- 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

are documented properly (see FS#220)


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15337 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@15330 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15328 2fb0f335-1f38-0410-981e-8018bf24f1b0

It was checked in add_dumux_test whether the to be linked input file exists
but then another file was linked in some occations. 
Use the path relative to the source directory to fix the broken links.


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15326 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@15318 2fb0f335-1f38-0410-981e-8018bf24f1b0

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15316 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

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15309 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

problems; The list contains currently  only features of the implicit
test problems. Everybody is welcome to contribute the completion of the list. 


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15302 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

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15293 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

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15259 2fb0f335-1f38-0410-981e-8018bf24f1b0

threshold.

Otherwise we compare non-zero with zero values.

Review by bernd


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15258 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

removed -ffast-math, because this caused slightly different solutions in the automatic testing

reviewed by timok


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15256 2fb0f335-1f38-0410-981e-8018bf24f1b0

- Parameters with more than one component are split into components for
  comparison
- The absoulte criteria gets scaled with the maximum absolute value in
  the parameter set
- It is possible to pass a zero threshold, i.e. the threshold under which
  values get treated as zero, for each parameter or
  parameter component via runtest as follows
  --zeroThreshold = {"vel":1e-9,"bla":10}
  The format is a python dictionary except single quotes are not allowed
  (because it uses json)
- More verbose output


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15254 2fb0f335-1f38-0410-981e-8018bf24f1b0

within dumux.


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15245 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

exception is caught. 

The parameter list was printed every time a parameter exception was
thrown in the parameter class. This made it impossible to catch
parameter exceptions without having a paramter list output every time.
Now it is printed only if the start function exits with a parameter
error.



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15229 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

The emphasis is now on the elements of the linear system
and to make it more clean how the physical equations are
related to the linear system.


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15214 2fb0f335-1f38-0410-981e-8018bf24f1b0

todos from chapter 4:
- beautified the folder structure picture
- added hint how compiler can be changed


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15213 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

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15208 2fb0f335-1f38-0410-981e-8018bf24f1b0

- adaption to style of other models (replaced use of \nabla by use of div or grad)
- replaced use of mass fraction with mole fraction in diffusion term and added
  comment about use of binary diffusion
- fixed typos

[doxygen,material]
- fixed typos and line break



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15207 2fb0f335-1f38-0410-981e-8018bf24f1b0

(e.g., replaced mass with mole fractions)

Reviewed by Thomas


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15206 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

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15202 2fb0f335-1f38-0410-981e-8018bf24f1b0