From 0dfb8f57086062ceb417c07cbfbe47f3cc87c624 Mon Sep 17 00:00:00 2001
From: Timo Koch <timo.koch@iws.uni-stuttgart.de>
Date: Wed, 20 Dec 2017 15:53:55 +0100
Subject: [PATCH] [doc] Improve documentation in folder common
---
dumux/common/balanceequationopts.hh | 12 +-
dumux/common/boundaryconditions.hh | 26 +--
dumux/common/boundaryflag.hh | 12 +-
dumux/common/boundarytypes.hh | 3 +-
dumux/common/defaultusagemessage.hh | 7 +-
dumux/common/dimensionlessnumbers.hh | 32 +--
dumux/common/dumuxmessage.hh | 7 +-
dumux/common/eigenvalues.hh | 9 +-
dumux/common/entitymap.hh | 2 +
dumux/common/exceptions.hh | 7 +-
dumux/common/fixedlengthspline_.hh | 8 +-
dumux/common/fvproblem.hh | 212 +++---------------
dumux/common/geometry/boundingboxtree.hh | 26 ++-
.../geometry/boundingboxtreeintersection.hh | 2 +
dumux/common/geometry/geometricentityset.hh | 7 +
dumux/common/geometry/geometryintersection.hh | 2 +
dumux/common/geometry/intersectingentities.hh | 24 +-
.../geometry/intersectspointgeometry.hh | 16 +-
.../common/geometry/intersectspointsimplex.hh | 31 ++-
dumux/common/intersectionmapper.hh | 14 +-
dumux/common/intrange.hh | 5 +-
dumux/common/loggingparametertree.hh | 6 +-
dumux/common/math.hh | 31 ++-
dumux/common/optional.hh | 9 +-
dumux/common/parameters.hh | 53 +++--
dumux/common/pointsource.hh | 1 +
dumux/common/properties.hh | 9 +-
dumux/common/properties/grid.hh | 9 +-
dumux/common/properties/model.hh | 13 +-
dumux/common/properties/propertysystem.hh | 2 +-
dumux/common/quad.hh | 2 +-
dumux/common/reorderingdofmapper.hh | 6 +
dumux/common/spline.hh | 3 +-
dumux/common/splinecommon_.hh | 6 +-
dumux/common/staggeredfvproblem.hh | 5 +-
dumux/common/start.hh | 3 +-
dumux/common/tabulated2dfunction.hh | 6 +-
dumux/common/timeloop.hh | 19 +-
dumux/common/timemanager.hh | 12 +-
dumux/common/timesteppingscheme.hh | 3 +
dumux/common/valgrind.hh | 3 +-
dumux/common/variablelengthspline_.hh | 9 +-
42 files changed, 320 insertions(+), 354 deletions(-)
diff --git a/dumux/common/balanceequationopts.hh b/dumux/common/balanceequationopts.hh
index ad401689f2..7a96e74474 100644
--- a/dumux/common/balanceequationopts.hh
+++ b/dumux/common/balanceequationopts.hh
@@ -18,7 +18,8 @@
*****************************************************************************/
/*!
* \file
- * \brief Class to set options used by the local residual when
+ * \ingroup Common
+ * \brief Traits class to set options used by the local residual when
* when evaluating the balance equations.
*/
#ifndef BALANCE_EQUATION_OPTIONS_HH
@@ -28,8 +29,11 @@ namespace Dumux
{
/*!
- * \ingroup BC
- * \brief Class to specify the type of a boundary.
+ * \ingroup Common
+ * \brief Traits class to set options used by the local residual when
+ * when evaluating the balance equations.
+ * \todo include useMoles here
+ * \todo include replaceCompIdx here
*/
template <class TypeTag>
class BalanceEquationOptions
@@ -44,6 +48,6 @@ public:
{ return true; }
};
-}
+} // end namespace Dumux
#endif
diff --git a/dumux/common/boundaryconditions.hh b/dumux/common/boundaryconditions.hh
index de8e0f0d26..5b6759ef01 100644
--- a/dumux/common/boundaryconditions.hh
+++ b/dumux/common/boundaryconditions.hh
@@ -16,21 +16,21 @@
* 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
+ * \ingroup Common
+ * \brief Definition of boundary condition types, extend if necessary
+ * \todo can this be removed for the sake of boundarytypes.hh?
+ */
#ifndef DUMUX_BOUNDARYCONDITIONS_HH
#define DUMUX_BOUNDARYCONDITIONS_HH
-/**
-* @file
-* @brief Definition of boundary condition types, extend if necessary
-*/
-namespace Dumux
-{
-/**
- * \ingroup BC
- * @brief Define a class containing boundary condition flags
- */
+namespace Dumux {
-//! base Class that defines boundary condition flags
+/*!
+ * \ingroup Common
+ * \brief Define a class containing boundary condition flags
+ */
struct BoundaryConditions
{
/** \brief These values are ordered according to precedence */
@@ -42,6 +42,6 @@ struct BoundaryConditions
};
};
-/** @} */
-}
+} // end namespace Dumux
+
#endif
diff --git a/dumux/common/boundaryflag.hh b/dumux/common/boundaryflag.hh
index 29dae7b445..dec09f7778 100644
--- a/dumux/common/boundaryflag.hh
+++ b/dumux/common/boundaryflag.hh
@@ -18,7 +18,7 @@
*****************************************************************************/
/*!
* \file
- *
+ * \ingroup Common
* \brief Boundary flag to store e.g. in sub control volume faces
*/
#ifndef DUMUX_BOUNDARY_FLAG_HH
@@ -29,10 +29,14 @@
#include <dune/alugrid/grid.hh>
#endif
-namespace Dumux
-{
+namespace Dumux {
-//! a boundary flag class specialized on the grid type
+/*!
+ * \file
+ * \ingroup Common
+ * \brief Boundary flag to store e.g. in sub control volume faces
+ * \tparam Grid the type of the gri
+ */
template<class Grid>
class BoundaryFlag
{
diff --git a/dumux/common/boundarytypes.hh b/dumux/common/boundarytypes.hh
index 46c68d431e..3ac652e3a3 100644
--- a/dumux/common/boundarytypes.hh
+++ b/dumux/common/boundarytypes.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Class to specify the type of a boundary.
*/
#ifndef DUMUX_BOUNDARY_TYPES_HH
@@ -27,7 +28,7 @@ namespace Dumux
{
/*!
- * \ingroup BC
+ * \ingroup Common
* \brief Class to specify the type of a boundary.
*/
template <int numEq>
diff --git a/dumux/common/defaultusagemessage.hh b/dumux/common/defaultusagemessage.hh
index c2b7ba4bfe..7991724e4f 100644
--- a/dumux/common/defaultusagemessage.hh
+++ b/dumux/common/defaultusagemessage.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Function printing a default usage message
*/
#ifndef DUMUX_DEFAULT_USAGE_MESSAGE_HH
@@ -25,12 +26,10 @@
#include <string>
-namespace Dumux
-{
+namespace Dumux {
/*!
- * \ingroup Start
- *
+ * \ingroup Common
* \brief Provides a general text block, that is part of error/ help messages.
*
* \return The string that is the help / error message.
diff --git a/dumux/common/dimensionlessnumbers.hh b/dumux/common/dimensionlessnumbers.hh
index 2934f884d6..8efc0366da 100644
--- a/dumux/common/dimensionlessnumbers.hh
+++ b/dumux/common/dimensionlessnumbers.hh
@@ -17,12 +17,12 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
/*!
- * \file dimensionlessnumbers.hh
- *
+ * \file
+ * \ingroup Common
* \brief Collection of functions, calculating dimensionless numbers.
*
- * All the input to the dimensionless numbers has to be provided as function arguments.
- * Rendering this collection generic in the sense that it can be used by any model.
+ * All the input to the dimensionless numbers has to be provided as function arguments.
+ * Rendering this collection generic in the sense that it can be used by any model.
*/
#ifndef DIMENSIONLESS_NUMBERS_HH
#define DIMENSIONLESS_NUMBERS_HH
@@ -31,14 +31,14 @@
#include <dune/common/exceptions.hh>
-namespace Dumux
-{
+namespace Dumux {
+
/*!
* \brief Collection of functions which calculate dimensionless numbers.
- *
- * Each number has it's own function.
- * All the parameters for the calculation have to be handed over.
- * Rendering this collection generic in the sense that it can be used by any model.
+ * \ingroup Common
+ * Each number has it's own function.
+ * All the parameters for the calculation have to be handed over.
+ * Rendering this collection generic in the sense that it can be used by any model.
*/
template <class Scalar>
class DimensionlessNumbers
@@ -48,11 +48,11 @@ public:
/*!
* \brief Calculate the Reynolds Number [-] (Re).
*
- * The Reynolds number is a measure for the relation of inertial to viscous forces.
- * The bigger the value, the more important inertial (as compared to viscous) effects become.
- * According to Bear [Dynamics of fluids in porous media (1972)] Darcy's law is valid for Re<1.
+ * The Reynolds number is a measure for the relation of inertial to viscous forces.
+ * The bigger the value, the more important inertial (as compared to viscous) effects become.
+ * According to Bear [Dynamics of fluids in porous media (1972)] Darcy's law is valid for Re<1.
*
- * source for Reynolds number definition: http://en.wikipedia.org/wiki/Reynolds_number
+ * Source for Reynolds number definition: http://en.wikipedia.org/wiki/Reynolds_number
*
* \param darcyMagVelocity The absolute value of the darcy velocity. In the context of box models this
* leads to a problem: the velocities are defined on the faces while other things (storage, sources, output)
@@ -296,7 +296,9 @@ static Scalar thermalDiffusivity(const Scalar & thermalConductivity ,
{
return thermalConductivity / (phaseDensity * heatCapacity);
}
-}; // end class
+
+}; // end class DimensionlessNumbers
+
} // end namespace Dumux
#endif // DIMENSIONLESS_NUMBERS_HH
diff --git a/dumux/common/dumuxmessage.hh b/dumux/common/dumuxmessage.hh
index 7102b83129..7176d2519f 100644
--- a/dumux/common/dumuxmessage.hh
+++ b/dumux/common/dumuxmessage.hh
@@ -18,7 +18,8 @@
*****************************************************************************/
/*!
* \file
- * \brief Provides the class creating the famous dumux start and end messages
+ * \ingroup Common
+ * \brief Provides the class creating the famous DuMu<sup>x</sup> start and end messages
*/
#ifndef DUMUX_MESSAGE_HH
#define DUMUX_MESSAGE_HH
@@ -31,8 +32,8 @@ namespace Dumux
{
/*!
- * \ingroup Start
- * \brief Dumux start and end message.
+ * \ingroup Common
+ * \brief DuMu<sup>x</sup> start and end message.
*/
class DumuxMessage
{
diff --git a/dumux/common/eigenvalues.hh b/dumux/common/eigenvalues.hh
index 6746502049..11f4de1806 100644
--- a/dumux/common/eigenvalues.hh
+++ b/dumux/common/eigenvalues.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Defines a functions to calculate eigenvalues and eigenvectors of n x n matrices. For n > 2 a cyclic jacobi method is used.
* This implementation is not efficient for larg matrices!
*/
@@ -29,8 +30,7 @@
#include "math.hh"
-namespace Dumux
-{
+namespace Dumux {
template<int dim, class Matrix>
void identityMatrix(Matrix& matrix)
@@ -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
@@ -214,7 +214,6 @@ bool calculateEigenValues(EVVectorType &eigVel, MatrixType& eigVec, MatrixType&
return true;
}
-
-}
+} // end namespace Dumux
#endif
diff --git a/dumux/common/entitymap.hh b/dumux/common/entitymap.hh
index de4a42b773..365655aea2 100644
--- a/dumux/common/entitymap.hh
+++ b/dumux/common/entitymap.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief A map from indices to entities using grid entity seeds
*/
#ifndef DUMUX_ENTITY_INDEX_MAP_HH
@@ -26,6 +27,7 @@
namespace Dumux {
/*!
+ * \ingroup Common
* \brief A map from indices to entities using grid entity seeds
*/
template <class GridView, int codim = 0>
diff --git a/dumux/common/exceptions.hh b/dumux/common/exceptions.hh
index 4f6d620e01..7a5f6fe94b 100644
--- a/dumux/common/exceptions.hh
+++ b/dumux/common/exceptions.hh
@@ -18,7 +18,8 @@
*****************************************************************************/
/*!
* \file
- * \brief Some exceptions thrown in DUMUX
+ * \ingroup Common
+ * \brief Some exceptions thrown in DuMu<sup>x</sup>
*/
#ifndef DUMUX_EXCEPTIONS_HH
#define DUMUX_EXCEPTIONS_HH
@@ -29,7 +30,7 @@
namespace Dumux {
/*!
- * \ingroup Exception
+ * \ingroup Common
* \brief Exception thrown if a fixable numerical problem occurs.
*
* (e.g. time step too big, etc.)
@@ -52,7 +53,7 @@ public:
};
/*!
- * \ingroup Exception
+ * \ingroup Common
* \brief Exception thrown if a run-time parameter is not specified correctly.
*/
class ParameterException : public Dune::Exception
diff --git a/dumux/common/fixedlengthspline_.hh b/dumux/common/fixedlengthspline_.hh
index 0341b22252..575e897940 100644
--- a/dumux/common/fixedlengthspline_.hh
+++ b/dumux/common/fixedlengthspline_.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Implements a spline with a fixed number of sampling points
*/
#ifndef DUMUX_FIXED_LENGTH_SPLINE_HH
@@ -29,9 +30,10 @@
#include "splinecommon_.hh"
-namespace Dumux
-{
+namespace Dumux {
+
/*!
+ * \ingroup Common
* \brief The common code for all 3rd order polynomial splines with
* more than two sampling points.
*/
@@ -407,6 +409,6 @@ protected:
BlockVector m_;
};
-}
+} // end namespace Dumux
#endif
diff --git a/dumux/common/fvproblem.hh b/dumux/common/fvproblem.hh
index 15819a5eaa..807f4741c2 100644
--- a/dumux/common/fvproblem.hh
+++ b/dumux/common/fvproblem.hh
@@ -18,7 +18,8 @@
*****************************************************************************/
/*!
* \file
- * \brief Base class for all problems
+ * \ingroup Common
+ * \brief Base class for all finite volume problems
*/
#ifndef DUMUX_FV_PROBLEM_HH
#define DUMUX_FV_PROBLEM_HH
@@ -33,12 +34,10 @@
#include <dumux/common/parameters.hh>
#include <dumux/discretization/methods.hh>
-//#include <dumux/io/restart.hh>
+namespace Dumux {
-namespace Dumux
-{
/*!
- * \ingroup Problems
+ * \ingroup Common
* \brief Base class for all finite-volume problems
*
* \note All quantities (regarding the units) are specified assuming a
@@ -81,8 +80,7 @@ class FVProblem
public:
/*!
* \brief Constructor
- *
- * \param gridView The simulation's idea about physical space
+ * \param fvGridGeometry The finite volume grid geometry
*/
FVProblem(std::shared_ptr<const FVGridGeometry> fvGridGeometry)
: fvGridGeometry_(fvGridGeometry)
@@ -178,10 +176,11 @@ public:
/*!
* \brief Evaluate the boundary conditions for a dirichlet
- * control volume.
+ * control volume face.
*
* \param element The finite element
* \param scvf the sub control volume face
+ * \note used for cell-centered discretization schemes
*
* The method returns the boundary types information.
*/
@@ -196,6 +195,16 @@ public:
return asImp_().dirichletAtPos(scvf.ipGlobal());
}
+ /*!
+ * \brief Evaluate the boundary conditions for a dirichlet
+ * control volume.
+ *
+ * \param element The finite element
+ * \param scv the sub control volume
+ * \note used for cell-centered discretization schemes
+ *
+ * The method returns the boundary types information.
+ */
PrimaryVariables dirichlet(const Element &element, const SubControlVolume &scv) const
{
// forward it to the method which only takes the global coordinate
@@ -214,8 +223,6 @@ public:
* \param globalPos The position of the center of the finite volume
* for which the dirichlet condition ought to be
* set in global coordinates
- *
- * For this method, the \a values parameter stores primary variables.
*/
PrimaryVariables dirichletAtPos(const GlobalPosition &globalPos) const
{
@@ -232,23 +239,19 @@ public:
* boundary segment.
*
* This is the method for the case where the Neumann condition is
- * potentially solution dependent and requires some quantities that
- * are specific to the fully-implicit method.
+ * potentially solution dependent
*
- * \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
* \param scvf The sub control volume face
*
- * For this method, the \a values parameter stores the flux
- * in normal direction of each phase. Negative values mean influx.
+ * Negative values mean influx.
* E.g. for the mass balance that would the mass flux in \f$ [ kg / (m^2 \cdot s)] \f$.
*/
ResidualVector neumann(const Element& element,
const FVElementGeometry& fvGeometry,
- const ElementVolumeVariables& elemVolvars,
+ const ElementVolumeVariables& elemVolVars,
const SubControlVolumeFace& scvf) const
{
// forward it to the interface with only the global position
@@ -261,8 +264,7 @@ public:
*
* \param globalPos The position of the boundary face's integration point in global coordinates
*
- * For this method, the \a values parameter stores the flux
- * in normal direction of each phase. Negative values mean influx.
+ * Negative values mean influx.
* E.g. for the mass balance that would be the mass flux in \f$ [ kg / (m^2 \cdot s)] \f$.
*/
ResidualVector neumannAtPos(const GlobalPosition &globalPos) const
@@ -285,7 +287,7 @@ public:
* \param elemVolVars All volume variables for the element
* \param scv The sub control volume
*
- * For this method, the \a values parameter stores the conserved quantity rate
+ * For this method, the return parameter stores the conserved quantity rate
* generated or annihilate per volume unit. Positive values mean
* that the conserved quantity is created, negative ones mean that it vanishes.
* E.g. for the mass balance that would be a mass rate in \f$ [ kg / (m^3 \cdot s)] \f$.
@@ -307,7 +309,7 @@ public:
* for which the source term ought to be
* specified in global coordinates
*
- * For this method, the \a values parameter stores the conserved quantity rate
+ * For this method, the values parameter stores the conserved quantity rate
* generated or annihilate per volume unit. Positive values mean
* that the conserved quantity is created, negative ones mean that it vanishes.
* E.g. for the mass balance that would be a mass rate in \f$ [ kg / (m^3 \cdot s)] \f$.
@@ -326,7 +328,7 @@ public:
* \param pointSources A vector of PointSource s that contain
source values for all phases and space positions.
*
- * For this method, the \a values method of the point source
+ * For this method, the values method of the point source
* has to return the absolute rate values in units
* \f$ [ \textnormal{unit of conserved quantity} / s ] \f$.
* Positive values mean that the conserved quantity is created, negative ones mean that it vanishes.
@@ -339,8 +341,7 @@ public:
* for all phases within a given sub-control-volume.
*
* This is the method for the case where the point source is
- * solution dependent and requires some quantities that
- * are specific to the fully-implicit method.
+ * solution dependent
*
* \param source A single point source
* \param element The finite element
@@ -348,7 +349,7 @@ public:
* \param elemVolVars All volume variables for the element
* \param scv The sub control volume
*
- * For this method, the \a values() method of the point sources returns
+ * For this method, the values() method of the point sources returns
* the absolute conserved quantity rate generated or annihilate in
* units \f$ [ \textnormal{unit of conserved quantity} / s ] \f$.
* Positive values mean that the conserved quantity is created, negative ones mean that it vanishes.
@@ -453,7 +454,7 @@ public:
/*!
* \brief Applies the initial solution for all degrees of freedom of the grid.
- *
+ * \param sol the initial solution vector
*/
void applyInitialSolution(SolutionVector& sol) const
{
@@ -524,165 +525,6 @@ public:
// \}
- /*!
- * \name Simulation steering
- */
- // \{
-
- /*!
- * \brief TODO serialization
- */
- // void timeIntegration()
- // {
- // // if the simulation run is about to abort, write restart files for the current and previous time steps:
- // // write restart file for the current time step
- // serialize();
-
- // //write restart file for the previous time step:
- // //set the time manager and the solution vector to the previous time step
- // const Scalar time = timeManager().time();
- // timeManager().setTime(time - timeManager().previousTimeStepSize());
- // const auto curSol = model_.curSol();
- // model_.curSol() = model_.prevSol();
- // //write restart file
- // serialize();
- // //reset time manager and solution vector
- // model_.curSol() = curSol;
- // timeManager().setTime(time);
- // }
-
- // TODO could be move to the episode manager that is user implemented?
- // /*!
- // * \brief Called when the end of an simulation episode is reached.
- // *
- // * Typically a new episode should be started in this method.
- // */
- // void episodeEnd()
- // {
- // std::cerr << "The end of an episode is reached, but the problem "
- // << "does not override the episodeEnd() method. "
- // << "Doing nothing!\n";
- // }
- // \}
-
- /*!
- * \name TODO: Restart mechanism
- */
- // \{
-
- /*!
- * \brief This method writes the complete state of the simulation
- * to the harddisk.
- *
- * The file will start with the prefix returned by the name()
- * method, has the current time of the simulation clock in it's
- * name and uses the extension <tt>.drs</tt>. (Dumux ReStart
- * file.) See Restart for details.
- */
- // void serialize()
- // {
- // using Restarter = Restart;
- // Restarter res;
- // res.serializeBegin(asImp_());
- // if (gridView().comm().rank() == 0)
- // std::cout << "Serialize to file '" << res.fileName() << "'\n";
-
- // timeManager().serialize(res);
- // asImp_().serialize(res);
- // res.serializeEnd();
- // }
-
- /*!
- * \brief This method writes the complete state of the problem
- * to the harddisk.
- *
- * The file will start with the prefix returned by the name()
- * method, has the current time of the simulation clock in it's
- * name and uses the extension <tt>.drs</tt>. (Dumux ReStart
- * file.) See Restart for details.
- *
- * \tparam Restarter The serializer type
- *
- * \param res The serializer object
- */
- // template <class Restarter>
- // void serialize(Restarter &res)
- // {
- // vtkOutputModule_->serialize(res);
- // model().serialize(res);
- // }
-
- /*!
- * \brief Load a previously saved state of the whole simulation
- * from disk.
- *
- * \param tRestart The simulation time on which the program was
- * written to disk.
- */
- // void restart(const Scalar tRestart)
- // {
- // using Restarter = Restart;
-
- // Restarter res;
-
- // res.deserializeBegin(asImp_(), tRestart);
- // if (gridView().comm().rank() == 0)
- // std::cout << "Deserialize from file '" << res.fileName() << "'\n";
- // timeManager().deserialize(res);
- // asImp_().deserialize(res);
- // res.deserializeEnd();
- // }
-
- /*!
- * \brief This method restores the complete state of the problem
- * from disk.
- *
- * It is the inverse of the serialize() method.
- *
- * \tparam Restarter The deserializer type
- *
- * \param res The deserializer object
- */
- // template <class Restarter>
- // void deserialize(Restarter &res)
- // {
- // vtkOutputModule_->deserialize(res);
- // model().deserialize(res);
- // }
-
- // \}
-
- // TODO this can probably be a setter function for the assembler
- /*!
- * \brief Function to add additional DOF dependencies, i.e. the residual of DOF globalIdx depends
- * on additional DOFs not included in the discretization schemes' occupation pattern
- *
- * \param globalIdx The index of the DOF that depends on additional DOFs
- * \return A vector of the additional DOFs the DOF with index globalIdx depends on
- *
- * \note This will lead to additional matrix entries and derivative computations automatically
- * This function is used when creating the matrix and when computing entries of the jacobian matrix
- * Per default we don't have additional DOFs
- */
- // std::vector<IndexType> getAdditionalDofDependencies(IndexType globalIdx) const
- // { return std::vector<IndexType>(); }
-
- // TODO is this necessary or can it just be meshed?
- /*!
- * \brief Function to set intersections as interior boundaries. This functionality is only
- * available for models using cell-centered schemes. The corresponding boundary
- * types and conditions are obtained from the standard methods.
- *
- * \param element The finite element
- * \param intersection The intersection within the element
- * \return boolean to mark an intersection as an interior boundary
- *
- * Per default we don't have interior boundaries
- */
- // template<class T = TypeTag>
- // bool isInteriorBoundary(const Element& element, const Intersection& intersection) const
- // { return false; }
-
//! The finite volume grid geometry
const FVGridGeometry& fvGridGeometry() const
{ return *fvGridGeometry_; }
diff --git a/dumux/common/geometry/boundingboxtree.hh b/dumux/common/geometry/boundingboxtree.hh
index e3aec399d1..5c5a0f6647 100644
--- a/dumux/common/geometry/boundingboxtree.hh
+++ b/dumux/common/geometry/boundingboxtree.hh
@@ -16,6 +16,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief An axis-aligned bounding box volume hierarchy for dune grids
*
* Dumux implementation of an AABB tree
@@ -42,6 +43,7 @@ namespace Dumux
{
/*!
+ * \ingroup Common
* \brief An axis-aligned bounding box volume tree implementation
*
* The class constructs a hierarchical structure of bounding box volumes around
@@ -293,7 +295,7 @@ private:
};
/*!
- * \brief Check whether a point is intersectin a bounding box
+ * \brief Check whether a point is intersectin a bounding box (dimworld == 3)
* \param point The point
* \param b Pointer to bounding box coordinates
*/
@@ -309,6 +311,11 @@ inline bool intersectsPointBoundingBox(const Dune::FieldVector<ctype, dimworld>&
b[2] - eps2 <= point[2] && point[2] <= b[5] + eps2);
}
+/*!
+ * \brief Check whether a point is intersectin a bounding box (dimworld == 2)
+ * \param point The point
+ * \param b Pointer to bounding box coordinates
+ */
template<class ctype, int dimworld, typename std::enable_if_t<dimworld == 2, int> = 0>
inline bool intersectsPointBoundingBox(const Dune::FieldVector<ctype, dimworld>& point, const ctype* b)
{
@@ -319,6 +326,11 @@ inline bool intersectsPointBoundingBox(const Dune::FieldVector<ctype, dimworld>&
b[1] - eps1 <= point[1] && point[1] <= b[3] + eps1);
}
+/*!
+ * \brief Check whether a point is intersectin a bounding box (dimworld == 1)
+ * \param point The point
+ * \param b Pointer to bounding box coordinates
+ */
template<class ctype, int dimworld, typename std::enable_if_t<dimworld == 1, int> = 0>
inline bool intersectsPointBoundingBox(const Dune::FieldVector<ctype, dimworld>& point, const ctype* b)
{
@@ -328,7 +340,7 @@ inline bool intersectsPointBoundingBox(const Dune::FieldVector<ctype, dimworld>&
}
/*!
- * \brief Check whether a bounding box is intersecting another bounding box
+ * \brief Check whether a bounding box is intersecting another bounding box (dimworld == 3)
* \param a Pointer to first bounding box coordinates
* \param b Pointer to second bounding box coordinates
*/
@@ -346,6 +358,11 @@ inline bool intersectsBoundingBoxBoundingBox(const ctypea* a, const ctypeb* b)
}
+/*!
+ * \brief Check whether a bounding box is intersecting another bounding box (dimworld == 2)
+ * \param a Pointer to first bounding box coordinates
+ * \param b Pointer to second bounding box coordinates
+ */
template<int dimworld, class ctypea, class ctypeb, typename std::enable_if_t<dimworld == 2, int> = 0>
inline bool intersectsBoundingBoxBoundingBox(const ctypea* a, const ctypeb* b)
{
@@ -357,6 +374,11 @@ inline bool intersectsBoundingBoxBoundingBox(const ctypea* a, const ctypeb* b)
b[1] - eps1 <= a[3] && a[1] <= b[3] + eps1);
}
+/*!
+ * \brief Check whether a bounding box is intersecting another bounding box (dimworld == 1)
+ * \param a Pointer to first bounding box coordinates
+ * \param b Pointer to second bounding box coordinates
+ */
template<int dimworld, class ctypea, class ctypeb, typename std::enable_if_t<dimworld == 1, int> = 0>
inline bool intersectsBoundingBoxBoundingBox(const ctypea* a, const ctypeb* b)
{
diff --git a/dumux/common/geometry/boundingboxtreeintersection.hh b/dumux/common/geometry/boundingboxtreeintersection.hh
index d80b906c45..d3f32aa2be 100644
--- a/dumux/common/geometry/boundingboxtreeintersection.hh
+++ b/dumux/common/geometry/boundingboxtreeintersection.hh
@@ -16,6 +16,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief A class storing intersections from intersecting two bounding box trees
*/
#ifndef DUMUX_BOUNDING_BOX_TREE_INTERSECTION_HH
@@ -28,6 +29,7 @@ namespace Dumux
{
/*!
+ * \ingroup Common
* \brief An intersection object resulting from the intersection of two bounding box tree primitives
*
* After is has been found that two leaf bounding boxes intersect a primitive test has to be
diff --git a/dumux/common/geometry/geometricentityset.hh b/dumux/common/geometry/geometricentityset.hh
index e298cb14d0..50a921eeb3 100644
--- a/dumux/common/geometry/geometricentityset.hh
+++ b/dumux/common/geometry/geometricentityset.hh
@@ -16,6 +16,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief An interface for a set of geometric entities
* \note This can be used e.g. to contruct a bounding box volume hierarchy of a grid
* It defines the minimum requirement for such a set
@@ -29,6 +30,12 @@
namespace Dumux {
+/*!
+ * \ingroup Common
+ * \brief An interface for a set of geometric entities
+ * \note This can be used e.g. to contruct a bounding box volume hierarchy of a grid
+ * It defines the minimum requirement for such a set
+ */
template <class GridView, int codim = 0>
class GridViewGeometricEntitySet
{
diff --git a/dumux/common/geometry/geometryintersection.hh b/dumux/common/geometry/geometryintersection.hh
index 8095a07bb3..f541a17758 100644
--- a/dumux/common/geometry/geometryintersection.hh
+++ b/dumux/common/geometry/geometryintersection.hh
@@ -16,6 +16,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief A class for collision detection of two geometries
* and computation of intersection corners
*/
@@ -32,6 +33,7 @@ namespace Dumux
{
/*!
+ * \ingroup Common
* \brief A class for geometry collision detection and intersection calculation
* The class can be specialized for combinations of dimworld, dim1, dim2, where
* dimworld is the world dimension embedding a grid of dim1 and a grid of dim2.
diff --git a/dumux/common/geometry/intersectingentities.hh b/dumux/common/geometry/intersectingentities.hh
index 0673c61ea5..132e61f3b4 100644
--- a/dumux/common/geometry/intersectingentities.hh
+++ b/dumux/common/geometry/intersectingentities.hh
@@ -16,6 +16,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Algorithms that finds which geometric entites intersect
*/
#ifndef DUMUX_INTERSECTING_ENTITIES_HH
@@ -30,10 +31,12 @@
#include <dumux/common/geometry/geometryintersection.hh>
#include <dumux/common/geometry/boundingboxtreeintersection.hh>
-namespace Dumux
-{
+namespace Dumux {
-//! Compute all intersections between entities and a point
+/*!
+ * \ingroup Common
+ * \brief Compute all intersections between entities and a point
+ */
template<class EntitySet, class ctype, int dimworld>
inline std::vector<std::size_t>
intersectingEntities(const Dune::FieldVector<ctype, dimworld>& point,
@@ -45,7 +48,10 @@ intersectingEntities(const Dune::FieldVector<ctype, dimworld>& point,
return entities;
}
-//! Compute collisions with point for a node of the bounding box tree
+/*!
+ * \ingroup Common
+ * \brief Compute intersections with point for all nodes of the bounding box tree recursively
+ */
template<class EntitySet, class ctype, int dimworld>
void intersectingEntities(const Dune::FieldVector<ctype, dimworld>& point,
const BoundingBoxTree<EntitySet>& tree,
@@ -77,7 +83,10 @@ void intersectingEntities(const Dune::FieldVector<ctype, dimworld>& point,
}
}
-//! Compute all intersections between two bounding box trees
+/*!
+ * \ingroup Common
+ * \brief Compute all intersections between two bounding box trees
+ */
template<class EntitySet0, class EntitySet1>
inline std::vector<BoundingBoxTreeIntersection<EntitySet0, EntitySet1>>
intersectingEntities(const BoundingBoxTree<EntitySet0>& treeA,
@@ -99,7 +108,10 @@ intersectingEntities(const BoundingBoxTree<EntitySet0>& treeA,
return intersections;
}
-//! Compute all intersections between two bounding box tree nodes recursively
+/*!
+ * \ingroup Common
+ * \brief Compute all intersections between two all bounding box tree nodes recursively
+ */
template<class EntitySet0, class EntitySet1>
void intersectingEntities(const BoundingBoxTree<EntitySet0>& treeA,
const BoundingBoxTree<EntitySet1>& treeB,
diff --git a/dumux/common/geometry/intersectspointgeometry.hh b/dumux/common/geometry/intersectspointgeometry.hh
index 4b13fd0359..cf944fc2f1 100644
--- a/dumux/common/geometry/intersectspointgeometry.hh
+++ b/dumux/common/geometry/intersectspointgeometry.hh
@@ -16,6 +16,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Detect if a point intersects a geometry
*/
#ifndef DUMUX_INTERSECTS_POINT_GEOMETRY_HH
@@ -29,7 +30,10 @@
namespace Dumux {
-//! Find out whether a point is inside a three-dimensional geometry
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a three-dimensional geometry
+ */
template <class ctype, int dimworld, class Geometry, typename std::enable_if_t<(Geometry::mydimension == 3), int> = 0>
bool intersectsPointGeometry(const Dune::FieldVector<ctype, dimworld>& point, const Geometry& g)
{
@@ -74,7 +78,10 @@ bool intersectsPointGeometry(const Dune::FieldVector<ctype, dimworld>& point, co
<< type << " in " << dimworld << "-dimensional world.");
}
-//! Find out whether a point is inside a two-dimensional geometry
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a two-dimensional geometry
+ */
template <class ctype, int dimworld, class Geometry, typename std::enable_if_t<(Geometry::mydimension == 2), int> = 0>
bool intersectsPointGeometry(const Dune::FieldVector<ctype, dimworld>& point, const Geometry& g)
{
@@ -99,7 +106,10 @@ bool intersectsPointGeometry(const Dune::FieldVector<ctype, dimworld>& point, co
<< type << " in " << dimworld << "-dimensional world.");
}
-//! Find out whether a point is inside a one-dimensional geometry
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a one-dimensional geometry
+ */
template <class ctype, int dimworld, class Geometry, typename std::enable_if_t<(Geometry::mydimension == 1), int> = 0>
bool intersectsPointGeometry(const Dune::FieldVector<ctype, dimworld>& point, const Geometry& g)
{
diff --git a/dumux/common/geometry/intersectspointsimplex.hh b/dumux/common/geometry/intersectspointsimplex.hh
index 601f189057..603eb7bc61 100644
--- a/dumux/common/geometry/intersectspointsimplex.hh
+++ b/dumux/common/geometry/intersectspointsimplex.hh
@@ -16,6 +16,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Detect if a point intersects a simplex (including boundary)
*/
#ifndef DUMUX_INTERSECTS_POINT_SIMPLEX_HH
@@ -27,7 +28,10 @@
namespace Dumux {
-//! Find out whether a point is inside a tetrahedron (p0, p1, p2, p3) (dimworld is 3)
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a tetrahedron (p0, p1, p2, p3) (dimworld is 3)
+ */
template<class ctype, int dimworld, typename std::enable_if_t<(dimworld == 3), int> = 0>
bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
const Dune::FieldVector<ctype, dimworld>& p0,
@@ -66,7 +70,10 @@ bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
return true;
}
-//! Find out whether a point is inside a triangle (p0, p1, p2) (dimworld is 3)
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a triangle (p0, p1, p2, p3) (dimworld is 3)
+ */
template<class ctype, int dimworld, typename std::enable_if_t<(dimworld == 3), int> = 0>
bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
const Dune::FieldVector<ctype, dimworld>& p0,
@@ -112,7 +119,10 @@ bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
return true;
}
-//! Find out whether a point is inside a triangle (p0, p1, p2) (dimworld is 2)
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a triangle (p0, p1, p2, p3) (dimworld is 2)
+ */
template<class ctype, int dimworld, typename std::enable_if_t<(dimworld == 2), int> = 0>
bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
const Dune::FieldVector<ctype, dimworld>& p0,
@@ -136,7 +146,10 @@ bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
&& (s + t) < 2*A*sign + eps);
}
-//! Find out whether a point is inside an interval (p0, p1) (dimworld is 3)
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a interval (p0, p1, p2, p3) (dimworld is 3)
+ */
template<class ctype, int dimworld, typename std::enable_if_t<(dimworld == 3), int> = 0>
bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
const Dune::FieldVector<ctype, dimworld>& p0,
@@ -173,7 +186,10 @@ bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
return (v1.dot(v2) > 0.0 && v2norm < v1norm*(1 + eps_));
}
-//! Find out whether a point is inside an interval (p0, p1) (dimworld is 2)
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a interval (p0, p1, p2, p3) (dimworld is 2)
+ */
template<class ctype, int dimworld, typename std::enable_if_t<(dimworld == 2), int> = 0>
bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
const Dune::FieldVector<ctype, dimworld>& p0,
@@ -211,7 +227,10 @@ bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
return (v1.dot(v2) > 0.0 && v2norm < v1norm*(1 + eps_));
}
-//! Find out whether a point is inside an interval (p0, p1) (dimworld is 1)
+/*!
+ * \ingroup Common
+ * \brief Find out whether a point is inside a interval (p0, p1, p2, p3) (dimworld is 1)
+ */
template<class ctype, int dimworld, typename std::enable_if_t<(dimworld == 1), int> = 0>
bool intersectsPointSimplex(const Dune::FieldVector<ctype, dimworld>& point,
const Dune::FieldVector<ctype, dimworld>& p0,
diff --git a/dumux/common/intersectionmapper.hh b/dumux/common/intersectionmapper.hh
index d69b376e79..558b310117 100644
--- a/dumux/common/intersectionmapper.hh
+++ b/dumux/common/intersectionmapper.hh
@@ -15,6 +15,11 @@
* 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
+ * \ingroup Common
+ * \brief defines intersection mappers.
+ */
#ifndef DUMUX_INTERSECTIONITERATOR_HH
#define DUMUX_INTERSECTIONITERATOR_HH
@@ -26,15 +31,12 @@
#include <dune/common/version.hh>
-/*!
- * \file
- * \brief defines intersection mappers.
- */
namespace Dumux
{
/*!
+ * \ingroup Common
* \brief defines a standard intersection mapper for mapping of global DOFs assigned
* to faces. It only works for conforming grids, without hanging nodes.
*/
@@ -79,6 +81,7 @@ private:
};
/*!
+ * \ingroup Common
* \brief defines an intersection mapper for mapping of global DOFs assigned
* to faces which also works for non-conforming grids and corner-point grids.
*/
@@ -177,6 +180,7 @@ private:
};
/*!
+ * \ingroup Common
* \brief defines an intersection mapper for mapping of global DOFs assigned
* to faces which also works for adaptive grids.
*/
@@ -391,6 +395,6 @@ protected:
std::unordered_map<int, int> standardLocalIdxMap_;
};
-}
+} // end namespace Dumux
#endif
diff --git a/dumux/common/intrange.hh b/dumux/common/intrange.hh
index 82dbef661d..ef9ad36f16 100644
--- a/dumux/common/intrange.hh
+++ b/dumux/common/intrange.hh
@@ -18,15 +18,16 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief A class to create an iterable integer range
*/
#ifndef DUMUX_INTEGER_RANGE_HH
#define DUMUX_INTEGER_RANGE_HH
-namespace Dumux
-{
+namespace Dumux {
/*!
+ * \ingroup Common
* \brief This class generates a IntRange [a,b) which can be used in a for loop, e.g.
* for(auto i : IntRange(3) { ... i = 0, 1, 2 } or
* for(auto i : IntRange(5, 8) { ... i = 5, 6, 7 }
diff --git a/dumux/common/loggingparametertree.hh b/dumux/common/loggingparametertree.hh
index 19d4b9c746..4a55800e4b 100644
--- a/dumux/common/loggingparametertree.hh
+++ b/dumux/common/loggingparametertree.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief A parameter tree that logs which parameters have been used
*/
#ifndef DUMUX_LOGGING_PARAMETER_TREE_HH
@@ -28,9 +29,7 @@
#include <string>
#include <dune/common/parametertree.hh>
-
#include <dumux/common/exceptions.hh>
-#include <dumux/common/parameters.hh>
namespace Dumux
{
@@ -76,7 +75,6 @@ public:
* Prints all entries with given prefix.
*
* \param stream Stream to print to
- * \param prefix for key and substructure names
*/
void reportAll(std::ostream& stream = std::cout) const
{
@@ -415,7 +413,7 @@ public:
/** \brief Find the keys that haven't been used yet
*
- * \retuns unusedParams Container storing unused keys
+ * \return unusedParams Container storing unused keys
* \note Useful for debugging purposes
*/
std::vector<std::string> getUnusedKeys() const
diff --git a/dumux/common/math.hh b/dumux/common/math.hh
index c1224fd0c7..c6777d5f8d 100644
--- a/dumux/common/math.hh
+++ b/dumux/common/math.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Define some often used mathematical functions
*/
#ifndef DUMUX_MATH_HH
@@ -34,7 +35,7 @@
namespace Dumux
{
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Calculate the harmonic mean of two scalar values.
*
* \param x The first input value
@@ -49,7 +50,7 @@ Scalar harmonicMean(Scalar x, Scalar y)
}
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Calculate the geometric mean of two scalar values.
*
* \param x The first input value
@@ -65,7 +66,7 @@ Scalar geometricMean(Scalar x, Scalar y)
}
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Calculate the harmonic mean of a fixed-size matrix.
*
* This is done by calculating the harmonic mean for each entry
@@ -94,7 +95,7 @@ void harmonicMeanMatrix(Dune::FieldMatrix<Scalar, m, n> &K,
}
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Invert a linear polynomial analytically
*
* The polynomial is defined as
@@ -120,7 +121,7 @@ int invertLinearPolynomial(SolContainer &sol,
}
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Invert a quadratic polynomial analytically
*
* The polynomial is defined as
@@ -193,7 +194,7 @@ void invertCubicPolynomialPostProcess_(SolContainer &sol,
//! \endcond
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Invert a cubic polynomial analytically
*
* The polynomial is defined as
@@ -382,7 +383,7 @@ int invertCubicPolynomial(SolContainer *sol,
}
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Comparison of two position vectors
*
* Compares an current position vector with a reference vector, and returns true
@@ -408,7 +409,7 @@ bool isLarger(const Dune::FieldVector<Scalar, dim> &pos,
}
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Comparison of two position vectors
*
* Compares an current position vector with a reference vector, and returns true
@@ -434,7 +435,7 @@ bool isSmaller(const Dune::FieldVector<Scalar, dim> &pos,
}
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Comparison of three position vectors
*
* Compares an current position vector with two reference vector, and returns true
@@ -464,7 +465,7 @@ bool isBetween(const Dune::FieldVector<Scalar, dim> &pos,
/*!
- * \ingroup Math
+ * \ingroup Common
* \brief Evaluates the Antoine equation used to calculate the vapour
* pressure of various liquids.
*
@@ -487,6 +488,7 @@ Scalar antoine(Scalar temperature,
}
/*!
+ * \ingroup Common
* \brief Sign or signum function.
*
* Returns 1 for a positive argument.
@@ -500,6 +502,7 @@ int sign(const ValueType& value)
}
/*!
+ * \ingroup Common
* \brief Cross product of two vectors in three-dimensional Euclidean space
*
* \param vec1 The first vector
@@ -515,6 +518,7 @@ Dune::FieldVector<Scalar, 3> crossProduct(const Dune::FieldVector<Scalar, 3> &ve
}
/*!
+ * \ingroup Common
* \brief Cross product of two vectors in two-dimensional Euclidean space retuning scalar
*
* \param vec1 The first vector
@@ -526,6 +530,7 @@ Scalar crossProduct(const Dune::FieldVector<Scalar, 2> &vec1,
{ return vec1[0]*vec2[1]-vec1[1]*vec2[0]; }
/*!
+ * \ingroup Common
* \brief Triple product of three vectors in three-dimensional Euclidean space retuning scalar
*
* \param vec1 The first vector
@@ -539,6 +544,7 @@ Scalar tripleProduct(const Dune::FieldVector<Scalar, 3> &vec1,
{ return crossProduct<Scalar>(vec1, vec2)*vec3; }
/*!
+ * \ingroup Common
* \brief Transpose a FieldMatrix
*
* \param M The matrix to be transposed
@@ -555,6 +561,7 @@ Dune::FieldMatrix<Scalar, n, m> getTransposed(const Dune::FieldMatrix<Scalar, m,
}
/*!
+ * \ingroup Common
* \brief Transpose a DynamicMatrix
*
* \param M The matrix to be transposed
@@ -575,6 +582,7 @@ Dune::DynamicMatrix<Scalar> getTransposed(const Dune::DynamicMatrix<Scalar>& M)
}
/*!
+ * \ingroup Common
* \brief Multiply two dynamic matrices
*
* \param M1 The first dynamic matrix
@@ -600,6 +608,7 @@ Dune::DynamicMatrix<Scalar> multiplyMatrices(const Dune::DynamicMatrix<Scalar> &
}
/*!
+ * \ingroup Common
* \brief Trace of dynamic matrix
*
* \param M The dynamic matrix
@@ -620,6 +629,7 @@ Scalar trace(const Dune::DynamicMatrix<Scalar>& M)
}
/*!
+ * \ingroup Common
* \brief Evaluates the scalar product of a vector v2, projected by
* a matrix M, with a vector v1.
*
@@ -644,6 +654,7 @@ vtmv(const Dune::DenseVector<V1>& v1,
}
/*!
+ * \ingroup Common
* \brief Evaluates the scalar product of a vector v2, scaled by
* a scalar m, with a vector v1.
*
diff --git a/dumux/common/optional.hh b/dumux/common/optional.hh
index 0207724e75..9f2b8aae36 100644
--- a/dumux/common/optional.hh
+++ b/dumux/common/optional.hh
@@ -18,9 +18,10 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief A wrapper that can either contain an object of T or be empty.
* This might be used as a workaround for non-default constructible classes.
- * \note This was adopted from dune-functions.
+ * \note Replace this with std::optional when C++17 is available
*/
#ifndef DUMUX_COMMON_OPTIONAL_HH
#define DUMUX_COMMON_OPTIONAL_HH
@@ -31,11 +32,9 @@
namespace Dumux {
-/**
+/*!
+ * \ingroup Common
* \brief A wrapper that can either contain an object of T or be empty
- *
- * \ingroup Utility
- *
* \tparam T Type of wrapped objects
*/
template<class T>
diff --git a/dumux/common/parameters.hh b/dumux/common/parameters.hh
index 97d6173c93..d81b5fd1b2 100644
--- a/dumux/common/parameters.hh
+++ b/dumux/common/parameters.hh
@@ -17,9 +17,8 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
/*!
- * \ingroup Parameter
* \file
- *
+ * \ingroup Common
* \brief The infrastructure to retrieve run-time parameters from
* Dune::ParameterTrees with the defaul value taken from the
* property system.
@@ -42,8 +41,9 @@
#include <dumux/common/defaultusagemessage.hh>
#include <dumux/common/loggingparametertree.hh>
+#ifndef DOXYGEN // hide deprecated macros from doxygen
/*!
- * \ingroup Parameter
+ * \ingroup Common
* \brief Retrieve a runtime parameter which _does_ have a default value taken from
* the Dumux property system.
*
@@ -59,7 +59,7 @@
// ::Dumux::template getParam_UsingDeprecatedMacro<ParamType>(std::string(#ParamName), GET_PROP_VALUE(TypeTag, ParamName))
/*!
- * \ingroup Parameter
+ * \ingroup Common
* \brief Retrieve a runtime parameter which _does_ have a default value taken from
* the Dumux property system.
*
@@ -79,7 +79,7 @@
/*!
- * \ingroup Parameter
+ * \ingroup Common
* \brief Retrieve a runtime parameter which _does not_ have a default value taken from
* the Dumux property system.
*
@@ -94,7 +94,7 @@
::Dumux::template getParam_UsingDeprecatedMacro<ParamType>(std::string(#ParamName))
/*!
- * \ingroup Parameter
+ * \ingroup Common
* \brief Retrieve a runtime parameter which _does not_ have a default value taken from
* the Dumux property system.
*
@@ -123,7 +123,7 @@
::Dumux::template getParam_UsingDeprecatedMacro<ParamType>(std::string(ParamName))
/*!
- * \ingroup Parameter
+ * \ingroup Common
* \brief Retrieve a runtime parameter which _does not_ have a default value taken from
* the Dumux property system.
*
@@ -141,7 +141,7 @@
::Dumux::template getParam_UsingDeprecatedMacro<ParamType>(std::string(#GroupName) + "." + std::string(#ParamName))
/*!
- * \ingroup Parameter
+ * \ingroup Common
* \brief Retrieve a runtime parameter which _does not_ have a default value taken from
* the Dumux property system.
*
@@ -171,10 +171,15 @@
#define GET_RUNTIME_PARAM_FROM_GROUP_CSTRING(TypeTag, ParamType, GroupName, ParamName) \
::Dumux::template getParam_UsingDeprecatedMacro<ParamType>(std::string(GroupName) + "." + std::string(#ParamName))
-namespace Dumux
-{
+#endif // DOXYGEN
-//! The runtime parameter managing class
+namespace Dumux {
+
+/*!
+ * \ingroup Common
+ * \brief Parameter class managing runtime input parameters
+ * \todo Doc me!
+ */
class Parameters {
using DefaultParams = std::function<void (Dune::ParameterTree&)>;
@@ -399,8 +404,11 @@ void setParam(Dune::ParameterTree& params,
params[group + "." + key] = value;
}
-// a free function to get a parameter from the parameter tree singleton
-// e.g. auto endTime = getParam<double>("TimeManager.TEnd");
+/*!
+ * \ingroup Common
+ * \brief A free function to get a parameter from the parameter tree singleton
+ * \note \code auto endTime = getParam<double>("TimeManager.TEnd"); \endcode
+ */
template<typename T, typename... Args>
T getParam(Args&&... args)
{
@@ -408,8 +416,11 @@ T getParam(Args&&... args)
return p.template get<T>(std::forward<Args>(args)... );
}
-// a free function to get a parameter from the parameter tree singleton
-// e.g. auto endTime = getParam<double>("TimeManager.TEnd");
+/*!
+ * \ingroup Common
+ * \brief A free function to get a parameter from the parameter tree singleton with a model group
+ * \note \code auto endTime = getParamFromGroup<double>("FreeFlow", "TimeManager.TEnd"); \endcode
+ */
template<typename T, typename... Args>
T getParamFromGroup(Args&&... args)
{
@@ -417,14 +428,20 @@ T getParamFromGroup(Args&&... args)
return p.template getFromGroup<T>(std::forward<Args>(args)... );
}
-// a free function to check whether a key exists
+/*!
+ * \ingroup Common
+ * \brief Check whether a key exists in the parameter tree
+ */
bool haveParam(const std::string& param)
{
const auto& p = Parameters::getTree();
return p.hasKey(param);
}
-// a free function to check whether a key exists
+/*!
+ * \ingroup Common
+ * \brief Check whether a key exists in the parameter tree with a model group prefix
+ */
template<typename... Args>
bool haveParamInGroup(const std::string& paramGroup, const std::string& param)
{
@@ -435,6 +452,7 @@ bool haveParamInGroup(const std::string& paramGroup, const std::string& param)
return p.hasKey(paramGroup + "." + param);
}
+#ifndef DOXYGEN
template<typename T, typename... Args>
DUNE_DEPRECATED_MSG("Using preprocessor MACROS for getting parameters is deprecated on next. Please use the new getParam method.")
T getParam_UsingDeprecatedMacro(Args&&... args)
@@ -442,6 +460,7 @@ T getParam_UsingDeprecatedMacro(Args&&... args)
const auto& p = Parameters::getTree();
return p.template get<T>(std::forward<Args>(args)... );
}
+#endif
} // namespace Dumux
diff --git a/dumux/common/pointsource.hh b/dumux/common/pointsource.hh
index b2ed400a45..4fdbfcbc4e 100644
--- a/dumux/common/pointsource.hh
+++ b/dumux/common/pointsource.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief A point source class,
* i.e. sources located at a single point in space
*/
diff --git a/dumux/common/properties.hh b/dumux/common/properties.hh
index 95dbf79f5a..ad0a554530 100644
--- a/dumux/common/properties.hh
+++ b/dumux/common/properties.hh
@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
/*!
- * \ingroup Properties
+ * \ingroup Common
* \file
*
* \brief _Declares_ all properties used in Dumux.
@@ -31,10 +31,9 @@
#include <dumux/common/properties/propertysystem.hh>
#endif
-namespace Dumux
-{
-namespace Properties
-{
+namespace Dumux {
+namespace Properties {
+
///////////////////////////////////////
// Basic properties of numeric models:
///////////////////////////////////////
diff --git a/dumux/common/properties/grid.hh b/dumux/common/properties/grid.hh
index eae670a9f1..2c0c581bc5 100644
--- a/dumux/common/properties/grid.hh
+++ b/dumux/common/properties/grid.hh
@@ -17,23 +17,20 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
/*!
- * \ingroup Properties
* \file
- *
+ * \ingroup Properties
* \brief Defines a type tags and some fundamental grid-related properties
*/
#ifndef DUMUX_GRID_PROPERTIES_HH
#define DUMUX_GRID_PROPERTIES_HH
-#include <dumux/common/properties.hh>
-
+#include <dune/common/version.hh>
#include <dune/grid/common/mcmgmapper.hh>
+#include <dumux/common/properties.hh>
#include <dumux/common/pointsource.hh>
#include <dumux/io/gridcreator.hh>
-#include <dune/common/version.hh>
-
namespace Dumux
{
namespace Properties
diff --git a/dumux/common/properties/model.hh b/dumux/common/properties/model.hh
index cb787a87d4..94ab4fb277 100644
--- a/dumux/common/properties/model.hh
+++ b/dumux/common/properties/model.hh
@@ -17,11 +17,9 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
/*!
- * \ingroup Properties
* \file
- *
- * \brief Defines a type tags and some fundamental properties for
- * all models
+ * \ingroup Properties
+ * \brief Defines a type tags and some fundamental properties for all models
*/
#ifndef DUMUX_MODEL_PROPERTIES_HH
#define DUMUX_MODEL_PROPERTIES_HH
@@ -35,10 +33,9 @@
// Forward declaration
namespace Dune { class ParameterTree; }
-namespace Dumux
-{
-namespace Properties
-{
+namespace Dumux {
+namespace Properties {
+
//! Type tag for numeric models.
NEW_TYPE_TAG(ModelProperties);
diff --git a/dumux/common/properties/propertysystem.hh b/dumux/common/properties/propertysystem.hh
index 85b1725ded..e5adf3cddc 100644
--- a/dumux/common/properties/propertysystem.hh
+++ b/dumux/common/properties/propertysystem.hh
@@ -19,8 +19,8 @@
/*!
* \file
* \brief Provides the magic behind the DuMuX property system.
- *
* \ingroup Properties
+ *
* Properties allow to associate arbitrary data types to
* identifiers. A property is always defined on a pair (TypeTag,
* PropertyTag) where TypeTag is the identifier for the object the
diff --git a/dumux/common/quad.hh b/dumux/common/quad.hh
index 7ff9842975..f0a50fc500 100644
--- a/dumux/common/quad.hh
+++ b/dumux/common/quad.hh
@@ -18,7 +18,7 @@
*****************************************************************************/
/*!
* \file
- *
+ * \ingroup Common
* \brief This file provides the infrastructure to use quad-precision
* floating point values in the numerical models.
*/
diff --git a/dumux/common/reorderingdofmapper.hh b/dumux/common/reorderingdofmapper.hh
index e15fc11391..56ed39360e 100644
--- a/dumux/common/reorderingdofmapper.hh
+++ b/dumux/common/reorderingdofmapper.hh
@@ -19,6 +19,7 @@
/*!
* \file
+ * \ingroup Common
* \brief An SCSG element mapper that sorts the indices in order to optimize the matrix sparsity pattern
* \note The reordering needs the SCOTCH library
*/
@@ -33,6 +34,11 @@
namespace Dumux
{
+/*!
+ * \ingroup Common
+ * \brief An SCSG element mapper that sorts the indices in order to optimize the matrix sparsity pattern
+ * \note The reordering needs the SCOTCH library
+ */
template<class GridView, int codimension>
class ReorderingDofMapper
: public Dune::Mapper<typename GridView::Grid, ReorderingDofMapper<GridView, codimension>, typename GridView::IndexSet::IndexType>
diff --git a/dumux/common/spline.hh b/dumux/common/spline.hh
index de3758578f..edcb038eef 100644
--- a/dumux/common/spline.hh
+++ b/dumux/common/spline.hh
@@ -17,6 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
*****************************************************************************/
/*!
+ * \ingroup Common
* \file
* \brief Provides 3rd order polynomial splines.
*/
@@ -30,7 +31,7 @@
namespace Dumux
{
/*!
- * \ingroup Spline
+ * \ingroup Common
* \brief A 3rd order polynomial spline.
* This class implements a spline \f$s(x)\f$ for which, given \f$n\f$ sampling
diff --git a/dumux/common/splinecommon_.hh b/dumux/common/splinecommon_.hh
index 194d1a420f..fd9a8ff038 100644
--- a/dumux/common/splinecommon_.hh
+++ b/dumux/common/splinecommon_.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief The common code for all 3rd order polynomial splines.
*/
#ifndef DUMUX_SPLINE_COMMON__HH
@@ -33,9 +34,10 @@
#include "math.hh"
#include "valgrind.hh"
-namespace Dumux
-{
+namespace Dumux {
+
/*!
+ * \ingroup Common
* \brief The common code for all 3rd order polynomial splines.
*/
template<class ScalarT, class ImplementationT>
diff --git a/dumux/common/staggeredfvproblem.hh b/dumux/common/staggeredfvproblem.hh
index a311c1e5dc..89d1e90fcd 100644
--- a/dumux/common/staggeredfvproblem.hh
+++ b/dumux/common/staggeredfvproblem.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Base class for all problems
*/
#ifndef DUMUX_STAGGERD_FV_PROBLEM_HH
@@ -30,6 +31,7 @@ namespace Dumux
{
/*!
* \ingroup Problems
+ * \ingroup Common
* \brief Base class for all finite-volume problems
*
* \note All quantities (regarding the units) are specified assuming a
@@ -67,8 +69,7 @@ class StaggeredFVProblem : public FVProblem<TypeTag>
public:
/*!
* \brief Constructor
- *
- * \param gridView The simulation's idea about physical space
+ * \param fvGridGeometry The finite volume grid geometry
*/
StaggeredFVProblem(std::shared_ptr<const FVGridGeometry> fvGridGeometry)
: ParentType(fvGridGeometry)
diff --git a/dumux/common/start.hh b/dumux/common/start.hh
index 62dd1fd384..f8583ec925 100644
--- a/dumux/common/start.hh
+++ b/dumux/common/start.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Provides a few default main functions for convenience.
*/
#ifndef DUMUX_START_HH
@@ -45,7 +46,7 @@ NEW_PROP_TAG(TimeManager);
}
/*!
- * \ingroup Start
+ * \ingroup Common
*
* \brief Provides a main function which reads in parameters from the
* command line and a parameter file.
diff --git a/dumux/common/tabulated2dfunction.hh b/dumux/common/tabulated2dfunction.hh
index 81bcbcb383..b1dc7b7f56 100644
--- a/dumux/common/tabulated2dfunction.hh
+++ b/dumux/common/tabulated2dfunction.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Implements tabulation for a two-dimensional function.
*/
#ifndef DUMUX_TABULATED_2D_FUNCTION_HH
@@ -26,9 +27,10 @@
#include <vector>
#include <cassert>
-namespace Dumux
-{
+namespace Dumux {
+
/*!
+ * \ingroup Common
* \brief Implements tabulation for a two-dimensional function.
*
* This class can be used to tabulate a two dimensional function
diff --git a/dumux/common/timeloop.hh b/dumux/common/timeloop.hh
index 8fc7f64fd4..d9e25ffe10 100644
--- a/dumux/common/timeloop.hh
+++ b/dumux/common/timeloop.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Manages the handling of time dependent problems
*/
#ifndef DUMUX_TIME_LOOP_HH
@@ -35,7 +36,7 @@
namespace Dumux
{
/*!
- * \ingroup SimControl
+ * \ingroup Common
* \brief Manages the handling of time dependent problems.
*
* This class facilitates the time management of the simulation.
@@ -54,14 +55,6 @@ namespace Dumux
* the (simulation) time it starts, its length and a consecutive
* index starting at 0.
*/
-
-//! The abstract base class
-//! only contains the methods needed during the assembly
-////////////////////////////////////////////////////////////////////
-//! TODO this might not be necessary if t and dt are actually passed into
-//! a time stepping method that forwards it everywhere nedded
-//! Then the time loop always stays contained in the main file
-////////////////////////////////////////////////////////////////////
template<class Scalar>
class TimeLoopBase
{
@@ -196,7 +189,7 @@ public:
/*!
* \brief Set the maximum time step size to a given value.
*
- * \param dt The new value for the maximum time step size \f$\mathrm{[s]}\f$
+ * \param maxDt The new value for the maximum time step size \f$\mathrm{[s]}\f$
*/
void setMaxTimeStepSize(Scalar maxDt)
{ maxTimeStepSize_ = maxDt; }
@@ -402,9 +395,9 @@ public:
}
/*!
- * \brief Set the maximum time step size to a given value.
- *
- * \param dt The new value for the maximum time step size \f$\mathrm{[s]}\f$
+ * \brief Set a periodic check point
+ * \note You can query if we are at a time check point with isCheckPoint()
+ * \param interval Set a periodic checkout every [interal] seconds
*/
void setPeriodicCheckPoint(Scalar interval)
{
diff --git a/dumux/common/timemanager.hh b/dumux/common/timemanager.hh
index 5dbbd2905a..df85af76f9 100644
--- a/dumux/common/timemanager.hh
+++ b/dumux/common/timemanager.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Manages the handling of time dependent problems
*/
#ifndef DUMUX_TIME_MANAGER_HH
@@ -34,16 +35,11 @@
#include "properties.hh"
#include "parameters.hh"
-namespace Dumux
-{
-namespace Properties
-{
-NEW_PROP_TAG(Scalar);
-NEW_PROP_TAG(Problem);
-}
+namespace Dumux {
/*!
- * \ingroup SimControl
+ * \ingroup Common
+ * \deprecated
* \brief Manages the handling of time dependent problems.
*
* This class facilitates the time management of the simulation.
diff --git a/dumux/common/timesteppingscheme.hh b/dumux/common/timesteppingscheme.hh
index a093729736..e6e033e4e3 100644
--- a/dumux/common/timesteppingscheme.hh
+++ b/dumux/common/timesteppingscheme.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Manages the handling of time dependent problems
*/
#ifndef DUMUX_TIME_STEPPING_SCHEME_HH
@@ -29,6 +30,7 @@ namespace Dumux
{
/*!
+ * \ingroup Common
* \brief The abstract time stepping parameter interface
*/
template <class Scalar>
@@ -59,6 +61,7 @@ public:
};
/*!
+ * \ingroup Common
* \brief The time stepping scheme class
*/
template <class Scalar>
diff --git a/dumux/common/valgrind.hh b/dumux/common/valgrind.hh
index b055d2ee09..e53098aab4 100644
--- a/dumux/common/valgrind.hh
+++ b/dumux/common/valgrind.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Some templates to wrap the valgrind macros
*/
#ifndef DUMUX_VALGRIND_HH
@@ -42,7 +43,7 @@ void voidBlubb() { }
namespace Valgrind
{
/*!
- * \ingroup Valgrind
+ * \ingroup Common
* \brief Returns whether the program is running under Valgrind or not.
*/
inline bool Running()
diff --git a/dumux/common/variablelengthspline_.hh b/dumux/common/variablelengthspline_.hh
index 21ba8d52a1..c02ea486a4 100644
--- a/dumux/common/variablelengthspline_.hh
+++ b/dumux/common/variablelengthspline_.hh
@@ -18,6 +18,7 @@
*****************************************************************************/
/*!
* \file
+ * \ingroup Common
* \brief Implements a spline with a variable number of sampling points
*/
#ifndef DUMUX_VARIABLE_LENGTH_SPLINE_HH
@@ -30,9 +31,10 @@
#include "splinecommon_.hh"
-namespace Dumux
-{
+namespace Dumux {
+
/*!
+ * \ingroup Common
* \brief The common code for all 3rd order polynomial splines with
* where the number of sampling points only known at run-time.
*/
@@ -424,6 +426,7 @@ protected:
Vector yPos_;
Vector m_;
};
-}
+
+} // end namespace Dumux
#endif
--
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