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



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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(...).



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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



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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)

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- 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

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threshold.

Otherwise we compare non-zero with zero values.

Review by bernd


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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


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

reviewed by timok


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- 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


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within dumux.


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fixed wrong guardian macros

reviewed by martins


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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.



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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



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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.


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


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conventions, review by vishal


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- 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



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

Reviewed by Thomas


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- 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.

   

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No visible differences to the solution before.



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Replace

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

by

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

Reviewed by fetzer.



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To follow the naming concenvention "brine_varSalinity" is moved to "brineversalinity". Moreover, a missing binary coefficient file brine_air is added (Reviewed by Johannes).

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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

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- Properties for models 2pnc and 2pncmin modified so that they can be used for both box and cc methods.
- The Chemistry property is removed from volume veriables so it has to be checked for reaction test cases first.
- The minimum prorsity after mineralization can be selected now from spatial parameters.


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Several explicit loops over the coordinate index can be replaced by
using the corresponding FieldVector functionality.

This implements FS#271.

Reviewed by fetzer.


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