Restructured handbook and handbook files as we discussed
it in the handbook meeting. This change is hardly reviewable
so please compile and check whether you miss something in the
new version of the handbook or the structure appears weird.

The models have been removed, because they are just a copy from the
doxygen description and we decided to refer to the doxygen homepage
for a detailed description (which also upgrades doxygen).



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15030 2fb0f335-1f38-0410-981e-8018bf24f1b0

fixed warnings from doxygen

[plotthermalconductivitymodel]
deprecated the old class constructor call

reviewed by nicolas


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15029 2fb0f335-1f38-0410-981e-8018bf24f1b0

reviewed by gruenich
wq


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15027 2fb0f335-1f38-0410-981e-8018bf24f1b0

It prevented the automatically building of the executable.
(revelead and reviewed by nicolas)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15026 2fb0f335-1f38-0410-981e-8018bf24f1b0

added guardian macros for the case of missing multidomain


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15025 2fb0f335-1f38-0410-981e-8018bf24f1b0

fixed definition of the HAVE_GNUPLOT macro

reviewed by nicolas


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15024 2fb0f335-1f38-0410-981e-8018bf24f1b0

doxygen
- added zeroeq and multidomain models
- add model and problem descriptions

handbook
- changes in the model description of models which do not use a free
  flow are just related to changes in doxygen
- added equation subsections for multidomain and zeroeq models

naming
- applied naming convention to stokes, zeroeq, and multidomain
  models/problems

reviewed by fetzer



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15023 2fb0f335-1f38-0410-981e-8018bf24f1b0

changed wrong macro guard

reviewed by fetzer



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15022 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15004 2fb0f335-1f38-0410-981e-8018bf24f1b0

before at all). Approved by Bernd


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15000 2fb0f335-1f38-0410-981e-8018bf24f1b0

- remove trailing whitespace
- replace tabs by spaces
- remove pointless returns
- remove superfluous semicolons
- use an auto
(reviewed by fetzer)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14999 2fb0f335-1f38-0410-981e-8018bf24f1b0

fixed bug in the calculation of the diffusion and conduction term in the
stokes equation
updated reference solutions and added new tests for diffusion and
conduction

reviewed by bernd


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14997 2fb0f335-1f38-0410-981e-8018bf24f1b0

defaulted newton controller properties

reviewed by bernd


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14996 2fb0f335-1f38-0410-981e-8018bf24f1b0

For ages, the method centerUnitOuterNormal exists which does not require
a local coordinate on the intersection. Therefore, we can also get rid
of the assumption.

Reviewed by gruenich.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14957 2fb0f335-1f38-0410-981e-8018bf24f1b0

Remove deprecated, Autotools-based build system.
Use CMake-based one instead.
(reviewed by bernd)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14939 2fb0f335-1f38-0410-981e-8018bf24f1b0

fixed bug when massUpwindWeight < 1 is used in stokes

reviewed by bernd


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14916 2fb0f335-1f38-0410-981e-8018bf24f1b0

Small cleanup in stokes(nc,ncni).
(reviewed by fetzer)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14913 2fb0f335-1f38-0410-981e-8018bf24f1b0

This fixes a bug that resulted from the recent changes to the Newton
convergence measures. Instead of storing the residual, the residual
reduction is stored, but it has been forgotten to initialize this
reduction with 1.0 instead of the initial residual.

This only affected the line search where the current residual/reduction
is compared to the last one.

Reviewed by Alex.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14895 2fb0f335-1f38-0410-981e-8018bf24f1b0

- added test problems for coupling turbulent free flow using zero eq.
turbulence models with flow in porous media
- documentation will follow

[CHANGELOG]
updated changelog to latest commits

reviewed by gruenich


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14886 2fb0f335-1f38-0410-981e-8018bf24f1b0

added possibility to pass user-defined options (in gnuplot language),
datafile separator can now be chosen, and always a gnuplot script will be
produced

[plotoverline2d.hh]
added switch to rewrite instead of append to data file, removed
superfluous tabs

[evaporationatmosphereproblem.hh]
added example for use of gnuplotinterface and plotoverline2d

reviewed by gruenich



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14876 2fb0f335-1f38-0410-981e-8018bf24f1b0

updated version number in start message and user meeting invitation to
thank you

reviewed by gruenich


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14868 2fb0f335-1f38-0410-981e-8018bf24f1b0

added the zeroeq turbulence models from dumux-devel
added zeroeq test problems
to be done:
 - general docu and doxygen docu
 - model description for handbook
 - dune compatibilites 2.3 and >2.3

reviewed by gruenich


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14861 2fb0f335-1f38-0410-981e-8018bf24f1b0

added functionality to pass gnuplot options for each plot

reviewed by gruenich


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14851 2fb0f335-1f38-0410-981e-8018bf24f1b0

Reviewed by Thomas


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14837 2fb0f335-1f38-0410-981e-8018bf24f1b0

fixed call of thermalconductivity plot (initializing with pressure and
temperature) without deprecation

[material]
unified output for out-of-range messages in h2o component

reviewed by gruenich


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14831 2fb0f335-1f38-0410-981e-8018bf24f1b0

The reference files are still wrong and need an update.
(reviewed by natalies)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14827 2fb0f335-1f38-0410-981e-8018bf24f1b0

values).

Reviewed by Martin S.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14820 2fb0f335-1f38-0410-981e-8018bf24f1b0

evalPhaseStorageDerivative

See FS#261 for details
http://www.dumux.org/flyspray/index.php?do=details&task_id=261

Reviewed by gruenich.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14799 2fb0f335-1f38-0410-981e-8018bf24f1b0

Test more decoupled 2p models in 3d.

Reviewed by Martin S.


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14791 2fb0f335-1f38-0410-981e-8018bf24f1b0

This fixes FS#266.
(reviewed by fetzer)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14789 2fb0f335-1f38-0410-981e-8018bf24f1b0

(reviewed by natalies)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14785 2fb0f335-1f38-0410-981e-8018bf24f1b0

- Rename mainpage, modules and parameterlist to *.txt
  to work around new behavior in Doxygen 1.8.8 or newer.
- Fix missing closing brackets in brine_co2.hh.
- Add missing ! in plotoverline (by fetzer)
(reviewed by fetzer)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14763 2fb0f335-1f38-0410-981e-8018bf24f1b0

updated call of masstransfermodel class

[multidomain]
- if a boundarylayer model for mass transfer is used, now this also means a boundary layer
  model for energy transfer is used too (which is more consistent)
- added a test for the masstransfer and boundary layer models

reviewed by gruenich



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14757 2fb0f335-1f38-0410-981e-8018bf24f1b0

Removed if-condtion requiring DUNE_TRHOW only for  rank==0  in  updateStaticData function of compositional models. Now all failing processes call DUNE_THROW. This is supposed to make parallel runs more stable.

Revieved by Alex

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14747 2fb0f335-1f38-0410-981e-8018bf24f1b0

- added individual headers for boundary layer and mass transfer models, which were implemented in the couplinglocaloperator

[multidomain]
- uses above mentioned new header and classes
- improved own start function, especially the usage function
- updated parts of the reference solutions, due to marginal deviations

[implicit]
- added convenience function for the viscosity in the 2p2c model 


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14743 2fb0f335-1f38-0410-981e-8018bf24f1b0

(reviewed by martinb)

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14727 2fb0f335-1f38-0410-981e-8018bf24f1b0

The richards model has now an additional flag useHead, which can be used to switch between pressure-saturation definition and pressureHead-watercontent definition. The primary variables are either pressure in [Pa] or pressure head in [cm]. Default is useHead = false.

tested and reviewed by Bernd



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14716 2fb0f335-1f38-0410-981e-8018bf24f1b0

- binarycoefficients
- constraintsolver
- eos

- Units were added where required
- All units were checked that they are expressed in latex
- No additional doxygen errors or wanrings

Work done by Scholz
Reviewed and committed by Alexk

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14706 2fb0f335-1f38-0410-981e-8018bf24f1b0

(reviewed by fetzer)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14665 2fb0f335-1f38-0410-981e-8018bf24f1b0

Until now it was not possbile to store the velocity in the
2p2c flux data object. This adds velocity and setVelocity methods.

Reviewed by bernd


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@14661 2fb0f335-1f38-0410-981e-8018bf24f1b0