 500 # [s] limiting the time step size speeds up the simulation, avoiding failed Newton iterations
+
+[Grid]
+UpperRight = 0.7112 # [m] upper right corner coordinates, the actual experiment was 0.61m long, extended the domain to reduce BC effects
+Cells = 56 # [-] number of cells in x,y-direction
+
+[SpatialParams]
+ReferencePorosity = 0.4 # [-]
+ReferencePermeability = 2e-10 # [m^2]
+
+[BioCoefficients]
+Ca1 = 8.3753e-8 # [1/s] fitted parameter, see Hommel et al. 2015
+Ca2 = 8.5114e-7 # [1/s] fitted parameter, see Hommel et al. 2015
+Cd1 = 2.894e-8 # [1/s] Ebigbo et al. 2010
+Dc0 = 3.183e-7 # [1/s] Taylor and Jaffe 1990
+Kmue = 4.1667e-5 # [1/s] Connolly et al. 2013
+F = 0.5 # [-] Mateles 1971
+Ke = 2e-5 # [kg/m³] Hao et al. 1983
+Ks = 7.99e-4 # [kg/m³] Taylor and Jaffe 1990
+Yield = 0.5 # [-] Seto and Alexander 1985
+BiofilmDensity = 6.9 # [kg/m³] fittet parameter, see Hommel et al. 2015
+
+[UreolysisCoefficients]
+Kub = 3.81e-4 # [kg_urease/kg_bio] fitted parameter, see Hommel et al. 2015
+Kurease = 706.6667 # [mol_urea/(kg_urease s)] Lauchnor et al. 2014
+Ku = 0.355 # [mol/kgH2O] Lauchnor et al. 2014
diff --git a/examples/biomineralization/problem.hh b/examples/biomineralization/problem.hh
new file mode 100644
index 0000000000..701336e782
--- /dev/null
+++ b/examples/biomineralization/problem.hh
@@ -0,0 +1,590 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+#ifndef DUMUX_MICP_COLUMN_SIMPLE_CHEM_PROBLEM_HH
+#define DUMUX_MICP_COLUMN_SIMPLE_CHEM_PROBLEM_HH
+
+// ## Initial and boundary conditions (`problem.hh`)
+//
+// This file contains the __problem class__ which defines the initial and boundary
+// conditions for the biominearalization example.
+//
+// [[content]]
+//
+// ### Include files
+// [[codeblock]]
+// This header contains the PorousMediumFlowProblem class
+#include <dumux/porousmediumflow/problem.hh>
+#include <dumux/common/properties.hh> // GetPropType
+#include <dumux/material/components/ammonia.hh>
+#include <dumux/discretization/evalgradients.hh>
+#include <dumux/io/container.hh>
+#include <algorithm> // for std::transform
+// [[/codeblock]]
+
+// ### The problem class
+// The problem class defines the boundary and initial conditions.
+// As this is a biomineralization problem in porous media, we inherit from the porous-media-flow problem
+
+// [[codeblock]]
+namespace Dumux {
+
+template <class TypeTag>
+class MICPColumnProblemSimpleChemistry : public PorousMediumFlowProblem<TypeTag>
+{
+ using ParentType = PorousMediumFlowProblem<TypeTag>;
+ using Scalar = GetPropType<TypeTag, Properties::Scalar>;
+ using NH3 = Components::Ammonia<Scalar>; // for molar mass of Ammonia
+ using FluidSystem = GetPropType<TypeTag, Properties::FluidSystem>;
+ using SolidSystem = GetPropType<TypeTag, Properties::SolidSystem>;
+ using VolumeVariables = GetPropType<TypeTag, Properties::VolumeVariables>;
+ using FluxVariables = GetPropType<TypeTag, Properties::FluxVariables>;
+ using Indices = typename GetPropType<TypeTag, Properties::ModelTraits>::Indices;
+
+ // We define some indices for convenience to be used later when defining the initial and boundary conditions
+ enum {
+ numComponents = FluidSystem::numComponents,
+
+ pressureIdx = Indices::pressureIdx,
+ switchIdx = Indices::switchIdx, //Saturation
+ xwNaIdx = FluidSystem::NaIdx,
+ xwClIdx = FluidSystem::ClIdx,
+ xwCaIdx = FluidSystem::CaIdx,
+ xwUreaIdx = FluidSystem::UreaIdx,
+ xwO2Idx = FluidSystem::O2Idx,
+ xwBiosubIdx = FluidSystem::GlucoseIdx,
+ xwSuspendedBiomassIdx = FluidSystem::SuspendedBiomassIdx,
+ phiBiofilmIdx = numComponents,
+ phiCalciteIdx = numComponents + 1,
+
+ //Indices of the components
+ wCompIdx = FluidSystem::wCompIdx,
+ nCompIdx = FluidSystem::nCompIdx,
+ NaIdx = FluidSystem::NaIdx,
+ ClIdx = FluidSystem::ClIdx,
+ CaIdx = FluidSystem::CaIdx,
+ UreaIdx = FluidSystem::UreaIdx,
+ O2Idx = FluidSystem::O2Idx,
+ BiosubIdx = FluidSystem::GlucoseIdx,
+ SuspendedBiomassIdx = FluidSystem::SuspendedBiomassIdx,
+
+ wPhaseIdx = FluidSystem::wPhaseIdx,
+ conti0EqIdx = Indices::conti0EqIdx,
+
+ // Phase State
+ wPhaseOnly = Indices::firstPhaseOnly,
+ bothPhases = Indices::bothPhases
+ };
+
+ using PrimaryVariables = GetPropType<TypeTag, Properties::PrimaryVariables>;
+ using NumEqVector = GetPropType<TypeTag, Properties::NumEqVector>;
+ using BoundaryTypes = GetPropType<TypeTag, Properties::BoundaryTypes>;
+ using ElementVolumeVariables = typename GetPropType<TypeTag, Properties::GridVolumeVariables>::LocalView;
+ using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>;
+ using GridView = typename GridGeometry::GridView;
+ using Element = typename GridView::template Codim<0>::Entity;
+ using FVElementGeometry = typename GridGeometry::LocalView;
+ using SubControlVolume = typename GridGeometry::SubControlVolume;
+ using GlobalPosition = typename Element::Geometry::GlobalCoordinate;
+ static constexpr int dim = GridView::dimension;
+// [[/codeblock]]
+//
+// We define an enum class to distinguish between different injection processes.
+// We will use these later in the definition of the Neumann boundary conditions.
+ enum class InjectionProcess : int
+ {
+ noInjection = -99,
+ noFlow = -9,
+ rinse = -1,
+ resuscitation = 3,
+ inoculation = 2,
+ mineralization = 1
+ };
+//
+// ### Reading of parameters specified in the params.input file
+// [[details]] parameters
+// [[codeblock]]
+public:
+ // This is the constructor of our problem class.
+ MICPColumnProblemSimpleChemistry(std::shared_ptr<const GridGeometry> gridGeometry)
+ : ParentType(gridGeometry)
+ {
+ // We read the parameters from the params.input file.
+ name_ = getParam<std::string>("Problem.Name");
+ temperature_ = getParam<Scalar>("Problem.Temperature");
+
+ // biomass parameters
+ ca1_ = getParam<Scalar>("BioCoefficients.Ca1");
+ ca2_ = getParam<Scalar>("BioCoefficients.Ca2");
+ cd1_ = getParam<Scalar>("BioCoefficients.Cd1");
+ dc0_ = getParam<Scalar>("BioCoefficients.Dc0");
+ kmue_ = getParam<Scalar>("BioCoefficients.Kmue");
+ f_ = getParam<Scalar>("BioCoefficients.F");
+ ke_ = getParam<Scalar>("BioCoefficients.Ke");
+ ks_ = getParam<Scalar>("BioCoefficients.Ks");
+ yield_ = getParam<Scalar>("BioCoefficients.Yield");
+
+ // ureolysis kinetic parameters
+ kub_ = getParam<Scalar>("UreolysisCoefficients.Kub");
+ kurease_ = getParam<Scalar>("UreolysisCoefficients.Kurease");
+ ku_ = getParam<Scalar>("UreolysisCoefficients.Ku");
+
+ // initial values
+ densityW_ = getParam<Scalar>("Initial.DensityW");
+ initPressure_ = getParam<Scalar>("Initial.Pressure");
+
+ initxwTC_ = getParam<Scalar>("Initial.XwTC");
+ initxwNa_ = getParam<Scalar>("Initial.XwNa");
+ initxwCl_ = getParam<Scalar>("Initial.XwCl");
+ initxwCa_ = getParam<Scalar>("Initial.XwCa");
+ initxwUrea_ = getParam<Scalar>("Initial.XwUrea");
+ initxwTNH_ = getParam<Scalar>("Initial.XwTNH");
+ initxwO2_ = getParam<Scalar>("Initial.XwO2");
+ initxwBiosub_ = getParam<Scalar>("Initial.XwSubstrate");
+ initxwBiosusp_ = getParam<Scalar>("Initial.XwSuspendedBiomass");
+ initCalcite_ = getParam<Scalar>("Initial.Calcite");
+ initBiofilm_ = getParam<Scalar>("Initial.Biofilm");
+
+ xwNaCorr_ = getParam<Scalar>("Initial.XwNaCorr");
+ xwClCorr_ = getParam<Scalar>("Initial.XwClCorr");
+
+ // injection values
+ injQ_ = getParam<Scalar>("Injection.FlowRate");
+
+ injTC_ = getParam<Scalar>("Injection.MassFracTC");
+ injNa_ = getParam<Scalar>("Injection.ConcentrationNa");
+ injCa_ = getParam<Scalar>("Injection.ConcentrationCa");
+ injUrea_ = getParam<Scalar>("Injection.ConcentrationUrea");
+ injTNH_ = getParam<Scalar>("Injection.ConcentrationTNH");
+ injO2_ = getParam<Scalar>("Injection.ConcentrationO2");
+ injSub_ = getParam<Scalar>("Injection.ConcentrationSubstrate");
+ injBiosusp_= getParam<Scalar>("Injection.ConcentrationSuspendedBiomass");
+ injNaCorr_ = getParam<Scalar>("Injection.ConcentrationNaCorr");
+ // [[/codeblock]]
+ // [[/details]]
+ //
+ // ### Reading of the temporal sequence of the different types of injection
+ // Here, the number of injections and the corresponding parameters are defined based on what is specified in the input files.
+ // [[codeblock]]
+ // We get the number of injections and the injection data file name from params.input
+ numInjections_ = getParam<int>("Injection.NumInjections");
+
+ // We resize the permeability vector contaning the permeabilities for the additional output
+ permeability_.resize(gridGeometry->numDofs());
+
+ // We read from the injection data file which injection type we have in each episode.
+ // We will use this in the Neumann boundary condition to set time dependend, changing boundary conditions.
+ // We do this similarly to the episode ends in the main file.
+ const auto injType = readFileToContainer<std::vector<int>>("injection_type.dat");
+ // translate integer to InjectionProcess type
+ std::transform(injType.begin(), injType.end(), std::back_inserter(injectionType_),
+ [](int n){ return static_cast<InjectionProcess>(n); });
+
+
+ // [[/codeblock]]
+
+ // We check the injection data against the number of injections specified in the parameter file
+ // and print an error message if the test fails
+ // [[codeblock]]
+ if (injectionType_.size() != numInjections_)
+ DUNE_THROW(Dune::IOError, "numInjections from the parameterfile and the number of injection types "
+ << "specified in the injection data file do not match!\n"
+ << "numInjections from parameter file: " << numInjections_ << "\n"
+ << "numInjTypes from injection data file: "<< injectionType_.size());
+
+ // Initialize the fluidsystem
+ FluidSystem::init(/*startTemp=*/temperature_ -5.0, /*endTemp=*/temperature_ +5.0, /*tempSteps=*/5,
+ /*startPressure=*/1e4, /*endPressure=*/1e6, /*pressureSteps=*/500);
+ }
+ // [[/codeblock]]
+
+ // In the follwing, functions to set the time, time step size and the index of the episode
+ // are declared which are used the time loop in main.cc
+ // [[codeblock]]
+ void setTime(const Scalar t)
+ { time_ = t; }
+
+ // We need the time step size to regularize the reactive source terms.
+ void setTimeStepSize(const Scalar dt)
+ { timeStepSize_ = dt; }
+
+ // We need the episode index to choose the right Neumann boundary condition for each episode based on the injection data.
+ void setEpisodeIdx(const Scalar epIdx)
+ { episodeIdx_ = epIdx; }
+ // [[/codeblock]]
+
+ // Here, functions to return the injectionType, the name of the problem and the temperature
+ // are defined
+ // [[codeblock]]
+ int injectionType(int episodeIdx) const
+ { return injectionType_[episodeIdx]; }
+
+ // Get the problem name. It is used as a prefix for files generated by the simulation.
+ const std::string& name() const
+ { return name_; }
+
+ // Return the temperature
+ Scalar temperature() const
+ { return temperature_; }
+ // [[/codeblock]]
+
+ // #### Boundary conditions
+ // With the following function we define the type of boundary conditions depending on the location. Two types of boundary conditions
+ // can be specified: Dirichlet or Neumann boundary condition. On a Dirichlet boundary, the values of the
+ // primary variables need to be fixed. On a Neumann boundary condition, values for derivatives need to be fixed.
+
+ // [[codeblock]]
+ BoundaryTypes boundaryTypesAtPos(const GlobalPosition &globalPos) const
+ {
+ BoundaryTypes bcTypes;
+ // We set all to Neumann, except for the top boundary, which is set to Dirichlet.
+ const Scalar zmax = this->gridGeometry().bBoxMax()[dim - 1];
+ bcTypes.setAllNeumann();
+ if (globalPos[dim - 1] > zmax - eps_)
+ bcTypes.setAllDirichlet();
+
+ return bcTypes;
+ }
+ // [[/codeblock]]
+
+ // We define the Dirichlet boundary conditions
+ // [[codeblock]]
+ PrimaryVariables dirichletAtPos(const GlobalPosition &globalPos) const
+ {
+ PrimaryVariables priVars(0.0);
+ priVars.setState(wPhaseOnly);
+ // We recycle the initial conditions, but additionally enforce that substrate and oxygen necessary for biomass growth are zero.
+ priVars = initial_(globalPos);
+ priVars[xwBiosubIdx] = 0.0;
+ priVars[xwO2Idx] = 0.0;
+ return priVars;
+ }
+ // [[/codeblock]]
+
+ // The injections can be described with a Neumann boundary condition.
+ // Since we have multiple injections durng the whole simulation period, the Neumann boundary conditions in this case are time or rather episode depended.
+ // [[codeblock]]
+ NumEqVector neumannAtPos(const GlobalPosition& globalPos) const
+ {
+ // We only have injection at the bottom, negative values for injection
+ if (globalPos[dim - 1] > eps_)
+ return NumEqVector(0.0);
+
+ // We calculate the injected water velocity based on the volume flux injected into a 1 inch diameter column.
+ const Scalar diameter = 0.0254;
+ const Scalar waterFlux = injQ_/(3.14*diameter*diameter/4.); //[m/s]
+ const auto injProcess = injectionType_[episodeIdx_];
+
+ // We also have no-injection, no-flow periods, which are coded for by -99 or 9.
+ // Thus, for no flow, we set the Neumann BC to zero for all components.
+ if (injProcess == InjectionProcess::noInjection || injProcess == InjectionProcess::noFlow)
+ return NumEqVector(0.0);
+
+ // We set the injection BC to the basic rinse injection and later only change the BC for those components that are different.
+ NumEqVector values(0.0);
+
+ values[conti0EqIdx + wCompIdx] = -waterFlux * 996/FluidSystem::molarMass(wCompIdx);
+ values[conti0EqIdx + nCompIdx] = -waterFlux * injTC_*996 /FluidSystem::molarMass(nCompIdx);
+ values[conti0EqIdx + xwCaIdx] = 0;
+ values[conti0EqIdx + xwSuspendedBiomassIdx] = 0;
+ values[conti0EqIdx + xwBiosubIdx] = -waterFlux * injSub_ /FluidSystem::molarMass(xwBiosubIdx);
+ values[conti0EqIdx + xwO2Idx] = -waterFlux * injO2_ /FluidSystem::molarMass(O2Idx);
+ values[conti0EqIdx + xwUreaIdx] = 0;
+ values[conti0EqIdx + phiCalciteIdx] = 0;
+ values[conti0EqIdx + phiBiofilmIdx] = 0;
+ values[conti0EqIdx + xwNaIdx] = -waterFlux * (injNa_ + injNaCorr_) /FluidSystem::molarMass(NaIdx);
+ values[conti0EqIdx + xwClIdx] = -waterFlux *injTNH_ /NH3::molarMass() //NH4Cl ---> mol Cl = mol NH4
+ -waterFlux *injNa_ /FluidSystem::molarMass(NaIdx); //NaCl ---> mol Cl = mol Na
+ // rinse, used as standard injection fluid
+ if (injProcess == InjectionProcess::rinse)
+ {
+ return values; // do not change anything.
+ }
+
+ // injProcess == 1 codes for an injection of mineralization medium containing urea and calcium chloride.
+ // Thus, we add BC terms for those components.
+ // Additionally, we need to adjust the amount of water injected due to the high concentration of other components injected.
+ // Finally, we need to adapt the injected NaCorr concentration to account fo the lower pH.
+ else if (injProcess == InjectionProcess::mineralization)
+ {
+ values[conti0EqIdx + wCompIdx] = - waterFlux * 0.8716 * densityW_ /FluidSystem::molarMass(wCompIdx); //0.8716 factor accounts for less water per volume due to relatively high solute concentrations!
+ values[conti0EqIdx + nCompIdx] = - waterFlux * injTC_ * densityW_ /FluidSystem::molarMass(nCompIdx);
+ values[conti0EqIdx + xwCaIdx] = - waterFlux * injCa_/FluidSystem::molarMass(CaIdx);
+ values[conti0EqIdx + xwUreaIdx] = - waterFlux * injUrea_ /FluidSystem::molarMass(UreaIdx);
+ values[conti0EqIdx + xwNaIdx] = - waterFlux * injNa_ /FluidSystem::molarMass(NaIdx)
+ - waterFlux * injNaCorr_ /FluidSystem::molarMass(NaIdx)* 0.032;
+ values[conti0EqIdx + xwClIdx] = - waterFlux * injTNH_ /NH3::molarMass() //NH4Cl ---> mol Cl = mol NH4
+ - waterFlux * 2 * injCa_/FluidSystem::molarMass(CaIdx) //+CaCl2 ---> mol Cl = mol Ca*2
+ -waterFlux *injNa_ /FluidSystem::molarMass(NaIdx); //NaCl ---> mol Cl = mol Na
+ return values;
+ }
+
+ // injProcess == 3 codes for a resuscitation injection to regrow biomass.
+ // It is similar to a rinse injection, but with added urea, which is what we add to the basic rinse
+ else if (injProcess == InjectionProcess::resuscitation )
+ {
+ values[conti0EqIdx + xwUreaIdx] = - waterFlux * injUrea_ /FluidSystem::molarMass(UreaIdx);
+ return values;
+ }
+
+ // injProcess == 2 codes for a inoculation or biomass injection.
+ // It is similar to a rinse injection, but with added suspended biomass, which is what we add to the basic rinse
+ else if (injProcess == InjectionProcess::inoculation)
+ {
+ values[conti0EqIdx + xwSuspendedBiomassIdx] = -waterFlux * injBiosusp_ /FluidSystem::molarMass(xwSuspendedBiomassIdx);
+ return values;
+ }
+ else
+ DUNE_THROW(Dune::InvalidStateException, "Invalid injection process " << static_cast<int>(injProcess));
+ }
+ // [[/codeblock]]
+
+ // #### Initial conditions
+ // We specify the initial conditions for the primary variable depending
+ // on the location. Here, we set zero model fractions everywhere in the domain except for a strip
+ // at the bottom of the domain where we set an initial mole fraction of $`1e-9`$.
+ // [[codeblock]]
+ PrimaryVariables initialAtPos(const GlobalPosition& globalPos) const
+ { return initial_(globalPos); }
+
+ // [[/codeblock]]
+
+ // #### Reactive source and sink terms
+ // We calculate the reactive source and sink terms.
+ // For the details, see the "simplified chemistry case" in the dissertation of Hommel available at https://elib.uni-stuttgart.de/handle/11682/8787
+ // [[codeblock]]
+ NumEqVector source(const Element &element,
+ const FVElementGeometry& fvGeometry,
+ const ElementVolumeVariables& elemVolVars,
+ const SubControlVolume &scv) const
+ {
+ const auto elemSol = elementSolution(element, elemVolVars, fvGeometry);
+ const auto gradPw = evalGradients(element,
+ element.geometry(),
+ this->gridGeometry(),
+ elemSol,
+ scv.center())[pressureIdx];
+ const Scalar scvPotGradNorm = gradPw.two_norm();
+
+ //define and compute some parameters for siplicity:
+ const Scalar porosity = elemVolVars[scv].porosity();
+ Scalar initialPorosity = 1.0;
+ constexpr int numActiveComps = SolidSystem::numComponents-SolidSystem::numInertComponents;
+ for (int i = numActiveComps; i<SolidSystem::numComponents; ++i)
+ initialPorosity -= elemVolVars[scv].solidVolumeFraction(i);
+
+ const Scalar Sw = elemVolVars[scv].saturation(wPhaseIdx);
+ const Scalar xlSalinity = elemVolVars[scv].moleFraction(wPhaseIdx,NaIdx)
+ + elemVolVars[scv].moleFraction(wPhaseIdx,CaIdx)
+ + elemVolVars[scv].moleFraction(wPhaseIdx,ClIdx);
+ const Scalar densityBiofilm = elemVolVars[scv].solidComponentDensity(SolidSystem::BiofilmIdx);
+ const Scalar densityCalcite = elemVolVars[scv].solidComponentDensity(SolidSystem::CalciteIdx);
+ const Scalar cBio = std::max(0.0, elemVolVars[scv].moleFraction(wPhaseIdx, SuspendedBiomassIdx)
+ * elemVolVars[scv].molarDensity(wPhaseIdx)
+ * FluidSystem::molarMass(SuspendedBiomassIdx)); //[kg_suspended_Biomass/m³_waterphase]
+ const Scalar volFracCalcite = std::max(0.0, elemVolVars[scv].solidVolumeFraction(SolidSystem::CalciteIdx));
+ const Scalar volFracBiofilm = std::max(0.0, elemVolVars[scv].solidVolumeFraction(SolidSystem::BiofilmIdx));
+ const Scalar massBiofilm = densityBiofilm * volFracBiofilm;
+ const Scalar cSubstrate = std::max(0.0, elemVolVars[scv].moleFraction(wPhaseIdx, BiosubIdx)
+ * elemVolVars[scv].molarDensity(wPhaseIdx)
+ * FluidSystem::molarMass(BiosubIdx)); //[kg_substrate/m³_waterphase]
+ const Scalar cO2 = std::max(0.0, elemVolVars[scv].moleFraction(wPhaseIdx, O2Idx)
+ * elemVolVars[scv].molarDensity(wPhaseIdx)
+ * FluidSystem::molarMass(O2Idx)); //[kg_oxygen/m³_waterphase]
+ const Scalar mUrea = std::max(0.0, moleFracToMolality(elemVolVars[scv].moleFraction(wPhaseIdx,UreaIdx),
+ xlSalinity,
+ elemVolVars[scv].moleFraction(wPhaseIdx,nCompIdx))); //[mol_urea/kg_H2O]
+ // compute rate of ureolysis:
+ const Scalar vmax = kurease_;
+ const Scalar Zub = kub_ * massBiofilm; // [kgurease/m³]
+ const Scalar rurea = vmax * Zub * mUrea / (ku_ + mUrea); //[mol/m³s]
+
+ // compute precipitation rate of calcite, no dissolution! Simplification: rprec = rurea
+ // additionally regularize the precipitation rate that we do not precipitate more calcium than available.
+ const Scalar maxPrecipitationRate = elemVolVars[scv].moleFraction(wPhaseIdx,CaIdx) * Sw * porosity
+ * elemVolVars[scv].molarDensity(wPhaseIdx) / timeStepSize_;
+ const Scalar rprec = std::min(rurea, maxPrecipitationRate);
+
+ //compute biomass growth coefficient and rate
+ const Scalar mue = kmue_ * cSubstrate / (ks_ + cSubstrate) * cO2 / (ke_ + cO2);// [1/s]
+ const Scalar rgf = mue * massBiofilm; //[kg/m³s]
+ const Scalar rgb = mue * porosity * Sw * cBio; //[kg/m³s]
+
+ // compute biomass decay coefficient and rate:
+ const Scalar dcf = dc0_ + (rprec * SolidSystem::molarMass(SolidSystem::CalciteIdx)
+ /(densityCalcite * (initialPorosity - volFracCalcite)));
+ const Scalar dcb = dc0_; //[1/s]
+ const Scalar rdcf = dcf * massBiofilm; //[kg/m³s]
+ const Scalar rdcb = dcb * porosity * Sw * cBio; //[kg/m³s]
+
+ // compute attachment coefficient and rate:
+ const Scalar ka = ca1_ * volFracBiofilm + ca2_; //[1/s]
+ const Scalar ra = ka * porosity * Sw * cBio; //[kg/m³s]
+
+ // compute detachment coefficient and rate:
+ const Scalar cd2 = volFracBiofilm / (initialPorosity - volFracCalcite); //[-]
+ const Scalar kd = cd1_ * std::pow((porosity * Sw * scvPotGradNorm),0.58) + cd2 * mue; //[1/s]
+ const Scalar rd = kd * massBiofilm; //[kg/m³s]
+
+ // rprec[mol/m³s]
+ // rurea[mol/m³s]
+ // rgb + rdcb + ra + rd [kg/m³s]
+ // source[kg/m³s]
+ NumEqVector source(0.0);
+ source[wCompIdx] += 0;
+ source[nCompIdx] += rurea - rprec;
+ source[NaIdx] += 0;
+ source[ClIdx] += 0;
+ source[CaIdx] += - rprec;
+ source[UreaIdx] += - rurea;
+ source[O2Idx] += -(rgf + rgb) *f_/yield_ / FluidSystem::molarMass(O2Idx);
+ source[BiosubIdx] += -(rgf + rgb) / yield_ / FluidSystem::molarMass(BiosubIdx);
+ source[SuspendedBiomassIdx] += (rgb - rdcb - ra + rd) / FluidSystem::molarMass(SuspendedBiomassIdx);
+ source[phiBiofilmIdx] += (rgf - rdcf + ra - rd) / SolidSystem::molarMass(SolidSystem::BiofilmIdx);
+ source[phiCalciteIdx] += + rprec;
+
+ return source;
+ }
+ // [[/codeblock]]
+
+ // The permeability is added to the vtk output
+ // [[codeblock]]
+ // Function to return the permeability for additional vtk output
+ const std::vector<Scalar>& getPermeability()
+ { return permeability_; }
+
+ // Function to update the permeability for additional vtk output
+ template<class SolutionVector>
+ void updateVtkOutput(const SolutionVector& curSol)
+ {
+ for (const auto& element : elements(this->gridGeometry().gridView()))
+ {
+ const auto elemSol = elementSolution(element, curSol, this->gridGeometry());
+ auto fvGeometry = localView(this->gridGeometry());
+ fvGeometry.bindElement(element);
+ for (const auto& scv : scvs(fvGeometry))
+ {
+ VolumeVariables volVars;
+ volVars.update(elemSol, *this, element, scv);
+ const auto dofIdxGlobal = scv.dofIndex();
+ permeability_[dofIdxGlobal] = volVars.permeability();
+ }
+ }
+ }
+ // [[/codeblock]]
+
+// ### Declaring all necessary variables and private fuctions
+// The internal methods are defined here
+// [[codeblock]]
+private:
+ // Internal method for the initial condition reused for the dirichlet conditions.
+ PrimaryVariables initial_(const GlobalPosition &globalPos) const
+ {
+ PrimaryVariables priVars(0.0);
+ priVars.setState(wPhaseOnly);
+ priVars[pressureIdx] = initPressure_ ; //70e5; // - (maxHeight - globalPos[1])*densityW_*9.81; //p_atm + rho*g*h
+ priVars[switchIdx] = initxwTC_;
+ priVars[xwNaIdx] = initxwNa_ + xwNaCorr_;
+ priVars[xwClIdx] = initxwCl_ + initxwTNH_ + 2*initxwCa_ + xwClCorr_;
+ priVars[xwCaIdx] = initxwCa_;
+ priVars[xwUreaIdx] = initxwUrea_;
+ priVars[xwO2Idx] = initxwO2_;
+ priVars[xwBiosubIdx] = initxwBiosub_;
+ priVars[xwSuspendedBiomassIdx] = initxwBiosusp_;
+ priVars[phiBiofilmIdx] = initBiofilm_; // [m^3/m^3]
+ priVars[phiCalciteIdx] = initCalcite_; // [m^3/m^3]
+ return priVars;
+ }
+
+ // Internal method to calculate the molality of a component based on its mole fraction.
+ static Scalar moleFracToMolality(Scalar moleFracX, Scalar moleFracSalinity, Scalar moleFracCTot)
+ {
+ const Scalar molalityX = moleFracX / (1 - moleFracSalinity - moleFracCTot)
+ / FluidSystem::molarMass(FluidSystem::H2OIdx);
+ return molalityX;
+ }
+ // [[/codeblock]]
+
+ // The remainder of the class contains an epsilon value used for floating point comparisons
+ // and parameters needed to describe the chemical processess.
+ // Additionally the problem name, the peremability vector as well as some time-parameters are declared
+ // [[details]] private members
+ // eps is used as a small value for the definition of the boundary conditions
+ static constexpr Scalar eps_ = 1e-6;
+
+ // initial condition parameters
+ Scalar initPressure_;
+ Scalar densityW_;//1087; // rhow=1087;
+ Scalar initxwTC_;//2.3864e-7; // [mol/mol]
+ Scalar initxwNa_;//0;
+ Scalar initxwCl_;//0;
+ Scalar initxwCa_;//0;
+ Scalar initxwUrea_;//0;
+ Scalar initxwTNH_;//3.341641e-3;
+ Scalar initxwO2_;//4.4686e-6;
+ Scalar initxwBiosub_;//2.97638e-4;
+ Scalar initxwBiosusp_;//0;
+ Scalar xwNaCorr_;//2.9466e-6;
+ Scalar xwClCorr_;//0;
+ Scalar initBiofilm_;
+ Scalar initCalcite_;
+ Scalar temperature_;
+
+ // biomass parameters for source/sink calculations
+ Scalar ca1_;
+ Scalar ca2_;
+ Scalar cd1_;
+ Scalar dc0_;
+ Scalar kmue_ ;
+ Scalar f_;
+ Scalar ke_;
+ Scalar ks_;
+ Scalar yield_;
+ // urease parameters for source/sink calculations
+ Scalar kub_;
+ Scalar kurease_;
+ Scalar ku_;
+
+ // injection parameters
+ Scalar injQ_;
+ Scalar injTC_; // [kg/kg]
+ Scalar injNa_; // [kg/m³]
+ Scalar injCa_; // [kg/m³] //computed from CaCl2
+ Scalar injUrea_; // [kg/m³]
+ Scalar injTNH_; // [kg/m³] //computed from NH4Cl
+ Scalar injO2_; // [kg/m³]
+ Scalar injSub_; // [kg/m³]
+ Scalar injBiosusp_; // [kg/m³]
+ Scalar injNaCorr_; // [kg/m³]
+ int numInjections_;
+ std::vector<InjectionProcess> injectionType_;
+
+ // the problem name
+ std::string name_;
+ // the permeability for output
+ std::vector<Scalar> permeability_;
+
+ // timing parameters
+ Scalar time_ = 0.0;
+ Scalar timeStepSize_ = 0.0;
+ int episodeIdx_ = 0;
+};
+} // end namespace Dumux
+// [[/details]]
+// [[/content]]
+#endif
diff --git a/examples/biomineralization/properties.hh b/examples/biomineralization/properties.hh
new file mode 100644
index 0000000000..86dd9660ad
--- /dev/null
+++ b/examples/biomineralization/properties.hh
@@ -0,0 +1,125 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 3 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#ifndef DUMUX_MICP_COLUMN_SIMPLE_CHEM_PROPERTIES_HH
+#define DUMUX_MICP_COLUMN_SIMPLE_CHEM_PROPERTIES_HH
+
+// ## `TypeTag` and compile-time settings (`properties.hh`)
+//
+// This file defines the `TypeTag` used for the biomineralization example,
+// for which we then specialize `properties` to the needs of this setup.
+//
+// [[content]]
+//
+// ### Include files
+// <details>
+//
+// This type tag specializes most of the `properties` required for two phase flow with
+// multiple components including mineralisation simulations (2pncmin) in DuMuX
+// We will use this in the following to inherit the respective properties and
+// subsequently specialize those `properties` for our `TypeTag`, which we want to
+// modify or for which no meaningful default can be set.
+#include <dumux/common/properties.hh>
+#include <dumux/porousmediumflow/2pncmin/model.hh>
+
+// We want to use `YaspGrid`, an implementation of the dune grid interface for structured grids:
+#include <dune/grid/yaspgrid.hh>
+
+// In this example, we want to discretize the equations with the box scheme
+#include <dumux/discretization/box.hh>
+
+// We include the necessary material files
+#include <examples/biomineralization/material/fluidsystems/biominsimplechemistry.hh>
+#include <examples/biomineralization/material/solidsystems/biominsolids.hh>
+#include <examples/biomineralization/material/co2tableslaboratory.hh>
+
+// We include the problem and spatial parameters headers used for this simulation.
+#include "problem.hh"
+#include "spatialparams.hh"
+
+// </details>
+//
+// ### Definition of the `TypeTag` used for the biomineralization problem
+//
+// We define a `TypeTag` for our simulation with the name `MICPColumnSimpleChemistry`
+// and inherit the `properties` specialized for the type tags `TwoPNCMin` and `BoxModel` respectively.
+// This way, most of the `properties` required for this simulations
+// using the box scheme are conveniently specialized for our new `TypeTag`.
+// However, some properties depend on user choices and no meaningful default value can be set.
+// Those properties will be adressed later in this file.
+// [[codeblock]]
+namespace Dumux::Properties {
+
+// We create new type tag for our simulation which inherits from the 2pncmin model and the box discretization
+namespace TTag {
+struct MICPColumnSimpleChemistry { using InheritsFrom = std::tuple<TwoPNCMin, BoxModel>; };
+} // end namespace TTag
+// [[/codeblock]]
+
+// ### Property specializations
+//
+// In the following piece of code, mandatory `properties` for which no meaningful
+// dafault can be set, are specialized for our type tag `MICPColumnSimpleChemistry`.
+
+// [[codeblock]]
+// We set the grid to a 1D Yasp Grid
+template<class TypeTag>
+struct Grid<TypeTag, TTag::MICPColumnSimpleChemistry>
+{ using type = Dune::YaspGrid<1>; };
+
+// We set the problem used for our simulation, defining boundary and initial conditions (see below)
+template<class TypeTag>
+struct Problem<TypeTag, TTag::MICPColumnSimpleChemistry>
+{ using type = MICPColumnProblemSimpleChemistry<TypeTag>; };
+
+// We set the fluidSystem used for our simulation
+template<class TypeTag>
+struct FluidSystem<TypeTag, TTag::MICPColumnSimpleChemistry>
+{
+ using Scalar = GetPropType<TypeTag, Properties::Scalar>;
+ using CO2Tables = Dumux::ICP::CO2Tables;
+ using H2OTabulated = Components::TabulatedComponent<Components::H2O<Scalar>>;
+ using type = Dumux::FluidSystems::BioMinSimpleChemistryFluid<Scalar, CO2Tables, H2OTabulated>;
+};
+
+// We set the solidSystem used for our simulation
+template<class TypeTag>
+struct SolidSystem<TypeTag, TTag::MICPColumnSimpleChemistry>
+{
+ using Scalar = GetPropType<TypeTag, Properties::Scalar>;
+ using type = SolidSystems::BioMinSolidPhase<Scalar>;
+};
+
+// We define the spatial parameters for our simulation. The values are specified in the corresponding spatialparameters header file, which is included above.
+template<class TypeTag>
+struct SpatialParams<TypeTag, TTag::MICPColumnSimpleChemistry>
+{
+ using type = ICPSpatialParams<GetPropType<TypeTag, Properties::GridGeometry>,
+ GetPropType<TypeTag, Properties::Scalar>>;
+};
+
+// We set the two-phase primary variable formulation used for our simulation
+template<class TypeTag>
+struct Formulation<TypeTag, TTag::MICPColumnSimpleChemistry>
+{ static constexpr auto value = TwoPFormulation::p0s1; };
+
+}// We leave the namespace Dumux::Properties.
+// [[/codeblock]]
+// [[/content]]
+#endif
diff --git a/examples/biomineralization/spatialparams.hh b/examples/biomineralization/spatialparams.hh
new file mode 100644
index 0000000000..68ab59cfe0
--- /dev/null
+++ b/examples/biomineralization/spatialparams.hh
@@ -0,0 +1,149 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#ifndef DUMUX_MICP_COLUMN_SIMPLE_CHEM_SPATIAL_PARAMS_HH
+#define DUMUX_MICP_COLUMN_SIMPLE_CHEM_SPATIAL_PARAMS_HH
+
+// ## Parameter distributions (`spatialparams_1p.hh`)
+//
+// [[content]]
+//
+// This file contains the __spatial parameters class__ which defines the
+// distributions for the porous medium parameters permeability and porosity
+// over the computational grid
+//
+// ### Include files
+// [[details]] includes
+// We include the basic spatial parameters for finite volumes file from which we will inherit
+#include <dumux/material/spatialparams/fv.hh>
+// We include the files for the two-phase laws: the linear material law
+#include <dumux/material/fluidmatrixinteractions/2p/linearmaterial.hh>
+// We include the files for the two-phase laws: the regularized Brooks-Corey pc-Sw and relative permeability laws
+#include <dumux/material/fluidmatrixinteractions/2p/regularizedbrookscorey.hh>
+// We include the files for the two-phase laws: the scaling from effective to absolute saturations
+#include <dumux/material/fluidmatrixinteractions/2p/efftoabslaw.hh>
+// We include the laws for changing porosity due to precipitation
+#include <dumux/material/fluidmatrixinteractions/porosityprecipitation.hh>
+// We include the laws for changing permeability based on porosity change according to Kozeny-Carman
+#include <dumux/material/fluidmatrixinteractions/permeabilitykozenycarman.hh>
+// [[/details]]
+//
+// ### The spatial parameters class
+// In the `ICPSpatialParams` class, we define all functions needed to describe
+// the porous medium, e.g. porosity and permeability.
+// We inherit from the `FVSpatialParams` class which is the base class for spatial paramters using finite volume discretization schemes.
+
+// [[codeblock]]
+namespace Dumux {
+
+// In the ICPSpatialParams class we define all functions needed to describe the spatial distributed parameters.
+template<class GridGeometry, class Scalar>
+class ICPSpatialParams
+: public FVSpatialParams<GridGeometry, Scalar, ICPSpatialParams<GridGeometry, Scalar>>
+{
+ // We introduce using declarations that are derived from the property system which we need in this class
+ using ThisType = ICPSpatialParams<GridGeometry, Scalar>;
+ using ParentType = FVSpatialParams<GridGeometry, Scalar, ThisType>;
+ using GridView = typename GridGeometry::GridView;
+ using EffectiveLaw = RegularizedBrooksCorey<Scalar>;
+ using SubControlVolume = typename GridGeometry::SubControlVolume;
+ using Element = typename GridView::template Codim<0>::Entity;
+ using GlobalPosition = typename Element::Geometry::GlobalCoordinate;
+
+public:
+ // type used for the permeability (i.e. tensor or scalar)
+ using PermeabilityType = Scalar;
+ using MaterialLaw = EffToAbsLaw<EffectiveLaw>;
+ using MaterialLawParams = typename MaterialLaw::Params;
+ // [[/codeblock]]
+ // #### Using porosity and permeability laws to return the updated values
+ // Due due calcium carbonate precipitation the porosity and the permeability change with time. At first, the initial values for the porosity and permeability are defined. Moreover, the functions that return the updated values, based on the chosen laws are defined.
+ // [[codeblock]]
+ ICPSpatialParams(std::shared_ptr<const GridGeometry> gridGeometry)
+ : ParentType(gridGeometry)
+ {
+ // We read reference values for porosity and permeability from the input
+ referencePorosity_ = getParam<Scalar>("SpatialParams.ReferencePorosity", 0.4);
+ referencePermeability_ = getParam<Scalar>("SpatialParams.ReferencePermeability", 2.e-10);
+
+ // Setting residual saturations
+ materialParams_.setSwr(0.2);
+ materialParams_.setSnr(0.05);
+
+ // Setting parameters for the Brooks-Corey law
+ materialParams_.setPe(1e4);
+ materialParams_.setLambda(2.0);
+ }
+
+ // We return the reference or initial porosity.
+ //This reference porosity is the porosity, for which the permeability is know and set as reference permeability
+ Scalar referencePorosity(const Element& element, const SubControlVolume &scv) const
+ { return referencePorosity_; }
+
+ // We return the volume fraction of the inert (unreactive) component
+ template<class SolidSystem>
+ Scalar inertVolumeFractionAtPos(const GlobalPosition& globalPos, int compIdx) const
+ { return 1.0-referencePorosity_; }
+
+ // [[codeblock]]
+ // We return the updated porosity using the specified porosity law
+ template<class ElementSolution>
+ Scalar porosity(const Element& element,
+ const SubControlVolume& scv,
+ const ElementSolution& elemSol) const
+ { return poroLaw_.evaluatePorosity(element, scv, elemSol, referencePorosity_); }
+
+ // We return the updated permeability using the specified permeability law
+ template<class ElementSolution>
+ PermeabilityType permeability(const Element& element,
+ const SubControlVolume& scv,
+ const ElementSolution& elemSol) const
+ {
+ const auto poro = porosity(element, scv, elemSol);
+ return permLaw_.evaluatePermeability(referencePermeability_, referencePorosity_, poro);
+ }
+ // [[/codeblock]]
+ // Return the brooks-corey context depending on the position
+ const MaterialLawParams& materialLawParamsAtPos(const GlobalPosition& globalPos) const
+ { return materialParams_; }
+
+ // Define the wetting phase
+ template<class FluidSystem>
+ int wettingPhaseAtPos(const GlobalPosition& globalPos) const
+ { return FluidSystem::H2OIdx; }
+
+ // The remainder of this class contains the data members and defines the porosity law which describes the change of porosity due to calcium carbonate precipitation.
+ // Additionally the change of porosity results in a change of permeability. This relation is described in the permeability law, in this case the Kozeny-Carman porosity-permeability relation
+ // [[codeblock]]
+private:
+
+ MaterialLawParams materialParams_;
+ // Setting porosity precipitation as the porosity law
+ PorosityPrecipitation<Scalar, /*numFluidComponents*/9, /*activeComponents*/2> poroLaw_;
+ // Setting the Kozeny-Carman porosity-permeability relation as the permeability law
+ PermeabilityKozenyCarman<PermeabilityType> permLaw_;
+ //The reference porosity is the porosity, for which the permeability is know and set as reference permeability
+ Scalar referencePorosity_;
+ //The reference permeability is the known (measured) permeability, of the porous medium in the initial condition, before the solid phases change during the simulation
+ PermeabilityType referencePermeability_ = 0.0;
+};// end class definition of ICPSpatialParams
+} //end namespace Dumux
+// [[/codeblock]]
+// [[/content]]
+#endif
diff --git a/test/references/example_biomineralization-reference.vtp b/test/references/example_biomineralization-reference.vtp
new file mode 100644
index 0000000000..697e123337
--- /dev/null
+++ b/test/references/example_biomineralization-reference.vtp
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