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

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[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).

git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15197 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

- 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.


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15195 2fb0f335-1f38-0410-981e-8018bf24f1b0

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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updated todo list with changes from last meeting
improved the structure of the model section



git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15190 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

No major changes.


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[mainpage.txt]: added links to Modules overview page and to
parameterlist.txt

Reviewed by Thomas


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conventions

Reviewed by gruenich.



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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.



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Updated solution patch files.

reviewed by fetzer


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15177 2fb0f335-1f38-0410-981e-8018bf24f1b0

update of chapter 4+5
 - restructured and combined different sections
 - shortened text

done by gruenich and fetzer


git-svn-id: svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/trunk@15168 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