- All headers and source files are moved to the specfied include directory during installation.

- Existing CMakeLists.txt files were appended.
- CMakeLists.txt were added in folders that did not contain any CMakeLists.txt files but contain headers
- The installed version of dumux has been tested by Bernd with the dumux-lecture module

Reviewed, modified and tested by Bernd.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15347 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15346 2fb0f335-1f38-0410-981e-8018bf24f1b0

  - added functionality and properties to refine grid in all directions
  - naming (comp -> dimIdx)

[multidomain]
  - adapted to changes in the interfacegridcreator
  - removed unused properties from input file
  - in coupled zeroeq problem added output at beginning of simulations

[freeflow]
  - removed one unused property from test_zeroeq2c.input

reviewed by timok



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15341 2fb0f335-1f38-0410-981e-8018bf24f1b0

This solves FS#237, see further details there.

The solution is to be aware of a restart already in the GridCreator.
Then, it is possible to construct the grid there that will be used for
the restarted simulation. This requires that the parameter Problem.Name
is set in the input file in order to deduct the correct restart file
names.

Reviewed and improved by Timo.


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15336 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15325 2fb0f335-1f38-0410-981e-8018bf24f1b0

Since only one test run is needed, but different VTK files need to be
compared, the corresponding capability of fuzzycompare can be used.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15324 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15315 2fb0f335-1f38-0410-981e-8018bf24f1b0

The gridcreator interface was slightly changes (see CHANGELOG)
The gridPtr method is no longer publicly available. All grid
methds can bee called through a reference to the grid obtained
by the grid() method. The parameter method for dgf parameters
is now accessible through GridCreator::parameters(...).



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15314 2fb0f335-1f38-0410-981e-8018bf24f1b0

Everything can be controlled by the input file: Changing

[Grid]
File = ./grid.dgf

into

[Grid]
File = ./grid.gmsh

or into

[Grid]
LowerLeft = 0 0 0
UpperRight = 1 1 1
Cells = 20 30 10

will construct a gmsh grid or a structured grid instead of the dgf grid.
The grid creator is the new standard grid creator.
To use all features dune 2.4 is required (e.g. structured grid factory)
but it dgf/gmsh works with dune 2.3. The structured grid factories can
be deprecated as soon as dune 2.4 is released.

additional feature:
- set inital refinement in Grid.Refinement  (oder options can be easily
  added, write me)
- grid specific parameter in input file, e.g.  UGGrid: Grid.ClosureType
  = None
turns off green refinement (triangles closure).
- new property GridParameterGroup sets the input file group the grid
  creator is looking in. Particularly useful for two grid simulations:

[DarcyGrid]
File = bla.dgf

[StokesGrid]
File = blub.dgf



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15307 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15303 2fb0f335-1f38-0410-981e-8018bf24f1b0

* Remove trailing whitespace and tabs
* Move electrochemistry output to the test problem (not related to 2pnc in general)
* Make electrochemistry have static members
* Use naming conventions for indices in the model
* Try to make the model work with cellcentered too (No cell-centered test available so far)
* Make electrochemistry input parameters part of a group "ElectroChemistry"
* Make the electrochemistry model a named enum (ElectroChemistryModel)for readability

Reviewed by martins 



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15298 2fb0f335-1f38-0410-981e-8018bf24f1b0

- BuildBot failed for commit -r 15292. The possible reason was the usage of static const int as template parameter for electrochemistry. (checked with M.Schneider)
- Unused variable removed from h2on2o2fluidsystem.hh 
- Unnecessary headers removed from test_box2pnc.cc 

Reviewed by (M.Schneider)

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15296 2fb0f335-1f38-0410-981e-8018bf24f1b0

- The required binary coefficients are added.
- Electrochemistry equations added for both isothermal and non-isothermal cases (Non-isothermal are not used till now).
- pc-s relation for hydrophobic material  added
- h2ON2o2 fluid system added
- fuelcell test case is the new test problem for 2pnc model.

Moreover, some updated related to 2pncmin model are included

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15292 2fb0f335-1f38-0410-981e-8018bf24f1b0

compare

This is the 1. iteration. The thresholds might have to be adapted for
more tests by knowledgable people

This and the last commit on tests were
reviewed by fetzer


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15257 2fb0f335-1f38-0410-981e-8018bf24f1b0

fixed wrong guardian macros

reviewed by martins


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15240 2fb0f335-1f38-0410-981e-8018bf24f1b0

Reference solution for 2pncmin test is changed (Now solution for the last timestep and is used for comparison). 
The similation endtime is also reduced.

- REVIEWED BY J.HOMMEL

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15216 2fb0f335-1f38-0410-981e-8018bf24f1b0

[richards-test] adding a new richards test that compares an analytical solution to a numerical one - created during the Bachelor Thesis of M.H. Baccour, supervised by C. Grueninger

reviewed by Christoph



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15215 2fb0f335-1f38-0410-981e-8018bf24f1b0

conventions, review by vishal


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15209 2fb0f335-1f38-0410-981e-8018bf24f1b0

- Units in the fluidsystem/brinevariablesalinity and components/nacl checked. Additional commented units removed.
- Commented cout statements removed from computefromfugacities2pncmin, computefromreferencephase2pnc and miscible2pnccomposition
- The ccommented out removed from problem file and input file corrected.
- The test case is checked for both debug and optim model with clang compiler.

   

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15203 2fb0f335-1f38-0410-981e-8018bf24f1b0

No visible differences to the solution before.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15201 2fb0f335-1f38-0410-981e-8018bf24f1b0

Replace

if (!useMoles)
  // mass stuff
else
  // mole stuff

by

if (useMoles)
  // mole stuff
else
  // mass stuff 

Reviewed by fetzer.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15200 2fb0f335-1f38-0410-981e-8018bf24f1b0

New test case for 2pncmin model added to dumux/test. For this following additional files are needed (Reviewde by Johannes)

- For variation of salinity in brine the needed constitutive relations are implemented in components brine_VerSalinity.hh and nacl.hh
- Additional constraint solvers (compositionfromfugacities2pncmin and computefromreferencephase2pncmin) are needed, specially for the case nPhaseOnly
- Additional constraint solvers (computefromreferencephase2pnc and miscible2pnccomposition) are needed for 2pnc cases in general.
- Fluidsystem brineairfluidsystem is updated
- Binerycoefficient file for brine_air case is included. 

- A test case for 2pncmin model is included for flusiong of precipitated salt in gas reserviors. The includes corresponding problem file, spatial parameters file, input file and *.cc file.
- For this the CMakeLists.txt is also updated.
- A reference solution 2pncmin test case "injectionbox2pncmin-reference" is included to test/references folder

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15196 2fb0f335-1f38-0410-981e-8018bf24f1b0

References have to be updated due to differences between test system and
the system of the reference solution creator. The differences are small,
but still too large for fuzzycompare. This is a known issue, see FS#281
for details.

The two ni-multidomain tests use the same names for the output. This
leads to conflicts when the tests are executed in parallel. The names of
one test are changed to fix this.


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15189 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15186 2fb0f335-1f38-0410-981e-8018bf24f1b0

conventions

Reviewed by gruenich.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15185 2fb0f335-1f38-0410-981e-8018bf24f1b0

Introduce a grid creator that reads from a Petrel output / Eclipse input
file and generates a CpGrid that is offered by the OPM module
dune-cornerpoint. Enhance the fully-implicit cell-centered models to be
able to deal with cornerpoint grids, test the functionality. This patch
consists of several parts:

- patches/ and dune.module: the CMake buildsystems from Dune and OPM are
  not compatible. The patches change some CMake files in the required
  OPM modules opm-parser, opm-core and dune-cornerpoint in such a way
  that those modules can serve as a dependency for Dumux. In addition,
  some specific CMake options have to be passed to dunecontrol. See
  patches/README for details.

- dumux/io/: defines the CpGridCreator which behaves like any other grid
  creator that reads from a file. In addition, it offers the Eclipse
  input deck in form of a static function deck(). This deck can be used
  to extract further simulation parameters, most prominently porosity
  and permeability values.

- dumux/implicit/cornerpoint/: changes some of the cell-centered
  classes to be able to deal with a CpGrid. The changes in the
  ElementVolumeVariables and the FVElementGeometry are minor and
  required by the facts that a CpGrid doesn't offer codim-1/2 entities
  and that the geometries don't offer local-to-global mappings. The
  changes in the DarcyFluxVariables are made for enhancing the
  robustness of the two-point flux approximation by forcing the
  inter-element transmissibilities to be positive.

- test/implicit/2p: runs a fully-implicit two-phase immiscible model on
  a CpGrid. An element index with an injection rate can be given in the
  input file. The grid provided in grids/ consists of only four
  elements, but exhibits typical cornerpoint features like a
  nonconforming situation and general hexahedrons. A more realistic grid
  will be provided in dumux-lecture soon.

Reviewed by gruenich.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15183 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15180 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15179 2fb0f335-1f38-0410-981e-8018bf24f1b0

The new test employs the function
setDirichlet(pvIdx, eqIdx)
with pvIdx != eqIdx.

On the right boundary, a Dirichlet value for the nonwetting-phase
pressure should be set. At the same time, nonwetting phase should
be allowed to leave the domain by means of an outflow boundary
condition. In order to achieve this the general 'setDirichlet'
method is used in the function 'boundaryTypesAtPos' which allows
to set the value of a primary variable by replacing an arbitrary
balance equation. In this case, the index of the primary variable
is Indices::pnIdx, while the index of the replaced equation is
Indices::contiWEqIdx. This allows to set the outflow condition for
equation index Indices::contiNEqIdx.

This completes FS#270.

Reviewed by Timo.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15167 2fb0f335-1f38-0410-981e-8018bf24f1b0

test_boxmpnckinetic now uses the start.hh and the
interfacegridcreator.hh
updated parameters and removed tabs from input file

test still fails, but the results with/without these changes are
identical

reviewed by kilian


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15165 2fb0f335-1f38-0410-981e-8018bf24f1b0

adapted the interfacegridcreator to the common GridCreator type structure
and for the use in the common start.hh
deprecated the interfacemeshcreator.hh

[multidomain]
adapted multidomain to be used with the common start.hh
deprecated the old multidomainproblem constructor

thanks to and reviewed by bernd and gruenich



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15161 2fb0f335-1f38-0410-981e-8018bf24f1b0

added cmake macro which, when called, links all input files of a folder

reviewed by martinb


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15155 2fb0f335-1f38-0410-981e-8018bf24f1b0

[fix] Remove unknown cmake macro. It is not needed here since the parameterfiles are given with the source path.

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15133 2fb0f335-1f38-0410-981e-8018bf24f1b0

Adapt all Ctests to the new architecture of runtest

Reviewd by timok


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15131 2fb0f335-1f38-0410-981e-8018bf24f1b0

Adapt all Ctests to the new, architecture.

Reviewd by fetzer


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15129 2fb0f335-1f38-0410-981e-8018bf24f1b0

(reviewed by timok)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15127 2fb0f335-1f38-0410-981e-8018bf24f1b0

The general setDirichlet function takes two parameters (pvIdx, eqIdx)
corresponding to the index of the primary variable and the index of the
balance equation. A convenience function that only takes one parameter
exists which calls the general version with two equal parameters. So
far, this one parameter has been documented as equation index. However,
it is better to refer to the parameter as a primary variable index.

This commit changes the parameter name and improves the documentation.
Furthermore, it replaces calls in the tests, whenever the general
version was called with two parameters of different name but equal value
or whenever the simplified version was called with an equation index
instead of a primary variable index.

See FS#270 for details.

Reviewed by Timo.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15115 2fb0f335-1f38-0410-981e-8018bf24f1b0

Deprecate unused function simulate from MultiDomainProblem.
(reviewed and tested by fetzer)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15109 2fb0f335-1f38-0410-981e-8018bf24f1b0

- updated output
  - eddy coefficient are now printed to vtk
  - fluxVariables data is printed to csv file
- fixed small bug with the crossLength for Baldwin Lomax Model
- further removing of unused properties

reviewed by gruenich



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15103 2fb0f335-1f38-0410-981e-8018bf24f1b0

shortened setting of properties

reviewed by gruenich


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15094 2fb0f335-1f38-0410-981e-8018bf24f1b0