diff --git a/doc/doxygen/DoxygenDumuxLayout.xml b/doc/doxygen/DoxygenDumuxLayout.xml
index 3cfe34c877d9e8546d0bb6917fc5d309eb2dbb60..e9d42835a406e55851c77235a7c7022907aacfd5 100644
--- a/doc/doxygen/DoxygenDumuxLayout.xml
+++ b/doc/doxygen/DoxygenDumuxLayout.xml
@@ -131,7 +131,7 @@
<variables title=""/>
</memberdef>
<includegraph visible="yes"/>
- <includedbygraph visible="yes"/>
+ <includedbygraph visible="no"/>
<authorsection/>
</file>
diff --git a/doc/doxygen/Doxylocal b/doc/doxygen/Doxylocal
index 3dfd4bec026c05ab508b8b2f748c859b3f2428ca..7c2abc2116908d639910132f928d1620c1858b5f 100644
--- a/doc/doxygen/Doxylocal
+++ b/doc/doxygen/Doxylocal
@@ -14,8 +14,8 @@ INPUT += @srcdir@/mainpage.txt \
@srcdir@/modules.txt \
@top_srcdir@/dumux \
@top_srcdir@/test \
- @srcdir@/extradoc/parameterlist.txt \
- @srcdir@/extradoc/featurelist.txt
+ # @srcdir@/extradoc/parameterlist.txt \ # we currently do not have a parameter list. Should be back for 3.1
+ # @srcdir@/extradoc/featurelist.txt # we currently do not have a feature list. Should be back for 3.1
EXAMPLE_PATH += @srcdir@/extradoc
diff --git a/doc/doxygen/customdoxygendumux.css b/doc/doxygen/customdoxygendumux.css
index df09ae1acf454c85e2d3b535801af27e11559061..ad8a591e2929be995fb0689ff12d8098e583e75a 100644
--- a/doc/doxygen/customdoxygendumux.css
+++ b/doc/doxygen/customdoxygendumux.css
@@ -2,6 +2,7 @@
body, table, div, p, dl {
font: 400 14px/22px Roboto,sans-serif;
+ min-width: 500px
}
p.reference, p.definition {
diff --git a/doc/doxygen/modules.txt b/doc/doxygen/modules.txt
index eedaf67e9ab17dbbb5a06789b136a1fbf6390d5f..151586de80ec7b7ddcf29c770ae04b751d706aec 100644
--- a/doc/doxygen/modules.txt
+++ b/doc/doxygen/modules.txt
@@ -375,7 +375,7 @@
*/
/* ***************** Flux ******************/
/*!
- * \defgroup Flux
+ * \defgroup Flux Flux
* \brief All flux related things available in DuMu<sup>x</sup>
*/
/* ***************** Material ******************/
diff --git a/doc/doxygen/sanitizelinks.sh b/doc/doxygen/sanitizelinks.sh
index 3c07e38642e5d47dcfa12633fecafd0990b9284b..76a4079b17e28991a5845e49c5cb76f57ee32790 100755
--- a/doc/doxygen/sanitizelinks.sh
+++ b/doc/doxygen/sanitizelinks.sh
@@ -2,3 +2,6 @@
if [ -e html/modules.html ]; then
sed -i 's/\(init_search();\)/\1 toggleLevel(1);/' html/modules.html
fi
+if [ -e html/modules.HTML ]; then
+ sed -i 's/\(init_search();\)/\1 toggleLevel(1);/' html/modules.HTML
+fi
diff --git a/doc/handbook/dumux-handbook.bib b/doc/handbook/dumux-handbook.bib
index 4e61894b70634f753934f53935d74bc45eec32a1..4ea2fe68427f72273c3fd379acb35dd5807b71fd 100644
--- a/doc/handbook/dumux-handbook.bib
+++ b/doc/handbook/dumux-handbook.bib
@@ -464,6 +464,29 @@
url={https://dx.doi.org/10.1021/jp021943g}
}
+@article{witherspoon1965,
+author = {Witherspoon, P. A. and Saraf, D. N.},
+title = {{Diffusion of Methane, Ethane, Propane, and n-Butane in Water from 25 to 43°}},
+journal = {The Journal of Physical Chemistry},
+volume = {69},
+number = {11},
+pages = {3752--3755},
+year = {1965},
+doi = {10.1021/j100895a017},
+url = {https://doi.org/10.1021/j100895a017},
+}
+
+@article{han2003,
+ title={{Description of fluid flow around a wellbore with stress-dependent porosity and permeability}},
+ author={Han, Gang and Dusseault, Maurice B},
+ journal={Journal of Petroleum science and engineering},
+ volume={40},
+ number={1-2},
+ pages={1--16},
+ year={2003},
+ publisher={Elsevier}
+}
+
@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
@@ -1715,6 +1738,19 @@ url={http://dx.doi.org/10.1007/s11242-015-0599-1}
url = {https://doi.org/10.2514/1.36541}
}
+@Article{launder1974a,
+author = {B.E. Launder and B.I. Sharma},
+title = {{Application of the energy-dissipation model of turbulence to the calculation of flow near a spinning disc}},
+journal = {Letters in Heat and Mass Transfer},
+volume = {1},
+number = {2},
+pages = {131 -- 137},
+year = {1974},
+issn = {0094--4548},
+doi = {https://doi.org/10.1016/0094-4548(74)90150-7},
+url = {http://www.sciencedirect.com/science/article/pii/0094454874901507},
+}
+
@Book{Versteeg2009a,
title = {{An Introduction to Computational Fluid Dynamics}},
publisher = {Pearson Education},
diff --git a/dumux/discretization/cellcentered/elementsolution.hh b/dumux/discretization/cellcentered/elementsolution.hh
index 47dc7b7e026da179ceb486f56e5bb09233e1d410..892ffe0c818009ba12356836fbfb9365a8734212 100644
--- a/dumux/discretization/cellcentered/elementsolution.hh
+++ b/dumux/discretization/cellcentered/elementsolution.hh
@@ -18,7 +18,7 @@
*****************************************************************************/
/*!
* \file
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief The local element solution class for cell-centered methods
*/
#ifndef DUMUX_CC_ELEMENT_SOLUTION_HH
@@ -32,7 +32,7 @@
namespace Dumux {
/*!
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief The element solution vector
*/
template<class FVElementGeometry, class PV>
@@ -106,7 +106,7 @@ private:
};
/*!
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief Make an element solution for cell-centered schemes
*/
template<class Element, class SolutionVector, class FVGridGeometry>
@@ -122,7 +122,7 @@ auto elementSolution(const Element& element, const SolutionVector& sol, const FV
}
/*!
-* \ingroup CCDiscretization
+* \ingroup Discretization
* \brief Make an element solution for cell-centered schemes
*/
template<class Element, class ElementVolumeVariables, class FVElementGeometry>
@@ -136,7 +136,7 @@ auto elementSolution(const Element& element, const ElementVolumeVariables& elemV
}
/*!
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief Make an element solution for cell-centered schemes
* \note This is e.g. used to contruct an element solution at Dirichlet boundaries
*/
@@ -150,7 +150,7 @@ auto elementSolution(PrimaryVariables&& priVars)
}
/*!
- * \ingroup CCDiscretization
+ * \ingroup Discretization
* \brief Make an element solution for cell-centered schemes
* \note This is e.g. used to contruct an element solution at Dirichlet boundaries
*/
diff --git a/dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh b/dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh
index 483bcc0eccc25f7b4644a6a6c8ff8b672b1297cc..f1fe3f285220bd08555941e4f1e88ea44a437329 100644
--- a/dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh
+++ b/dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh
@@ -73,6 +73,7 @@ namespace CCMpfa {
* \param volVars The container where the volume variables are stored
* \param volVarIndices The container where the volume variable indices are stored
* \param problem The problem containing the Dirichlet boundary conditions
+ * \param element The element to which the finite volume geometry is bound
* \param fvGeometry The element finite volume geometry
* \param nodalIndexSet The dual grid index set around a node
*/
diff --git a/dumux/discretization/staggered/elementsolution.hh b/dumux/discretization/staggered/elementsolution.hh
index 846c94adcd15c4cd1f69512b9e568223a1b2aeb4..140c38b24ebd734c6af2424c2b2029e838c04403 100644
--- a/dumux/discretization/staggered/elementsolution.hh
+++ b/dumux/discretization/staggered/elementsolution.hh
@@ -18,7 +18,7 @@
*****************************************************************************/
/*!
* \file
- * \ingroup StaggeredDiscretization
+ * \ingroup Discretization
* \brief The local element solution class for staggered methods
*/
#ifndef DUMUX_STAGGERED_ELEMENT_SOLUTION_HH
@@ -31,7 +31,7 @@
namespace Dumux {
/*!
- * \ingroup StaggeredDiscretization
+ * \ingroup Discretization
* \brief Helper function to create a PrimaryVariables object from CellCenterPrimaryVariables
* \tparam PrimaryVariables The type of the desired primary variables object
* \tparam CellCenterPrimaryVariables The type of the cell center (input) primary variables object
@@ -54,7 +54,7 @@ template<class PrimaryVariables>
using StaggeredElementSolution = Dune::BlockVector<PrimaryVariables>;
/*!
- * \ingroup StaggeredDiscretization
+ * \ingroup Discretization
* \brief Make an element solution for staggered schemes
* \note This is e.g. used to construct an element solution at Dirichlet boundaries
*/
@@ -67,7 +67,7 @@ auto elementSolution(PrimaryVariables&& priVars)
}
/*!
- * \ingroup StaggeredDiscretization
+ * \ingroup Discretization
* \brief Helper function to create an elementSolution from cell center primary variables
* \tparam PrimaryVariables The type of the desired primary variables object
* \tparam CellCenterPrimaryVariables The type of the cell center (input) primary variables object
diff --git a/dumux/freeflow/navierstokes/iofields.hh b/dumux/freeflow/navierstokes/iofields.hh
index b38b8f5a07b566ad3faf9dfd0ffb3f7c0d1b0d38..e50a4199694e2f1d835edb82b0dbcb1926138bdf 100644
--- a/dumux/freeflow/navierstokes/iofields.hh
+++ b/dumux/freeflow/navierstokes/iofields.hh
@@ -37,7 +37,6 @@ namespace Dumux
{
/*!
- * \ingroup InputOutput
* \ingroup NavierStokesModel
* \brief helper function to determine the names of cell-centered primary variables of a model with staggered grid discretization
* \note use this as input for the load solution function
@@ -58,7 +57,6 @@ std::function<std::string(int,int)> createCellCenterPVNameFunction(const std::st
}
/*!
- * \ingroup InputOutput
* \ingroup NavierStokesModel
* \brief helper function to determine the names of primary variables on the cell faces of a model with staggered grid discretization
* \note use this as input for the load solution function
diff --git a/dumux/freeflow/rans/twoeq/kepsilon/model.hh b/dumux/freeflow/rans/twoeq/kepsilon/model.hh
index bd94bd8329dc24f906cda1d91f20355d362d489d..2eabe5fed4cd7e8fbcff4b4b9e9a916c4f14b57b 100644
--- a/dumux/freeflow/rans/twoeq/kepsilon/model.hh
+++ b/dumux/freeflow/rans/twoeq/kepsilon/model.hh
@@ -26,7 +26,8 @@
*
* The k-epsilon models calculate the eddy viscosity with two additional PDEs,
* one for the turbulent kinetic energy (k) and for the dissipation (\f$ \varepsilon \f$).
- * The model uses the one proposed by Launder and Sharma \cite{Launder1994a}.
+ * The model uses the one proposed by Launder and Sharma \cite launder1974a
+ * https://doi.org/10.1016/0094-4548(74)90150-7.
*
* The turbulent kinetic energy balance is:
* \f[
diff --git a/dumux/linear/seqsolverbackend.hh b/dumux/linear/seqsolverbackend.hh
index fa408d4ff054efa5fd6cf3e31feee0bacb8d23a7..70bdd880c3ed022d2a007d72de7a97fe57d13c35 100644
--- a/dumux/linear/seqsolverbackend.hh
+++ b/dumux/linear/seqsolverbackend.hh
@@ -831,7 +831,7 @@ private:
*/
// \{
-/*
+/*!
* A simple ilu0 block diagonal preconditioner
*/
template<class M, class X, class Y, int blockLevel = 2>
@@ -875,17 +875,8 @@ public:
static_assert(blockLevel >= 2, "Only makes sense for MultiTypeBlockMatrix!");
}
- /*!
- \brief Prepare the preconditioner.
-
- \copydoc Dune::Preconditioner::pre(X&,Y&)
- */
void pre (X& v, Y& d) final {}
- /*!
- * \brief Apply the preconditoner.
- * \copydoc Dune::Preconditioner::apply(X&,const Y&)
- */
void apply (X& v, const Y& d) final
{
using namespace Dune::Hybrid;
@@ -895,10 +886,6 @@ public:
});
}
- /*!
- * \brief Clean up.
- * \copydoc Dune::Preconditioner::post(X&)
- */
void post (X&) final {}
//! Category of the preconditioner (see SolverCategory::Category)
@@ -1006,9 +993,20 @@ public:
}
/*!
- \brief Prepare the preconditioner.
-
- \copydoc Dune::Preconditioner::pre(X&,Y&)
+ * \brief Prepare the preconditioner.
+ *
+ * A solver solves a linear operator equation A(v)=d by applying
+ * one or several steps of the preconditioner. The method pre()
+ * is called before the first apply operation.
+ * d and v are right hand side and solution vector of the linear
+ * system respectively. It may. e.g., scale the system, allocate memory or
+ * compute a (I)LU decomposition.
+ * Note: The ILU decomposition could also be computed in the constructor
+ * or with a separate method of the derived method if several
+ * linear systems with the same matrix are to be solved.
+ *
+ * \param v The left hand side of the equation.
+ * \param d The right hand side of the equation.
*/
void pre (X& v, Y& d) final
{
@@ -1020,8 +1018,15 @@ public:
}
/*!
- * \brief Apply the preconditoner.
- * \copydoc Dune::Preconditioner::apply(X&,const Y&)
+ * \brief Apply one step of the preconditioner to the system A(v)=d.
+ *
+ * On entry v=0 and d=b-A(x) (although this might not be
+ * computed in that way. On exit v contains the update, i.e
+ * one step computes \f$ v = M^{-1} d \f$ where \f$ M \f$ is the
+ * approximate inverse of the operator \f$ A \f$ characterizing
+ * the preconditioner.
+ * \param v The update to be computed
+ * \param d The current defect.
*/
void apply (X& v, const Y& d) final
{
@@ -1034,7 +1039,12 @@ public:
/*!
* \brief Clean up.
- * \copydoc Dune::Preconditioner::post(X&)
+ *
+ * This method is called after the last apply call for the
+ * linear system to be solved. Memory may be deallocated safely
+ * here. v is the solution of the linear equation.
+ *
+ * \param v The right hand side of the equation.
*/
void post (X& v) final
{
diff --git a/dumux/material/binarycoefficients/h2o_ch4.hh b/dumux/material/binarycoefficients/h2o_ch4.hh
index c90f35ad8a6d5ac833fba5fd2814b97c45f50683..c7c5d63803df2cc26133d13ca21e68d6bcef3c0d 100644
--- a/dumux/material/binarycoefficients/h2o_ch4.hh
+++ b/dumux/material/binarycoefficients/h2o_ch4.hh
@@ -96,8 +96,8 @@ public:
* linear dependency on temperature. We thus simply scale the
* experimentally obtained diffusion coefficient of Ferrell and
* Himmelblau by the temperature.<br>
- * This function use an interpolation of the data by \cite{Whitherspoon1965}
- * \url{http://dx.doi.org/10.1021/j100895a017}
+ * This function use an interpolation of the data by \cite witherspoon1965
+ * http://dx.doi.org/10.1021/j100895a017
*/
template <class Scalar>
static Scalar liquidDiffCoeff(Scalar temperature, Scalar pressure)
diff --git a/dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh b/dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh
index 049d7b57bafa06fde5adbbb213540ed19a0b328d..0a75f5149e4ca5477601b6921f6c5e6ddf93a185 100644
--- a/dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh
+++ b/dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh
@@ -61,7 +61,7 @@ public:
* \param values Container for the return values
* \param params Array of Parameters
* \param state The fluid state
- * \param wPhaseIdx the phase index of the wetting phase
+ * \param wPhaseIdx The phase index of the wetting phase
*/
template <class ContainerT, class FluidState>
static void capillaryPressures(ContainerT &values,
@@ -82,6 +82,7 @@ public:
* \param values Container for the return values
* \param params Array of Parameters
* \param state The fluid state
+ * \param wPhaseIdx the phase index of the wetting phase
*/
template <class ContainerT, class FluidState>
static void relativePermeabilities(ContainerT &values,
diff --git a/dumux/material/fluidmatrixinteractions/porositydeformation.hh b/dumux/material/fluidmatrixinteractions/porositydeformation.hh
index c40c61d3dec854e953041b0f9eefde1cff1be16a..3e0001a0721217739881a7f3b5779ca16a36f8d5 100644
--- a/dumux/material/fluidmatrixinteractions/porositydeformation.hh
+++ b/dumux/material/fluidmatrixinteractions/porositydeformation.hh
@@ -44,7 +44,6 @@ public:
* the displacements in the different grid directions are stored
* in the first entries of the primary variable vector.
*
- *
* \param fvGridGeometry The finite volume grid geometry
* \param element The finite element
* \param elemSol The element solution
@@ -53,10 +52,10 @@ public:
* \param minPoro A minimum porosity value
* \param maxPoro A maximum porosity value
*
- * \note Han and Dusseault (2003, doi 10.1016/S0920-4105(03)00047-0)
- * provide a derivation for \f$\text{d} \phi = -(1 - \phi ) \text{d} \epsilon_v\f$.
- * Here, \f$\epsilon_v\f$ is equal to \f$text{div} \mathbf{u}\f$.
- * By using an initial porosity \f$\phi_0\f$ and assuming \epsilon_{v, 0} = 0,
+ * \note \cite han2003 ( https://doi.org/10.1016/S0920-4105(03)00047-0 )
+ * provide a derivation for \f$\text{d} \phi = -(1 - \phi ) \text{d} \epsilon_v \f$.
+ * Here, \f$\epsilon_v\f$ is equal to \f$\text{div} \mathbf{u}\f$.
+ * By using an initial porosity \f$\phi_0\f$ and assuming \f$ \epsilon_{v, 0} = 0 \f$,
* one obtains \f$\phi = \frac{\phi_0 - \text{div} \mathbf{u}}{1 - \text{div} \mathbf{u}}\f$,
* which is the formulation for the rock mechanics sign convention. Here we are
* using the continuum mechanics sign convention, thus, the final formula reads:
diff --git a/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh b/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
index 09f7a680db0a3fd983db9294ad7039d254c141c2..0272454a15e2724cc649ec42f70d148db087ae44 100644
--- a/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
+++ b/dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
@@ -91,7 +91,6 @@ public:
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,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
@@ -120,7 +119,6 @@ public:
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx3, int idx6);
-
/*!
* \brief Constructs a FvMpfaL3dTransmissibilityCalculator object
* \param problem A problem class object
diff --git a/dumux/porousmediumflow/2p2c/sequential/fvpressure.hh b/dumux/porousmediumflow/2p2c/sequential/fvpressure.hh
index e8766b1a25aa6a4be03ad505b8ace5935340f6a4..7d9bf004a3390e86fe74683cc3d87ba6c5025489 100644
--- a/dumux/porousmediumflow/2p2c/sequential/fvpressure.hh
+++ b/dumux/porousmediumflow/2p2c/sequential/fvpressure.hh
@@ -33,21 +33,22 @@
#include <dumux/io/vtkmultiwriter.hh>
#include <dumux/porousmediumflow/2p2c/sequential/properties.hh>
-/**
- * @file
- * @brief Finite Volume 2p2c Pressure Model
+/*!
+ * \file
+ * \brief Finite Volume 2p2c Pressure Model
*/
-
namespace Dumux
{
-//! The finite volume model for the solution of the compositional pressure equation
-/*! \ingroup multiphase
- * Provides a Finite Volume implementation for the pressure equation of a compressible
- * system with two components. An IMPES-like method is used for the sequential
- * solution of the problem. Diffusion is neglected, capillarity can be regarded.
- * Isothermal conditions and local thermodynamic
- * equilibrium are assumed. Gravity is included.
- * \f[
+/*!
+ * \ingroup multiphase
+ * \brief The finite volume model for the solution of the compositional pressure equation
+ *
+ * Provides a Finite Volume implementation for the pressure equation of a compressible
+ * system with two components. An IMPES-like method is used for the sequential
+ * solution of the problem. Diffusion is neglected, capillarity can be regarded.
+ * Isothermal conditions and local thermodynamic
+ * equilibrium are assumed. Gravity is included.
+ * \f[
c_{total}\frac{\partial p}{\partial t} + \sum_{\kappa} \frac{\partial v_{total}}{\partial C^{\kappa}}
\nabla \cdot \left( \sum_{\alpha} X^{\kappa}_{\alpha} \varrho_{\alpha} \bf{v}_{\alpha}\right)
= \sum_{\kappa} \frac{\partial v_{total}}{\partial C^{\kappa}} q^{\kappa},
@@ -66,7 +67,6 @@ namespace Dumux
* whereas this class provides the actual entries for the matrix and RHS vector.
* The partial derivatives of the actual fluid volume \f$ v_{total} \f$ are gained by using a secant method.
*
- * \tparam TypeTag The Type Tag
*/
template<class TypeTag> class FVPressure2P2C
: public FVPressureCompositional<TypeTag>
@@ -104,11 +104,13 @@ template<class TypeTag> class FVPressure2P2C
wCompIdx = Indices::wPhaseIdx, nCompIdx = Indices::nPhaseIdx,
contiWEqIdx = Indices::contiWEqIdx, contiNEqIdx = Indices::contiNEqIdx
};
- //! Indices of matrix and rhs entries
- /** During the assembling of the global system of equations get-functions are called
+
+ /*!
+ * \brief Indices of matrix and rhs entries
+ * During the assembling of the global system of equations get-functions are called
* (getSource(), getFlux(), etc.), which return global matrix or right hand side entries
* in a vector. These can be accessed using following indices:
- */
+ */
enum
{
rhs = 1,//!<index for the right hand side entry
@@ -143,20 +145,20 @@ protected:
}
public:
- void getSource(EntryType&, const Element&, const CellData&, const bool);
- void getStorage(EntryType&, const Element&, const CellData&, const bool);
+ void getSource(EntryType& sourceEntry, const Element& elementI, const CellData& cellDataI, const bool first);
+
+ void getStorage(EntryType& storageEntry, const Element& elementI, const CellData& cellDataI, const bool first);
- void getFlux(EntryType&, const Intersection&, const CellData&, const bool);
+ void getFlux(EntryType& entries, const Intersection& intersection, const CellData& cellDataI, const bool first);
- void getFluxOnBoundary(EntryType&,
- const Intersection&, const CellData&, const bool);
+ void getFluxOnBoundary(EntryType& entries, const Intersection& intersection, const CellData& cellDataI, const bool first);
//updates secondary variables for one cell and stores in the variables object
void updateMaterialLawsInElement(const Element& elementI, bool postTimeStep);
- //! Constructs a FVPressure2P2C object
- /**
+ /*!
+ * \brief Constructs a FVPressure2P2C object
* \param problem a problem class object
*/
FVPressure2P2C(Problem& problem) : FVPressureCompositional<TypeTag>(problem),
@@ -196,9 +198,10 @@ private:
{ return *static_cast<const Implementation *>(this);}
};
-
-//! Assembles the source term
-/** for first == true, a source is implemented as in FVPressure2P.
+/*!
+ * \brief Assembles the source term
+ *
+ * for first == true, a source is implemented as in FVPressure2P.
* for first == false, the source is translated into a volumentric source term:
* \f[ V_i \sum_{\kappa} \frac{\partial v_{t}}{\partial C^{\kappa}} q^{\kappa}_i \f].
* \param sourceEntry The Matrix and RHS entries
@@ -241,8 +244,10 @@ void FVPressure2P2C<TypeTag>::getSource(Dune::FieldVector<Scalar, 2>& sourceEntr
return;
}
-//! Assembles the storage term
-/** for first == true, there is no storage contribution.
+/*!
+ * \brief Assembles the storage term
+ *
+ * for first == true, there is no storage contribution.
* for first == false, the storage term comprises the compressibility (due to a change in
* pressure from last timestep):
* \f[ V_i c_{t,i} \frac{p^t_i - p^{t-\Delta t}_i}{\Delta t} \f]
@@ -325,9 +330,10 @@ void FVPressure2P2C<TypeTag>::getStorage(Dune::FieldVector<Scalar, 2>& storageEn
return;
}
-
-//! Get flux at an interface between two cells
-/*! for first == true, the flux is calculated in traditional fractional-flow forn as in FVPressure2P.
+/*!
+ * \brief Get flux at an interface between two cells
+ *
+ * for first == true, the flux is calculated in traditional fractional-flow forn as in FVPressure2P.
* for first == false, the flux thorugh \f$ \gamma \f$ is calculated via a volume balance formulation
* \f[ - A_{\gamma} \mathbf{n}^T_{\gamma} \mathbf{K} \sum_{\alpha} \varrho_{\alpha} \lambda_{\alpha}
\mathbf{d}_{ij} \left( \frac{p_{\alpha,j}^t - p^{t}_{\alpha,i}}{\Delta x} + \varrho_{\alpha} \mathbf{g}^T \mathbf{d}_{ij} \right)
@@ -617,8 +623,10 @@ void FVPressure2P2C<TypeTag>::getFlux(Dune::FieldVector<Scalar, 2>& entries,
} // end !first
}
-//! Get flux on Boundary
-/** for first == true, the flux is calculated in traditional fractional-flow forn as in FVPressure2P.
+/*!
+ * \brief Get flux on Boundary
+ *
+ * for first == true, the flux is calculated in traditional fractional-flow forn as in FVPressure2P.
* for first == false, the flux thorugh \f$ \gamma \f$ is calculated via a volume balance formulation
* \f[ - A_{\gamma} \mathbf{n}^T_{\gamma} \mathbf{K} \sum_{\alpha} \varrho_{\alpha} \lambda_{\alpha} \mathbf{d}_{ij}
\left( \frac{p_{\alpha,j}^t - p^{t}_{\alpha,i}}{\Delta x} + \varrho_{\alpha} \mathbf{g}^T \mathbf{d}_{ij} \right)
@@ -882,8 +890,10 @@ void FVPressure2P2C<TypeTag>::getFluxOnBoundary(Dune::FieldVector<Scalar, 2>& en
return;
}
-//! updates secondary variables of one cell
-/*! For each element, the secondary variables are updated according to the
+/*!
+ * \brief Updates secondary variables of one cell
+ *
+ * For each element, the secondary variables are updated according to the
* primary variables. In case the method is called after the Transport,
* i.e. at the end / post time step, CellData2p2c.reset() resets the volume
* derivatives for the next time step.
diff --git a/dumux/porousmediumflow/2p2c/sequential/fvpressuremultiphysics.hh b/dumux/porousmediumflow/2p2c/sequential/fvpressuremultiphysics.hh
index 71c7e401e71edd69cba1add277ac68018aefc1f5..272a0323b0514c7fffdb7be91e2d6c4279912da1 100644
--- a/dumux/porousmediumflow/2p2c/sequential/fvpressuremultiphysics.hh
+++ b/dumux/porousmediumflow/2p2c/sequential/fvpressuremultiphysics.hh
@@ -120,14 +120,16 @@ public:
//function which assembles the system of equations to be solved
void assemble(bool first);
- void get1pSource(EntryType&, const Element&, const CellData&);
+ void get1pSource(EntryType& sourceEntry, const Element& elementI, const CellData& cellDataI);
- void get1pStorage(EntryType&, const Element&, CellData&);
+ void get1pStorage(EntryType& storageEntry, const Element& elementI, CellData& cellDataI);
- void get1pFlux(EntryType&, const Intersection&, const CellData&);
+ void get1pFlux(EntryType& entries, const Intersection& intersection,
+ const CellData& cellDataI);
- void get1pFluxOnBoundary(EntryType&,
- const Intersection&, const CellData&);
+ void get1pFluxOnBoundary(EntryType& entries,
+ const Intersection& intersection,
+ const CellData& cellDataI);
//initialize multi-physics-specific pressure model constituents
void initialize(bool solveTwice = false)
@@ -205,8 +207,8 @@ public:
return;
}
- //! Constructs a FVPressure2P2CPC object
- /**
+ /*!
+ * \brief Constructs a FVPressure2P2CPC object
* \param problem a problem class object
*/
FVPressure2P2CMultiPhysics(Problem& problem) : FVPressure2P2C<TypeTag>(problem),
@@ -226,8 +228,8 @@ protected:
static constexpr int pressureType = GET_PROP_VALUE(TypeTag, PressureFormulation);
Dune::Timer timer_; //!< A timer for the time spent on the multiphysics framework.
- //! Indices of matrix and rhs entries
- /**
+ /*!
+ * \brief Indices of matrix and rhs entries
* During the assembling of the global system of equations get-functions are called (getSource(),
* getFlux(), etc.), which return global matrix or right hand side entries in a vector.
* These can be accessed using following indices:
@@ -240,8 +242,10 @@ protected:
};
};
-//! function which assembles the system of equations to be solved
-/*! for first == true, this function assembles the matrix and right hand side for
+/*!
+ * \brief function which assembles the system of equations to be solved
+ *
+ * for first == true, this function assembles the matrix and right hand side for
* the solution of the pressure field in the same way as in the class FVPressure2P.
* for first == false, the approach is changed to \f[-\frac{\partial V}{\partial p}
* \frac{\partial p}{\partial t}+\sum_{\kappa}\frac{\partial V}{\partial m^{\kappa}}\nabla\cdot
@@ -346,8 +350,10 @@ void FVPressure2P2CMultiPhysics<TypeTag>::assemble(bool first)
return;
}
-//! Assembles the source term
-/** The source is translated into a volumentric source term:
+/*!
+ * \brief Assembles the source term
+ *
+ * The source is translated into a volumentric source term:
* \f[ V_i \sum_{\kappa} \frac{1}{\varrho} q^{\kappa}_i \; , \f]
* because under singlephase conditions
* \f[ \frac{\partial v_{t}}{\partial C^{\kappa}} \approx \frac{1}{\varrho} \f].
@@ -375,8 +381,10 @@ void FVPressure2P2CMultiPhysics<TypeTag>::get1pSource(Dune::FieldVector<Scalar,
return;
}
-//! Assembles the storage term for a 1p cell in a multiphysics framework
-/** The storage term comprises the (single-phase) compressibility (due to a change in
+/*!
+ * \brief Assembles the storage term for a 1p cell in a multiphysics framework
+ *
+ * The storage term comprises the (single-phase) compressibility (due to a change in
* pressure from last timestep):
* \f[ V_i c_{i} \frac{p^t_i - p^{t-\Delta t}_i}{\Delta t} \f]
* and the damped error introduced by the incorrect transport of the last timestep:
@@ -761,15 +769,16 @@ void FVPressure2P2CMultiPhysics<TypeTag>::get1pFluxOnBoundary(Dune::FieldVector<
}
-//! constitutive functions are updated once if new concentrations are calculated and stored in the variables container
/*!
+ * \brief constitutive functions are updated once if new concentrations are calculated and stored in the variables container
+ *
* In contrast to the standard sequential 2p2c model ( FVPressure2P2C<TypeTag>::updateMaterialLaws() ),
* this method also holds routines to adapt the subdomain. The subdomain indicates weather we are in 1p domain (value = 1)
* or in the two phase subdomain (value = 2).
* Note that the type of flash, i.e. the type of FluidState (FS), present in each cell does not have to
* coincide with the subdomain. If a cell will be simple and was complex, a complex FS is available, so next time step
* will use this complex FS, but updateMaterialLaw afterwards will finally transform that to simple FS.
- * \param postTimeStep Flag indicating method is called from Problem::postTimeStep()
+ * \param postTimeStep Flag indicating method is called from Problem::postTimeStep()
*/
template<class TypeTag>
void FVPressure2P2CMultiPhysics<TypeTag>::updateMaterialLaws(bool postTimeStep)
@@ -887,8 +896,10 @@ void FVPressure2P2CMultiPhysics<TypeTag>::updateMaterialLaws(bool postTimeStep)
return;
}
-//! updates secondary variables of one single phase cell
-/*! For each element, the secondary variables are updated according to the
+/*!
+ * \brief updates secondary variables of one single phase cell
+ *
+ * For each element, the secondary variables are updated according to the
* primary variables. Only a simple flash calulation has to be carried out,
* as phase distribution is already known: single-phase.
* \param elementI The element
diff --git a/dumux/porousmediumflow/2p2c/sequential/fvtransport.hh b/dumux/porousmediumflow/2p2c/sequential/fvtransport.hh
index c8186435949c486033c1e3c94becbb32c1891b8c..a5742763e84d2ad54d0ffb924f2b6a97c6f98f2c 100644
--- a/dumux/porousmediumflow/2p2c/sequential/fvtransport.hh
+++ b/dumux/porousmediumflow/2p2c/sequential/fvtransport.hh
@@ -30,15 +30,16 @@
#include <dumux/common/math.hh>
#include <dumux/linear/vectorexchange.hh>
-/**
- * @file
- * @brief Finite Volume discretization of the component transport equation
+/*!
+ * \file
+ * \brief Finite Volume discretization of the component transport equation
*/
-
namespace Dumux
{
-//! Compositional transport step in a Finite Volume discretization
-/*! \ingroup multiphase
+/*!
+ * \ingroup Sequential
+ * \brief Compositional transport step in a Finite Volume discretization
+ *
* The finite volume model for the solution of the transport equation for compositional
* two-phase flow.
* \f[
@@ -52,7 +53,6 @@ namespace Dumux
* Corresponding functions (<tt>getFlux()</tt> and <tt>getFluxOnBoundary()</tt>) are provided,
* internal sources are directly treated.
*
- *
* \tparam TypeTag The Type Tag
*/
template<class TypeTag>
@@ -134,17 +134,21 @@ public:
void updateConcentrations(TransportSolutionType& updateVector, Scalar dt);
// Function which calculates the flux update
- void getFlux(ComponentVector&, EntryType&,
- const Intersection&, CellData&);
+ void getFlux(ComponentVector& fluxEntries, EntryType& timestepFlux,
+ const Intersection& intersection, CellData& cellDataI);
// Function which calculates the boundary flux update
- void getFluxOnBoundary(ComponentVector&, EntryType&,
- const Intersection&, const CellData&);
+ void getFluxOnBoundary(ComponentVector& fluxEntries, EntryType& timestepFlux,
+ const Intersection& intersection, const CellData& cellDataI);
+
+ void evalBoundary(GlobalPosition globalPosFace,
+ const Intersection& intersection,
+ FluidState& BCfluidState,
+ PhaseVector& pressBound);
- void evalBoundary(GlobalPosition,const Intersection&,FluidState &, PhaseVector &);
- //! Set the initial values before the first pressure equation
/*!
+ * \brief Set the initial values before the first pressure equation
* This method is called before first pressure equation is solved from IMPET.
*/
void initialize()
@@ -159,8 +163,10 @@ public:
}
}
- //! \brief Write transport variables into the output files
- /* \param writer applied VTK-writer */
+ /*!
+ * \brief Write transport variables into the output files
+ * \param writer applied VTK-writer
+ */
template<class MultiWriter>
void addOutputVtkFields(MultiWriter &writer)
{
@@ -197,10 +203,11 @@ public:
/*! \name Access functions for protected variables */
//@{
- //! Return the vector of the transported quantity
- /*! For an immiscible IMPES scheme, this is the saturation. For compositional simulations, however,
- * the total concentration of all components is transported.
- * @param transportedQuantity Vector of both transported components
+ /*!
+ * \brief Return the vector of the transported quantity
+ * For an immiscible IMPES scheme, this is the saturation. For compositional simulations, however,
+ * the total concentration of all components is transported.
+ * \param transportedQuantity Vector of both transported components
*/
void getTransportedQuantity(TransportSolutionType& transportedQuantity)
{
@@ -214,11 +221,12 @@ public:
/*! \name Access functions for protected variables */
//@{
- //! Return the the total concentration stored in the transport vector
- /*! To get real cell values, do not acess this method, but rather
+ /*!
+ * \brief Return the the total concentration stored in the transport vector
+ * To get real cell values, do not acess this method, but rather
* call the respective function in the cell data object.
- * @param compIdx The index of the component
- * @param eIdxGlobal The global index of the current cell.
+ * \param compIdx The index of the component
+ * \param eIdxGlobal The global index of the current cell.
*/
Scalar& totalConcentration(int compIdx, int eIdxGlobal)
{
@@ -229,9 +237,10 @@ public:
{}
- //! Function to control the abort of the transport-sub-time-stepping depending on a physical parameter range
/*!
- * @param entry Cell entries of the update vector
+ * \brief Function to control the abort of the transport-sub-time-stepping
+ * depending on a physical parameter range
+ * \param entry Cell entries of the update vector
*/
template<class DataEntry>
bool inPhysicalRange(DataEntry& entry)
@@ -254,8 +263,8 @@ public:
}
//@}
- //! Constructs a FVTransport2P2C object
/*!
+ * \brief Constructs a FVTransport2P2C object
* Currently, the compositional transport scheme can not be applied with a global pressure / total velocity
* formulation.
*
@@ -332,8 +341,9 @@ private:
{ return *static_cast<const Implementation *>(this); }
};
-//! \brief Calculate the update vector and determine timestep size
+
/*!
+ * \brief Calculate the update vector and determine timestep size
* This method calculates the update vector \f$ u \f$ of the discretized equation
* \f[
C^{\kappa , new} = C^{\kappa , old} + u,
@@ -345,8 +355,8 @@ private:
* employing a CFL condition.
*
* \param t Current simulation time \f$\mathrm{[s]}\f$
- * \param[out] dt Time step size \f$\mathrm{[s]}\f$
- * \param[out] updateVec Update vector, or update estimate for secants, resp. Here in \f$\mathrm{[kg/m^3]}\f$
+ * \param dt Time step size \f$\mathrm{[s]}\f$
+ * \param updateVec Update vector, or update estimate for secants, resp. Here in \f$\mathrm{[kg/m^3]}\f$
* \param impet Flag that determines if it is a real impet step or an update estimate for volume derivatives
*/
template<class TypeTag>
@@ -499,10 +509,11 @@ void FVTransport2P2C<TypeTag>::update(const Scalar t, Scalar& dt,
Dune::dinfo << " Averageing done for " << averagedFaces_ << " faces. "<< std::endl;
}
}
-/* Updates the transported quantity once an update is calculated.
- * This method updates both, the internal transport solution vector and the entries in the cellData.
- * \param updateVec Update vector, or update estimate for secants, resp. Here in \f$\mathrm{[kg/m^3]}\f$
+/*!
+ * \brief Updates the transported quantity once an update is calculated.
*
+ * This method updates both, the internal transport solution vector and the entries in the cellData.
+ * \param updateVector Update vector, or update estimate for secants, resp. Here in \f$\mathrm{[kg/m^3]}\f$
*/
template<class TypeTag>
void FVTransport2P2C<TypeTag>::updateTransportedQuantity(TransportSolutionType& updateVector)
@@ -513,10 +524,12 @@ void FVTransport2P2C<TypeTag>::updateTransportedQuantity(TransportSolutionType&
updateConcentrations(updateVector, problem().timeManager().timeStepSize());
}
-/* Updates the transported quantity once an update is calculated.
- * This method updates both, the internal transport solution vector and the entries in the cellData.
- * \param updateVec Update vector, or update estimate for secants, resp. Here in \f$\mathrm{[kg/m^3]}\f$
+/*!
+ * \brief Updates the transported quantity once an update is calculated.
*
+ * This method updates both, the internal transport solution vector and the entries in the cellData.
+ * \param updateVector Update vector, or update estimate for secants, resp. Here in \f$\mathrm{[kg/m^3]}\f$
+ * \param dt Time step size \f$\mathrm{[s]}\f$
*/
template<class TypeTag>
void FVTransport2P2C<TypeTag>::updateTransportedQuantity(TransportSolutionType& updateVector, Scalar dt)
@@ -524,10 +537,12 @@ void FVTransport2P2C<TypeTag>::updateTransportedQuantity(TransportSolutionType&
updateConcentrations(updateVector, dt);
}
-/* Updates the concentrations once an update is calculated.
- * This method updates both, the internal transport solution vector and the entries in the cellData.
- * \param updateVec Update vector, or update estimate for secants, resp. Here in \f$\mathrm{[kg/m^3]}\f$
+/*!
+ * \brief Updates the concentrations once an update is calculated.
*
+ * This method updates both, the internal transport solution vector and the entries in the cellData.
+ * \param updateVector Update vector, or update estimate for secants, resp. Here in \f$\mathrm{[kg/m^3]}\f$
+ * \param dt Time step size \f$\mathrm{[s]}\f$
*/
template<class TypeTag>
void FVTransport2P2C<TypeTag>::updateConcentrations(TransportSolutionType& updateVector, Scalar dt)
@@ -544,8 +559,9 @@ void FVTransport2P2C<TypeTag>::updateConcentrations(TransportSolutionType& updat
}
}
-//! Get flux at an interface between two cells
-/** The flux through \f$ \gamma \f$ is calculated according to the underlying pressure field,
+/*!
+ * \brief Get flux at an interface between two cells
+ * The flux through \f$ \gamma \f$ is calculated according to the underlying pressure field,
* calculated by the pressure model.
* \f[ - A_{\gamma} \mathbf{n}^T_{\gamma} \mathbf{K} \sum_{\alpha} \varrho_{\alpha} \lambda_{\alpha}
\mathbf{d}_{ij} \left( \frac{p_{\alpha,j}^t - p^{t}_{\alpha,i}}{\Delta x} + \varrho_{\alpha} \mathbf{g}^T \mathbf{d}_{ij} \right)
@@ -848,8 +864,11 @@ void FVTransport2P2C<TypeTag>::getFlux(ComponentVector& fluxEntries,
return;
}
-//! Get flux on Boundary
-/** The flux through \f$ \gamma \f$ is calculated according to the underlying pressure field,
+
+/*!
+ * \brief Get flux on Boundary
+ *
+ * The flux through \f$ \gamma \f$ is calculated according to the underlying pressure field,
* calculated by the pressure model.
* \f[ - A_{\gamma} \mathbf{n}^T_{\gamma} \mathbf{K} \mathbf{d}_{i-Boundary}
\sum_{\alpha} \varrho_{\alpha} \lambda_{\alpha} \sum_{\kappa} X^{\kappa}_{\alpha}
@@ -939,9 +958,9 @@ void FVTransport2P2C<TypeTag>::getFluxOnBoundary(ComponentVector& fluxEntries,
// read boundary values
this->evalBoundary(globalPosFace,
- intersection,
- BCfluidState,
- pressBound);
+ intersection,
+ BCfluidState,
+ pressBound);
// determine fluid properties at the boundary
Scalar densityWBound = BCfluidState.density(wPhaseIdx);
@@ -1069,8 +1088,10 @@ void FVTransport2P2C<TypeTag>::getFluxOnBoundary(ComponentVector& fluxEntries,
return;
}
-//! evaluate the boundary conditions
+
/*!
+ * \brief Evaluate the boundary conditions
+ *
* As the transport primary variable in this formulation is the total component
* concentration, \f$ C^{\kappa} \f$ it seems natural that the boundary values
* are also total concentrations. However, as for the initial conditions, it is
diff --git a/test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh b/test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh
index 0606c2bf86a7118ea591e52d39b591388962b93a..cb45b31911f25b6c15f67c85e3b1cc1b8a6b8ae5 100644
--- a/test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh
+++ b/test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh
@@ -255,8 +255,6 @@ public:
* potentially solution dependent and requires some quantities that
* are specific to the fully-implicit method.
*
- * \param values The neumann values for the conservation equations in units of
- * \f$ [ \textnormal{unit of conserved quantity} / (m^2 \cdot s )] \f$
* \param element The finite element
* \param fvGeometry The finite-volume geometry
* \param elemVolVars All volume variables for the element
@@ -267,9 +265,9 @@ public:
* E.g. for the mass balance that would the mass flux in \f$ [ kg / (m^2 \cdot s)] \f$.
*/
NumEqVector neumann(const Element& element,
- const FVElementGeometry& fvGeometry,
- const ElementVolumeVariables& elemVolVars,
- const SubControlVolumeFace& scvf) const
+ const FVElementGeometry& fvGeometry,
+ const ElementVolumeVariables& elemVolVars,
+ const SubControlVolumeFace& scvf) const
{
return NumEqVector(0.0);
}