Commit 10da7726 authored by Simon Scholz's avatar Simon Scholz

Merge branch 'cleanup/doxygen' into 'master'

[cleanup][doxygen] remove ingroups and general cleanup

See merge request !67
parents 0dcf1916 e797691f
......@@ -84,7 +84,6 @@ public:
} // end namespace Properties
/*!
* \ingroup TwoPBoxProblems
* \brief Exercise to show the diffusive spreading of contaminants.
*
* The whole problem is symmetric.
......@@ -102,8 +101,6 @@ public:
* The Dirichlet boundaries on the top boundary can be chosen
* differently to the bottom pressure.
*
* This problem uses the \ref OnePTwoCBoxModel.
*
* Typical simulation parameters can be found in the input file:
* exercise3.input
*
......@@ -134,9 +131,8 @@ class LensOnePTwoCProblem : public PorousMediumFlowProblem<TypeTag>
public:
/*!
* \brief The constructor
*
* \param fvGridGeometry The finite volume grid geometry
*/
LensOnePTwoCProblem(std::shared_ptr<const FVGridGeometry> fvGridGeometry )
: ParentType(fvGridGeometry)
{
......@@ -170,8 +166,7 @@ public:
* \brief Specifies which kind of boundary condition should be
* used for which equation on a given boundary segment.
*
* \param values The boundary types for the conservation equations
* \param globalPos DOC ME!
* \param globalPos The position for which the bc type should be evaluated
*
*/
BoundaryTypes boundaryTypesAtPos(const GlobalPosition& globalPos) const
......@@ -190,10 +185,7 @@ public:
* \brief Evaluate the boundary conditions for a dirichlet
* control volume.
*
* \param values The dirichlet values for the primary variables
* \param globalPos DOC ME!
*
* For this method, the \a values parameter stores primary variables.
* \param globalPos The position for which the Dirichlet condition should be evaluated
*/
PrimaryVariables dirichletAtPos(const GlobalPosition& globalPos) const
{
......@@ -215,34 +207,25 @@ public:
/*!
* \brief Evaluate the boundary conditions for a neumann
* boundary segment.
* \param values DOC ME!
* \param globalPos DOC ME!
*
* For this method, the \a values parameter stores the mass flux
* in normal direction of each phase. Negative values mean influx.
* \param globalPos The position for which the neumann condition should be evaluated
*/
PrimaryVariables neumannAtPos(const GlobalPosition &globalPos) const
{
return PrimaryVariables(0.0);
}
// \}
/*!
* \name Volume terms
*/
// \{
/*!
* \brief Evaluate the source term for all phases within a given
* sub-control-volume.
*
* \param values The source and sink values for the conservation equations in units of
* \f$ [ \textnormal{unit of conserved quantity} / (m^3 \cdot s )] \f$
* \param globalPos The position of the center of the finite volume
* for which the source term ought to be
* specified in global coordinates
*
* For this method, the \a values parameter stores the rate mass
* generated or annihilate per volume unit. Positive values mean
* that mass is created, negative ones mean that it vanishes.
* \param globalPos The position for which the source should be evaluated
*/
NumEqVector sourceAtPos(const GlobalPosition &globalPos) const
{
......@@ -252,11 +235,8 @@ public:
/*!
* \brief Evaluate the initial value for a control volume.
*
* \param values DOC ME!
* \param globalPos DOC ME!
* \param globalPos The position for which the initial condition should be evaluated
*
* For this method, the \a values parameter stores primary
* variables.
*/
PrimaryVariables initialAtPos( const GlobalPosition& globalPos) const
{
......@@ -270,6 +250,7 @@ public:
return values;
}
// \}
private:
/*!
......@@ -290,8 +271,8 @@ private:
}
/*!
* \brief DOC ME!
* \param globalPos DOC ME!
* \brief returns true if point is located between the given points
* \param globalPos The position of the point in global coordinates
*/
bool isInitial_(const GlobalPosition &globalPos) const
{
......
......@@ -16,7 +16,10 @@
* 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 Class for defining spatial parameters
*/
#ifndef DUMUX_1P2C_SPATIALPARAMS_HH
#define DUMUX_1P2C_SPATIALPARAMS_HH
......@@ -24,12 +27,6 @@
#include <dumux/material/spatialparams/fv1p.hh>
/**
* @file
* @brief Class for defining spatial parameters
* @author Bernd Flemisch, Klaus Mosthaf, Markus Wolff
*/
namespace Dumux {
//forward declaration
......@@ -53,8 +50,9 @@ public:
} // end namespace Properties
/** \todo Please doc me! */
/*!
* \brief Class for defining spatial parameters
*/
template<class FVGridGeometry, class Scalar>
class Lens1p2cSpatialParams : public FVSpatialParamsOneP<FVGridGeometry, Scalar, Lens1p2cSpatialParams<FVGridGeometry, Scalar> >
{
......@@ -73,8 +71,9 @@ public:
using PermeabilityType = Scalar;
/*!
* \brief DOC ME!
* \param gridView DOC ME!
* \brief The constructor
*
* \param fvGridGeometry The finite volume grid geometry
*/
Lens1p2cSpatialParams(std::shared_ptr<const FVGridGeometry> fvGridGeometry)
: ParentType(fvGridGeometry)
......@@ -93,13 +92,12 @@ public:
}
/*!
* \brief Apply the intrinsic permeability tensor to a pressure
* potential gradient.
* \brief Function for defining the (intrinsic) permeability \f$[m^2]\f$
*
* \param element The current finite element
* \param fvElemGeom The current finite volume geometry of the element
* \param scvIdx The index sub-control volume face where the
* intrinsic velocity ought to be calculated.
* \param element The current element
* \param scv The sub-control volume inside the element.
* \param elemSol The solution at the dofs connected to the element.
* \return permeability
*/
template<class ElementSolution>
Scalar permeability(const Element& element,
......@@ -112,16 +110,15 @@ public:
else
return outerK_;
}
/*!
* \brief Define the porosity \f$[-]\f$ of the spatial parameters
*
* \param element The current finite element
* \param fvElemGeom The current finite volume geometry of the element
* \param scvIdx The local index of the sub-control volume where
* the porosity needs to be defined
* \param globalPos DOC ME!
* \brief Function for defining the porosity.
* That is possibly solution dependent.
* \param element The current element
* \param scv The sub-control volume inside the element.
* \param elemSol The solution at the dofs connected to the element.
* \return the porosity
*/
template<class ElementSolution>
Scalar porosity(const Element& element,
const SubControlVolume& scv,
......@@ -133,13 +130,10 @@ public:
else
return outerPorosity_;
}
/*!
* \brief DOC ME!
* \param lensLowerLeft DOC ME!
* \param lensUpperRight
* \brief set the lens coordinates
*/
//! Set the bounding box of the fine-sand lens
void setLensCoords(const GlobalPosition& lensLowerLeft, const GlobalPosition& lensUpperRight)
{
lensLowerLeft_ = lensLowerLeft;
......@@ -147,10 +141,6 @@ public:
}
private:
/*!
* \brief DOC ME!
* \param pos DOC ME!
*/
bool isInLens_(const GlobalPosition &pos) const
{
for (int i = 0; i < dimWorld; ++i)
......
......@@ -19,7 +19,7 @@
/*!
* \file
*
* \brief DOC ME!
* \brief Exercise to show the diffusive spreading of contaminants.
*/
#include <config.h>
......
......@@ -19,7 +19,7 @@
/*!
* \file
*
* \brief DOC ME!
* \brief Exercise to show the diffusive spreading of contaminants.
*/
#ifndef DUMUX_LENS_2P2C_PROBLEM_HH
......@@ -82,17 +82,26 @@ public:
} // end namespace Properties
/*!
* \ingroup TwoPTwoCModel
* \brief Problem where air is injected under a low permeable layer in a depth of 800m.
* \brief Exercise to show the diffusive spreading of contaminants.
*
* The domain is sized 60m times 40m and consists of two layers, a moderately
* permeable spatial parameters (\f$ K=10e-12\f$) for \f$ y>22m\f$ and one with a lower permeablility (\f$ K=10e-13\f$)
* in the rest of the domain.
* The whole problem is symmetric.
*
* The domain is sized 2m times 4m and features a rectangular lens
* with low permeablility which is located in the lower half of the domain.
*
* On the top and the bottom of the domain Dirichlet boundary conditions
* are used, while Neumann conditions apply on the left and right
* boundaries.
*
* The contaminant is initially located in the middle of the domain,
* but only in the upper layer.
*
* The Dirichlet boundaries on the top boundary can be chosen
* differently to the bottom pressure.
*
* Typical simulation parameters can be found in the input file:
* exercise3.input
*
* Air enters a water-filled aquifer, which is situated 800m below sea level, at the right boundary
* (\f$ 5m<y<15m\f$) and migrates upwards due to buoyancy. It accumulates and
* partially enters the lower permeable aquitard.
* This problem uses the \ref TwoPTwoCModel.
*/
template<class TypeTag>
class LensTwoPTwoCProblem: public PorousMediumFlowProblem<TypeTag>
......@@ -120,7 +129,6 @@ public:
/*!
* \brief The constructor
*
* \param gridView The grid view
*/
LensTwoPTwoCProblem(std::shared_ptr<const FVGridGeometry> fvGridGeometry )
: ParentType(fvGridGeometry)
......@@ -147,12 +155,6 @@ public:
/*!
* \brief Returns the temperature within the domain.
*
* \param temperature DOC ME!
* \param values DOC ME!
* \param globalPos DOC ME!
*
* This problem assumes a temperature of 10 degrees Celsius.
*/
Scalar temperature() const
{
......@@ -169,7 +171,6 @@ public:
* \brief Specifies which kind of boundary condition should be
* used for which equation on a given boundary control volume.
*
* \param values The boundary types for the conservation equations
* \param globalPos The position of the center of the finite volume
*/
BoundaryTypes boundaryTypesAtPos( const GlobalPosition &globalPos) const
......@@ -188,10 +189,7 @@ public:
* \brief Evaluate the boundary conditions for a dirichlet
* control volume.
*
* \param values The dirichlet values for the primary variables
* \param globalPos DOC ME!
*
* For this method, the \a values parameter stores primary variables.
* \param globalPos The position for which the Dirichlet condition should be evaluated
*/
PrimaryVariables dirichletAtPos(const GlobalPosition &globalPos) const
{
......@@ -216,16 +214,6 @@ public:
/*!
* \brief Evaluate the boundary conditions for a neumann
* boundary segment.
*
* \param values The neumann values for the conservation equations
* \param element The finite element
* \param fvElemGeom The finite-volume geometry in the box scheme
* \param is The intersection between element and boundary
* \param scvIdx The local vertex index
* \param boundaryFaceIdx The index of the boundary face
*
* For this method, the \a values parameter stores the mass flux
* in normal direction of each phase. Negative values mean influx.
*/
PrimaryVariables neumannAtPos( const GlobalPosition &globalPos) const
{
......@@ -242,15 +230,9 @@ public:
* \brief Evaluate the source term for all phases within a given
* sub-control-volume.
*
* \param values The source and sink values for the conservation equations in units of
* \f$ [ \textnormal{unit of conserved quantity} / (m^3 \cdot s )] \f$
* \param globalPos The position of the center of the finite volume
* for which the source term ought to be
* specified in global coordinates
*
* For this method, the \a values parameter stores the rate mass
* generated or annihilate per volume unit. Positive values mean
* that mass is created, negative ones mean that it vanishes.
*/
NumEqVector sourceAtPos(const GlobalPosition &globalPos) const
{
......@@ -260,13 +242,6 @@ public:
/*!
* \brief Evaluate the initial value for a control volume.
*
* \param values The initial values for the primary variables
* \param element The finite element
* \param fvElemGeom The finite-volume geometry in the box scheme
* \param scvIdx The local vertex index
*
* For this method, the \a values parameter stores primary
* variables.
*/
PrimaryVariables initialAtPos(const GlobalPosition &globalPos) const
{
......@@ -314,8 +289,8 @@ private:
}
/*!
* \brief DOC ME!
* \param globalPos DOC ME!
* \brief returns true if point is located between the given points
* \param globalPos The position of the point in global coordinates
*/
bool isInitial_(const GlobalPosition &globalPos) const
{
......
......@@ -19,7 +19,7 @@
/*!
* \file
*
* \brief DOC ME!
* \brief Exercise to show the spreading of contaminants.
*/
#ifndef DUMUX_LENS2P_PROBLEM_HH
......@@ -86,37 +86,26 @@ public:
} // end namespace Properties
/*!
* \ingroup TwoPBoxProblems
* \brief DOC ME!
* \brief Exercise to show the spreading of contaminants.
*
* DOC ME! The domain is sized 5m times 4m and features a rectangular lens
* with low permeablility which spans from (1 m , 2 m) to (4 m, 3 m)
* and is surrounded by a medium with higher permability. Note that
* this problem is discretized using only two dimensions, so from the
* point of view of the two-phase model, the depth of the domain
* implicitly is 1 m everywhere.
* The whole problem is symmetric.
*
* On the top and the bottom of the domain neumann boundary conditions
* are used, while dirichlet conditions apply on the left and right
* The domain is sized 2m times 4m and features a rectangular lens
* with low permeablility which is located in the lower half of the domain.
*
* On the top and the bottom of the domain Dirichlet boundary conditions
* are used, while Neumann conditions apply on the left and right
* boundaries.
*
* DNAPL is injected at the top boundary from 3m to 4m at a rate of
* 0.04 kg/(s m^2), the remaining neumann boundaries are no-flow
* boundaries.
*
* The dirichlet boundaries on the left boundary is the hydrostatic
* pressure scaled by a factor of 1.125, while on the right side it is
* just the hydrostatic pressure. The DNAPL saturation on both sides
* is zero.
* The contaminant is initially located in the middle of the domain,
* but only in the upper layer.
*
* This problem uses the \ref TwoPBoxModel.
* The Dirichlet boundaries on the top boundary can be chosen
* differently to the bottom pressure.
*
* This problem should typically be simulated until \f$t_{\text{end}}
* \approx 50\,000\;s\f$ is reached. A good choice for the initial time step
* size is \f$t_{\text{inital}} = 1\,000\;s\f$.
* Typical simulation parameters can be found in the input file:
* exercise3.input
*
* To run the simulation execute the following line in shell:
* <tt>./test_2p -parameterFile test_2p.input</tt>
*/
template <typename TypeTag>
class LensTwoPProblem : public PorousMediumFlowProblem<TypeTag>
......@@ -154,7 +143,6 @@ public:
/*!
* \brief Returns the temperature within the domain.
* \param temperature DOC ME!
* This problem assumes a uniform temperature of 10 degrees Celsius.
*/
Scalar temperature() const
......@@ -172,8 +160,6 @@ public:
/*!
* \brief Specifies which kind of boundary condition should be
* used for which equation on a given boundary control volume.
*
* \param values The boundary types for the conservation equations
* \param globalPos The position of the center of the finite volume
*/
BoundaryTypes boundaryTypesAtPos(const GlobalPosition &globalPos) const
......@@ -191,11 +177,8 @@ public:
/*!
* \brief Evaluate the boundary conditions for a dirichlet
* control volume.
* \param globalPos the global position
*
* \param values The dirichlet values for the primary variables
* \param globalPos DOC ME!
*
* For this method, the \a values parameter stores primary variables.
*/
PrimaryVariables dirichletAtPos( const GlobalPosition &globalPos) const
{
......@@ -220,11 +203,8 @@ public:
* \brief Evaluate the boundary conditions for a neumann
* boundary segment.
*
* \param values The neumann values for the conservation equations [kg / (m^2 *s )]
* \param globalPos The position of the integration point of the boundary segment.
*
* For this method, the \a values parameter stores the mass flux
* in normal direction of each phase. Negative values mean influx.
*/
PrimaryVariables neumannAtPos( const GlobalPosition &globalPos) const
{
......@@ -240,15 +220,10 @@ public:
* \brief Evaluate the source term for all phases within a given
* sub-control-volume.
*
* \param values The source and sink values for the conservation equations in units of
* \f$ [ \textnormal{unit of conserved quantity} / (m^3 \cdot s )] \f$
* \param globalPos The position of the center of the finite volume
* for which the source term ought to be
* specified in global coordinates
*
* For this method, the \a values parameter stores the rate mass
* generated or annihilate per volume unit. Positive values mean
* that mass is created, negative ones mean that it vanishes.
*/
NumEqVector sourceAtPos( const GlobalPosition &globalPos) const
{
......@@ -258,11 +233,8 @@ public:
/*!
* \brief Evaluate the initial value for a control volume.
*
* \param values The initial values for the primary variables
* \param globalPos The center of the finite volume which ought to be set.
*
* For this method, the \a values parameter stores primary
* variables.
*/
PrimaryVariables initialAtPos(const GlobalPosition &globalPos) const
{
......@@ -302,8 +274,8 @@ private:
}
/*!
* \brief DOC ME!
* \param globalPos DOC ME!
* \brief returns true if point is located between the given points
* \param globalPos The position of the point in global coordinates
*/
bool isInitial_(const GlobalPosition &globalPos) const
{
......
......@@ -33,8 +33,10 @@
namespace Dumux {
/** \todo Please doc me! */
/*!
* \brief Definition of the spatial parameters for the lens
* problem which uses the isothermal 2p or 2p2c box model
*/
template<class FVGridGeometry, class Scalar>
class Lens2pSpatialParams
: public FVSpatialParams<FVGridGeometry, Scalar, Lens2pSpatialParams<FVGridGeometry, Scalar>>
......@@ -56,8 +58,6 @@ public:
/*!
* \brief The constructor
*
* \param gridView DOC ME!
*/
Lens2pSpatialParams(std::shared_ptr<const FVGridGeometry> fvGridGeometry)
: ParentType(fvGridGeometry)
......@@ -85,13 +85,12 @@ public:
}
/*!
* \brief Apply the intrinsic permeability tensor to a pressure
* potential gradient.
* \brief Function for defining the (intrinsic) permeability \f$[m^2]\f$
*
* \param element The current finite element
* \param fvElemGeom The current finite volume geometry of the element
* \param scvIdx The index sub-control volume face where the
* intrinsic velocity ought to be calculated.
* \param element The current element
* \param scv The sub-control volume inside the element.
* \param elemSol The solution at the dofs connected to the element.
* \return permeability
*/
template<class ElementSolution>
PermeabilityType permeability(const Element& element,
......@@ -104,15 +103,13 @@ public:
}
/*!
* \brief Define the porosity \f$[-]\f$ of the spatial parameters
*
* \param element The current finite element
* \param fvElemGeom The current finite volume geometry of the element
* \param scvIdx The local index of the sub-control volume where
* the porosity needs to be defined
* \param globalPos DOC ME!
* \brief Function for defining the porosity.
* That is possibly solution dependent.
* \param element The current element
* \param scv The sub-control volume inside the element.
* \param elemSol The solution at the dofs connected to the element.
* \return the porosity
*/
template<class ElementSolution>
Scalar porosity(const Element& element,
const SubControlVolume& scv,
......@@ -126,12 +123,10 @@ public:
/*!
* \brief return the brooks-corey context depending on the position
*
* \param element The current finite element
* \param fvElemGeom The current finite volume geometry of the element
* \param scvIdx The index of the sub-control volume
* \param globalPos DOC ME!
*/
* \param element The current element
* \param scv The sub-control volume inside the element.
* \param elemSol The solution at the dofs connected to the element.
*/
template<class ElementSolution>
const MaterialLawParams& materialLawParams(const Element& element,
const SubControlVolume& scv,
......
......@@ -19,7 +19,8 @@
/*!
* \file
*
* \brief DOC ME!
* \brief Soil decontamination problem where a contaminant infiltrates a fully
* water saturated medium.
*/
#ifndef DUMUX_LENS_1P2C_PROBLEM_HH
......@@ -79,7 +80,6 @@ public:
} // end namespace Properties
/*!
* \ingroup TwoPBoxProblems
* \brief Soil decontamination problem where a contaminant infiltrates a fully
* water saturated medium.
*
......@@ -103,8 +103,6 @@ public:
* 50\,000\;s\f$ is reached. A good choice for the initial time step size
* is \f$t_{\text{inital}} = 1\,000\;s\f$.
*
* To run the simulation execute the following line in shell:
* <tt>./lens_1p2c 50000 100</tt>
*/
template <class TypeTag>
class LensOnePTwoCProblem : public PorousMediumFlowProblem<TypeTag>
......@@ -201,9 +199,7 @@ public:
/*!
* \brief Evaluate the boundary conditions for a dirichlet
* control volume.
*
* \param values The dirichlet values for the primary variables
* \param globalPos DOC ME!
* \param globalPos he position for which the dirichlet condition should be evaluated
*
* For this method, the \a values parameter stores primary variables.
*/
......@@ -227,8 +223,7 @@ public:
/*!
* \brief Evaluate the boundary conditions for a neumann
* boundary segment.
* \param values DOC ME!
* \param globalPos DOC ME!
* \param globalPos he position for which the neumann condition should be evaluated
*
* For this method, the \a values parameter stores the mass flux
* in normal direction of each phase. Negative values mean influx.
......@@ -250,8 +245,7 @@ public:
/*!
* \brief Evaluate the source term for all phases within a given
* sub-control-volume.
* \param values DOC ME!
* \param globalPos DOC ME!
* \param globalPos he position for which the source should be evaluated
*
* For this method, the \a values parameter stores the rate mass
* generated or annihilate per volume unit. Positive values mean
......@@ -265,11 +259,8 @@ public:
/*!
* \brief Evaluate the initial value for a control volume.
*
* \param values DOC ME!
* \param globalPos DOC ME!
* \param globalPos the position for which the initial condition should be evaluated
*
* For this method, the \a values parameter stores primary
* variables.
*/
PrimaryVariables initialAtPos(const GlobalPosition& globalPos) const
{
......@@ -312,8 +303,8 @@ private:
}
/*!
* \brief DOC ME!
* \param globalPos DOC ME!
* \brief returns true if point is located between the given points
* \param globalPos The position of the point in global coordinates
*/
bool onInlet_(const GlobalPosition &globalPos) const
{
......
......@@ -19,7 +19,8 @@
/*!
* \file
*
* \brief DOC ME!
* \brief Soil decontamination problem where DNAPL infiltrates a fully
* water saturated medium.
*/
#include <config.h>
......
......@@ -19,7 +19,8 @@
/*!
* \file
*
* \brief DOC ME!
* \brief Soil decontamination problem where DNAPL infiltrates a fully
* water saturated medium.
*/
#ifndef DUMUX_LENS2P_EXERCISE1_PROBLEM_HH
......@@ -83,7 +84,6 @@ public:
} // end namespace Properties
/*!
* \ingroup TwoPBoxProblems
* \brief Soil decontamination problem where DNAPL infiltrates a fully
* water saturated medium.
*
......@@ -149,8 +149,6 @@ public:
/*!
* \brief The constructor
*
* \param timeManager The time manager
* \param gridView The grid view
*/
LensTwoPProblem(std::shared_ptr<const FVGridGeometry> fvGridGeometry)
: ParentType(fvGridGeometry)
......@@ -191,7 +189,6 @@ public:
* \brief Specifies which kind of boundary condition should be
* used for which equation on a given boundary control volume.
*
* \param values The boundary types for the conservation equations
* \param globalPos The position of the center of the finite volume
*/
BoundaryTypes boundaryTypesAtPos(const GlobalPosition &globalPos) const
......@@ -213,10 +210,8 @@ public:
* \brief Evaluate the boundary conditions for a dirichlet
* control volume.
*
* \param values The dirichlet values for the primary variables
* \param globalPos DOC ME!
* \param globalPos The position for which the Dirichlet condition should be evaluated
*
* For this method, the \a values parameter stores primary variables.
*/
PrimaryVariables dirichletAtPos( const GlobalPosition &globalPos) const
{
......@@ -240,13 +235,8 @@ public: