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Commit 8aef937c authored by Simon Scholz's avatar Simon Scholz
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[doxygen] cleanup warnings generated from doxygen, remove included_by_graph, introduce min-width

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doc/doxygen/DoxygenDumuxLayout.xml
View file @ 8aef937c
......@@ -131,7 +131,7 @@
<variables title=""/>
</memberdef>
<includegraph visible="yes"/>
<includedbygraph visible="yes"/>
<includedbygraph visible="no"/>
<authorsection/>
</file>
......
doc/doxygen/Doxylocal
View file @ 8aef937c
......@@ -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
......
doc/doxygen/customdoxygendumux.css
View file @ 8aef937c
......@@ -2,6 +2,7 @@
body, table, div, p, dl {
font: 400 14px/22px Roboto,sans-serif;
min-width: 500px
}
p.reference, p.definition {
......
doc/doxygen/modules.txt
View file @ 8aef937c
......@@ -375,7 +375,7 @@
*/
/* ***************** Flux ******************/
/*!
* \defgroup Flux
* \defgroup Flux Flux
* \brief All flux related things available in DuMu<sup>x</sup>
*/
/* ***************** Material ******************/
......
doc/doxygen/sanitizelinks.sh
View file @ 8aef937c
......@@ -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
doc/handbook/dumux-handbook.bib
View file @ 8aef937c
......@@ -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},
......
dumux/discretization/cellcentered/elementsolution.hh
View file @ 8aef937c
......@@ -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
*/
......
dumux/discretization/cellcentered/mpfa/elementvolumevariables.hh
View file @ 8aef937c
......@@ -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
*/
......
dumux/discretization/staggered/elementsolution.hh
View file @ 8aef937c
......@@ -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
......
dumux/freeflow/navierstokes/iofields.hh
View file @ 8aef937c
......@@ -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
......
dumux/freeflow/rans/twoeq/kepsilon/model.hh
View file @ 8aef937c
......@@ -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[
......
dumux/linear/seqsolverbackend.hh
View file @ 8aef937c
......@@ -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
{
......
dumux/material/binarycoefficients/h2o_ch4.hh
View file @ 8aef937c
......@@ -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)
......
dumux/material/fluidmatrixinteractions/mp/mplinearmaterial.hh
View file @ 8aef937c
......@@ -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,
......
dumux/material/fluidmatrixinteractions/porositydeformation.hh
View file @ 8aef937c
......@@ -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$,
* which is the formulation for the rock mechanics sign convention. Here we are
* using the continuum mechanics sign convention, thus, the final formula reads:
......
dumux/porousmediumflow/2p/sequential/diffusion/mpfa/lmethod/3dtransmissibilitycalculator.hh
View file @ 8aef937c
......@@ -91,7 +91,6 @@ public:
int idx1, int idx2, int idx3, int idx4, int idx5, int idx6,
Dune::FieldVector<bool, 4> &useCases);
int transmissibilityTPFA(Dune::FieldMatrix<Scalar,dim,2*dim-dim+1>& transmissibility,
InteractionVolume& interactionVolume,
std::vector<DimVector >& lambda,
......@@ -120,7 +119,6 @@ public:
std::vector<DimVector >& lambda,
int idx1, int idx2, int idx3, int idx6);
/*!
* \brief Constructs a FvMpfaL3dTransmissibilityCalculator object
* \param problem A problem class object
......
test/porousmediumflow/1pnc/implicit/1p2c/nonisothermal/transientbc/problem.hh
View file @ 8aef937c
......@@ -255,8 +255,6 @@ public:
* potentially solution dependent and requires some quantities that
* are specific to the fully-implicit method.
*
* \param values The neumann values for the conservation equations in units of
* \f$ [ \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);
}
......
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