diff --git a/doc/doxygen/Doxylocal b/doc/doxygen/Doxylocal
index b45d87babb0442b42f01e48e74a0a31e22bd4eba..fcf6e7271f042d5209912c0f35c924da536bcc38 100644
--- a/doc/doxygen/Doxylocal
+++ b/doc/doxygen/Doxylocal
@@ -1,5 +1,5 @@
# This file contains local changes to the doxygen configuration
-# please us '+=' to add file/directories to the lists
+# please use '+=' to add file/directories to the lists
PREDEFINED += "NEW_PROP_TAG(name)=Property tag name" \
"NEW_TYPE_TAG(name)=Type tag name" \
@@ -10,6 +10,7 @@ INPUT += @srcdir@/mainpage.txt \
@top_srcdir@/dumux \
@top_srcdir@/test \
@top_srcdir@/tutorial \
+ @srcdir@/extradoc/binaries.txt \
@srcdir@/extradoc/parameterlist.txt \
@srcdir@/extradoc/featurelist.txt
diff --git a/doc/doxygen/extradoc/binaries.txt b/doc/doxygen/extradoc/binaries.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d88910ba1c18582788e97bc76220db92a34e132f
--- /dev/null
+++ b/doc/doxygen/extradoc/binaries.txt
@@ -0,0 +1,14 @@
+/*!
+ * \page Binaries Scripts
+ *
+ * \brief List of auxiliary scripts provided with DuMuX
+ *
+ * | Folder | Filename | Functionality |
+ * | :- | :- | :- |
+ * | bin | installexternal.sh | Easily install external modules (e.g. opm, dune-pdelab, gstat, ug, ...). |
+ * | bin/postprocessing | extractlinedata.py | Extract all data point from a vtu over a defined line (requires pvpython). |
+ * | bin/postprocessing | extractpointdataovertime.py | Extract transient data from a .pvd for a specific point (requires pvpython). |
+ * | bin/postprocessing | l2error.py | Calculate the L2-error between two vectors. |
+ * | bin/testing | fuzzycomparevtu.py | Compare to vtu files allowing for a tiny mismatch. |
+ * | bin/testing | runtest.py | Start a test including fuzzy-comparison. |
+ */
diff --git a/doc/doxygen/extradoc/featurelist.txt b/doc/doxygen/extradoc/featurelist.txt
index 091b69f3641a0879a454807cf87e1685f9644fd3..7293950a9aa0e00dd56b7309fa10ab3751b32073 100644
--- a/doc/doxygen/extradoc/featurelist.txt
+++ b/doc/doxygen/extradoc/featurelist.txt
@@ -1,8 +1,6 @@
/*!
- *\file
- *\ingroup Feature
- *
- *\brief List of Features implemented in the DuMuX-test-problems
+ * \page featureList Feature List
+ * \brief List of Features implemented in the DuMuX-test-problems
*
* The list gives an overview over features that are already
* implemented in DuMuX and in which respective test problem
diff --git a/doc/doxygen/extradoc/parameterlist.txt b/doc/doxygen/extradoc/parameterlist.txt
index 130e603aec960bbba3add9e6a8f38da93641ca3e..3d29b563869fb43a651318efe3d8e5e42230c51c 100644
--- a/doc/doxygen/extradoc/parameterlist.txt
+++ b/doc/doxygen/extradoc/parameterlist.txt
@@ -1,8 +1,7 @@
/*!
- *\file
- *\ingroup Parameter
+ * \page parameterList Parameter List
*
- *\brief List of currently useable run-time parameters
+ * \brief List of currently useable run-time parameters
*
* The listed run-time parameters are in general available,
* but we point out that a certain model might not be able
@@ -11,8 +10,9 @@
* | Group | Parameter | Type | Default Value | Explanation |
* | :- | :- | :- | :- | :-
* | - | ParameterFile | std::string | executable.input | name of the parameter file |
- * | \b BoundaryLayer | Model | int | 0 | 0 for none, 1 Blasius, 2 and 3 turbulent BL, 9 constant thickness |
- * | | ConstThickness | Scalar | - | constant BL thickness (BL model 9) |
+ * | \b BoundaryLayer | Model | int | 0 | 0 for none; 1 constant thickness; 2 Blasius laminar; 3 turbulent; 4, 5, 6, 7 viscous sublayer |
+ * | | ConstThickness | Scalar | - | constant BL thickness (BL model 1) |
+ * | | HydraulicDiameter | Scalar | - | hydraulic diameter for BL model 7 |
* | | Offset | Scalar | - | virtual run-up distance for BL models |
* | | RoughnessLength | Scalar | - | Equivalent sand grain roughness [m] |
* | | YPlus | Scalar | - | Conversion factor between dimensionless wall distance y^+ and actual wall distance |
@@ -20,13 +20,10 @@
* | | RefTemperature | Scalar | - | free stream temperature |
* | | RefVelocity | Scalar | - | free stream velocity |
* | \b Grid | File | std::string | - | name of the grid file, if a corresponding GridCreator is used |
- * | | InterfacePosX | Scalar | 0.0 | x-coordinate of the refinement point/line (only Interface-GridCreator) |
- * | | InterfacePosY | Scalar | 0.0 | y-coordinate of the refinement point/line (only Interface-GridCreator) |
* | | LowerLeft | globalPosition | - | coordinates of the lower front left corner for the Cube/Simplex/Interface-GridCreator |
* | | Cells | globalPosition | - | number of cells in respective coordinate directions for the Cube/SimplexGridCreator |
- * | | RefineTopX | bool | false | Refine to the right of the domain (only Interface-GridCreator) |
- * | | RefineTopY | bool | false | Refine to the top of the domain (only Interface-GridCreator) |
* | | UpperRight | globalPosition | - | coordinates of the upper back right corner for the Cube/Simplex/Interface-GridCreator |
+ * | | Verbosity | bool | - | whether the grid construction should output to standard out |
* | \b GridAdapt | AdaptionInterval | int | 1 | time step interval for adaption |
* | | CoarsenPercentileFlux | Scalar | 0.2 | percentile of cells coarsened because of flux criterion |
* | | CoarsenPercentileSat | Scalar | 0.2 | percentile of cells coarsened because of saturation criterion |
@@ -98,10 +95,12 @@
* | | WriteConvergence | bool | false | specifies whether the convergence rate and the global residual gets written out to disk for every Newton iteration |
* | \b Pardiso | NumProcessors | int | - | |
* | \b Problem | EnableGravity | bool | true | returns whether gravity is considered in the problem |
- * | | GasDensity | Scalar | - | The density of the gas (only components/constant.hh) |
- * | | GasKinematicViscosity | Scalar | - | The kinematic viscosity of the gas (only components/constant.hh) |
- * | | LiquidDensity | Scalar | - | The density of the liquid (only components/constant.hh) |
- * | | LiquidKinematicViscosity | Scalar | - | The kinematic viscosity of the liquid (only components/constant.hh) |
+ * | | GasDensity | Scalar | 1.0 | The density of the gas (only components/constant.hh) |
+ * | | GasKinematicViscosity | Scalar | 1.0 | The kinematic viscosity of the gas (only components/constant.hh) |
+ * | | InteractingContinuaType | int | 0 | defines interaction of the nested continua (0: constant volume fractions, 1: equally distanced nested continua, 2: DFM generated volume fractions) |
+ * | | LiquidDensity | Scalar | 1.0 | The density of the liquid (only components/constant.hh) |
+ * | | LiquidKinematicViscosity | Scalar | 1.0 | The kinematic viscosity of the liquid (only components/constant.hh) |
+ * | | MolarMass | Scalar | 1.0 | The molar mass (only components/constant.hh) |
* | | Name | std::string | - | The name of the current problem, used for output |
* | | Salinity | Scalar | 1e-3 | |
* | \b SpatialParams | ForchCoeff | Scalar | 0.55 | property for the forchheimer coefficient |
diff --git a/doc/doxygen/mainpage.txt b/doc/doxygen/mainpage.txt
index f608923d87cd4dae576b8d06daf70746163839ee..80eacb795c57032fd5222a37571b8d2e67c2e5f9 100644
--- a/doc/doxygen/mainpage.txt
+++ b/doc/doxygen/mainpage.txt
@@ -1,9 +1,3 @@
-/*!
- * \file
- *
- * \brief documentation for the doxygen main page
- */
-
/** \mainpage DuMuX Documentation
\section intro Introduction
@@ -12,17 +6,19 @@ Welcome to the DuMuX documentation pages. This documentation has been
generated using <a href="http://www.doxygen.org/index.html">Doxygen</a>, a free source code documentation system for
documenting C/C++ code.
-\section mods Modules
-
-The best way to start is from the page <a href="modules.html">Modules</a> which gives
-you access to the documentation by category.
+\section relatedPages Related pages
-\section params Parameters
+The <a href="pages.html">Related Pages</a> gives a good overview on everything beyond the
+actual DuMuX code.
+This includes a Bibliography of the publications DuMuX is based on.<br>
+Further, a \ref parameterList containing all implemented parameters and
+a \ref featureList of special features used in the test problems is available.<br>
+Auxiliary script files can be find in \ref Binaries.<br>
+In addition, the current Todo List, Warning List, and Deprecated List are given (if available).
-An overview of all availabe parameters is given in \ref parameterlist.txt.
-
-\section features Features
+\section mods Modules
-An overview of special features implemented in the DuMuX-test-problems is given in \ref featurelist.txt.
+The best way to start is from the page <a href="modules.html">Modules</a> which gives
+you access to the documentation by the model categories.
*/
diff --git a/doc/doxygen/modules.txt b/doc/doxygen/modules.txt
index 11a3cc1fae44be0faf5da24e28ec75cfb68d7e71..55d99389c7d02ddc51c5563b757681fc3cbd2b21 100644
--- a/doc/doxygen/modules.txt
+++ b/doc/doxygen/modules.txt
@@ -1,17 +1,12 @@
-/*!
- * \file
- *
- * \brief This file contains all module definitions for the doxygen documentation.
- *
- */
-
/* ***************** Porousmediaflow ******************/
/*!
- * \defgroup Porousmediaflow Porous-Medium Flow (fully implicit if not denoted otherwise)
+ * \defgroup Porousmediaflow Porous-Medium Flow
+ * \brief fully implicit if not denoted otherwise
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup OnePModels 1p (one-phase Darcy flow)
+ * \defgroup OnePModels 1p
+ * \brief one-phase Darcy flow
*/
/*!
* \ingroup OnePModels
@@ -27,13 +22,15 @@
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup OnePTwoCModel 1p2c (one-phase, two-component Darcy flow)
+ * \defgroup OnePTwoCModel 1p2c
+ * \brief one-phase, two-component Darcy flow
*
* \copydetails Dumux::OnePTwoCModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup TwoPModels 2p (two-phase Darcy flow)
+ * \defgroup TwoPModels 2p
+ * \brief two-phase Darcy flow
*/
/*!
* \ingroup TwoPModels
@@ -56,19 +53,22 @@
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup TwoPOneCModel 2p1c (two-phase, one-component Darcy flow)
+ * \defgroup TwoPOneCModel 2p1c
+ * \brief two-phase, one-component Darcy flow
*
* \copydetails Dumux::TwoPOneCModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup TwoPOneCModel 2p1c (two-phase, one-component Darcy flow)
+ * \defgroup TwoPOneCModel 2p1c
+ * \brief two-phase, one-component Darcy flow
*
* \copydetails Dumux::TwoPOneCModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup TwoPTwoCModels 2p2c (two-phase, two-component Darcy flow)
+ * \defgroup TwoPTwoCModels 2p2c
+ * \brief two-phase, two-component Darcy flow
*/
/*!
* \ingroup TwoPTwoCModels
@@ -88,67 +88,78 @@
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup TwoPDFMModel 2pdfm (two-phase Darcy flow in discrete fracture-matrix)
+ * \defgroup TwoPDFMModel 2pdfm
+ * \brief two-phase Darcy flow in discrete fracture-matrix
*
* \copydetails Dumux::TwoPDFMModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup TwoPMincModel 2pminc (two-phase Darcy flow dual continuum)
+ * \defgroup TwoPMincModel 2pminc
+ * \brief two-phase Darcy flow dual continuum
*
* \copydetails Dumux::TwoPMincModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup TwoPNCModel 2pnc (two-phase, n-component Darcy flow)
+ * \defgroup TwoPNCModel 2pnc
+ * \brief two-phase, n-component Darcy flow
*
* \copydetails Dumux::TwoPNCModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup TwoPNCMinModel 2pncmin (two-phase, n-component Darcy flow with mineralization)
+ * \defgroup TwoPNCMinModel 2pncmin
+ * \brief two-phase, n-component Darcy flow with mineralization
*
* \copydetails Dumux::TwoPNCMinModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup ThreePModel 3p (three-phase Darcy flow)
+ * \defgroup ThreePModel 3p
+ * \brief three-phase Darcy flow
*
* \copydetails Dumux::ThreePModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup ThreePThreeCModel 3p3c (three-phase, three-component Darcy flow)
+ * \defgroup ThreePThreeCModel 3p3c
+ * \brief three-phase, three-component Darcy flow
*
* \copydetails Dumux::ThreePThreeCModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup ThreePWaterOilModel 3pwateroil (three-phase, two-component Darcy flow)
+ * \defgroup ThreePWaterOilModel 3pwateroil
+ * \brief three-phase, two-component Darcy flow
*
* \copydetails Dumux::ThreePWaterOilModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup CO2Model CO2 (two-phase, two-component Darcy flow)
+ * \defgroup CO2Model CO2
+ * \brief two-phase, two-component Darcy flow
*
* \copydetails Dumux::CO2Model
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup MPNCModel MpNc (m-phase, n-component Darcy flow)
+ * \defgroup MPNCModel MpNc
+ * \brief m-phase, n-component Darcy flow
*
* \copydetails Dumux::MPNCModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup NIModel Non-isothermal (energy equation, to be added to an isothermal model)
+ * \defgroup NIModel Non-isothermal
+ * \brief energy equation, to be added to an isothermal model
*
* \copydetails Dumux::NIModel
*/
/*!
* \ingroup Porousmediaflow
- * \defgroup RichardsModel Richards (Richards flow)
+ * \defgroup RichardsModel Richards
+ * \brief Richards flow
*
* \copydetails Dumux::RichardsModel
*/
@@ -159,19 +170,22 @@
*/
/*!
* \ingroup Geomechanics
- * \defgroup ElOnePTwoCBoxModel El1p2c (one-phase, two-component Darcy flow, linear elastic deformation model)
+ * \defgroup ElOnePTwoCBoxModel El1p2c
+ * \brief one-phase, two-component Darcy flow, linear elastic deformation model
*
* \copydetails Dumux::ElOnePTwoCModel
*/
/*!
* \ingroup Geomechanics
- * \defgroup ElTwoPBoxModel El2p (two-phase Darcy flow, linear elastic deformation model)
+ * \defgroup ElTwoPBoxModel El2p
+ * \brief two-phase Darcy flow, linear elastic deformation model
*
* \copydetails Dumux::ElTwoPModel
*/
/*!
* \ingroup Geomechanics
- * \defgroup ElasticBoxModel Elastic (linear elastic deformation model)
+ * \defgroup ElasticBoxModel Elastic
+ * \brief linear elastic deformation model
*
* \copydetails Dumux::ElasticModel
*/
@@ -182,37 +196,43 @@
*/
/*!
* \ingroup Freeflow
- * \defgroup BoxStokesModel Stokes (one-phase Stokes flow)
+ * \defgroup BoxStokesModel Stokes
+ * \brief one-phase Stokes flow
*
* \copydetails Dumux::StokesModel
*/
/*!
* \ingroup Freeflow
- * \defgroup BoxStokesncModel Stokesnc (one-phase, n-component Stokes flow)
+ * \defgroup BoxStokesncModel Stokesnc
+ * \brief one-phase, n-component Stokes flow
*
* \copydetails Dumux::StokesncModel
*/
/*!
* \ingroup Freeflow
- * \defgroup BoxStokesncniModel Stokesncni (one-phase, n-component, non-isothermal Stokes flow)
+ * \defgroup BoxStokesncniModel Stokesncni
+ * \brief one-phase, n-component, non-isothermal Stokes flow
*
* \copydetails Dumux::StokesncniModel
*/
/*!
* \ingroup Freeflow
- * \defgroup BoxZeroEqModel Zeroeq (one-phase Stokes flow with zero-eq turbulence model)
+ * \defgroup BoxZeroEqModel Zeroeq
+ * \brief one-phase Stokes flow with zero-eq turbulence model
*
* \copydetails Dumux::ZeroEqModel
*/
/*!
* \ingroup Freeflow
- * \defgroup BoxZeroEqncModel Zeroeqnc (one-phase, n-component Stokes flow with zero-eq turbulence model)
+ * \defgroup BoxZeroEqncModel Zeroeqnc
+ * \brief one-phase, n-component Stokes flow with zero-eq turbulence model
*
* \copydetails Dumux::ZeroEqncModel
*/
/*!
* \ingroup Freeflow
- * \defgroup BoxZeroEqncniModel Zeroeqncni (one-phase, n-component, non-isothermal Stokes flow with zero-eq turbulence model)
+ * \defgroup BoxZeroEqncniModel Zeroeqncni
+ * \brief one-phase, n-component, non-isothermal Stokes flow with zero-eq turbulence model
*
* \copydetails Dumux::ZeroEqncniModel
*/
@@ -224,10 +244,12 @@
/*!
* \ingroup Multidomain
* \defgroup MultidomainModel Multidomain
+ * \brief Multidomain
*/
/*!
* \ingroup Multidomain
- * \defgroup TwoPTwoCStokesTwoCModel 2cstokes2p2c (1p2c Stokes flow coupled to 2p2c Darcy flow)
+ * \defgroup TwoPTwoCStokesTwoCModel 2cstokes2p2c
+ * \brief 1p2c Stokes flow coupled to 2p2c Darcy flow
*
* # Coupling Conditions
* \copydetails Dumux::TwoCStokesTwoPTwoCLocalOperator
@@ -240,7 +262,8 @@
*/
/*!
* \ingroup Multidomain
- * \defgroup TwoPTwoCNIStokesTwoCNIModel 2cnistokes2p2cni (1p2cni Stokes flow coupled to 2p2cni Darcy flow)
+ * \defgroup TwoPTwoCNIStokesTwoCNIModel 2cnistokes2p2cni
+ * \brief 1p2cni Stokes flow coupled to 2p2cni Darcy flow
*
* # Coupling Conditions
* \copydetails Dumux::TwoCNIStokesTwoPTwoCNILocalOperator
@@ -256,7 +279,8 @@
*/
/*!
* \ingroup Multidomain
- * \defgroup TwoPTwoCZeroEqTwoCModel 2czeroeq2p2c (1p2c Stokes flow with zero-eq turbulence model coupled to 2p2c Darcy flow)
+ * \defgroup TwoPTwoCZeroEqTwoCModel 2czeroeq2p2c
+ * \brief 1p2c Stokes flow with zero-eq turbulence model coupled to 2p2c Darcy flow
*
* # Coupling Conditions
* \copydetails Dumux::TwoCStokesTwoPTwoCLocalOperator
@@ -269,7 +293,8 @@
*/
/*!
* \ingroup Multidomain
- * \defgroup TwoPTwoCNIZeroEqTwoCNIModel 2cnizeroeq2p2cni (1p2cni Stokes flow with zero-eq turbulence model coupled to 2p2cni Darcy flow)
+ * \defgroup TwoPTwoCNIZeroEqTwoCNIModel 2cnizeroeq2p2cni
+ * \brief 1p2cni Stokes flow with zero-eq turbulence model coupled to 2p2cni Darcy flow
*
* # Coupling Conditions
* \copydetails Dumux::TwoCNIStokesTwoPTwoCNILocalOperator
@@ -286,70 +311,85 @@
/* ***************** Fully Implicit ******************/
/*!
- * \defgroup ImplicitModel Fully-Coupled Fully-Implicit Scheme
+ * \defgroup ImplicitModel Implicit Scheme
+ * \brief Fully-Coupled Fully-Implicit Scheme
*/
/*!
* \ingroup ImplicitModel
* \defgroup ImplicitBaseProblems Base Problems
+ * \brief Base Problems
*/
/*!
* \ingroup ImplicitModel
* \defgroup Discretizations Discretizations
+ * \brief Discretizations
*/
/*!
* \ingroup Discretizations
- * \defgroup CCModel Fully-implicit cell-centered discretization
+ * \defgroup CCModel CCModel
+ * \brief Fully-implicit cell-centered discretization
*/
/*!
* \ingroup Discretizations
- * \defgroup BoxModel Fully-implicit box discretization
+ * \defgroup BoxModel BoxModel
+ * \brief Fully-implicit box discretization
*/
/*!
* \ingroup ImplicitModel
* \defgroup ImplicitBoundaryTypes Boundary Types
+ * \brief Boundary Types
*/
/*!
* \ingroup ImplicitModel
* \defgroup ImplicitFluxVariables Flux Variables
+ * \brief Flux Variables
*/
/*!
* \ingroup ImplicitModel
* \defgroup ImplicitIndices Indices
+ * \brief Indices
*/
/*!
* \ingroup ImplicitModel
* \defgroup ImplicitLocalJacobian Local Jacobian
+ * \brief Local Jacobian
*/
/*!
* \ingroup ImplicitModel
* \defgroup ImplicitLocalResidual Local Residual
+ * \brief Local Residual
*/
/*!
* \ingroup ImplicitModel
* \defgroup ImplicitProperties Properties
+ * \brief Properties
*/
/*!
* \ingroup ImplicitModel
* \defgroup ImplicitVolumeVariables Volume Variables
+ * \brief Volume Variables
*/
/* ***************** Sequential ******************/
/*!
- * \defgroup Sequential Sequential Scheme (Implicit Pressure, Explicit Transport)
+ * \defgroup Sequential Sequential Scheme
+ * \brief Implicit Pressure, Explicit Transport
*/
/*!
* \ingroup Sequential
- * \defgroup IMPETproblems Base Problems
+ * \defgroup IMPETproblems Base problems
+ * \brief Base Problems
*/
/*!
* \ingroup Sequential
* \defgroup IMPETProperties Properties
+ * \brief Properties
*/
/* ***************** Material ******************/
/*!
* \defgroup Material Material and Fluid Framework
- * Short description of the most important concepts of the material and fluid framework:
+ * \brief Short description of the most important concepts of the material and fluid framework:
*
* - __Binary coefficient:__ @copydoc Binarycoefficients
*
@@ -380,8 +420,10 @@
/*!
* \ingroup Material
* \defgroup Binarycoefficients Binary Coefficients
- * Binary coefficients describe the relations
- * of a mixture of two components. Typical binary coefficients are
+ * \brief Binary coefficients describe the relations
+ * of a mixture of two components.
+ *
+ * Typical binary coefficients are
* Henry coefficients or binary molecular diffusion
* coefficients. So far, the programming interface for accessing binary
* coefficients has not been standardized in Dumux.
@@ -389,9 +431,11 @@
/*!
* \ingroup Material
* \defgroup Components Components
- * Components are fluid systems which provide the
+ * \brief Components are fluid systems which provide the
* thermodynamic relations for the liquid and gas phase of a single
- * chemical species or a fixed mixture of species. Their main purpose
+ * chemical species or a fixed mixture of species.
+ *
+ * Their main purpose
* is to provide a convenient way to access these quantities from
* full-fledged fluid systems. Components are not supposed to be used
* by models directly.
@@ -399,13 +443,16 @@
/*!
* \ingroup Components
* \defgroup IAPWS IAPWS
+ * \brief Properties of water and steam, see \cite IAPWS1997
*/
/*!
* \ingroup Material
* \defgroup ConstraintSolver Constraint Solver
- * Constraint solvers are auxiliary tools to
+ * \brief Constraint solvers are auxiliary tools to
* make sure that a fluid state is consistent with some thermodynamic
- * constraints. All constraint solvers specify a well defined set of
+ * constraints.
+ *
+ * All constraint solvers specify a well defined set of
* input variables and make sure that the resulting fluid state is
* consistent with a given set of thermodynamic equations.
* Constraint solvers connect the thermodynamic relations expressed by
@@ -416,20 +463,25 @@
*/
/*!
* \ingroup Material
- * \defgroup EOS Equation of State
+ * \defgroup EOS Equations of State
+ * \brief Equation of State
*
- * Equations of state (EOS) are auxiliary
+ * \brief Equations of state (EOS) are auxiliary
* classes which provide relations between a fluid phase's temperature,
- * pressure, composition and density. Since these classes are only used
+ * pressure, composition and density.
+ *
+ * Since these classes are only used
* internally in fluid systems, their programming interface is
* currently ad-hoc.
*/
/*!
* \ingroup Material
* \defgroup FluidStates Fluid States
- * Fluid states are responsible for representing the
+ * \brief Fluid states are responsible for representing the
* complete thermodynamic configuration of a system at a given spatial
- * and temporal position. A fluid state always provides access methods
+ * and temporal position.
+ *
+ * A fluid state always provides access methods
* to __all__ thermodynamic quantities, but the concept of a fluid state does not
* mandate what assumptions are made to store these thermodynamic
* quantities. What fluid states also do __not__ do is to make sure
@@ -439,9 +491,11 @@
/*!
* \ingroup Material
* \defgroup Fluidsystems Fluid Systems
- * Fluid systems express the thermodynamic relations
+ * \brief Fluid systems express the thermodynamic relations.
* Strictly speaking, these relations are
- * functions, mathematically.} between quantities. Since functions do
+ * functions, dealing mathematically between quantities.
+ *
+ * Since functions do
* not exhibit any internal state, fluid systems are stateless classes,
* i.e. all member functions are static. This is a conscious
* decision since the thermodynamic state of the system is expressed by
@@ -450,30 +504,35 @@
/*!
* \ingroup Material
* \defgroup fluidmatrixinteractions Fluid-Matrix Interactions
- * Some parameters are functions of the fluid state as well as parameters of
- * the matrix. For example the capillary pressure is a function of the phase saturation
+ * \brief Some parameters are functions of the fluid state as well as parameters of
+ * the matrix.
+ *
+ * For example the capillary pressure is a function of the phase saturation
* and the shape parameter \f$\lambda\f$ which is dependent on the material. All such relations
* are gathered in this module.
*/
/*!
* \ingroup fluidmatrixinteractions
* \defgroup fluidmatrixinteractionslaws Laws for Fluid-Matrix Interactions
+ * \brief Laws for Fluid-Matrix Interactions
*/
/*!
* \ingroup fluidmatrixinteractions
* \defgroup fluidmatrixinteractionsparams Parameters for Fluid-Matrix Interactions
+ * \brief Parameters for Fluid-Matrix Interactions
*/
/*!
* \ingroup Material
* \defgroup ParameterCache Parameter Cache
- * Fluid systems sometimes require
+ * \brief Fluid systems sometimes require
* computationally expensive parameters for multiple relations. Such
* parameters can be cached using a so-called parameter
- * cache. Parameter cache objects are specific for each fluid system
+ * cache.
+ *
+ * Parameter cache objects are specific for each fluid system
* but they must provide a common interface to update the internal
* parameters depending on the quantities which changed since the last
- * update.
- * All fluid systems must export a type for their __ParameterCache__
+ * update. All fluid systems must export a type for their __ParameterCache__
* objects. Parameter caches can be used to cache parameter that are
* expensive to compute and are required in multiple thermodynamic
* relations. For fluid systems which do need to cache parameters,
@@ -486,7 +545,7 @@
* Note, that the parameter cache interface only guarantees that if a
* more specialized <tt>update()</tt> method is called, it is not slower
* than the next more-general method (e.g. calling <tt>updateSingleMoleFraction()</tt>
- * may be as expensive as <tt>updateAll()}</tt>. It is thus advisable to
+ * may be as expensive as <tt>updateAll()</tt>. It is thus advisable to
* rather use a more general <tt>update()</tt> method once than multiple
* calls to specialized <tt>update()</tt> methods.
* To make usage of parameter caches easier for the case where all cached
@@ -497,9 +556,11 @@
/*!
* \ingroup Material
* \defgroup SpatialParameters Spatial Parameters
- * All parameters which depend on the matrix and
+ * \brief All parameters which depend on the matrix and
* therefore on the position within the model domain are defined as spatial
- * parameters. For example permeability, porosity etc.
+ * parameters.
+ *
+ * For example permeability, porosity etc.
*
*/
@@ -510,45 +571,55 @@
/*!
* \ingroup Common
* \defgroup BC Boundary Conditions
+ * \brief Boundary Conditions
*/
/*!
* \ingroup Common
* \defgroup Math Elementary Math Functions
+ * \brief Elementary Math Functions
*/
/*!
* \ingroup Common
* \defgroup Exception Exceptions
+ * \brief Exceptions
*/
/*!
* \ingroup Common
* \defgroup Linear Linear Solver Backends
+ * \brief Linear Solver Backends
*/
/*!
* \ingroup Common
* \defgroup Newton Newton Solver
+ * \brief Newton Solver
*/
/*!
* \ingroup Common
* \defgroup Parameter Parameters
- * See the file parameterlist for available parameters.
+ * \brief See the \ref parameterList for available parameters.
*/
/*!
* \ingroup Common
* \defgroup Properties Property System
+ * \brief Property System
*/
/*!
* \ingroup Common
* \defgroup Spline Splines
+ * \brief Splines
*/
/*!
* \ingroup Common
* \defgroup Start Starting the Simulation
+ * \brief Starting the Simulation
*/
/*!
* \ingroup Common
* \defgroup SimControl Time Manager
+ * \brief Time Manager
*/
/*!
* \ingroup Common
* \defgroup Valgrind Valgrind
+ * \brief Valgrind
*/
diff --git a/doc/doxygen/sanitizelinks.sh b/doc/doxygen/sanitizelinks.sh
index f23c1417bd50ac515cbdf71db756eda02913c623..bd1d9ef8e304f67c389b2ef7dc622fb1c452e7ba 100755
--- a/doc/doxygen/sanitizelinks.sh
+++ b/doc/doxygen/sanitizelinks.sh
@@ -3,10 +3,16 @@
sanitizelinks () {
NEW_FILE=`grep -l "\"title\">$1" html/*html | egrep -o [0-9]+`
OLD_FILE=`awk -v a=$NEW_FILE 'BEGIN {printf("%05d", a-1)}'`
- sed -i "s/$OLD_FILE/$NEW_FILE/g" html/*html
+# echo $1: $OLD_FILE $NEW_FILE
+ if [ $OLD_FILE -gt 0 ]; then
+ sed -i "s#$OLD_FILE#$NEW_FILE#g" html/a*html
+ sed -i "s# $1 # <a href=\"a$NEW_FILE.html\">$1</a> #g" html/index.html
+ sed -i "s# $1,# <a href=\"a$NEW_FILE.html\">$1</a>,#g" html/index.html
+ fi
}
-sanitizelinks "Todo List"
+sanitizelinks "Deprecated List" # has to be called before Todo List
+sanitizelinks "Todo List" # has to be called before Warning List
+sanitizelinks "Warning List"
sanitizelinks "Bug List"
-sanitizelinks "Deprecated List"
sanitizelinks "Bibliography"
diff --git a/doc/handbook/dumux-handbook.bib b/doc/handbook/dumux-handbook.bib
index 7568018740ef07921af64da45ffbea6b5b7b7165..575958ece9e8e6a62e05b6396cca309ba23cdd3b 100644
--- a/doc/handbook/dumux-handbook.bib
+++ b/doc/handbook/dumux-handbook.bib
@@ -8,7 +8,7 @@
@ARTICLE{VANGENUCHTEN1980,
author = {M. T. {van Genuchten}},
title = {{A Closed-form Equation for Predicting the Hydraulic Conductivity
- of Unsaturated Soils}},
+ of Unsaturated Soils}},
journal = {Journal of the Soil Science Society of America},
year = {1980},
pages = {892--898},
@@ -19,7 +19,7 @@
@PHDTHESIS{Fritz2010,
author = {J. Fritz},
title = {{A Decoupled Model for Compositional Non-Isothermal Multiphase Flow
- in Porous Media and Multiphysics Approaches for Two-Phase Flow}},
+ in Porous Media and Multiphysics Approaches for Two-Phase Flow}},
school = {Universit\"at Stuttgart},
year = {2010},
owner = {rodrigog},
@@ -63,7 +63,7 @@
@ARTICLE{LENHARD1987,
author = {R. J. Lenhard and J. C. Parker},
title = {{A Model for Hysteretic Constitutive Relations Governing Multiphase
- Flow. 2. Permeability-Saturation Relations}},
+ Flow. 2. Permeability-Saturation Relations}},
journal = {Water Resources Research},
year = {1987},
volume = {23},
@@ -84,11 +84,11 @@
@INPROCEEDINGS{A3:freiboth:2004,
author = {S. H\"olzemann and H. Class and R. Helmig},
title = {{A New Concept for the Numerical Simulation and Parameter Identification
- of Multiphase Flow and Transport Processes in Cohesive Soils}},
+ of Multiphase Flow and Transport Processes in Cohesive Soils}},
booktitle = {{Unsaturated Soils: Numerical and Theoretical Approaches -- Proceedings
- of the International Conference ``From Experimental Evidence towards
- Numerical Modelling of Unsaturated Soils'' (18. - 19. September 2003,
- Bauhaus-Universit\"at Weimar)}},
+ of the International Conference ``From Experimental Evidence towards
+ Numerical Modelling of Unsaturated Soils'' (18. - 19. September 2003,
+ Bauhaus-Universit\"at Weimar)}},
year = {2004},
editor = {Schanz, T.},
publisher = {Springer-Verlag},
@@ -115,14 +115,15 @@
volume = {15},
number = {03},
pages = {658--669},
- publisher = {Society of Petroleum Engineers}
+ publisher = {Society of Petroleum Engineers},
+ url= {https://doi.org/10.2118/106435-PA}
}
@ARTICLE{MUALEM1976,
author = {Y. Mualem},
title = {{A new model for predicting the hydraulic conductivity of unsaturated
- porous media}},
+ porous media}},
journal = {Water Resources Research},
year = {1976},
volume = {12},
@@ -145,7 +146,7 @@
@ARTICLE{PARKER1987,
author = {J. C. Parker and R. J. Lenhard and T. Kuppusamy},
title = {{A Parametric Model for Constitutive Properties Governing Multiphase
- Flow in Porous Media}},
+ Flow in Porous Media}},
journal = {Water Resources Research},
year = {1987},
volume = {23},
@@ -181,13 +182,14 @@
volume = {42},
number = {2-3},
pages = {296--305},
- publisher = {Springer}
+ publisher = {Springer},
+ url={https://doi.org/10.1007/s00254-001-0499-2}
}
@ARTICLE{BELIAEV2001,
author = {A. Y. Beliaev and S. M. Hassanizadeh},
title = {{A Theoretical Model of Hysteresis and Dynamic Effects in the Capillary
- Relation for Two-phase Flow in Porous Media}},
+ Relation for Two-phase Flow in Porous Media}},
journal = {Transport in Porous Media},
year = {2001},
volume = {43},
@@ -276,14 +278,14 @@
publisher = {SFB 404},
year = {2003},
author = {Helmig, R. and Class, H. and Jakobs, H. and Bierlinski, A. and \"Olmann,
- U.},
+ U.},
month = {May}
}
@PHDTHESIS{A3:oelmann:2006a,
author = {\"Olmann, Ulrich},
title = {{Behandlung anisotroper Mobilit\"aten als Resultat von Upscalingverfahren
- mittels Mehrpunktflu{\ss}approximationen}},
+ mittels Mehrpunktflu{\ss}approximationen}},
school = {Institut f\"ur Wasserbau, Universit\"at Stuttgart},
year = {to be published 2006}
}
@@ -292,7 +294,7 @@
@MISC{A3:oelmann:2006b,
author = {\"Olmann, U. and Aavatsmark, I. and Helmig, R.},
title = {{Buckley-Leverett heterogen --- Konstruktion der L\"osung mit der
- Charakteristikenmethode}},
+ Charakteristikenmethode}},
howpublished = {Preprint-Reihe des SFB404},
month = {March},
year = {2006},
@@ -302,7 +304,7 @@
@ARTICLE{LAND1968,
author = {C. S. Land},
title = {{Calculation of Imbibition Relative Permeability for Two- and Three-Phase
- Flow from Rock Properties}},
+ Flow from Rock Properties}},
journal = {Journal of the Society of Petroleum Engineers},
year = {1968},
volume = {8},
@@ -358,7 +360,7 @@
@PHDTHESIS{HUBER2000,
author = {R. U. Huber},
title = {{Compositional Multiphase Flow and Transport in Heterogeneous Porous
- Media}},
+ Media}},
school = {University of Stuttgart},
year = {2000}
}
@@ -406,15 +408,15 @@
@ARTICLE{A3:Braun:2002,
author = {Braun, C. and Helmig, R. and Manthey, S.},
title = {{Determination of constitutive relationships for two-phase flow processes
- in heterogeneous porous media with emphasis on the relative permeability-saturation-relationship}},
+ in heterogeneous porous media with emphasis on the relative permeability-saturation-relationship}},
journal = {Journal of Contaminant Hydrology},
year = {2005}
}
-@phdthesis{nuske2009,
+@mastersthesis{nuske2009,
title={{Determination of interfacial area-capillary pressure-saturation relationships for a single fracture}},
author={Nuske, K. P.},
year={2009},
- school={Master’s thesis, Universit{\"a}t Stuttgart}
+ school={Universit{\"a}t Stuttgart}
}
@article{ferrell1967,
@@ -444,7 +446,7 @@
@INPROCEEDINGS{A3:aavatsmark:1994,
author = {Aavatsmark, I. and Barkve, T. and B{\o}e, {\O}. and Mannseth, T.},
title = {{Discretization on non-orthogonal, curvilinear grids for multiphase
- flow}},
+ flow}},
booktitle = {Proc.\ of the 4th European Conf.\ on the Mathematics of Oil Recovery},
year = {1994},
address = {Norway}
@@ -453,7 +455,7 @@
@ARTICLE{A3:aavatsmark:1996,
author = {Aavatsmark, I. and Barkve, T. and B{\o}e, {\O}. and Mannseth, T.},
title = {{Discretization on Non-Orthogonal, Quadrilateral Grids for Inhomogeneous
- Anisotropic Media}},
+ Anisotropic Media}},
journal = {Journal of Computational Physics},
year = {1996},
volume = {127},
@@ -472,7 +474,7 @@
@ARTICLE{A3:bastian:1999,
author = {Bastian, P. and Helmig, R.},
title = {{Efficient Fully-Coupled Solution Techniques for Two Phase Flow in
- Porous Media. Parallel Multigrid Solution and Large Scale Computations}},
+ Porous Media. Parallel Multigrid Solution and Large Scale Computations}},
journal = {Advances in Water Resources},
year = {1999}
}
@@ -480,7 +482,7 @@
@ARTICLE{BASTIAN-HELMIG1999,
author = {P. Bastian and R. Helmig},
title = {{Efficient Fully-Coupled Solution Techniques for Two Phase Flow in
- Porous Media. Parallel Multigrid Solution and Large Scale Computations}},
+ Porous Media. Parallel Multigrid Solution and Large Scale Computations}},
journal = {Advances in Water Resources},
year = {1999},
volume = {23},
@@ -563,7 +565,8 @@
title = {{Fifth Comparative Solution Project: Evaluation of Miscible Flood Simulators}},
journal = {Society of Petroleum Engineers},
year = {1987},
- volume = {SPE 16000}
+ volume = {SPE 16000},
+ url={https://doi.org/10.2118/16000-MS}
}
@ARTICLE{WHITAKER1985,
@@ -691,7 +694,7 @@
@ARTICLE{A3:nordbotten:2005a,
author = {Nordbotten, J. M. and Celia, M. A. and Bachu, S.},
title = {{Injection and Storage of {CO$_2$} in Deep Saline Aquifers: Analytical
- Solution for {CO$_2$} Plume Evolution During Injection}},
+ Solution for {CO$_2$} Plume Evolution During Injection}},
journal = {Transport in Porous Media},
year = {2005},
volume = {58(3)},
@@ -713,7 +716,7 @@
@ARTICLE{NIESSNER2005,
author = {J. Niessner and R. Helmig and H. Jakobs and J. Roberts},
title = {{Interface Condition and Exact Linearization in the Newton Iterations
- for Two-phase Flow in Heterogeneous Porous Media}},
+ for Two-phase Flow in Heterogeneous Porous Media}},
journal = {Advances in Water Resources},
year = {2005},
volume = {28},
@@ -796,9 +799,9 @@
@ARTICLE{A3:acosta:2006,
author = {Acosta, M. and Merten, C. and Eigenberger, G. and Class, H. and Helmig,
- R. and Thoben, B. and M\"uller-Steinhagen, H.},
+ R. and Thoben, B. and M\"uller-Steinhagen, H.},
title = {{Modeling non-isothermal two-phase multicomponent flow in the cathode
- of PEM fuel cells}},
+ of PEM fuel cells}},
journal = {Journal of Power Sources},
year = {2006},
pages = {in print},
@@ -807,7 +810,7 @@
@BOOK{CLASS2007,
title = {{Models for Non-Isothermal Compositional Gas-Liquid Flow and Transport
- in Porous Media}},
+ in Porous Media}},
publisher = {University of Stuttgart},
year = {2007},
author = {H. Class},
@@ -823,7 +826,7 @@
@INPROCEEDINGS{A3:HelmigEtAl:2006,
author = {Helmig, R. and Miller, C. T. and Jakobs, H. and Class, H. and Hilpert,
- M. and Kees, C. E. and Niessner, J.},
+ M. and Kees, C. E. and Niessner, J.},
title = {{Multiphase Flow and Transport Modeling in Heterogeneous Porous Media}},
booktitle = {Progress in Industrial Mathematics at ECMI 2004},
year = {2006},
@@ -838,7 +841,7 @@
@BOOK{A3:helmig:1997,
title = {{Multiphase Flow and Transport Processes in the Subsurface --- A Contribution
- to the Modeling of Hydrosystems}},
+ to the Modeling of Hydrosystems}},
publisher = {Springer Verlag},
year = {1997},
author = {Helmig, R.}
@@ -846,7 +849,7 @@
@BOOK{HELMIG1997,
title = {{Multiphase Flow and Transport Processes in the Subsurface: A Contribution
- to the Modeling of Hydrosystems}},
+ to the Modeling of Hydrosystems}},
publisher = {Springer},
year = {1997},
author = {R. Helmig},
@@ -893,7 +896,7 @@
@PHDTHESIS{PAPAFOTIOU2008,
author = {A. Papafotiou},
title = {{Numerical investigations of the role of hysteresis in heterogeneous
- two-phase flow systems}},
+ two-phase flow systems}},
school = {University of Stuttgart},
year = {2008}
}
@@ -917,7 +920,7 @@
@ARTICLE{A3:falta:1992,
author = {Falta, R. W. and Pruess, K. and Javandel, I. and Witherspoon, P. A.},
title = {{Numerical Modeling of Steam Injection for the Removal of Nonaqueous
- Phase Liquids From the Subsurface. 1. Numerical Formulation}},
+ Phase Liquids From the Subsurface. 1. Numerical Formulation}},
journal = {Water Resoures Research},
year = {1992},
volume = {28,2},
@@ -939,7 +942,7 @@
publisher = {Springer Verlag},
year = {2000},
author = {Bastian, P. and Chen, Z. and Ewing, R. E. and Helmig, R. and Jakobs
- H. and Reichenberger V.},
+ H. and Reichenberger V.},
series = {Lecture Notes in Physics, Chen, Ewing and Shi (eds.)}
}
@@ -957,17 +960,18 @@
@ARTICLE{A3:class:2002b,
author = {Class, H. and Helmig, R.},
title = {{Numerical Simulation of Nonisothermal Multiphase Multicomponent Processes
- in Porous Media -- 2. Applications for the Injection of Steam and
- Air}},
+ in Porous Media -- 2. Applications for the Injection of Steam and
+ Air}},
journal = {Advances in Water Resources},
year = {2002},
volume = {25},
- pages = {551--564}
+ pages = {551--564},
+ url = {http://dx.doi.org/10.1016/S0309-1708(02)00015-5}
}
@BOOK{MEISTER2008,
title = {{Numerik linearer Gleichungssysteme: Eine Einf\"{u}hrung in moderne
- Verfahren.}},
+ Verfahren.}},
publisher = {Vieweg},
year = {2008},
author = {A. Meister},
@@ -1001,7 +1005,7 @@
@PHDTHESIS{A3:emmert:1997,
author = {Emmert, M.},
title = {{Numerische Simulation von isothermen/nichtisothermen Mehrphasenprozessen
- unter Ber\"ucksichtigung der Ver\"anderung der Fluideigenschaften}},
+ unter Ber\"ucksichtigung der Ver\"anderung der Fluideigenschaften}},
school = {Institut f\"ur Wasserbau, Universit\"at Stuttgart},
year = {1997}
}
@@ -1021,7 +1025,7 @@ url = {http://www.sciencedirect.com/science/article/pii/S0169772204001160}
@ARTICLE{KOOL1987,
author = {J. Kool and J. C. Parker and M. T. van Genuchten},
title = {{Parameter Estimation for Unsaturated Flow and Transport Models -
- A Review}},
+ A Review}},
journal = {Journal of Hydrology},
year = {1987},
volume = {91},
@@ -1064,7 +1068,7 @@ url = {http://www.sciencedirect.com/science/article/pii/S0169772204001160}
author = {N. T. Burdine},
title = {{Relative permeability calculations from pore size distribution data}},
journal = {Transactions of the American Institute of Mining and Metallurgical
- Engineers},
+ Engineers},
year = {1953},
volume = {198},
pages = {71--78}
@@ -1073,24 +1077,25 @@ url = {http://www.sciencedirect.com/science/article/pii/S0169772204001160}
title={{Release of the IAPWS formulation 2008 for the viscosity of ordinary water substance}},
author={Cooper, J. R. and Dooley, R. B.},
year={2008},
- publisher={The International Association of the Properties of Water and Steam, Berlin, Germany}
+ publisher={The International Association of the Properties of Water and Steam, Berlin, Germany},
+ url={http://www.iapws.org/relguide/visc.pdf}
}
@MISC{A3:IAPWS:2003,
author = {IAPWS (The International Association for the Properties of Water
- and Steam)},
+ and Steam)},
title = {{Revised Release on the IAPS Formulation 1985 for the Viscosity of
- Ordinary Water Substance}},
+ Ordinary Water Substance}},
howpublished = {\url{http://www.iapws.org/}},
year = {2003}
}
@MISC{IAPWS1997,
author = {IAPWS (The International Association for the Properties of Water
- and Steam)},
+ and Steam)},
title = {{Revised Release on the IAPWS Industrial Formulation 1997 for the
- Thermodynamic Properties of Water and Steam}},
- howpublished = {\url{http://www.iapws.org/IF97-Rev.pdf}},
+ Thermodynamic Properties of Water and Steam}},
+ url={http://www.iapws.org/relguide/IF97-Rev.pdf},
year = {1997}
}
@@ -1107,7 +1112,7 @@ url = {http://www.sciencedirect.com/science/article/pii/S0169772204001160}
author = {Allan, J. and Ewing, J. and Helmig, R. and Braun, J.},
title = {{Scale effects in multiphase flow modeling}},
booktitle = {1. International conference on remediation of chlorinated and recalcitrant
- compounds},
+ compounds},
year = {1998},
editor = {Wickramanayake, G.B. and Hinchee, R.E.},
address = {Monterey, California, USA},
@@ -1130,7 +1135,7 @@ url = {http://www.sciencedirect.com/science/article/pii/S0169772204001160}
@ARTICLE{A3:nordbotten:2005b,
author = {Nordbotten, J. M. and Celia, M. A. and Bachu, S. and Dahle, H.},
title = {{Semi-Analytical Solution for {CO$_2$} Leakage through an Abandoned
- Well}},
+ Well}},
journal = {Environmental Science and Technology},
year = {2005},
volume = {39(2)},
@@ -1140,16 +1145,16 @@ url = {http://www.sciencedirect.com/science/article/pii/S0169772204001160}
@ARTICLE{A3:Williams:1989,
author = {Williams, J. K.},
title = {{Simple Renormalisation Schemes for Calculating Effective Properties
- of Heterogeneous Reservoirs}},
+ of Heterogeneous Reservoirs}},
journal = {1st European Conference on the Mathematics of Oil Recovery, Cambridge,
- UK, July 1989},
+ UK, July 1989},
year = {1989}
}
@PHDTHESIS{SHETA1999,
author = {H. Sheta},
title = {{Simulation von Mehrphasenvorg\"{a}engen in por\"{o}sen Medien unter
- Einbeziehung von Hystereseeffekten}},
+ Einbeziehung von Hystereseeffekten}},
school = {University of Stuttgart},
year = {1999}
}
@@ -1169,7 +1174,7 @@ url = {http://www.sciencedirect.com/science/article/pii/S0169772204001160}
@ARTICLE{A3:gimse:1992,
author = {Gimse, T. and Risebro, N. H.},
title = {{Solution of the Cauchy Problem for a Conservation Law with a Discontinuous
- Flux Function}},
+ Flux Function}},
journal = {SIAM J.\ Math.\ Anal.},
year = {1992},
volume = {23},
@@ -1311,7 +1316,7 @@ url={http://dx.doi.org/10.1007/s11242-015-0599-1}
volume={5},
year={2001},
publisher={McGraw-Hill New York},
- url={https://dx.doi.org/10.1036/0070116822}
+ url = { http://www.academia.edu/download/39241893/_EBOOK__Properties_of_Gases_and_Liquids_Prausnitz_5th.pdf}
}
@BOOK{reid1987,
@@ -1335,19 +1340,20 @@ url={http://dx.doi.org/10.1007/s11242-015-0599-1}
@PHDTHESIS{CLASS2001,
author = {H. Class},
title = {{Theorie und numerische Modellierung nichtisothermer Mehrphasenprozesse
- in NAPL-kontaminierten por\"{o}sen Medien.}},
+ in NAPL-kontaminierten por\"{o}sen Medien.}},
school = {University of Stuttgart},
year = {2001}
}
@BOOK{A3:class:2001,
title = {{Theorie und numerische Modellierung nichtisothermer Mehrphasenprozesse
- in NAPL-kontaminierten por\"osen Medien}},
+ in NAPL-kontaminierten por\"osen Medien}},
publisher = {Institut f\"ur Wasserbau, Universit\"at Stuttgart},
year = {2001},
author = {Class, H.},
volume = {105},
- series = {Mitteilungsheft}
+ series = {Mitteilungsheft},
+ url = {http://dx.doi.org/10.18419/opus-223}
}
@BOOK{A3:lancaster:1969,
@@ -1378,12 +1384,11 @@ url={http://dx.doi.org/10.1007/s11242-015-0599-1}
url={http://oai.dtic.mil/oai/oai?verb=getRecord&metadataPrefix=html&identifier=ADA044002}
}
-@phdthesis{ebigbo2005,
+@mastersthesis{ebigbo2005,
title={{Thermal effects of carbon dioxide sequestration in the subsurface}},
author={Ebigbo, A.},
year={2005},
- school={Master’s thesis, Institut f{\"u}r Wasserbau, Universit{\"a}t Stuttgart},
- url={https://www.hydrosys.uni-stuttgart.de/institut/hydrosys/publikationen/paper/Dipl_Anozie_Ebigbo.pdf}
+ school={Master’s thesis, Institut f{\"u}r Wasserbau, Universit{\"a}t Stuttgart}
}
@article{michaelides1981,
@@ -1444,11 +1449,11 @@ url={http://dx.doi.org/10.1007/s11242-015-0599-1}
@INBOOK{A3:bastian:1997,
pages = {27--40},
title = {{UG: A flexible software toolbox for solving partial differential
- equations.}},
+ equations.}},
publisher = {Springer Verlag},
year = {1997},
author = {Bastian, P. and Birken, K. and Lang, S. and Johannsen, K. and Neuss,
- N. and Rentz-Reichert, H. and Wieners, C.},
+ N. and Rentz-Reichert, H. and Wieners, C.},
volume = {1},
series = {Computing and Visualization in Science}
}
@@ -1456,7 +1461,7 @@ url={http://dx.doi.org/10.1007/s11242-015-0599-1}
@MASTERSTHESIS{A3:grass:2005,
author = {Grass, C.},
title = {{Untersuchung von Randbedingungen bei der numerischen Simulation von
- Zweiphasenstr\"omungen in por\"osen Medien}},
+ Zweiphasenstr\"omungen in por\"osen Medien}},
school = {Institut f\"ur Wasserbau, Universit\"at Stuttgart},
year = {2005},
month = {January}
diff --git a/dumux/common/eigenvalues.hh b/dumux/common/eigenvalues.hh
index 674650204914d6792abdbfd41d5aaaa776e11164..4241ac2d932af778b4e5898849022a6a134099d9 100644
--- a/dumux/common/eigenvalues.hh
+++ b/dumux/common/eigenvalues.hh
@@ -56,7 +56,7 @@ double calcOffDiagonalNorm(Matrix& matrix)
}
/*!
- * \briefFunction to calculate eigenvalues of n x n matrices
+ * \brief Function to calculate eigenvalues of n x n matrices
*
* \param eigVel Vector for storing the eigenvalues
* \param matrix n x n matrices for which eigenvalues have to be calculated
diff --git a/dumux/common/parameters.hh b/dumux/common/parameters.hh
index f06f2d1c2cca33615b7c768387faa18c83042c16..9ae02e04c694bb7d1c66a5acd767ad242dffa458 100644
--- a/dumux/common/parameters.hh
+++ b/dumux/common/parameters.hh
@@ -278,6 +278,10 @@ void print(std::ostream &os = std::cout)
const char *getString_(const char *foo = 0)
{ return foo; }
+/*!
+ * \ingroup Parameter
+ * \brief Class sorting params and runTimeParams
+ */
template <class TypeTag>
class Param
{
diff --git a/dumux/common/pointsource.hh b/dumux/common/pointsource.hh
index 8a5595229cc0733ad52376512d7bdb700fffb0ee..a7ce7c56936f679dc231c16c6b54874ddc90102e 100644
--- a/dumux/common/pointsource.hh
+++ b/dumux/common/pointsource.hh
@@ -49,6 +49,10 @@ NEW_PROP_TAG(TimeManager);
} // end namespace Properties
// forward declarations
+/*!
+ * \ingroup Common
+ * \brief A point helper class
+ */
template<class TypeTag>
class PointSourceHelper;
diff --git a/dumux/common/reorderingdofmapper.hh b/dumux/common/reorderingdofmapper.hh
index e15fc113918c76220131d1245e7b24fd31cf64be..e5883d825abececbaa322ce35a37d6da818689e0 100644
--- a/dumux/common/reorderingdofmapper.hh
+++ b/dumux/common/reorderingdofmapper.hh
@@ -32,7 +32,9 @@
namespace Dumux
{
-
+/*!
+ * \brief An SCSG element mapper that sorts the indices in order to optimize the matrix sparsity pattern
+ */
template<class GridView, int codimension>
class ReorderingDofMapper
: public Dune::Mapper<typename GridView::Grid, ReorderingDofMapper<GridView, codimension>, typename GridView::IndexSet::IndexType>
diff --git a/dumux/geomechanics/el2p/newtoncontroller.hh b/dumux/geomechanics/el2p/newtoncontroller.hh
index ddc648b5afe25d3092e26ff67f877189235af59f..f0b174f863e5d8fd1936c508c92f0ff418b4bd5f 100644
--- a/dumux/geomechanics/el2p/newtoncontroller.hh
+++ b/dumux/geomechanics/el2p/newtoncontroller.hh
@@ -18,7 +18,14 @@
*****************************************************************************/
/*!
* \file
+ *
+ * \brief An el2p specific controller for the newton solver.
+ *
+ * This controller 'knows' what a 'physically meaningful' solution is
+ * which allows the newton method to abort quicker if the solution is
+ * way out of bounds.
*/
+
#ifndef DUMUX_EL2P_NEWTON_CONTROLLER_HH
#define DUMUX_EL2P_NEWTON_CONTROLLER_HH
diff --git a/dumux/geomechanics/el2p/propertydefaults.hh b/dumux/geomechanics/el2p/propertydefaults.hh
index 251008ce06e0a98914dc4c8d4038441fee61175b..0f3b634b386d1589d54327fe916f53badb199703 100644
--- a/dumux/geomechanics/el2p/propertydefaults.hh
+++ b/dumux/geomechanics/el2p/propertydefaults.hh
@@ -386,6 +386,8 @@ public:
typedef Dune::FieldVector<Scalar, numEq> type;
};
+/*! @copydoc Properties::NonoverlappingSolverTraits
+ */
template <class TypeTag, class MType, class VType, bool isParallel>
class ElasticTwoPSolverTraits
: public NonoverlappingSolverTraits<MType, VType, isParallel>
@@ -394,6 +396,8 @@ public:
typedef typename GET_PROP_TYPE(TypeTag, JacobianMatrix) JacobianMatrix;
};
+/*! @copydoc Properties::NonoverlappingSolverTraits
+ */
template <class TypeTag, class MType, class VType>
class ElasticTwoPSolverTraits<TypeTag, MType, VType, true>
: public NonoverlappingSolverTraits<MType, VType, true>
diff --git a/dumux/implicit/adaptive/adaptionhelper.hh b/dumux/implicit/adaptive/adaptionhelper.hh
index 36ddbb7eec79deb3f05c5bb718fdd4b24df7f679..b74bad049be97ae79c023cc9aa2e7bf41f07cc2d 100644
--- a/dumux/implicit/adaptive/adaptionhelper.hh
+++ b/dumux/implicit/adaptive/adaptionhelper.hh
@@ -67,9 +67,10 @@ public:
//! Constructs an adaptive helper object
/**
* In addition to providing a storage object for cell-centered Methods, this class provides
- * mapping functionality to adapt the grid.
+ * mapping functionality to adapt the grid. It uses gridView, a DUNE gridview object corresponding
+ * to diffusion and transport equation
*
- * @param gridView a DUNE gridview object corresponding to diffusion and transport equation
+ * @param problem The current problem
*/
ImplicitAdaptionHelper(Problem& problem)
{}
diff --git a/dumux/io/artgridcreator.hh b/dumux/io/artgridcreator.hh
index 1cde782284d9dc53eb6bbd40dbc7d1a368b46fca..cb4d18abde9e026e0d7be23a1f9b8b4732bc205a 100644
--- a/dumux/io/artgridcreator.hh
+++ b/dumux/io/artgridcreator.hh
@@ -501,6 +501,9 @@ class FractureMapper
typedef typename GET_PROP_TYPE(TypeTag, GridCreator) GridCreator;
public:
// mapper: one data element in every entity
+ /*!
+ * \brief Maps one data element in every entity
+ */
template<int dim>
struct FaceLayout
{
diff --git a/dumux/io/ploteffectivediffusivitymodel.hh b/dumux/io/ploteffectivediffusivitymodel.hh
index 70073ae5bef2714ce44d1e334ffb21ec3525a5d2..2807bfebcc4df3554a2925bef322d1e001bb4c42 100644
--- a/dumux/io/ploteffectivediffusivitymodel.hh
+++ b/dumux/io/ploteffectivediffusivitymodel.hh
@@ -65,7 +65,7 @@ public:
* \brief Add a effective diffusion factor-saturation data set to the plot
*
* \param gnuplot The gnuplot interface
- * \param params The material law parameters
+ * \param porosity The porosity
* \param lowerSat Minimum x-value for data set
* \param upperSat Maximum x-value for data set
* \param curveName Name of the data set
diff --git a/dumux/io/plotthermalconductivitymodel.hh b/dumux/io/plotthermalconductivitymodel.hh
index db4963bfb1c0e9a713cef05a2d71a1dd0d2b06ec..58f9ae8f76615052fe98051494c2b1d8b624afb8 100644
--- a/dumux/io/plotthermalconductivitymodel.hh
+++ b/dumux/io/plotthermalconductivitymodel.hh
@@ -109,7 +109,9 @@ public:
* \brief Add a effective thermal conductivity-saturation curve to the plot
*
* \param gnuplot The gnuplot interface
- * \param params The material law parameters
+ * \param porosity The porosity
+ * \param rhoSolid The solid density
+ * \param lambdaSolid Thermal conductivity of the solid
* \param lowerSat Minimum x-value for data set
* \param upperSat Maximum x-value for data set
* \param curveName Name of the data set
diff --git a/dumux/linear/amgproperties.hh b/dumux/linear/amgproperties.hh
index dbbb9780032bd7b1b1a5afcf71df3936281d1eeb..da2e6ccd9850f864bac83432a48107db703ad1d2 100644
--- a/dumux/linear/amgproperties.hh
+++ b/dumux/linear/amgproperties.hh
@@ -52,6 +52,8 @@ namespace Properties
//! The type traits required for using the AMG backend
NEW_PROP_TAG(AmgTraits);
+/*! \brief Non-overlapping solver traits for parallel computing
+ */
template <class MType, class VType, bool isParallel>
class NonoverlappingSolverTraits
{
@@ -63,6 +65,8 @@ public:
};
#if HAVE_MPI
+/*! \brief Non-overlapping solver traits for parallel computing if MPI available
+ */
template <class MType, class VType>
class NonoverlappingSolverTraits<MType, VType, true>
{
@@ -95,7 +99,8 @@ public:
typedef typename SolverTraits::ScalarProduct ScalarProduct;
typedef typename SolverTraits::Smoother Smoother;
};
-
+/*! \brief Overlapping solver traits for parallel computing
+ */
template <class MType, class VType, bool isParallel>
class OverlappingSolverTraits
{
@@ -107,6 +112,8 @@ public:
};
#if HAVE_MPI
+/*! \brief Non-overlapping solver traits for parallel computing if MPI available
+ */
template <class MType, class VType>
class OverlappingSolverTraits<MType, VType, true>
{
diff --git a/dumux/linear/pardisobackend.hh b/dumux/linear/pardisobackend.hh
index 7ed7894c5e901a24479298fcb63e3b9fc2bb1563..b3fb49782ef4bad1faaae8974d076835661a25f5 100644
--- a/dumux/linear/pardisobackend.hh
+++ b/dumux/linear/pardisobackend.hh
@@ -18,7 +18,7 @@
*****************************************************************************/
/*!
* \file
- * \brief Dumux solver backend the Pardiso direct solver.
+ * \brief Dumux solver backend for the Pardiso direct solver.
*/
#ifndef DUMUX_PARDISO_BACKEND_HH
#define DUMUX_PARDISO_BACKEND_HH
diff --git a/dumux/linear/scotchbackend.hh b/dumux/linear/scotchbackend.hh
index 9121848cdf3234fa5dce79a85b238f4aa299c511..86fceed8192955aa617602e5a4dcecc8d43d455c 100644
--- a/dumux/linear/scotchbackend.hh
+++ b/dumux/linear/scotchbackend.hh
@@ -39,7 +39,9 @@ extern "C"
namespace Dumux
{
-
+/*!
+ * \brief An interface to the scotch library for matrix reordering
+ */
template<class IndexType>
class ScotchBackend
{
diff --git a/dumux/material/constraintsolvers/compositionfromfugacities2pncmin.hh b/dumux/material/constraintsolvers/compositionfromfugacities2pncmin.hh
index e31eea5b77da5f94390a5dfe0c92eca1e0eb091a..bc4c1382bd9b0f2ec35b4b0b7103e44938a678b0 100644
--- a/dumux/material/constraintsolvers/compositionfromfugacities2pncmin.hh
+++ b/dumux/material/constraintsolvers/compositionfromfugacities2pncmin.hh
@@ -45,6 +45,11 @@ class DUNE_DEPRECATED_MSG("CompositionFromFugacities2pncmin is deprecated. Use C
: public CompositionFromFugacities<Scalar, FluidSystem>
{ };
+/*!
+ * \ingroup ConstraintSolver
+ * \brief Calculates the chemical equilibrium from the component
+ * fugacities in a phase.
+ */
template <class Scalar, class FluidSystem>
class DUNE_DEPRECATED_MSG("compositionFromFugacities2pncmin is deprecated. Use CompositionFromFugacities instead.")
compositionFromFugacities2pncmin
diff --git a/dumux/material/fluidmatrixinteractions/2p/thermalconductivityjohansen.hh b/dumux/material/fluidmatrixinteractions/2p/thermalconductivityjohansen.hh
index c0be8ad95fbbe70545bea790b5aff46eb1546994..ed1e45c36f0e2c81a222bd797eb5323dd8594ce2 100644
--- a/dumux/material/fluidmatrixinteractions/2p/thermalconductivityjohansen.hh
+++ b/dumux/material/fluidmatrixinteractions/2p/thermalconductivityjohansen.hh
@@ -30,7 +30,9 @@
namespace Dumux
{
-
+/*!
+ * \brief Contains the phase indices
+ */
struct JohansenIndices
{
static const int wPhaseIdx = 0;
diff --git a/dumux/material/fluidmatrixinteractions/2p/thermalconductivitysomerton.hh b/dumux/material/fluidmatrixinteractions/2p/thermalconductivitysomerton.hh
index f12b84be8d0c4b9289cd1fab38f1724efcc63ce4..6c350b9e939d6fcd674825afcfd0542eeaeb9260 100644
--- a/dumux/material/fluidmatrixinteractions/2p/thermalconductivitysomerton.hh
+++ b/dumux/material/fluidmatrixinteractions/2p/thermalconductivitysomerton.hh
@@ -28,7 +28,9 @@
namespace Dumux
{
-
+/*!
+ * \brief Indices for the wetting and the non-wetting Phase
+ */
struct SomertonIndices
{
static constexpr int wPhaseIdx = 0;
diff --git a/dumux/material/fluidmatrixinteractions/3p/thermalconductivitysomerton3p.hh b/dumux/material/fluidmatrixinteractions/3p/thermalconductivitysomerton3p.hh
index 12a39c1c6d9c91f9b5b6410cf85fbd92a9296390..ccf29e6188172c355094d917b2b4791f28969ea6 100644
--- a/dumux/material/fluidmatrixinteractions/3p/thermalconductivitysomerton3p.hh
+++ b/dumux/material/fluidmatrixinteractions/3p/thermalconductivitysomerton3p.hh
@@ -28,7 +28,9 @@
namespace Dumux
{
-
+/*!
+ * \brief Indices for three permanent phases
+ */
struct SimpleThreePIndices
{
static const int wPhaseIdx = 0;
diff --git a/dumux/material/fluidsystems/base.hh b/dumux/material/fluidsystems/base.hh
index ac2f479a3004b1f765d4c3023abd0e0635c5fa5b..d7df3931919eef749c31a03c4c9c95d8ea993ddf 100644
--- a/dumux/material/fluidsystems/base.hh
+++ b/dumux/material/fluidsystems/base.hh
@@ -20,6 +20,7 @@
* \file
*
* \brief @copybrief Dumux::FluidSystems::BaseFluidSystem
+ *
*/
#ifndef DUMUX_BASE_FLUID_SYSTEM_HH
#define DUMUX_BASE_FLUID_SYSTEM_HH
@@ -28,6 +29,8 @@
namespace Dumux
{
+namespace FluidSystems
+{
/*!
* \ingroup Fluidsystems
* \brief Fluid system base class.
@@ -36,10 +39,6 @@ namespace Dumux
* liquid phase. This contribution is probably not big, but somebody
* has to find out its influence.
*/
-
-namespace FluidSystems
-{
-
template <class Scalar, class Implementation>
class BaseFluidSystem
{
diff --git a/dumux/multidomain/newtoncontroller.hh b/dumux/multidomain/newtoncontroller.hh
index 1fefd9ac3d8ac123b1a4685b9956b7e383bad223..7fa9fa5fab045c6077052d7dfe73c03530b0803b 100644
--- a/dumux/multidomain/newtoncontroller.hh
+++ b/dumux/multidomain/newtoncontroller.hh
@@ -97,7 +97,7 @@ public:
<< std::endl;
}
- //! \copydoc ParentType::newtonUpdateShift()
+ //! \copydoc NewtonController::newtonUpdateShift()
void newtonUpdateShift(const SolutionVector &uLastIter,
const SolutionVector &deltaU)
{
diff --git a/dumux/porousmediumflow/2p/implicit/adaptionhelper.hh b/dumux/porousmediumflow/2p/implicit/adaptionhelper.hh
index 3c21b24524b410236e0309263e98e34c0f5bcd57..c9594e0ac2b2920bc71a7334331ec7f38161efdc 100644
--- a/dumux/porousmediumflow/2p/implicit/adaptionhelper.hh
+++ b/dumux/porousmediumflow/2p/implicit/adaptionhelper.hh
@@ -16,6 +16,12 @@
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
+/*!
+ * \file
+ *
+ * \brief Base class holding the variables for implicit models.
+ */
+
#ifndef DUMUX_TWOP_ADAPTIONHELPER_HH
#define DUMUX_TWOP_ADAPTIONHELPER_HH
@@ -90,9 +96,9 @@ private:
PersistentContainer adaptionMap_;
public:
- //! Constructs an adaption helper object
- /**
- * @param gridView a DUNE gridview object
+ /*! \brief Constructs an adaption helper object
+ /*
+ * @param problem The current problem
*/
TwoPAdaptionHelper(Problem& problem) : ParentType(problem), adaptionMap_(problem.grid(), 0)
{
@@ -101,7 +107,7 @@ public:
}
/*!
- * Store primary variables
+ * \brief Store primary variables
*
* To reconstruct the solution in father elements, problem properties might
* need to be accessed.
@@ -190,7 +196,7 @@ public:
}
/*!
- * Reconstruct missing primary variables (where elements are created/deleted)
+ * \brief Reconstruct missing primary variables (where elements are created/deleted)
*
* To reconstruct the solution in father elements, problem properties might
* need to be accessed.
@@ -445,8 +451,9 @@ public:
//#endif
}
- //! Stores sons entries into father element for averaging
- /**
+ /*!
+ * \brief Stores sons entries into father element for averaging
+ *
* Sum up the adaptedValues (sons values) into father element. We store from leaf
* upwards, so sons are stored first, then cells on the next leaf (=fathers)
* can be averaged.
@@ -471,14 +478,16 @@ public:
adaptedValuesFather.associatedMass += adaptedValues.associatedMass;
}
}
- //! Set adapted values in CellData
- /**
+ /*!
+ * \brief Set adapted values in CellData
+ *
* This methods stores reconstructed values into the cellData object, by
* this setting a newly mapped solution to the storage container of the
* sequential models.
*
* \param adaptedValues Container for model-specific values to be adapted
* \param u The variables to be stored
+ * \param scvIdx The SCV (sub-control-volume) index
*/
static void setAdaptionValues(AdaptedValues& adaptedValues, PrimaryVariables& u, int scvIdx)
{
diff --git a/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh b/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
index a93e9f84c287c7face3951be7517a361b17cd058..43c2d80ee0ae9d4b3caedabf0142d9db261a7267 100644
--- a/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
+++ b/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
@@ -72,47 +72,43 @@ class FvMpfaL3dTransmissibilityCalculator
public:
- typedef Dune::FieldMatrix<Scalar, dim, 2 * dim - dim + 1> TransmissibilityType;//!< Type of the transmissibility matrix
+ typedef Dune::FieldMatrix<Scalar,dim,2*dim-dim+1> TransmissibilityType;//!< Type of the transmissibility matrix
int chooseTransmissibility(TransmissibilityType& transmissibilityOne,
TransmissibilityType& transmissibilityTwo, int lTypeOne, int lTypeTwo);
- int transmissibility(Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
+ int transmissibility(TransmissibilityType& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx3, int idx4, int idx5, int idx6);
- int transmissibility(Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
+ int transmissibility(TransmissibilityType& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx3, int idx4, int idx5, int idx6,
Dune::FieldVector<bool, 4> &useCases);
-
- int transmissibilityTPFA(Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
+ int transmissibilityTPFA( TransmissibilityType& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
int idx1, int idx2);
- int transmissibilityCaseOne(
- Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
+ int transmissibilityCaseOne(TransmissibilityType& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx3, int idx5);
- int transmissibilityCaseTwo(
- Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
+ int transmissibilityCaseTwo(TransmissibilityType& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx4, int idx6);
- int transmissibilityCaseThree(
- Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
+
+ int transmissibilityCaseThree( TransmissibilityType& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx4, int idx5);
- int transmissibilityCaseFour(
- Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
+ int transmissibilityCaseFour( TransmissibilityType& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx3, int idx6);
diff --git a/dumux/porousmediumflow/2p2c/sequential/fvtransport.hh b/dumux/porousmediumflow/2p2c/sequential/fvtransport.hh
index 838b21efda692e304880d37030fe304642dadd01..4136eb1244dfb8c743026443537d41d28934c241 100644
--- a/dumux/porousmediumflow/2p2c/sequential/fvtransport.hh
+++ b/dumux/porousmediumflow/2p2c/sequential/fvtransport.hh
@@ -116,6 +116,9 @@ public:
typedef Dune::FieldVector<Scalar, 2> TimeStepFluxType;
protected:
+ /**
+ * \brief Data for local timestepping
+ */
struct LocalTimesteppingData
{
Dune::FieldVector<EntryType, 2*dim> faceFluxes;
diff --git a/dumux/porousmediumflow/2pminc/implicit/model.hh b/dumux/porousmediumflow/2pminc/implicit/model.hh
index 3459402cf242446cf599c4ec808644f9a0d2d521..fc9e30d29d02acb3d853e7d5e940f83729ed4424 100644
--- a/dumux/porousmediumflow/2pminc/implicit/model.hh
+++ b/dumux/porousmediumflow/2pminc/implicit/model.hh
@@ -39,6 +39,7 @@ namespace Dumux
/*!
* \ingroup TwoPMincModel
+ * \brief Adaption of the fully implicit scheme to the two-phase flow model.
*/
template<class TypeTag >
class TwoPMincModel : public TwoPModel<TypeTag>
diff --git a/dumux/porousmediumflow/mpnc/implicit/diffusion/fluxvariables.hh b/dumux/porousmediumflow/mpnc/implicit/diffusion/fluxvariables.hh
index ce4b0ea710f2718e48db68fb0aacddab786bb07c..2e864e020d265bef6ce934994d5cf051f4ebfb42 100644
--- a/dumux/porousmediumflow/mpnc/implicit/diffusion/fluxvariables.hh
+++ b/dumux/porousmediumflow/mpnc/implicit/diffusion/fluxvariables.hh
@@ -218,7 +218,11 @@ protected:
Scalar moleFraction_[numPhases][numComponents];
};
-
+/*!
+ * \ingroup MPNCModel
+ * \ingroup ImplicitFluxVariables
+ * \brief Variables for the diffusive fluxes in the MpNc model
+ */
template<class TypeTag>
class MPNCFluxVariablesDiffusion<TypeTag, false>
{
diff --git a/dumux/porousmediumflow/mpnc/implicit/diffusion/volumevariables.hh b/dumux/porousmediumflow/mpnc/implicit/diffusion/volumevariables.hh
index d3ccc4ac1b78b55b7577583d36abb48095b78399..7ba2efaf2116f9cba5aa91542419bea23f655cc7 100644
--- a/dumux/porousmediumflow/mpnc/implicit/diffusion/volumevariables.hh
+++ b/dumux/porousmediumflow/mpnc/implicit/diffusion/volumevariables.hh
@@ -144,6 +144,11 @@ protected:
Scalar diffCoeffG_[numComponents][numComponents];
};
+
+/*!
+ * \brief Variables for the disabled diffusive fluxes in the MpNc model within
+ * a finite volume.
+ */
// dummy class for the case where diffusion is disabled
template<class TypeTag>
class MPNCVolumeVariablesDiffusion<TypeTag, false>
diff --git a/dumux/porousmediumflow/mpnc/implicit/energy/fluxvariables.hh b/dumux/porousmediumflow/mpnc/implicit/energy/fluxvariables.hh
index 265bef607b35081d7e9590dfdc723afcde862665..a274c8e4e43c398bd786e4519292aebdd05a9ba4 100644
--- a/dumux/porousmediumflow/mpnc/implicit/energy/fluxvariables.hh
+++ b/dumux/porousmediumflow/mpnc/implicit/energy/fluxvariables.hh
@@ -34,7 +34,7 @@ namespace Dumux
/*!
* \ingroup MPNCModel
* \ingroup ImplicitFluxVariables
- * \brief Variables for the enthalpy fluxes in the MpNc model
+ * \brief Variables for the enthalpy fluxes in the MpNc model for the isothermal case
*/
template <class TypeTag, bool enableEnergy/*=false*/, int numEnergyEquations/*=0*/>
class MPNCFluxVariablesEnergy
@@ -81,6 +81,11 @@ public:
{}
};
+/*!
+ * \ingroup MPNCModel
+ * \ingroup ImplicitFluxVariables
+ * \brief Variables for the enthalpy fluxes in the MpNc model
+ */
template <class TypeTag>
class MPNCFluxVariablesEnergy<TypeTag, /*enableEnergy=*/true, /*numEnergyEquations=*/1>
{
diff --git a/dumux/porousmediumflow/mpnc/implicit/energy/localresidual.hh b/dumux/porousmediumflow/mpnc/implicit/energy/localresidual.hh
index 4c553ccc06670d2c3e8a5327624fcacc78f59695..4ade29ccc6dc175387fb346bf244147d1f2b004d 100644
--- a/dumux/porousmediumflow/mpnc/implicit/energy/localresidual.hh
+++ b/dumux/porousmediumflow/mpnc/implicit/energy/localresidual.hh
@@ -119,7 +119,10 @@ public:
}
};
-
+/*!
+ * \brief Specialization of the energy module for the nonisothermal case.
+ *
+ */
template <class TypeTag>
class MPNCLocalResidualEnergy<TypeTag, /*enableEnergy=*/true, /*numEnergyEquations=*/ 1 >
{
diff --git a/dumux/porousmediumflow/mpnc/implicit/newtoncontroller.hh b/dumux/porousmediumflow/mpnc/implicit/newtoncontroller.hh
index f6a030a36215e5896513cace4c1cadc28674366f..ea9755eb5530a03dc80cff608a4834fedc7f57fb 100644
--- a/dumux/porousmediumflow/mpnc/implicit/newtoncontroller.hh
+++ b/dumux/porousmediumflow/mpnc/implicit/newtoncontroller.hh
@@ -36,7 +36,7 @@
namespace Dumux {
/*!
- * \brief A MpNc specific controller for the newton solver, which knows
+ * \brief A MpNc specific controller for the newton solver assuming local thermal equilibrium, which knows
* 'physically meaningful' solution.
*/
template <class TypeTag, bool enableKinetic /* = false */>
@@ -97,6 +97,10 @@ private:
};
+/*!
+ * \brief A MpNc specific controller for the newton solver, which knows
+ * 'physically meaningful' solution.
+ */
template <class TypeTag>
class MpNcNewtonChop<TypeTag, /*enableKinetic=*/true>
{
diff --git a/dumux/porousmediumflow/mpnc/implicit/volumevariablesiakinetic.hh b/dumux/porousmediumflow/mpnc/implicit/volumevariablesiakinetic.hh
index 7374befbadbf1b5235d245259b8cc399b58f1687..3049b46778aa807b50ef4eacf889bef10c443f46 100644
--- a/dumux/porousmediumflow/mpnc/implicit/volumevariablesiakinetic.hh
+++ b/dumux/porousmediumflow/mpnc/implicit/volumevariablesiakinetic.hh
@@ -40,6 +40,11 @@ namespace Dumux
////////////////////////////////////////////////////////////////////////////////////////////////////
// specialization for the case of kinetic mass AND energy transfer
////////////////////////////////////////////////////////////////////////////////////////////////////
+/*!
+ * \brief Volume variables required for the modules which require the specific interfacial
+ * area between fluid phases. This is the specialization for the case of kinetic
+ * mass AND energy transfer
+ */
template <class TypeTag, bool enableKinetic >
class MPNCVolumeVariablesIA<TypeTag, enableKinetic, /*numEnergyEqs=*/3>
{
@@ -332,6 +337,11 @@ private:
/////////////////////////////////////////////////////////////////////////////////////////////////////////////
// specialization for the case of NO kinetic mass but kinteic energy transfer of a fluid mixture and solid
/////////////////////////////////////////////////////////////////////////////////////////////////////////////
+/*!
+ * \brief Volume variables required for the modules which require the specific interfacial
+ * area between fluid phases. This is the specialization for the case of NO kinetic
+ * mass but kinteic energy transfer of a fluid mixture and solid
+ */
template <class TypeTag>
class MPNCVolumeVariablesIA<TypeTag, /*enableKinetic=*/false, /*numEnergyEqs=*/2>
{
@@ -471,6 +481,11 @@ private:
////////////////////////////////////////////////////////////////////////////////////////////////////
// specialization for the case of (only) kinetic mass transfer
////////////////////////////////////////////////////////////////////////////////////////////////////
+/*!
+ * \brief Volume variables required for the modules which require the specific interfacial
+ * area between fluid phases. This is the specialization specialization for the case
+ * of (only) kinetic mass transfer
+ */
template <class TypeTag>
class MPNCVolumeVariablesIA<TypeTag, /*enableKinetic=*/true, /*numEnergyEqs=*/0>
{
diff --git a/test/common/boundingboxtree/test_bboxtree.cc b/test/common/boundingboxtree/test_bboxtree.cc
index 7829e41ce8fabaa2ad2540fd6cbba03139123641..f1079bc6f6d2acde325f213d0ecc97fa4474c985 100644
--- a/test/common/boundingboxtree/test_bboxtree.cc
+++ b/test/common/boundingboxtree/test_bboxtree.cc
@@ -1,3 +1,27 @@
+// -*- 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/>. *
+ *****************************************************************************/
+/*!
+ * \file
+ *
+ * \brief test for the boundnig box tree
+ */
+
#include <config.h>
#include <iostream>
#include <unordered_map>
@@ -23,6 +47,11 @@ namespace Properties
#endif
}
+/*!
+ *
+ * \brief Bounding box tree tests
+ */
+
template<class TypeTag>
class BBoxTreeTests
{
diff --git a/test/geomechanics/el2p/el2pco2tables.hh b/test/geomechanics/el2p/el2pco2tables.hh
index 74b3a6f958278623fc586bb433f50a383e7ffaff..f7d4913b67eae5e1b4009a0f77f9d5e725d8805f 100644
--- a/test/geomechanics/el2p/el2pco2tables.hh
+++ b/test/geomechanics/el2p/el2pco2tables.hh
@@ -31,9 +31,14 @@ namespace Dumux
{
namespace El2P
{
+/*!
+* \brief Class providing the tabulated values of CO2 for density and enthalpy
+*/
// the real work is done by some external program which provides
// ready-to-use tables.
+
#include "co2values.inc"
+
}
}
diff --git a/test/io/gridcreator/test_gridcreator_gmsh.cc b/test/io/gridcreator/test_gridcreator_gmsh.cc
index 1b37ca2a3380be2be3338280a041b652e5014d26..be3e9db1bfaf841de663355f15e4eb992ef77514 100644
--- a/test/io/gridcreator/test_gridcreator_gmsh.cc
+++ b/test/io/gridcreator/test_gridcreator_gmsh.cc
@@ -46,6 +46,10 @@ namespace Properties
SET_STRING_PROP(GridCreatorGmshTest, GridParameterGroup, "BifurcationGrid");
}
+/*!
+ *
+ * \brief Test for gmsh interface of the grid creator
+ */
template<class TypeTag>
class GridCreatorGmshTest
{
diff --git a/test/porousmediumflow/1p/sequential/test_diffusionproblem.hh b/test/porousmediumflow/1p/sequential/test_diffusionproblem.hh
index 5395e23e570ae402535199905690c381f32be05c..a1a98e2ddad1be8f5cf44cbb7b4fea842e66b804 100644
--- a/test/porousmediumflow/1p/sequential/test_diffusionproblem.hh
+++ b/test/porousmediumflow/1p/sequential/test_diffusionproblem.hh
@@ -40,7 +40,9 @@
namespace Dumux
{
-// A simple unit sqare grid creator
+/*!
+* \brief A simple unit sqare grid creator
+*/
template <class Grid>
class UnitCubeGridCreator
{
diff --git a/test/porousmediumflow/2p/implicit/cc2pcornerpointproblem.hh b/test/porousmediumflow/2p/implicit/cc2pcornerpointproblem.hh
index ed711f637e5236537836c1ceef738af18db02e87..f4dedae9ab3c3d76c08e062979162b57da88d14f 100644
--- a/test/porousmediumflow/2p/implicit/cc2pcornerpointproblem.hh
+++ b/test/porousmediumflow/2p/implicit/cc2pcornerpointproblem.hh
@@ -16,6 +16,14 @@
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
+/*!
+ * \file
+ *
+ * \brief Test for a cornerpoint grid applied on a gas injection scenario
+ */
+
+
+
#ifndef DUMUX_CC2P_CORNERPOINT_PROBLEM_HH
#define DUMUX_CC2P_CORNERPOINT_PROBLEM_HH
diff --git a/test/porousmediumflow/2p/implicit/cc2pcornerpointspatialparams.hh b/test/porousmediumflow/2p/implicit/cc2pcornerpointspatialparams.hh
index a3cbaf094074a07c26a6f9063d707034a4609a8e..0f6abd61d81ac108f2bcf6efc9adc3704dfdf646 100644
--- a/test/porousmediumflow/2p/implicit/cc2pcornerpointspatialparams.hh
+++ b/test/porousmediumflow/2p/implicit/cc2pcornerpointspatialparams.hh
@@ -16,6 +16,13 @@
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
+/*!
+ * \file
+ *
+ * \brief The spatial parameters for the CC2PCornerPointProblem
+ */
+
+
#ifndef DUMUX_CC2P_CORNERPOINT_SPATIAL_PARAMS_HH
#define DUMUX_CC2P_CORNERPOINT_SPATIAL_PARAMS_HH
@@ -53,7 +60,10 @@ public:
typedef EffToAbsLaw<EffectiveLaw> type;
};
}
-
+/*!
+ *
+ * \brief The spatial parameters for the CC2PCornerPointProblem
+ */
template<class TypeTag>
class CC2PCornerPointSpatialParams : public ImplicitSpatialParams<TypeTag>
{
diff --git a/test/porousmediumflow/2p/implicit/test_generalizeddirichlet.cc b/test/porousmediumflow/2p/implicit/test_generalizeddirichlet.cc
index 0a822952bd87b9e04254cb03065d2b5508a69e94..043645573562428a36c87307b1c19ad0a6a76bfd 100644
--- a/test/porousmediumflow/2p/implicit/test_generalizeddirichlet.cc
+++ b/test/porousmediumflow/2p/implicit/test_generalizeddirichlet.cc
@@ -16,6 +16,12 @@
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
+/*!
+ * \file
+ *
+ * \brief Test for a generalized Dirichlet boundary condition.
+ */
+
#include <config.h>
#include "generalizeddirichletproblem.hh"
#include <dumux/common/start.hh>
diff --git a/test/porousmediumflow/2p/sequential/buckleyleverettanalyticsolution.hh b/test/porousmediumflow/2p/sequential/buckleyleverettanalyticsolution.hh
index e25451dd4d73e7369c3093700ee6ae544ee99bcd..e15780692b957cd8aa3237258a85b43a65380ea4 100644
--- a/test/porousmediumflow/2p/sequential/buckleyleverettanalyticsolution.hh
+++ b/test/porousmediumflow/2p/sequential/buckleyleverettanalyticsolution.hh
@@ -44,6 +44,11 @@ struct CheckMaterialLaw
}
};
+/**
+ * \ingroup fracflow
+ * @brief IMplicit Pressure Explicit Saturation (IMPES) scheme for the solution of
+ * the Buckley-Leverett problem
+ */
template<typename Scalar>
struct CheckMaterialLaw<Scalar, LinearMaterial<Scalar> >
{
@@ -53,8 +58,13 @@ struct CheckMaterialLaw<Scalar, LinearMaterial<Scalar> >
}
};
+/**
+ * \ingroup fracflow
+ * @brief IMplicit Pressure Explicit Saturation (IMPES) scheme for the solution of
+ * the Buckley-Leverett problem
+ */
template<typename Scalar>
-struct CheckMaterialLaw<Scalar, EffToAbsLaw< LinearMaterial<Scalar> > >
+struct CheckMaterialLaw <Scalar, EffToAbsLaw< LinearMaterial<Scalar> > >
{
static bool isLinear()
{
@@ -62,6 +72,9 @@ struct CheckMaterialLaw<Scalar, EffToAbsLaw< LinearMaterial<Scalar> > >
}
};
+/**
+* @brief Analytical solution of the buckley-leverett problem
+*/
template<class TypeTag> class BuckleyLeverettAnalytic
{
typedef typename GET_PROP_TYPE(TypeTag, Problem) Problem;
diff --git a/test/porousmediumflow/2p/sequential/test_mpfa2pspatialparams.hh b/test/porousmediumflow/2p/sequential/test_mpfa2pspatialparams.hh
index 18afeb4fbf2bfccdb2da59129f0b5bb1600448ea..ae221d0322592a69f8193d5f138e81d2887b6e8e 100644
--- a/test/porousmediumflow/2p/sequential/test_mpfa2pspatialparams.hh
+++ b/test/porousmediumflow/2p/sequential/test_mpfa2pspatialparams.hh
@@ -30,7 +30,11 @@
namespace Dumux
{
-
+/*!
+ * \file
+ *
+ * \brief Spatial parameters for the sequential 2p test problems
+ */
template<class TypeTag>
class Test2PSpatialParams;
@@ -53,7 +57,8 @@ public:
};
}
-/** \todo Please doc me! */
+/*! \brief Spatial parameters for the sequential 2p test problems
+ */
template<class TypeTag>
class Test2PSpatialParams: public FVSpatialParams<TypeTag>
diff --git a/test/porousmediumflow/2pncmin/implicit/dissolutionspatialparams.hh b/test/porousmediumflow/2pncmin/implicit/dissolutionspatialparams.hh
index e0e993dea4aae8870f520a319b9fdcb4b0c2866c..fff42e0a05a0c30339f456032c4fe7ad662f99e8 100644
--- a/test/porousmediumflow/2pncmin/implicit/dissolutionspatialparams.hh
+++ b/test/porousmediumflow/2pncmin/implicit/dissolutionspatialparams.hh
@@ -16,6 +16,13 @@
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
+/*!
+ * \file
+ *
+ * \brief Definition of the spatial parameters for the DissolutionProblem
+ *
+ */
+
#ifndef DUMUX_INJECTION_SPATIAL_PARAMETERS_HH
#define DUMUX_INJECTION_SPATIAL_PARAMETERS_HH
diff --git a/test/porousmediumflow/co2/implicit/heterogeneousco2tables.hh b/test/porousmediumflow/co2/implicit/heterogeneousco2tables.hh
index be7a970c39a7a9b205d68bce11ab664e9205e862..d41457974e2d7dbb86d73d201b99a90c869170db 100644
--- a/test/porousmediumflow/co2/implicit/heterogeneousco2tables.hh
+++ b/test/porousmediumflow/co2/implicit/heterogeneousco2tables.hh
@@ -32,6 +32,9 @@ namespace Dumux
{
namespace HeterogeneousCO2Tables
{
+/*!
+* \brief Class providing the tabulated values of CO2 for density and enthalpy
+*/
// the real work is done by some external program which provides
// ready-to-use tables.
#include "co2values.inc"
diff --git a/test/porousmediumflow/mpnc/implicit/plotoverline2d.hh b/test/porousmediumflow/mpnc/implicit/plotoverline2d.hh
index 6606bf0163bd34cd85dd65fa9d59d7a05162a11c..55007b0fd49d188b3f6a376ce6ab8be34ecb4bcc 100644
--- a/test/porousmediumflow/mpnc/implicit/plotoverline2d.hh
+++ b/test/porousmediumflow/mpnc/implicit/plotoverline2d.hh
@@ -55,7 +55,12 @@ namespace Properties
NEW_PROP_TAG(AwnSurface);
NEW_PROP_TAG(AwnSurfaceParams);
}
-
+/*!
+ * \brief Plot variables over a line specified by two arguments.
+ * These output files are meant for visualization with another
+ * program (matlab, gnuplot...)
+ *
+ */
template<class TypeTag>
class PlotOverLine2D
{