diff --git a/doc/doxygen/modules b/doc/doxygen/modules
index b90a73683537172910e02956dcccdf4085629be9..8a53a51b7bdcc07cc86fa70164bca76fb911d51c 100644
--- a/doc/doxygen/modules
+++ b/doc/doxygen/modules
@@ -114,21 +114,37 @@
* \ingroup BoxModels
* \defgroup TwoPBoxModel Two-phase
*
- * \copydetails Dumux::TwoP
+ * \copydetails Dumux::TwoPModel
*/
/*!
* \ingroup BoxModels
* \defgroup TwoPNIModel Non-isothermal two-phase
+ *
+ * \copydetails Dumux::TwoPNIModel
*/
/*!
* \ingroup BoxModels
- * \defgroup TwoPTwoCModel Two-phase two-component
+ * \defgroup TwoPTwoCModel Two-phase, two-component
*
* \copydetails Dumux::TwoPTwoCModel
*/
/*!
* \ingroup BoxModels
- * \defgroup TwoPTwoCNIModel Non-isothermal two-phase two-component
+ * \defgroup TwoPTwoCNIModel Non-isothermal two-phase, two-component
+ *
+ * \copydetails Dumux::TwoPTwoCNIModel
+ */
+ /*!
+ * \ingroup BoxModels
+ * \defgroup ThreePThreeCModel Three-phase, three-component
+ *
+ * \copydetails Dumux::ThreePThreeCModel
+ */
+ /*!
+ * \ingroup BoxModels
+ * \defgroup ThreePThreeCNIModel Non-isothermal three-phase, three-component
+ *
+ * \copydetails Dumux::ThreePThreeCNIModel
*/
/*!
* \ingroup BoxModels
diff --git a/doc/handbook/Makefile.am b/doc/handbook/Makefile.am
index 15fd96748dd5cf79f52f1e389a33d6560d9b2c9b..afea73e17878924cdeaa7b9e4e3d4a0a40f0beba 100644
--- a/doc/handbook/Makefile.am
+++ b/doc/handbook/Makefile.am
@@ -43,4 +43,8 @@ EXTRA_TEXINPUTS=$(top_srcdir)
include $(top_srcdir)/am/global-rules
include $(top_srcdir)/am/latex
+else
+doc:
+ echo -n ""
endif
+
diff --git a/dumux/boxmodels/3p3c/3p3cmodel.hh b/dumux/boxmodels/3p3c/3p3cmodel.hh
index f465c1b418f57de5f0e7dd8d102600a2df2c77f7..cc32b1c576482a4e206f8b8d5da485b6d67a1a95 100644
--- a/dumux/boxmodels/3p3c/3p3cmodel.hh
+++ b/dumux/boxmodels/3p3c/3p3cmodel.hh
@@ -41,11 +41,6 @@
namespace Dumux
{
-/*!
- * \ingroup BoxModels
- * \defgroup ThreePThreeCModel Three-phase three-component box model
- */
-
/*!
* \ingroup ThreePThreeCModel
* \brief Adaption of the BOX scheme to the three-phase three-component flow model.
diff --git a/dumux/boxmodels/3p3cni/3p3cnimodel.hh b/dumux/boxmodels/3p3cni/3p3cnimodel.hh
index c3d57c228bc450c77ce69a7289dd5e0113074188..f13a52a4ac159f65c5f139393774cb4dbd61a438 100644
--- a/dumux/boxmodels/3p3cni/3p3cnimodel.hh
+++ b/dumux/boxmodels/3p3cni/3p3cnimodel.hh
@@ -34,11 +34,6 @@
#include <dumux/boxmodels/3p3c/3p3cmodel.hh>
namespace Dumux {
-/*!
- * \ingroup BoxModels
- * \defgroup ThreePThreeCNIModel Non-isothermal three-phase three-component box model
- */
-
/*!
* \ingroup ThreePThreeCNIModel
* \brief Adaption of the BOX scheme to the non-isothermal three-phase three-component flow model.
diff --git a/dumux/boxmodels/common/boxlocalresidual.hh b/dumux/boxmodels/common/boxlocalresidual.hh
index eaf68a38a3d1174ba2822ff580b8fd3275e013e1..6682727ccb1ee01570830b24757e1b63c621462e 100644
--- a/dumux/boxmodels/common/boxlocalresidual.hh
+++ b/dumux/boxmodels/common/boxlocalresidual.hh
@@ -536,7 +536,7 @@ protected:
PrimaryVariables tmp(0.);
// mass balance within the element. this is the
- // $\frac{m}{\partial t}$ term if using implicit
+ // \f$\frac{m}{\partial t}\f$ term if using implicit
// euler as time discretization.
//
// TODO (?): we might need a more explicit way for
diff --git a/dumux/common/fixedlengthspline_.hh b/dumux/common/fixedlengthspline_.hh
index 06141f819ed36d293b3d970a6438e2cd3554b063..29b210e2a80ceec62bdf2e1e7af34c5474d77364 100644
--- a/dumux/common/fixedlengthspline_.hh
+++ b/dumux/common/fixedlengthspline_.hh
@@ -34,7 +34,6 @@
namespace Dumux
{
-//! \cond INTERNAL
/*!
* \brief The common code for all 3rd order polynomial splines with
* more than two sampling points.
@@ -461,8 +460,6 @@ protected:
BlockVector m_;
};
-//! \endcond
-
}
#endif
diff --git a/dumux/common/splinecommon_.hh b/dumux/common/splinecommon_.hh
index ab7060f7325d70149868c28587b3cae533bd5207..58f2e1946023397561bbdf1be4575a8c15df1b3c 100644
--- a/dumux/common/splinecommon_.hh
+++ b/dumux/common/splinecommon_.hh
@@ -44,9 +44,7 @@ using tr1::get;
namespace Dumux
{
-//! \cond INTERNAL
/*!
- *
* \brief The common code for all 3rd order polynomial splines.
*/
template<class ScalarT, class ImplementationT>
@@ -143,7 +141,7 @@ public:
* \param extrapolate If this parameter is set to true, the spline
* will be extended beyond its range by
* straight lines, if false calling extrapolate
- * for \$f x \not [x_{min}, x_{max}]\f$ will
+ * for \f$ x \not [x_{min}, x_{max}]\f$ will
* cause a failed assertation.
*/
Scalar eval(Scalar x, bool extrapolate=false) const
@@ -176,7 +174,7 @@ public:
* \param extrapolate If this parameter is set to true, the spline
* will be extended beyond its range by
* straight lines, if false calling extrapolate
- * for \$f x \not [x_{min}, x_{max}]\f$ will
+ * for \f$ x \not [x_{min}, x_{max}]\f$ will
* cause a failed assertation.
*/
@@ -691,8 +689,6 @@ protected:
{ return asImp_().numSamples(); }
};
-//! \endcond
-
}
#endif
diff --git a/dumux/common/tabulated2dfunction.hh b/dumux/common/tabulated2dfunction.hh
index 869880382e4f67d939f43195e7e4f300d904d214..40e4de16232728a41a0e4a09396467cdff821eab 100644
--- a/dumux/common/tabulated2dfunction.hh
+++ b/dumux/common/tabulated2dfunction.hh
@@ -36,7 +36,7 @@ namespace Dumux
*
* This class can be used to tabulate a two dimensional function
* \f$f(x, y)\f$ over the range \f$[x_{min}, x_{max}] \times [y_{min},
- * y_{max}]\f$. For this, the ranges of the $x$ and $y$ axes are
+ * y_{max}]\f$. For this, the ranges of the \f$x\f$ and \f$y\f$ axes are
* divided into \f$m\f$ and \f$n\f$ sub-intervals and the values of
* \f$f(x_i, y_j)\f$ need to be provided. Here, \f$x_i\f$ and
* \f$y_j\f$ are the largest positions of the \f$i\f$-th and
diff --git a/dumux/common/variablelengthspline_.hh b/dumux/common/variablelengthspline_.hh
index cd3cee0481b584b6c5c4f8a9313dbc73dcd69e08..d4dee76a07c22e20e35c7f1636de50bdf7c49df8 100644
--- a/dumux/common/variablelengthspline_.hh
+++ b/dumux/common/variablelengthspline_.hh
@@ -35,8 +35,7 @@
namespace Dumux
{
-//! \cond INTERNAL
-/*
+/*!
* \brief The common code for all 3rd order polynomial splines with
* where the number of sampling points only known at run-time.
*/
@@ -488,7 +487,6 @@ protected:
Vector yPos_;
Vector m_;
};
-//! \endcond
}
#endif
diff --git a/dumux/freeflow/stokes/stokeslocaljacobian.hh b/dumux/freeflow/stokes/stokeslocaljacobian.hh
index 9b53fb756677339369a1e5cc9ab8657bc3d16286..81a7c56791cc66ce7aa178f07c9e6d571310cc0e 100644
--- a/dumux/freeflow/stokes/stokeslocaljacobian.hh
+++ b/dumux/freeflow/stokes/stokeslocaljacobian.hh
@@ -54,14 +54,12 @@ private:
dimWorld = GridView::dimensionworld
};
-public:
- //! \copydoc numericEpsilon_()
- Scalar numericEpsilon_(int scvIdx,
- int pvIdx) const
+ //! \copydoc BoxLocalJacobian::numericEpsilon()
+ Scalar numericEpsilon(int scvIdx,
+ int pvIdx) const
{
Scalar pv = this->curVolVars_[scvIdx].primaryVars()[pvIdx];
if (pvIdx == 0 || pvIdx == 1){
- // std::cout << "adjusting eps_ for momentum balance\n";
return 1e-7*(std::abs(pv) + 1);
}
return 1e-9*(std::abs(pv) + 1);
diff --git a/dumux/material/components/air.hh b/dumux/material/components/air.hh
index a2a52697fc623a0612dd8f976a1cc3ec9fe45138..5331caeb333243d373617582f5aea2e54b662d0d 100644
--- a/dumux/material/components/air.hh
+++ b/dumux/material/components/air.hh
@@ -189,7 +189,7 @@ public:
*
* Definition of enthalpy: \f$h= u + pv = u + p / \rho\f$.
* Rearranging for internal energy yields: \f$u = h - pv\f$.
- * Exploiting the \emph{Ideal Gas} assumption
+ * Exploiting the Ideal Gas assumption
* (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
*
* \param temperature temperature of component in \f$\mathrm{[K]}\f$
diff --git a/dumux/material/components/ch4.hh b/dumux/material/components/ch4.hh
index 2766db258f85cae81c61b6d46779ba82c6011b72..3854ea09e10cbef73fbffb6e743c4a2b8f5ed46b 100644
--- a/dumux/material/components/ch4.hh
+++ b/dumux/material/components/ch4.hh
@@ -170,9 +170,9 @@ public:
*
* Rearranging for internal energy yields: \f$u = h - pv\f$.
*
- * Exploiting the \emph{Ideal Gas} assumption (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
+ * Exploiting the Ideal Gas assumption (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
*
- * The \emph{universal} gas constant can only be used in the case of molar formulations.
+ * The universal gas constant can only be used in the case of molar formulations.
*
* \param temperature temperature of component in \f$\mathrm{[K]}\f$
* \param pressure pressure of component in \f$\mathrm{[Pa]}\f$
diff --git a/dumux/material/components/n2.hh b/dumux/material/components/n2.hh
index 8ac75b34bf2325b4f1484b0280eb8309a9e2acc1..61b7ae6f82f739fcc0bcfc2bf2577c0de8dedef4 100644
--- a/dumux/material/components/n2.hh
+++ b/dumux/material/components/n2.hh
@@ -204,9 +204,9 @@ public:
*
* Rearranging for internal energy yields: \f$u = h - pv\f$.
*
- * Exploiting the \emph{Ideal Gas} assumption (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
+ * Exploiting the Ideal Gas assumption (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
*
- * The \emph{universal} gas constant can only be used in the case of molar formulations.
+ * The universal gas constant can only be used in the case of molar formulations.
* \param temperature temperature of component in \f$\mathrm{[K]}\f$
* \param pressure pressure of component in \f$\mathrm{[Pa]}\f$
*/
diff --git a/dumux/material/components/simpleco2.hh b/dumux/material/components/simpleco2.hh
index a35fd645e911e259deff50d3e8fea48a0139611f..38159cdf73099a298371466486430647d681c861 100644
--- a/dumux/material/components/simpleco2.hh
+++ b/dumux/material/components/simpleco2.hh
@@ -114,9 +114,9 @@ public:
*
* Rearranging for internal energy yields: \f$u = h - pv\f$.
*
- * Exploiting the \emph{Ideal Gas} assumption (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
+ * Exploiting the Ideal Gas assumption (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
*
- * The \emph{universal} gas constant can only be used in the case of molar formulations.
+ * The universal gas constant can only be used in the case of molar formulations.
* \param temperature temperature of component in \f$\mathrm{[K]}\f$
* \param pressure pressure of component in \f$\mathrm{[Pa]}\f$
*/
diff --git a/dumux/material/components/simpleh2o.hh b/dumux/material/components/simpleh2o.hh
index 22308d17a12ae8f38c92098c1b197911005b2492..04a4d1acf3abbbf6a8ff33f808bd49030a8d5ceb 100644
--- a/dumux/material/components/simpleh2o.hh
+++ b/dumux/material/components/simpleh2o.hh
@@ -156,9 +156,9 @@ public:
*
* Rearranging for internal energy yields: \f$u = h - pv\f$.
*
- * Exploiting the \emph{Ideal Gas} assumption (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
+ * Exploiting the Ideal Gas assumption (\f$pv = R_{\textnormal{specific}} T\f$)gives: \f$u = h - R / M T \f$.
*
- * The \emph{universal} gas constant can only be used in the case of molar formulations.
+ * The universal gas constant can only be used in the case of molar formulations.
* \param temperature temperature of component in \f$\mathrm{[K]}\f$
* \param pressure pressure of component in \f$\mathrm{[Pa]}\f$
*/
diff --git a/dumux/material/eos/pengrobinsonmixture.hh b/dumux/material/eos/pengrobinsonmixture.hh
index 86e86c2b787cb5a67f10657b2770bbaab21a8936..a4de0ae20a9a541f918453455d2c66681d2c7e55 100644
--- a/dumux/material/eos/pengrobinsonmixture.hh
+++ b/dumux/material/eos/pengrobinsonmixture.hh
@@ -76,7 +76,7 @@ public:
* \brief Returns the fugacity coefficient of an individual
* component in the phase.
*
- * The fugacity coefficient \f$\phi_i\f$ of a component $i$ is
+ * The fugacity coefficient \f$\phi_i\f$ of a component \f$i\f$ is
* defined as
* \f[
f_i = \phi_i x_i \;,
diff --git a/dumux/material/fluidstates/compositionalfluidstate.hh b/dumux/material/fluidstates/compositionalfluidstate.hh
index 07b50171ff655e2eff7338fe2808ecab93e074f4..900de9ec2521cd56c5a45b831a13b1c7a8d1caf2 100644
--- a/dumux/material/fluidstates/compositionalfluidstate.hh
+++ b/dumux/material/fluidstates/compositionalfluidstate.hh
@@ -99,7 +99,7 @@ public:
* The average mass is the mean molar mass of a molecule of the
* fluid at current composition. It is defined as the sum of the
* component's molar masses weighted by the current mole fraction:
- * \[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \]
+ * \f[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \f]
*/
Scalar averageMolarMass(int phaseIdx) const
{ return averageMolarMass_[phaseIdx]; }
diff --git a/dumux/material/fluidstates/nonequilibriumfluidstate.hh b/dumux/material/fluidstates/nonequilibriumfluidstate.hh
index a71705865eed5a2b7f00862eb005ad1d2753b180..b5373f6b395a156cb096adda2858f6610ab1a7d8 100644
--- a/dumux/material/fluidstates/nonequilibriumfluidstate.hh
+++ b/dumux/material/fluidstates/nonequilibriumfluidstate.hh
@@ -98,7 +98,7 @@ public:
* The average mass is the mean molar mass of a molecule of the
* fluid at current composition. It is defined as the sum of the
* component's molar masses weighted by the current mole fraction:
- * \[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \]
+ * \f[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \f]
*/
Scalar averageMolarMass(int phaseIdx) const
{ return averageMolarMass_[phaseIdx]; }
diff --git a/dumux/material/fluidstates/pressureoverlayfluidstate.hh b/dumux/material/fluidstates/pressureoverlayfluidstate.hh
index 05000211094a3ec6b9ceac2d8a1e18620628f46e..eb2b50cec1f3f9ba9d44ab944fe23ba8ece3de86 100644
--- a/dumux/material/fluidstates/pressureoverlayfluidstate.hh
+++ b/dumux/material/fluidstates/pressureoverlayfluidstate.hh
@@ -104,7 +104,7 @@ public:
* The average mass is the mean molar mass of a molecule of the
* fluid at current composition. It is defined as the sum of the
* component's molar masses weighted by the current mole fraction:
- * \[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \]
+ * \f[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \f]
*/
Scalar averageMolarMass(int phaseIdx) const
{ return fs_->averageMolarMass(phaseIdx); }
diff --git a/dumux/material/fluidstates/saturationoverlayfluidstate.hh b/dumux/material/fluidstates/saturationoverlayfluidstate.hh
index 5cbcaa0668b2976e0ebba96d1d0a28e5466a2d3a..9081a18f7648059c89d43aea3e9d2b3a23e09a81 100644
--- a/dumux/material/fluidstates/saturationoverlayfluidstate.hh
+++ b/dumux/material/fluidstates/saturationoverlayfluidstate.hh
@@ -103,7 +103,7 @@ public:
* The average mass is the mean molar mass of a molecule of the
* fluid at current composition. It is defined as the sum of the
* component's molar masses weighted by the current mole fraction:
- * \[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \]
+ * \f[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \f]
*/
Scalar averageMolarMass(int phaseIdx) const
{ return fs_->averageMolarMass(phaseIdx); }
diff --git a/dumux/material/fluidstates/temperatureoverlayfluidstate.hh b/dumux/material/fluidstates/temperatureoverlayfluidstate.hh
index 262632f8020356c6a86364287ca4e90e29dafc73..b1794dddda088b0abd24a829f105c9b9d4b402c8 100644
--- a/dumux/material/fluidstates/temperatureoverlayfluidstate.hh
+++ b/dumux/material/fluidstates/temperatureoverlayfluidstate.hh
@@ -105,7 +105,7 @@ public:
* The average mass is the mean molar mass of a molecule of the
* fluid at current composition. It is defined as the sum of the
* component's molar masses weighted by the current mole fraction:
- * \[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \]
+ * \f[ \bar M_\alpha = \sum_\kappa M^\kappa x_\alpha^\kappa \f]
*/
Scalar averageMolarMass(int phaseIdx) const
{ return fs_->averageMolarMass(phaseIdx); }
diff --git a/dumux/material/fluidsystems/spe5fluidsystem.hh b/dumux/material/fluidsystems/spe5fluidsystem.hh
index 92e74064dc87da8ad957e528ac0791d147d564fc..08835c9f1df2343e4fc0ea7bd737880853886746 100644
--- a/dumux/material/fluidsystems/spe5fluidsystem.hh
+++ b/dumux/material/fluidsystems/spe5fluidsystem.hh
@@ -390,12 +390,12 @@ public:
* \brief Calculate the binary molecular diffusion coefficient for
* a component in a fluid phase [mol^2 * s / (kg*m^3)]
*
- * Molecular diffusion of a compoent $\kappa$ is caused by a
+ * Molecular diffusion of a compoent \f$\kappa\f$ is caused by a
* gradient of the chemical potential and follows the law
*
* \f[ J = - D \grad mu_\kappa \f]
*
- * where \f$\mu_\kappa\$ is the component's chemical potential,
+ * where \f$\mu_\kappa\\f$ is the component's chemical potential,
* \f$D\f$ is the diffusion coefficient and \f$J\f$ is the
* diffusive flux. \f$mu_\kappa\f$ is connected to the component's
* fugacity \f$f_\kappa\f$ by the relation