CHANGELOG.md 105 KB
Newer Older
1
Differences Between DuMu<sup>x</sup> 3.4 and DuMu<sup>x</sup> 3.3
2
=============================================
3
4

### Improvements and Enhancements
Kilian Weishaupt's avatar
Kilian Weishaupt committed
5
6
7
8
9
- __Pore-network models added to DuMu<sup>x</sup>__:
    - Three fully implicit pore-network models (1p, 1pnc, 2p) have been added.
    - A quasi-static 2p PNM for the creation of pc-Sw curves has been added.
    - A new namespace `Dumux::PoreNetwork` has been introduced, containing all relevant classes and functions for pore-network modeling.
    - An example introduces the use of the 1p PNM for the estimation of the upscaled Darcy permeability.
10
    - Advection type including inertia effect for simulations in the non-creeping flow regime
Kilian Weishaupt's avatar
Kilian Weishaupt committed
11
    - Note that this is still considered a rather _experimental_ feature. Everything within namespace `Dumux::PoreNetwork` might undergo (backward-compatibility breaking) changes _without prior notice_.
12
13
14
15
- __Several scripts have been translated to Python__:
    - `getusedversions.sh` to extract the used Dumux/Dune versions of a module (new script: `bin/util/getusedversions.py`)
    - `extractmodulepart.sh` no longer creates an install file, instead, you can now generate install scripts for your module using the new script `bin/util/makeinstallscript.py`.
    - Note: the old shells script will be removed after release 3.4.
16
- __Law for water vapor viscosity in gas mixtures changed__: Polynomial laws for determining the viscosity of vater vapor in gas mixtures are introduced and applied by the new function `h2oGasViscosityInMixture`. The polynomial laws give a better approximation of the gas viscosity especially at higher temperatures ( >273.15 K) and a high water vapor content.
17

18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
- __Newton line search__: The line search algorithm decreases the step size until the residual decreases. The lower bound
of the step size can now be set in the input file via the parameter `Newton.LineSearchMinRelaxationFactor`.

- __Material / Constant component__: The `Component::Constant` can now be used in non-isothermal simulation. Simple relations
for internal energy and enthalpy depending on temperature and constant heat capacity have been added.

- __Ordering strategies for UMFPack__:
It is now possible to [choose an ordering strategy](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/linear/seqsolverbackend.hh#L851) for UMFPack via the runtime parameter `LinearSolver.UMFPackOrdering` or by calling the `setOrdering()` method of `UMFPackBackend`. This can have a positive effect on the solver's performance, depending on the matrix structure.

- __Add setRetryTimeStepReductionFactor() function  to NewtonSolver__:
This function allows to set the factor by which the time step is reduced after al failed iteration. Can be used, e.g., for custom Newton solvers inheriting from this class and using a more sophisticated time step management.

- __Improve upwind interface__:
    - Additional functions have been added to upwindscheme.hh which can be used to `apply` the upwind scheme without the need of FluxVariables and to get the `multiplier` by which the flux is multiplied.
    - These additional functions are now used in `CCTpfaForchheimersLaw` by providing the UpwindScheme as additional template argument.

- __Simplified use of SubGridManger__: It is now possible to specify pixel dimensions when reading an image file used as grid. For instance, `Grid.PixelDimension = 1e-3 1e-3` will scale the domain automatically such that the grid cells have a side length of 1e-3 m and you don't need to specify `Grid.UpperRight` anymore.

- __String utility__: There is a new header `common/stringutilities.hh` that implements two functions `tokenize` and `split`
that can split strings at a given delimiter.

- __Add linearRegression() function  to math.hh__:
This function gets a set of (x, y) data and calculates/returns the intercept and the slope of the regression line using linear least squares method.

- __Python bindings__: There is now a small finite volume example included in the Python tests using the wrapped grid geometry and problem

- __Shallow water__: Added a heuristic turbulence model based on a mixing length and resulting a turbulent viscosity term

46
47
48
### Immediate interface changes not allowing/requiring a deprecation period:
- __MPNC__: The `MPAdapter` can now also be called with a temporary `pcKrSw` objects. For this, the compiler needs to deduce the
            class's template argument types. You may need to adapt your `spatialParams` from
49
50
51
- __Newton__: The global parameter defaults have been substituted for local parameter defaults (in nonlinear/newtonsolver.hh). If
              you have been relying on global defaults (reading parameters without supplying a value in the input file nor a default)
              you will get a runtime ParameterException. To solve this simply provide a default or set the value in the input file.
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
```
using MPAdapter = Dumux::FluidMatrix::MPAdapter<PcKrSwCurve, 2>;
...
auto fluidMatrixInteractionAtPos(const GlobalPosition &globalPos) const
{
    return makeFluidMatrixInteraction(MPAdapter(pcKrSwCurve_));
}
```
to
```
// alias for MPAdapter is removed
auto fluidMatrixInteractionAtPos(const GlobalPosition &globalPos) const
{
    return makeFluidMatrixInteraction(FluidMatrix::MPAdapter(pcKrSwCurve_));
}
```
68
69
70
71
72
- __Grid-geometry__: The local views of grid geometries are now required to implement the interfaces
`element()` (returning the bound element) and `isBound()` returning a `bool` which is `true` if the
functions `bind` or `bindElement` have been called (i.e. the local geometry is in a bound state). These
interfaces are currently not used (except in the unit tests) but will be required
by the assembler in future Dumux versions.
73

74
75
### Deprecated properties/classes/functions/files, to be removed after 3.4:

76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
- `Dumux::IsIndexable<T, I>` is deprecated, use `Dune::IsIndexable<T, I>`directly.
- The property `NumEqVector` has been deprecated. The class `NumEqVector` is now defined in namespace `Dumux` in header file `dumux/common/numeqvector.hh`.

### New experimental features (possibly subject to backwards-incompatible changes in the future)

- __Time stepping__: a first implementation of a generic `Dumux::MultiStageTimeStepper` was introduced,
that allows for using different time integration schemes besides the currently supported implicit and explicit
Euler schemes. However, this poses new requirements on the linear system assemblers, which are not yet met by
the standard assemblers provided in Dumux. This will be extended in future versions.

### Continuous integration

- A first version of the Dumux GitLab CI is now at the disposal of all developers. While every night a complete
test pipeline is triggered automatically, developers have the possibility to manually start test pipelines
within merge requests that automatically identify and run only those tests affected by the changes introduced.

92

93
Differences Between DuMu<sup>x</sup> 3.3 and DuMu<sup>x</sup> 3.2
Timo Koch's avatar
Timo Koch committed
94
95
96
97
=============================================

### Improvements and Enhancements

Kilian Weishaupt's avatar
Kilian Weishaupt committed
98
99
100
101
102
103
104
- __Requirements__: DuMu<sup>x</sup> now requires Dune >=2.7 and CMake >= 3.13.
- __New way to use material laws__: The usage of laws for pc-Sw and kr-Sw has been completely revised. A caller does not have to pass a `parameters` object to the laws anymore. The `spatialParams` now provide a `fluidMatrixInteraction` function which bundles an arbitrary number of
 different interaction laws such as a pc-Sw and kr-Sw curve and interfacial areas.
 New pre-cached spline laws were added which can help to increase efficiency. The usage of the old interface is deprecated and warnings will be raised. The old interface will be removed after the release of 3.3.
- __New example__: We have added another free-flow example dealing with lid-driven cavity flow.
- __Install script written in Python__: The DuMu<sup>x</sup> install script has been translated to Python to improve portability. The old shell script will be removed after release 3.3.
- __Improved velocity reconstruction__: The velocity reconstruction for immiscible porous-media models has been improved, leading to slightly
Kilian Weishaupt's avatar
Kilian Weishaupt committed
105
  different velocity fields in the vicinity of Neumann boundaries.
Kilian Weishaupt's avatar
Kilian Weishaupt committed
106
- __Python bindings (experimental)__: Basic support for Python bindings has been added. Python bindings are an experimental feature
107
108
  and might undergo unannounced API changes until further notice. This concerns the files in the folders `python` and `dumux/python`. To activate
    - add `-DDUNE_ENABLE_PYTHONBINDINGS=TRUE` and `-DCMAKE_POSITION_INDEPENDENT_CODE=TRUE` to your CMAKE_FLAGS and run dunecontrol
Kilian Weishaupt's avatar
Kilian Weishaupt committed
109
    - run `python3 dune-common/bin/setup-dunepy.py`
Kilian Weishaupt's avatar
Kilian Weishaupt committed
110
    - adapt your PYTHONPATH environment variable as described [here](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/tree/master/python)
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
- __Obtain DuMux via pip__: The Dumux source code can now be installed using `pip install dumux`. This works for the Python bindings as well as the C++ source code. Matching Dune modules are also installed. Currently not all dune modules have Python packages available. We recommend trying this new feature in a virtual environment by typing
```sh
python3 -m virtualenv venv
source venv/bin/activate
pip install dumux
```
To test the setup you can use the following Python script
```py
from dune.grid import structuredGrid
from dumux.discretization import GridGeometry

gridView = structuredGrid([0,0],[1,1],[5,5])

gridGeometry = GridGeometry(gridView, discMethod="cctpfa")
gridGeometry.update()

print("The total number of scvs is {}".format(gridGeometry.numScv()))
print("The total number of scvfs is {}".format(gridGeometry.numScvf()))
```
Kilian Weishaupt's avatar
Kilian Weishaupt committed
130
- __fmt-library__: We now include a basic version of the [fmt-library](https://github.com/fmtlib/fmt) which implements `std::format` (coming with C++20) without the need for C++20.
Timo Koch's avatar
Timo Koch committed
131
132
  In order to use this, include `<dumux/io/format.hh>`. `format`, `format_to`, `format_to_n`, `formatted_size` are available in the `Dumux::Fmt` namespace.
  The string formatting is documented [here](https://en.cppreference.com/w/cpp/utility/format/formatter#Standard_format_specification) and follows the Python string formatting rules.
Kilian Weishaupt's avatar
Kilian Weishaupt committed
133
134
  The functions are documented on [cppreference](https://en.cppreference.com/w/cpp/utility/format).
 - __RANS__: The RANS models now include variable densities. Compositional or nonisothermal RANS models could produce slightly different, more accurate, results.
Timo Koch's avatar
Timo Koch committed
135
136

### Immediate interface changes not allowing/requiring a deprecation period:
137
- __Flash/Constraintsolver__: The flashes depending on material laws are immediately required to use new-style material laws (fluidMatrixInteraction interface in spatialparams)
Kilian Weishaupt's avatar
Kilian Weishaupt committed
138
- __Box interface solver__: The box interface solver immediately requires the new material law interface without deprecation period. Use the new class `BoxMaterialInterfaces` and update your spatial params to use the new fluidmatrixinteraction interface to be able to use the box interface solver in version 3.3.
139
- For the "sequential" models, the property `BoundaryTypes` has been simply renamed to `SequentialBoundaryTypes`
140
- __Quadmath__: Dumux::Quad has been removed without deprecation. Use Dune::Float128 instead.
141
142
- Within the RANS group, two additional runtime parameters have been included 'IsFlatWallBounded' and 'WriteFlatWallBoundedFields'.
For both the K-Epsilon and Zero-eq RANS models the 'IsFlatWallBounded' runtime parameter should be set as True,
143
as wall topology is not supported for these models with our geometric constraints. If not set as true, the geometry
144
will be checked before the model is run. If either the runtime parameter or the geometry check indicate non-flat walls,
145
the model will terminate. To add FlatWallBounded specific output to the vtk output, WriteFlatWallBoundedFields can be set as True.
146
- __1d3d coupling__: The kernel coupling manager has been replaced with the one from Koch et al (2020) JCP https://doi.org/10.1016/j.jcp.2020.109370
147
148
- __1d3d coupling__: The average and surface coupling managers has been updated with a slightly more accurate version to compute the stencils and the average operator.
The results might differ a bit when using coarse grids. However, both version are expected to converge to the same result with grid refinement.
149

Timo Koch's avatar
Timo Koch committed
150
151
### Deprecated properties/classes/functions/files, to be removed after 3.3:

152
153
- The property `BoundaryTypes` has been deprecated. The boundary condition type can now be deduced from the problem type using `ProblemTraits`.

Timo Koch's avatar
Timo Koch committed
154
155
### Deleted classes/files, property names, constants/enums:

156
- Everything that has been deprecated before release 3.2 has been removed.
157
- All of the geometry headers previously saved in `dumux/common/geometry` have been relocated to `dumux/geometry`.
Bernd Flemisch's avatar
Bernd Flemisch committed
158
  The headers in `dumux/common/geometry` are deprecated and will be removed after 3.3. The geometry tests have been moved from `test/common/geometry`
Ned Coltman's avatar
Ned Coltman committed
159
  and `test/common/boundingboxtree` to `test/geometry`.
160

161
### Other noteworthy changes:
Bernd Flemisch's avatar
Bernd Flemisch committed
162
- Releases earlier than 3.0 are no longer automatically tested or supported.
Timo Koch's avatar
Timo Koch committed
163

164
Differences Between DuMu<sup>x</sup> 3.2 and DuMu<sup>x</sup> 3.1
Timo Koch's avatar
Timo Koch committed
165
166
167
168
=============================================

### Improvements and Enhancements

169
- __C++17__: DuMu<sup>x</sup> now requires a C++ compiler supporting the C++17 features of GCC 7 (e.g. GCC 7, Clang 5).
170
171
- __Radially symmetric problems__: We now have support for radially symmetric problems (disc, ball, toroid). The support comes in form of wrappers for sub control volumes and faces that overload the respective `volume()` and `area()` function turning a 1d or 2d problem into a 2d or 3d radially symmetric problem.

172
173
- __Improvements of Beavers-Joseph(-Saffman) condition for the free flow model__: The naming for handling BJ(-S) boundary conditions has been adapted from `isBJS()` to `isBeaversJoseph()` / `setBJS()` to `setBeaversJoseph()`. In order to consider the velocity within the porous medium, the old `velocityPorousMedium(element, scvf)` method (returning a Scalar) has been renamed to `porousMediumVelocity(element, scvf)` (returning a velocity vector). The latter defaults to `VelocityVector(0.0)`.

174
175
- __Van Genuchten__: The VanGenuchten-Mualem material law now allows to set a parameter `l` (default to 0.5) which is sometimes fitted.

176
177
- __Runtime variable output precision e.g. Float64__: The VtkOutputModule has been adapted to allow easy changes of the vtk output precision. It is now possible to specify output precision in the input file using `Vtk.Precision` followed by either `Float32`, `Float64`, `UInt32`, `UInt8` or `Int32`. `Float32` stays the default. We especially advice the use of `Float64` when working with restart files.
An additional new option is `Vtk.CoordPrecision` which changes the precision of the coordinates only and uses the default of `Vtk.Precision`.
178
179
180

- __Effective Laws and Diffusion Coefficients__: The effective laws interface has been changed within !1684. The interface for these laws has been unified, and all coefficents are to be stored in containers that fit to the model. These quantities should then be added in the volumeVariables, meaning all effective quantities would be accessible from the volumevariables.

181
182
- __Examples__: The documentation of the examples has been improved further, focusing on readability and convenience. Further, three additional examples are included the folder `examples`. To get an overview, point your browser to https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/tree/master/examples.

183
- __Linear solvers__: There is a new ISTL solver factory backend which allows to choose solvers at runtime (requires dune-istl 2.7) and also enables more parallel solvers (requires dune-istl > 2.7.0).
184
185


Timo Koch's avatar
Timo Koch committed
186
187
### Immediate interface changes not allowing/requiring a deprecation period

Christoph Grüninger's avatar
Christoph Grüninger committed
188
- Remove `Grid.HeapSize` as dune-ugrid removed the according feature as well.
189
- __Van Genuchten__: Corrected VanGenuchten-Mualem exponent in the nonwetting saturation formula (`1/3` instead of `1/2` (or `l`, see above))
190
- __Van Genuchten__: Corrected VanGenuchten-Mualem implementation of `dkrn/dSw`
191
- __Brooks-Corey__: Corrected Brooks-Corey implementation of `dkrn/dSw` and added the derivatives for the regularized version
192
- __AMGBackend__: The internal structure of the AMGBackend and the ParallelISTLHelper has been overhauled, as only used by the AMG, we did not make the changes backwards-compatible
193
194
- The global default parameters for linear solvers have been removed and moved to the class `LinearSolver`.
This only affects users that directly obtain this parameter via `getParam` somewhere in the code.
Christoph Grüninger's avatar
Christoph Grüninger committed
195

Kilian Weishaupt's avatar
Kilian Weishaupt committed
196
197
198
- __Sequential linear solver backends__: Remove template argument `precondBlockLevel` from `solve` functions. The preconditioner block level is now determined automatically, assuming a value of
1 for regular BCRS matrices and a value of 2 for MultiTypeBlock matrices. The respective calls from the `NewtonSolver` and `PDESolver`classes have been adapted.

Kilian Weishaupt's avatar
Kilian Weishaupt committed
199
- __Change matrix block arrangement for staggered models__: The matrix block structure has been adapted such that it complies with the literature standard, i.e., having the velocity block (A) on `M[0][0]`
200
201
202
203
rather than on `M[1][1]`. This also requires re-arranging the submodels and properties in dumux-multidomain such that the face-related classes and vector entries now appear before the cell-centered ones.

```math
M = \begin{pmatrix}
Kilian Weishaupt's avatar
Kilian Weishaupt committed
204
205
  D & C\\
  B & A
206
207
208
209
210
\end{pmatrix}

\qquad => \qquad

M = \begin{pmatrix}
Kilian Weishaupt's avatar
Kilian Weishaupt committed
211
212
    A & B\\
    C & D
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
    \end{pmatrix}
```

Backwards-compatibility can only be provided to a certain extent. The following changes need to made in the main file:

1.) change the order of the arguments for the `assembler` such that it reads:
```c++
auto assembler = std::make_shared<Assembler>(std::make_tuple(ffProblem, ffProblem, otherProblem, ...),
                                             std::make_tuple(ffGridGeometry->faceFVGridGeometryPtr(),
                                                             ffFvGridGeometry->cellCenterFVGridGeometryPtr(),
                                                             otherFvGridGeometry, ...),
                                             std::make_tuple(ffGridVariables->faceGridVariablesPtr(),
                                                             ffGridVariables->cellCenterGridVariablesPtr(),
                                                             otherGridVariables, ...),
                                             couplingManager,
                                             timeLoop, solOld);

// Not changing the arguments will yield a deprecation warning stating this hint but the code still compiles and runs.
```

2.) change the order of arguments in the `partial` function:
```c++
ffSol = partial(sol, ffFaceIdx, ffCellCenterIdx);

// Not changing the argument will rise a compiler error which makes the MR not fully backwards-compatible.
```

240
241
242
Regarding changes made to the effective laws and diffusionCoefficient containters, Backwards-compatibility is maintined for a large extent, barring any volumevariable classes defined externally that inherit from the non-isothermal volumevariables.
If you use a self defined volumevariables class that inherits from the non-isothermal volumevariables, please adapt the your volumevariables class to fit to the non-isothermal volumevariables, and include the new methods for accessing the diffusion and effective diffusion coefficients.

243
244
- Tracer model: tracer fluid systems do no longer provide a `getMainComponent` function since this simply doesn't make sense -- the main bulk component is not modeled.

Timo Koch's avatar
Timo Koch committed
245
### Deprecated properties, to be removed after 3.2:
246
- __GridView__: The property `GridView` has been deprecated and can be accessed via `GridGeometry::GridView` instead.
Timo Koch's avatar
Timo Koch committed
247
248

### Deprecated classes/files, to be removed after 3.2:
249
250
- __AMGBackend__: The class AMGBackend is deprecated and has been replaced by AMGBiCGSTABBackend which gets some different template arguments
- __AMGTraits__: AMGTraits are deprecated, are to be replaced by LinearSolverTraits and restructured internally. As they were only used by the AMGBackend, we did not make the internal changes backwards-compatible
Timo Koch's avatar
Timo Koch committed
251
252

### Deprecated member functions, to be removed after 3.2:
253
254
- __DiffusionCoefficient(various arguments)__: These coefficients are now defined in the volvars and stored in a container fit to the model. To access these values, use the unified ```c++ diffusionCoefficient(int phaseIdx, int compIIdx, int compJIdx) ```
- __EffectiveDiffusivity(various arguments)__: These values are now defined in the volvars and stored in a container fit to the model. To access these values, use the unified ```c++ effectiveDiffusionCoefficient(int phaseIdx, int compIIdx, int compJIdx) ```
Timo Koch's avatar
Timo Koch committed
255
256

### Deleted classes/files, property names, constants/enums
Timo Koch's avatar
Timo Koch committed
257
Everything that has been deprecated before release 3.1 has been removed.
Timo Koch's avatar
Timo Koch committed
258

259
Differences Between DuMu<sup>x</sup> 3.1 and DuMu<sup>x</sup> 3.0
Timo Koch's avatar
Timo Koch committed
260
261
262
263
=============================================

### Improvements and Enhancements

264
- __Examples__: Three extensively documented examples have been added which highlight interesting features and show how to apply DuMu<sup>x</sup> to interesting problems. They can be found in the new folder `examples`. To get an overview, point your browser to https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/tree/master/examples.
265

Katharina Heck's avatar
Katharina Heck committed
266
- __Porousmediumflow__: Added a new porous medium model for the energy balance of a porous solid (general heat equation).
267

268
- __Multidomain__: It is now possible to use the facet coupling module together with the mpfa-o scheme in the bulk domain.
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284

- __Box__: The box scheme works now on grids with prism / wedge elements in 3D.

- __Diffusive fluxes__: We revised the formulation of the diffusion laws to allow for changes between mass-averaged velocity reference systems and molar-averaged velocity reference systems. The standard formulation is now set to mass-averaged velocity reference systems.

- __GridManager__:
    * Supports now reading unstructured grids and data from vtu/vtp files (ASCII, XML format) sequential.
      For UGGrid and FoamGrid you can specify a grid in such a format in the input file:
      `Grid.File = mygrid.vtu` / `Grid.File = mygrid.vtp`. The associated data is then available in the grid data object.
    * Instead of always including all grid manager specializations you can now only include the specialization that you need.
      For example, if you only use YaspGrid in your code, you only need to include `dumux/io/grid/gridmanager_yasp.hh`. The
      convenience header `dumux/io/grid/gridmanager.hh` still includes all specializations.
    * Added a `NetPBMReader` which allows to read simple raster images files (`*.pbm` and `*.pgm`). Can be used, e.g., with
      `dune-subgrid` in order to create a grid from an image file.

- __Freeflow__: A second order approximation of the convective term of all Navier-Stokes based models is now available.
Roman Winter's avatar
Roman Winter committed
285
  This can be enabled using the property `UpwindSchemeOrder`. This property defaults to a first order upwinding approximation,
286
  which is the method used for all models in release 3.0. If this property is set to `2`, a second order flux limiter method will be used.
287
288
289
290
  Various flux limiter functions have been implemented to maintain the monotonicity of this discretization. Per default the
  `Minmod` flux limiter is used, but `Vanleer`, `Vanalbada`, `Superbee`, `Umist`, `Mclimiter`, and `Wahyd` based flux limiters
  are also available. These can be specified using the input file entry `Flux.DifferencingScheme`. These methods are also
  implemented for non-uniform structured grids (e.g. YaspGrid - TensorProductCoordinates). Per default, a scheme assuming a
Ned Coltman's avatar
Ned Coltman committed
291
  uniform grid is used, but two other methods, `Li` and `Hou`, are both available for adaptations to non-uniform grids.
292
  These can be specified using the input file entry `Flux.TVDApproach`.
293

Ned Coltman's avatar
Ned Coltman committed
294
- __RANS__: The called RANS model, defined in the properties system, will specify, via the model traits,
295
296
297
  which RANS problem implementation should be used. In each problem file, the initial and boundary conditions can be
  set using templated functions based on the model type. Examples of these functions exist in the RANS based tests.
  No further preprocessor macros are required.
298
299
300
301
302
303

- __ShallowWater__: Thanks to Leopold Stadler we now have a shallow water equations solver / model. Have a look at freeflow/shallowwater and give it a try with the dam break test at test/freeflow/shallowwater. The are also some friction laws computing shear stresses (Manning, Nikuradse) to account for friction in a channel/river bed, thanks to Martin Utz.

- __Staggered__: Added a `StaggeredNewtonConvergenceWriter` for the staggered grid discretization scheme.

- __Solver__: There is a new abstract base class `PDESolver` that is a class that does linearize & assemble, solve and update.
Roman Winter's avatar
Roman Winter committed
304
  The NewtonSolver now derives from this class (interface is unchanged). A new class `LinearPDESolver` simplifies solving linear problems
305
  by reducing the code in the main file and streamlining the terminal output to look like the Newton output.
Katharina Heck's avatar
Katharina Heck committed
306

307

Timo Koch's avatar
Timo Koch committed
308
309
### Immediate interface changes not allowing/requiring a deprecation period

Roman Winter's avatar
Roman Winter committed
310
311
- `NewtonConvergenceWriter`'s first template argument has changed from `GridView` to `FVGridGeometry`. This allows to call the `resize()` method after a grid change without any arguments.
  Here is an example how to instatiate the convergence writer:
312
313
314
315
  ```
  using NewtonConvergenceWriter = Dumux::NewtonConvergenceWriter<FVGridGeometry, SolutionVector>;
  auto convergenceWriter = std::make_shared<NewtonConvergenceWriter>(*fvGridGeometry);
  ```
316

317
318
319
320
- The interface of the abstract `TimeLoopBase` class has been extended by `virtual void advanceTimeStep()`, `virtual void setTimeStepSize(Scalar dt)`,
  `virtual Scalar maxTimeStepSize()`, and `virtual bool finished()`, thus forcing the inheriting classes to implement those functions.
  `TimeLoop` is no longer a template argument in `NewtonSolver`'s `solve()` method, thereby increasing
  type safety and providing better compiler error messages.
321

Katharina Heck's avatar
Katharina Heck committed
322
323
- __RANS__: The base problems for all turbulence models e.g. `ZeroEqProblem` have been been renamed to one generic `RANSProblem`

324
325
326
327
328
329
330
331
### Deprecated properties, to be removed after 3.1:

- `FVGridGeometry` and `EnableFVGridGeometryCache` have been replaced by
  `GridGeometry` and `EnableGridGeometryCache`.

Unfortunately, clang doesn't emit deprecation warnings if an old property name is
used. Consider employing gcc for detecting occurrences of the old name.

Timo Koch's avatar
Timo Koch committed
332
333
### Deprecated classes/files, to be removed after 3.1:

334
335
336
337
338
339
- `BaseFVGridGeometry` from `dumux/discretization`. Use `BaseGridGeometry` instead.

- `CakeGridCreator` and `SubgridGridCreator` from `dumux/io/grid`. Use the corresponding `...Manager` instead.

- `IntRange` from `dumux/common`. Use `Dune::IntegralRange` instead.

Timo Koch's avatar
Timo Koch committed
340
341
### Deprecated member functions, to be removed after 3.1:

342
343
344
345
- The convergence writer is no longer passed to `NewtonSolver`'s `solve()` method.
  For outputting convergence data, please use `newtonSolver.attachConvergenceWriter(convWriter)` in `main.cc` (directly after instantiating the writer).
  To stop the output, the writer can also be detached again using `newtonSolver.detachConvergenceWriter()`.

Timo Koch's avatar
Timo Koch committed
346
347
### Deleted classes/files, property names, constants/enums

348
349
- Deprecated classes and files for the 3.0 release listed below stay deprecated
  for at least one more release cycle.
Timo Koch's avatar
Timo Koch committed
350

351
Differences Between DuMu<sup>x</sup> 2.12 and DuMu<sup>x</sup> 3.0
352
353
=============================================

Bernd Flemisch's avatar
Bernd Flemisch committed
354
355
## Important Notes

356
357
- DuMu<sup>x</sup> 3.0 is a major version update. It is not backward compatible in all aspects to 2.12.
  The following minor version updates will be, as before for the DuMu<sup>x</sup> 2-series, always backward compatible
358
359
      to at least the last minor version update.

Bernd Flemisch's avatar
Bernd Flemisch committed
360
361
- The tutorial has been replaced by the new module `dumux-course` which is
  accessible at https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-course.
362
  We recommend new users and also users experienced with DuMu<sup>x</sup> 2.X to clone
Bernd Flemisch's avatar
Bernd Flemisch committed
363
364
  the course and have a look at the exercises in there.

365
- DuMu<sup>x</sup> 3.0 is based on Dune 2.6 and is expected to run with the current Dune master.
Bernd Flemisch's avatar
Bernd Flemisch committed
366
367
368
  We will try to keep the compatibility with the Dune master
  as long as it is technically feasible and our resources allow it.

369
- DuMu<sup>x</sup> 3.0 requires at least GCC 4.9 or Clang 3.5 in their C++-14 mode.
Bernd Flemisch's avatar
Bernd Flemisch committed
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
  However, we suggest to use newer compiler versions, as we cannot test against all previous compiler versions.

- For employing corner-point grids by means of opm-grid, the OPM release 2018.10 has to be used.

## Improvements and Enhancements

### General

- __New style main files:__ 3.0 comes which a major overhaul of how the sequence of simulation steps is specified.
  Until 2.12 there was the start.hh header including the free function `start` that contained a predefined sequence of
  steps. Customization of the sequence was possible by many hooks implemented in classes used in this sequence. This
  made it hard to follow the course of the program and hard to implement customization at points where this was not previously envisioned.
  In contrast, in the new approach the sequence of simulation steps was linearized, meaning that each step is visible
  in the program's main file. In the new main files, one can clearly see the io, initialization, assembly, solving, update, time loop, etc.,
  of the program. Many parts of the simulation that were previously mandatory, i.e. simulations in 2.12 always contained a time loop,
  are now optional (stationary simulations just don't need a time loop). The new style main files make it easier two follow the course
  of the program, are easier to customize, and offer more flexibility concerning the customization of steps and components of a simulation.
  All tests and examples in the dumux repository have been adapted to the new style main files.
- __Property system:__ The property system is now usable without preprocessor macros. To this end it was completely reimplemented using C++14 techniques and
  variadic templates. The hierarchies can now be arbitrarily deep instead of being limited to 5 levels. The new implementation does not use
  C++ inheritance. Properties and TypeTag now have to be properly qualified with the namespaces `Properties::`, `TTag::`. Types that share the
  name with properties have to properly qualified with the `Dumux::` namespace. This update makes it hopefully more readable
  and removes the "magic" part from the property system.
- __Runtime parameters:__ Runtime parameters are no longer accessed with preprocessor macros. They have been replaced by C++ function templates
  `Dumux::getParam`, `Dumux::hasParam`, `Dumux::getParamFromGroup`. The `..FromGroup` version has been redesigned to allow the specification
  of parameters for different models in one input file. The concept of a parameter group string was extended to make it possible to
  use a single input file for complex multidomain simulation setups.
- __Restarting simulations:__ The old restart module was replaced by an implementation based on a VTK backend (other formats might be added later such as HDF5).
  Restarted simulations can read solutions from vtk files. For parallel runs, there is currently the restriction that the number of processors has to be the same
  as before the restart. Restarted simulations can read grids from vtk (currently only sequential, non-adaptive grids, support for parallel and adaptive
  will be added in a future version).
- __Assembly__: The assembler can now assemble implicit and explicit Euler time discretizations. An interface for implementing analytical Jacobians was added.
  The CCTpfa assembler has been significantly improved for complex models that spend a lot of time computing constitutive laws. Also the numerical
  differentiation scheme was improved by altering the order in which derivatives are computed.
404
405
- __TypeTag templates:__ Implementers of code in DuMu<sup>x</sup> 3.0 are advised to avoid TypeTag as a template argument for class templates.
  Many classes in the DuMu<sup>x</sup> core have been changed to have a small number of specific template arguments, including `GridGeometry`,
Bernd Flemisch's avatar
Bernd Flemisch committed
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
  `TimeLoop`, `Newton`, `LinearSolver`, `SpatialParams`. This makes it possible to share objects of these types between models using
  different TypeTags. This was not possible before as `Class<TypeTag1>` and `Class<TypeTag2>` are different types, even if they contain
  exactly the same implementation code.
  Furthermore, having TypeTag as a template argument leads to bad programming, and unnecessary dependencies that should be avoided in
  every object-oriented code.
- __The grid geometry concept:__ In version 3.0, discretization methods use grid geometries which are wrappers or adapters around a `Dune::GridView`,
  providing data structures and interfaces necessary to implement these discretization methods easily. In particular, the
  abstraction of sub-control-volumes (scv) and sub-control-volume-faces (scvf) are now separate classes and the grid geometry provides means to iterate
  over all scvs and scvfs of an element, using range-based-for loops.
- __The caching concept:__ Version 3.0 introduces a caching concept for the new grid geometry, the volume variables and the flux variables.
  There are classes with a `Grid` prefix, that store data for the current grid view, and classes with the `Element` prefix that store data locally
  for an element or element stencil. Depending on the caching concept used, data will be either stored completely in the `Grid` objects
  (e.g. `GridGeometry`) and the `Element` objects (e.g. `ElementGeometry`) are mere accessor objects, or, data will be partly only cached locally.
  Local caching uses less memory but might result in an increased runtime. Grid caching is memory intensive
  but can provide a significant run-time speedup. Choose whatever concept fits your available resources,
  the default being local caching.
- __Support__ for grid managers `dune-subgrid` (a meta grid selecting only certain elements from a host grid)
  and `dune-spgrid` (a structured parallel grid manager, supporting periodic boundaries).

### Models, Physics and Methods

427
428
- __MPFA schemes:__ The new design of the DuMu<sup>x</sup> core facilitates the incorporation of new finite-volume schemes. In particular, the new core comes with
  a framework for MPFA schemes, in which currently the only available scheme is the MPFA-O scheme. It can be used in conjunction with any DuMu<sup>x</sup> model and
Bernd Flemisch's avatar
Bernd Flemisch committed
429
  also works on surface grids. More schemes will be added in the future.
430
- __Box-dfm:__ The `2pdfm` model from version 2.12 has been generalized such that it can be used on any DuMu<sup>x</sup> model and in both two and three dimensions.
Bernd Flemisch's avatar
Bernd Flemisch committed
431
432
433
434
435
436
- __Tracer transport__: A new model for tracer transport with a given flow field has been added. The model can be also used to implement sequentially
  coupled simulations, or iterative solvers where flow and transport are decoupled / weakly coupled.
- __Mineralization__: An adapter model for mineralization has been added and can be used with all porousmediumflow models. A balance for the solid
  volume fraction of precipitating, adsorbed, or absorbed substances is added to the existing equations.
- __Solution-dependent spatial params:__ A redesign of the spatial params interface allows now to define spatial parameters such as permeability
  and porosity that depend on the solution. This makes it easier to implement mineralization models altering the solid structure of the porous medium.
437
- __Solid systems:__ DuMu<sup>x</sup> 3.0 introduces solid systems similar to fluid systems but for solid components. This allows a consistent
Bernd Flemisch's avatar
Bernd Flemisch committed
438
439
  implementation of mineralization models including reactions, dissolution, precipitation and other processes altering the solid
  phase of the porous medium.
440
- __Multidomain:__ DuMu<sup>x</sup> 3.0 introduces a new multidomain framework which does no longer depend on `dune-multidomain` and can be used for the coupling
Bernd Flemisch's avatar
Bernd Flemisch committed
441
  of an arbitrary number of subdomains. The sub-domains can be regions in which different sets of equations are solved and/or which have different
442
  dimensionalities. The implementation is such that any of the existing DuMu<sup>x</sup> models can be used in the subdomains, while the data and functionality
Bernd Flemisch's avatar
Bernd Flemisch committed
443
444
445
446
447
448
449
  required for the coupling of the sub-domains is implemented in a `CouplingManger` class. Three different coupling concepts are available, for which
  there are a number of available `CouplingManager` class implementations:
    - _Boundary:_ coupling across sub-domain boundaries
    - _Embedded:_ Coupling between a bulk domain and an embedded lower-dimensional sub-domain which has an independent grid
    - _Facet:_ Coupling betweeen a bulk domain and a codimension-one sub-domain, which is conforming with the element facets of the bulk domain
- __Free-flow models:__ The previous Navier-Stokes model using the box method has been replaced by one that employs a staggered grid discretization.
  The new method does not  require any stabilization techniques while those were necessary for the box method in order to avoid spurious oscillations.
450
  The free-flow models in DuMu<sup>x</sup> 3.0 consider single phase flow with or without component/energy transport. So far, only regular Cartesian grids are supported
Bernd Flemisch's avatar
Bernd Flemisch committed
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
  but local grid refinement will be added in a future release.
  Several RANS models for turbulent flow have been added: k-omega, k-epsilon, low-Re-k-epsilon, one-eq, zero-eq. The RANS models might be subject to further (interface)
  changes.
- __Thermal and chemical non-equilibrium:__ The possibility to consider thermal and/or chemical non-equilibrium of several types has been enabled for all
  porous medium models.
- __Interface solver:__ For the two-phase flow model in conjunction with the box scheme, an interface solver can now be used to reconstruct the saturations
  in the sub-control volumes adjacent to vertices that lie on material discontinuities. This allows a sharper representation of the saturation front evolving
  in heterogeneous porous media.
- __Components:__ Components can now derive from different base classes, `Base`, `Liquid`, `Solid`, `Gas`, depending on which
  phase states are implemented. This can be used to determine at compile time if a component supports a certain phase state.
- __Tabulation of fluid parameter laws:__ The tabulation of fluid parameter laws has been improved to only tabulate those functions actually used during the
  simulation. To this end, the tabulation is done on the first call of a corresponding fluid parameter.
- __MPNC:__ The general m-phase n-component model has been adapted in structure to the other porous medium flow models.
- __Different wettability:__ The 2p models can now model materials with different wettability (hydrophobic, hydrophilic) in different parts of the domain.
- __Maxwell-Stefan-diffusion:__ Most models can now use Maxwell-Stefan diffusion for multi-component diffusion instead of Fickian diffusion.
  There are also a few tests demonstrating how to use it.

## Immediate interface changes not allowing/requiring a deprecation period

- Many classes have been completely redesigned. See the numerous example applications included in 3.0 showcasing all new classes.
- The `GridCreator` has been replaced by the `GridManager`, which no longer uses a singleton for the grid object.
  This makes it possible to create two grids of the exact same type. The `GridManager` also handles user data provided in grid files.

## Deprecated classes/files, to be removed after 3.0
- All classes of the sequential models are deprecated. The sequential models will be ported to the new structure
  of porous medium models (formerly called implicit models). This way sequential and implicit model implementations
  no longer differ and use the same numerical infrastructure.
- The `TimeManager` class is to be replaced by the class `TimeLoop`.
- The `VtkMultiWriter` class is to be replaced by the class `VtkOutputModule`.
- The file `start.hh` is replaced by new style main files.

482
## Deleted classes/files/functions... which have been deprecated in DuMu<sup>x</sup> 2.12
Bernd Flemisch's avatar
Bernd Flemisch committed
483
- Everything listed as deprecated below has been removed.
484
485


486
Differences Between DuMu<sup>x</sup> 2.11 and DuMu<sup>x</sup> 2.12
487
488
489
=============================================

* IMPORTANT NOTES:
490
    - DuMu<sup>x</sup> 2.12 is expected to run based on Dune 2.4.1, 2.5, 2.6 and the Dune
491
492
      master. We will try to keep the compatibility with the Dune master
      as long as it is technically feasible and our resources allow it. If
493
      you want to use DuMu<sup>x</sup> multidomain models, you have to stick with the
494
      Dune 2.4 core and specific versions of other modules, see
495
496
      [test/multidomain/README](test/multidomain/README) for details.
      Also the geomechanics models require Dune 2.4 and PDELab 2.0.
497

498
    - DuMu<sup>x</sup> 2.12 requires at least GCC 4.9 or Clang 3.5 in their C++-14 mode.
499
500

    - For employing corner-point grids by means of opm-grid (former
501
      dune-cornerpoint), the OPM releases 2017.04 or 2017.10 have to be used.
502
503

* IMPROVEMENTS and ENHANCEMENTS:
504
505
506
507
508
509
510
511
    - Four new tutorial exercises have been added in the folder
      [tutorial](tutorial). They can be built by executing
      `make build_tutorials` in the build folder. Each exercise
      comes with detailed instructions:
        1. [Exercise 1](tutorial/ex1/README.md)
        2. [Exercise 2](tutorial/ex2/README.md)
        3. [Exercise 3](tutorial/ex3/README.md)
        4. [Exercise 4](tutorial/ex4/README.md)
512

513
514
515
516
517
518
    - Fixed bug in heatCapacity() of component air and replace
      the use of a constant value in  gasEnthalpy() by calling
      heatCapacity().

    - The GnuplotInterface now supports in-simulation generation of image
      files (*.png).
519

520
521
    - A paraview python script for exporting 2d pictures from *.vtu files
      has been added.
522

523
524
    - A class for estimating turbulence properties has been added with
      turbulenceproperties.hh.
525

526
527
528
529
* IMMEDIATE INTERFACE CHANGES not allowing/requiring a deprecation period:
    - gnuplotinterface.hh: The add...ToPlot() functions have changed signature,
      the curve name/title is not mandatory anymore and can be specified together
      with the curve options.
530
531

* DELETED classes/files, property names, constants/enums,
532
  member functions, which have been deprecated in DuMu<sup>x</sup> 2.11:
533
534
535
    - Everything listed as deprecated below has been removed.


536
Differences Between DuMu<sup>x</sup> 2.10 and DuMu<sup>x</sup> 2.11
Christoph Grüninger's avatar
Christoph Grüninger committed
537
538
539
=============================================

* IMPORTANT NOTES:
540
    - DuMu<sup>x</sup> 2.11 is expected to run based on Dune 2.4.1, 2.5 and the Dune
Christoph Grüninger's avatar
Christoph Grüninger committed
541
542
      master. We will try to keep the compatibility with the Dune master
      as long as it is technically feasible and our resources allow it. If
543
      you want to use DuMu<sup>x</sup> multidomain models, you have to stick with the
Christoph Grüninger's avatar
Christoph Grüninger committed
544
545
546
      Dune 2.4 core and specific versions of other modules, see
      `test/multidomain/README` for details.

547
    - DuMu<sup>x</sup> 2.11 requires at least GCC 4.9 or Clang 3.5 in their C++-14 mode.
Christoph Grüninger's avatar
Christoph Grüninger committed
548
549
550
551
552
553
554

    - For employing corner-point grids by means of opm-grid (former
      dune-cornerpoint), the OPM release 2016.04 has to be used.

* IMPROVEMENTS and ENHANCEMENTS:

* IMMEDIATE INTERFACE CHANGES not allowing/requiring a deprecation period:
555
556
557
558
    - A gridcreator for piece-of-cake-type grids has been added. It is capable
      of creating meshes with gradually in- and decreasing distances between nodes.
      It also allows the creation of a 360° cake where the last elements are
      connected to the first elements.
559
560
561
562
    - shouldWriteRestartFile() is now, as shouldWriteOutput() already was,
      called before the time level is advanced. So it might be necessary to use
      ...WillBeFinished instead of ...IsFinished for writing restart files at
      the correct time.
563
564
565
    - In the ZeroEq models, the properties BBoxMinIsWall and BBoxMaxIsWall have
      been replaced by the functions bBoxMaxIsWall() and bBoxMaxIsWall() in the
      problem file.
566
567
568
569
570
571
    - In the TwoPNC (and, consequently the TwoPNCMin) models, the old formulations
      pgSl, plSg as well as pnSw and pwSg have been replaced by the pnsw and pwsn,
      to satify the naming convention and be consistent with TwoPTwoC.
    - In the TwoPTwoC model, the indices are no longer dependent on the
      formulation. Further, the values of "nPhaseOnly" and "bothPhases"
      have been harmonized with those in TwoPNC
Christoph Grüninger's avatar
Christoph Grüninger committed
572
573
574
575
576
577
578
579
580
581
582

* Deprecated PROPERTY and PARAMETER NAMES, to be removed after 2.11: BEWARE: The
  compiler will not print any warning if a deprecated property or parameter name
  is used. If possible, a run-time warning will appear in the summary lines
  after the corresponding run.

* Deprecated CLASSES/FILES, to be removed after 2.11:

* Deprecated MEMBER FUNCTIONS, to be removed after 2.11:

* DELETED classes/files, property names, constants/enums,
583
  member functions, which have been deprecated in DuMu<sup>x</sup> 2.10:
Christoph Grüninger's avatar
Christoph Grüninger committed
584
585
586
    - Everything listed as deprecated below has been removed.


587
Differences Between DuMu<sup>x</sup> 2.9 and DuMu<sup>x</sup> 2.10
588
589
590
===================================================

* IMPORTANT NOTES:
591
    - DuMu<sup>x</sup> 2.10 is expected to run based on Dune 2.4.1, 2.5 and the Dune
592
593
      master. We will try to keep the compatibility with the Dune master
      as long as it is technically feasible and our resources allow it. If
594
      you want to use DuMu<sup>x</sup> multidomain models, you have to stick with the
595
596
      Dune 2.4 core and specific versions of other modules, see
      `test/multidomain/README` for details.
597

598
    - DuMu<sup>x</sup> 2.10 requires at least GCC 4.9 or Clang 3.5 in their C++-14 mode.
599

600
601
602
    - For employing corner-point grids by means of opm-grid (former
      dune-cornerpoint), the OPM release 2016.04 has to be used.

603
* IMPROVEMENTS and ENHANCEMENTS:
604
605
606
607
608
609
610
611
612
613
614
    - Two new fully-implicit models have been added: `ThreePWaterOil` and
      `TwoPOneC`. The first one admits two components water and oil that may be
      present in two liquid and one gaseous phase, see `test_box3pwateroil` in
      `test/porousmediumflow/3pwateroil/implicit` for details. The second one is
      dedicated to one generic component that may be present in liquid and
      gaseous state, see `test_boxsteaminjection` in
      `test/porousmediumflow/2p1c/implicit` for an example.

    - Numbering of the VTK files starts with `0` now.

    - Using the geostatistical tool gstat for generating random fields has been
615
616
      facilitated. See `test_cc1pwithgstat` in `test/porousmediumflow/1p/implicit`.
      This tool can be installed using the `bin/installexternal.sh` script.
617
618
      If cmake does not find gstat, one has to specify the GSTAT_ROOT variable,
      see the standard optim.opts or debug.opts.
Christoph Grüninger's avatar
Christoph Grüninger committed
619

620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
    - The multidomain models should now run with all compilers without
      segfaults, both with optimization and debug options.

    - Computation for two-dimensional fracture networks in three-dimensional
      space has been fixed and is tested now in
      `test/porousmediumflow/2p/implicit/test_fracture_box2p`.

    - The `bin` folder containing various helper scripts has been restructured.
      For example, the scripts `fuzzycompare.py` and `runtest.py` are now
      contained in the subfolder `testing`.

    - Two new scripts `extractlinedata.py` and `extractpointdataovertime.py`
      have been added to `bin/postprocessing`. They realize what their names
      suggest.

    - The computation of the tortuosity tau with the Millington-Quirk model has
      been optimized. Tests show a speedup of up to 5% for a 2p2c simulation.

    - The fully-implicit box scheme now fully supports prism-shaped elements.

    - Convenience functions for reading values from a file to a container and
      for writing values to a file from a container have been added, see
      `test_container_io` in `test/io/container`.
643
644

* IMMEDIATE INTERFACE CHANGES not allowing/requiring a deprecation period:
645
646
    - The problem class interface needs to provide the method maxTimeStepSize().
      This is important if you implement problem classes not deriving from the base
647
      problem classes in DuMu<sup>x</sup> (`ImplicitProblem`, `OneModelProblem`,
648
      `ImpetProblem`, and `MultidomainProblem`).
649
650
651
652
    - All name-related methods that previously returned / received `const char*`
      do now use the type-safe alternative `std::string`. An example is
      `FluidSystem::componentName()`. If you need a
      `const char*` for special operation use the string member `c_str()`.
653
654
655

* Deprecated PROPERTY and PARAMETER NAMES, to be removed after 2.10: BEWARE: The
  compiler will not print any warning if a deprecated property or parameter name
656
657
658
659
660
  is used. If possible, a run-time warning will appear in the summary lines
  after the corresponding run.
    - The pure run-time parameter `tau` has been renamed to the property and
      run-time parameter `TauTortuosity`. For the models 1p2c, 2p2c, 3p3c it got
      the default value 0.5.
661
662

* Deprecated CLASSES/FILES, to be removed after 2.10:
663
664
665
    - The class `DiffusivityConstantTau<TypeTag, Scalar>` was renamed to
      `DiffusivityConstant<TypeTag>` and is located in a according new header. The
      old class, its header and the property `tau` are deprecated.
666

667
668
669
670
671
672
    - `PointSourceHelper<TypeTag>` has been deprecated. Use
      `BoundingBoxTreePointSourceHelper<TypeTag>` instead.

    - The classes `Dumux::Liquid/GasPhase<Scalar, Component>` have been moved to
      the namespace `Dumux::FluidSystems`.

673
* Deprecated MEMBER FUNCTIONS, to be removed after 2.10:
674
675
    - `checkEffectiveSaturation` of the classes `PlotMaterialLaw<TypeTag>` in
      `dumux/io`.
676

677
678
    - `concentrationGrad` of the class `TwoPNCFluxVariables<TypeTag>`. Use
      `moleFractionGrad` instead, with the obviously different physical meaning.
679
680

* DELETED classes/files, property names, constants/enums,
681
  member functions, which have been deprecated in DuMu<sup>x</sup> 2.9:
682
683
684
    - Everything listed as deprecated below has been removed.


685
Differences Between DuMu<sup>x</sup> 2.8 and DuMu<sup>x</sup> 2.9
686
687
688
===================================================

* IMPORTANT NOTES:
689
    - DuMu<sup>x</sup> 2.9 is expected to run based on either Dune 2.4 or Dune 3.0. We will
Bernd Flemisch's avatar
Bernd Flemisch committed
690
      try to keep the compatibility with Dune 3.0 as long as it is technically
691
      feasible and our resources allow it. If you want to use DuMu<sup>x</sup> multidomain
Bernd Flemisch's avatar
Bernd Flemisch committed
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
      models, you have to stick with the Dune 2.4 core and specific versions of
      other modules, see `test/multidomain/README` for details.

    - The ALUGrid stand-alone library cannot be used any longer. Use the module
      [dune-alugrid](https://gitlab.dune-project.org/extensions/dune-alugrid)
      instead. Both the `releases/2.4` branch and the `master` should work.

    - The above is not true if you like to run a sequential MPFA model on an
      `ALUGrid`. Then, you currently have to use the `master-old` branch of
      dune-alugrid. We will try to fix this as soon as possible. Alternatively,
      `UGGrid` or `YaspGrid` can be chosen as grid managers.

    - Instead of using AlbertaGrid for the tests where dim < dimWorld, we now
      employ
      [dune-foamgrid](https://gitlab.dune-project.org/extensions/dune-foamgrid).
      Dune-foamgrid provides 1d and 2d simplex grids embedded in an arbitrary
      dimension world space. It features element parametrizations, runtime growth,
      runtime-movable vertices. You might still use AlbertaGrid, but it is not
      supported by our GridCreator.

    - If you like/have to use corner-point grids by means of the module
      dune-cornerpoint, you have to use (and partially patch) the 2015.10 release
      of [OPM](http://opm-project.org/?page_id=36). See `patches/README` for
      details.
716
717

* IMPROVEMENTS and ENHANCEMENTS:
Bernd Flemisch's avatar
Bernd Flemisch committed
718
719
720
721
722
    - The folder structure has been changed according to
      [FS#250](http://www.dumux.org/flyspray/index.php?do=details&task_id=250).
      This has been a rather massive change affecting more than 1000 files. Close
      to 400 files have been moved and/or renamed.
      We made everything backwards-compatible, the worst thing that should happen
723
      after switching to DuMu<sup>x</sup> 2.9, will be some warnings when including headers
Bernd Flemisch's avatar
Bernd Flemisch committed
724
725
726
727
728
729
730
731
732
733
      from old destinations/names. You can fix the include statements and get rid
      of the warnings by applying the bash script `bin/fix_includes.sh` to your
      source files, for example by executing
      ```
      bash ../dumux/bin/fix_includes.sh file1 [file2 ...]
      ```
      or
      ```
      find . -name '*.[ch][ch]' -exec bash ../dumux/bin/fix_includes.sh {} \;
      ```
734
      inside the folder that contains your files.
735
736
737
738
      A patch is available to remove deprecated header files:
      ```
      patch -p1 < patches/dumux-2.9-no-deprecated-headers.patch
      ```
Bernd Flemisch's avatar
Bernd Flemisch committed
739
      The benefits are hopefully:
740
        + A clearer structure in terms of the problems that you want to apply DuMu<sup>x</sup>
Bernd Flemisch's avatar
Bernd Flemisch committed
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
          for. Three main application areas on the top level: `porousmediumflow`,
          `freeflow` and `geomechanics`. The different numerical treatments "fully
          implicit" or "sequential" appear as discretization detail after the
          choice of the physical model. That's of course currently rather wishful
          thinking, but nevertheless where we are headed. The folder `implicit` on
          the top level now only contains physics-agnostic classes that can be used
          by any class of an application area.  Please note the change from
          "decoupled" to "sequential" according to the related task
          [FS#252](http://www.dumux.org/flyspray/index.php?do=details&task_id=252).

        + Nicer include statements due to relaxation of the naming conventions for
          the header files. Compare the old
          ```
          #include <dumux/multidomain/2cnistokes2p2cni/2cnistokes2p2cnilocaloperator.hh>
          ```
          with the new
          ```
758
          #include <dumux/multidomain/2cnistokes2p2cni/localoperator.hh>
Bernd Flemisch's avatar
Bernd Flemisch committed
759
760
761
762
763
764
765
766
767
768
769
          ```
      The structure change is reflected in the `test` folder:
        + The tests from`test/implicit/particular_model` have been moved to
          `test/porousmediumflow/particular_model/implicit`. For example,
          `test/implicit/2p` has been moved to `test/porousmediumflow/2p/implicit`.

        + Analogously, the tests from `test/decoupled/particular_model` have been
          moved to `test/porousmediumflow/particular_model/sequential`.

        + The subfolders `decoupled` and `implicit` of `test` have been removed.

770
        + If you have cloned the DuMu<sup>x</sup> Git repository and have local changes in the
Bernd Flemisch's avatar
Bernd Flemisch committed
771
772
773
774
775
776
777
          folders `test/implicit` or `test/decoupled`, you can expect merge
          conflicts for your next `git pull`. You can either deal with these
          conflicts directly or create a patch, remove the local changes, pull, and
          apply the patch afterwards with some care to respect the changed
          structure.

    - A two-phase multiple-interacting-continua (MINC) model has been added to
778
      the DuMu<sup>x</sup> model portfolio. See `test/porousmediumflow/2pminc/implicit` for
Bernd Flemisch's avatar
Bernd Flemisch committed
779
780
781
782
783
784
785
      details.

    - The multidomain models have been restructured. Duplicated code has been
      reduced; isothermal and non-isothermal models are treated in a more
      consistent manner.

    - It is now possible to specify point sources for implicit models. A point
786
      source is a source term specified at any point location in e.g. kg/s. DuMu<sup>x</sup>
Bernd Flemisch's avatar
Bernd Flemisch committed
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
      will compute the correct control volume the source belongs to for you. Point
      sources can be e.g. solution and/or time-dependent. See tests
      (1p/implicit/pointsources, 2p/implicit/pointsources) for examples.

    - All tests use our standard `GridCreator` now. If it is possible to specify
      the grid entirely in the input-file, the corresponding DGF files have been
      deleted. In particular, a YaspGrid tensor grid can now also be specified via
      the input file only.

    - Several sections on our fluid/material framework have been moved from the
      handbook to the Doxygen documentation.

    - The three-phase constitutive relations from
      `material/fluidmatrixinteractions` have been reworked to be consistent with
      their two-phase analogues. In particular, an `EffToAbsLaw` and
      regularization classes have been implemented.

    - In case of a simulation stop due to too many timestep subdivisions, restart
      files of both the current and the old solution are automatically generated.
806

807
* IMMEDIATE INTERFACE CHANGES not allowing/requiring a deprecation period:
Bernd Flemisch's avatar
Bernd Flemisch committed
808
809
810
811
    - All flux variables are now default-constructible. While the non-trivial
      constructors are deprecated, model implementers might be required to make
      their flux variables default-constructible too. In particular, this affects
      you if you develop your own flux variables that
812
        + inherit from flux variables from dumux-stable, such as the
Bernd Flemisch's avatar
Bernd Flemisch committed
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
          `ImplicitDaryFluxVariables`,
        + and/or are used in a local residual from dumux-stable.
      See the
      [mailing list](https://listserv.uni-stuttgart.de/pipermail/dumux/2016q1/001551.html)
      for details.

    - For the multidomain models, the notation of the boundary condition types
      has changed. This is especially important for all momentum boundary
      conditions. In general:
        + `couplingInflow`  -> `couplingNeumann`
        + `couplingOutflow` -> `couplingDirichlet`
    - But for the momentum balances:
        + `couplingInflow`  -> `couplingDirichlet`
        + `couplingOutflow` -> `couplingNeumann`

    - Due to the change in the three-phase fluid-matrix-interactions, you might
      have to adjust your spatial parameters. You should get a compiler warning
      message that gives you more details.

    - The TypeTags `ImplicitModel` and `ExplicitModel` have been deleted. They
      haven't been used apart from one internal inheritance. See FS#304 for
      details.
835

Timo Koch's avatar
Timo Koch committed
836
* Deprecated PROPERTY and PARAMETER NAMES, to be removed after 2.9: BEWARE: The
837
838
839
  compiler will not print any warning if a deprecated property or parameter name
  is used. However, a run-time warning should appear in the summary lines after
  the corresponding run.
Bernd Flemisch's avatar
Bernd Flemisch committed
840
841
842
843
844
845
    - The word `Decoupled` in the TypeTags has been replaced by `Sequential`:
        + `DecoupledModel` -> `SequentialModel`
        + `DecoupledOneP` -> `SequentialOneP`
        + `DecoupledTwoP` -> `SequentialTwoP`
        + `DecoupledTwoPTwoC` -> `SequentialTwoPTwoC`
        + `DecoupledTwoPTwoCAdaptive` -> `SequentialTwoPTwoCAdaptive`
846

847

Timo Koch's avatar
Timo Koch committed
848
* Deprecated CLASSES/FILES, to be removed after 2.9:
Bernd Flemisch's avatar
Bernd Flemisch committed
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
    - Self-written parallel linear solvers and corresponding infrastructure,
      according to
      [FS#293](http://www.dumux.org/flyspray/index.php?do=details&task_id=293).
      For parallel runs, use the `AMGBackend` instead. For sequential runs,
      direct replacements are:
        + `BoxBiCGStabILU0Solver` -> `ILU0BiCGSTABBackend`
        + `BoxBiCGStabSORSolver` -> `SORBiCGSTABBackend`
        + `BoxBiCGStabSSORSolver` -> `SSORBiCGSTABBackend`
        + `BoxBiCGStabJacSolver` -> `JacBiCGSTABBackend`
        + `BoxBiCGStabGSSolver` -> `GSBiCGSTABBackend`
        + `BoxCGILU0Solver` -> `ILUnCGBackend`
        + `BoxCGSORSolver` -> `SORCGBackend`
        + `BoxCGSSORSolver` -> `SSORCGBackend`
        + `BoxCGJacSolver` -> `JacCGBackend`
        + `BoxCGGSSolver` -> `GSCGBackend`
        + `IMPETBiCGStabILU0Solver` -> `ILU0BiCGSTABBackend`

    - `CubeGridCreator`, functionality available in default `GridCreator`

    - `SimplexGridCreator`, functionality available in default `GridCreator`

    - `DgfGridCreator`, functionality available in default `GridCreator` (since 2.8)

    - `Decoupled...Indices` -> `Sequential...Indices` (BEWARE: maybe no compiler
    warnings)
874

Timo Koch's avatar
Timo Koch committed
875
* Deprecated MEMBER FUNCTIONS, to be removed after 2.9:
876

Timo Koch's avatar
Timo Koch committed
877
* Deprecated protected MEMBER VARIABLES, to be removed after 2.9: BEWARE: Older
878
879
880
881
  compilers will not print any warning if a deprecated protected member variable
  is used.

* DELETED classes/files, property names, constants/enums,
882
  member functions, which have been deprecated in DuMu<sup>x</sup> 2.8:
Bernd Flemisch's avatar
Bernd Flemisch committed
883
884
    - Everything listed as deprecated below has been removed.

885

886
Differences Between DuMu<sup>x</sup> 2.7 and DuMu<sup>x</sup> 2.8
Thomas Fetzer's avatar
Thomas Fetzer committed
887
888
889
===================================================

* IMPORTANT NOTES:
890
  - DuMu<sup>x</sup> 2.8 is expected to run based on either Dune 2.3 or Dune 2.4. However,
Bernd Flemisch's avatar
Bernd Flemisch committed
891
892
893
894
895
    no attempt has been made to fix the warnings arising from the deprecation of
    EntityPointer in Dune 2.4. This will be made during the next release cycle.
    Moreover, using the multidomain models based on Dune 2.4 is currently only
    possible by patching dune-multidomaingrid. See test/multidomain/README for
    details.
Thomas Fetzer's avatar
Thomas Fetzer committed
896

897
898
899
* DELETED BUILD SYSTEM: The Autotools based build system was removed, use the
  CMake based build system as it is default since Dune 2.4.

Thomas Fetzer's avatar
Thomas Fetzer committed
900
* IMPROVEMENTS and ENHANCEMENTS:
Bernd Flemisch's avatar
Bernd Flemisch committed
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
  - New fully-implicit porous-media models for two fluid phases that may consist
    of an arbitrary number of components have been added. The basic one is
    associated with the property TwoPNC, see test/implicit/2pnc. A more advanced
    one that incorporates solid-fluid phase changes is indicated by TwoPNCMin,
    see test/implicit/2pncmin.

  - The implicit cell-centered models now can use adaptive grid refinement. To
    make a test problem adaptive, just set the property AdaptiveGrid to true and
    choose corresponding indicators via AdaptionInitializationIndicator and
    AdaptionIndicator, see test/implicit/2p/lensproblem.hh for an example. So
    far, indicators are only provided for the TwoPModel. Indicators for other
    models will be provided in the future, as well as parallelization and box
    discretization.

  - With the CpGridCreator, a grid creator has been introduced that reads from a
    Petrel output / Eclipse input file and generates a CpGrid that is offered by
    the OPM module dune-cornerpoint. The fully-implicit cell-centered models are
    now able to deal with cornerpoint grids. See
    test/implicit/2p/test_cc2pcornerpoint for a test of the functionality. A
    realistic corner-point grid will be provided in dumux-lecture soon. The OPM
    modules need to be patched to be compatible with Dune's CMake based build
    system, see patches/README for details.

Thomas Fetzer's avatar
[docu]    
Thomas Fetzer committed
924
  - Zero equation turbulence models (zeroeq) have been added as new models
Bernd Flemisch's avatar
Bernd Flemisch committed
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
    to the freeflow folder. Tests for coupling a turbulent free flow using
    zeroeq turbulence models with flow in a porous medium have been added.

  - A new class GridCreator is now the new standard grid creator replacing
    DgfGridCreator. It comprises all functionality from the DgfGridCreator (see
    also immediate interface changes), plus the ability to read gmsh, or to
    build a structured grid (only with Dune 2.4) by merely changing the input
    file.

  - Multidomain problems can now be run by using the general start routine,
    just as most other problems. For this, the constructor of the multidomain
    problems has been changed and the InterfaceMeshCreator has been replaced by
    the InterfaceGridCreator, see below.

  - The Richards model has now an additional flag useHead, which can be used to
    switch between a pressure-saturation and a pressureHead-watercontent
    formulation. The primary variables are either pressure in [Pa] or pressure
    head in [cm], respectively. Default is useHead = false. See
    test/implicit/richards for details.

  - A bug in the diffusion term in the freeflow models has been fixed.

  - A lot of work has been devoted to improving the testing environment, adding
    new tests, restructuring the handbook and improving the documentation.
Thomas Fetzer's avatar
Thomas Fetzer committed
949
950

* IMMEDIATE INTERFACE CHANGES not allowing/requiring a deprecation period:
Bernd Flemisch's avatar
Bernd Flemisch committed
951

952
953
  - The (new standard) GridCreator's public method gridPtr has been removed. For
    using PARAMETERS from DGF files use the GridCreators parameters method via
Bernd Flemisch's avatar
Bernd Flemisch committed
954
955
956
957
    GridCreator::parameters(...). See test/implicit/co2 for an example.

  - The use and support for SGrid is dropped. SGrid is deprecated in Dune 2.4.
    Use YaspGrid instead.
Thomas Fetzer's avatar
Thomas Fetzer committed
958

959
* Deprecated PROPERTY and PARAMETER NAMES, to be removed after 2.8: BEWARE: The
Thomas Fetzer's avatar
Thomas Fetzer committed
960
961
962
963
  compiler will not print any warning if a deprecated property or parameter name
  is used. However, a run-time warning should appear in the summary lines after
  the corresponding run.

964
* Deprecated CLASSES/FILES, to be removed after 2.8:
Thomas Fetzer's avatar
[io]    
Thomas Fetzer committed
965
966
967
  - The InterfaceMeshCreator has been moved to InterfaceGridCreator and adapted
    to the structure of other grid creators, it can simply be used by specifying
    the GridCreator TypeTag.
Thomas Fetzer's avatar
Thomas Fetzer committed
968

969
* Deprecated MEMBER FUNCTIONS, to be removed after 2.8:
Bernd Flemisch's avatar
Bernd Flemisch committed
970
971
972
973
  - The constructor of the multidomain problems has changed. They will now be
    called directly from the start.hh, identical to the other problems. The new
    parameters are the TimeManager and the HostGrid.

974
  - The method simulate(Scalar dtInitial, Scalar tEnd) from MultiDomainProblem,
Bernd Flemisch's avatar
Bernd Flemisch committed
975
976
977
978
979
980
981
    is unused and will be dropped.

  - The GnuplotInterface functions are now called without giving a window
    number. If plots should be plotted in different windows, different
    GnuplotInterface objects are now required. This affects also all other plots
    in the "io" folder.

Thomas Fetzer's avatar
[io]    
Thomas Fetzer committed
982
983
  - The write() function in plotoverline2d.hh now has an append function, to be
    able to decide whether the previously written file should be kept or not.
Thomas Fetzer's avatar
Thomas Fetzer committed
984

985
986
* Deprecated protected MEMBER VARIABLES, to be removed after 2.8: BEWARE: Older
  compilers will not print any warning if a deprecated protected member variable
Thomas Fetzer's avatar
Thomas Fetzer committed
987
988
989
  is used.

* DELETED classes/files, property names, constants/enums,
990
  member functions, which have been deprecated in DuMu<sup>x</sup> 2.7:
Thomas Fetzer's avatar
Thomas Fetzer committed
991
992
  Everything listed as deprecated below has been removed.

993
Differences Between DuMu<sup>x</sup> 2.6 and DuMu<sup>x</sup> 2.7
Bernd Flemisch's avatar
Bernd Flemisch committed
994
===================================================
Bernd Flemisch's avatar
Bernd Flemisch committed
995

996
* IMPORTANT NOTES:
997
  - DuMu<sup>x</sup> 2.7 should work with DUNE 2.3 as well as 2.4. However, at the time of
998
    writing, DUNE-multidomain(grid) doesn't work with DUNE 2.4. Therefore, if a
999
    DuMu<sup>x</sup> multidomain model should be used, DUNE 2.3 is required. See
1000
1001
    test/multidomain/README for details.

1002
1003
1004
  - The 2.3 branch of dune-alugrid has no CMake support, use dune-alugrid master
    respectivly 2.4. Or you can fall back to Autotools or use legacy ALUGrid
    1.52.
1005

Bernd Flemisch's avatar
Bernd Flemisch committed
1006
* IMPROVEMENTS and ENHANCEMENTS:
Bernd Flemisch's avatar
Bernd Flemisch committed
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
  - Since 2.6, all isothermal implicit porous-media models (except 2pdfm) can be
    easily enhanced with the energy equation. For 2.7, this has been also
    carried out for the models that were only isothermal before, namely, 1p, 3p
    and richards. Tests have been written and are provided in test/implicit. In
    order to keep the number of subfolders bearable, isothermal as well as
    thermal tests are gathered in the model folders "1p", "1p2c", ..., "3p3c",
    "mpnc", "richards" (without the "ni") and the corresponding "ni"-folders
    have been deleted.

  - All implicit porous-media models (except 2pdfm) are now able to run on grids
    with dim < dimWorld. In implicit/1p, four new tests are added that run the
    1p test problem on 1d-3d and 2d-3d Alberta grids with box and cell-centered,
    respectively. Compilation has been tested also for all other models, but no
    runtime testing has been performed.

Bernd Flemisch's avatar
Bernd Flemisch committed
1022
1023
1024
1025
1026
1027
  - The terminology for the Newton method has been improved according to FS#238.
    In particular, what has been referred to as "relative error" is now termed
    "maximum relative shift", while "absolute error" has been renamed to
    "residual reduction". This is particularly important, if corresponding
    parameters or properties are set, see below.

1028
1029
1030
1031
  - The geomechanics ElTwoPModel runs in parallel now. This is made possible by
    a dedicated solver, the El2PAMGBackend which has to be set for the property
    LinearSolver in the problem file. See test/geomechanics/el2p for details.

Bernd Flemisch's avatar
Bernd Flemisch committed
1032
1033
1034
1035
  - Before, velocity output for the implicit porous-media models only worked for
    cube grids. This has been generalized to simplices (box and cc) and prisms/
    pyramids (box only).

Thomas Fetzer's avatar
Thomas Fetzer committed
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
  - Revised and fixed restart capability for the multidomain models.

  - A gnuplot interface has been added (works only with CMake). With
    this interface it is possible to plot material laws (like in the 2p2cni test),
    or to generate live-updating output (like in test_2cnistokes2p2cni).
    The gnuplot interface reads analytical functions, data file or data arrays.

  - The fuzzycompare script for automatic testing has been improved. Instead of
    printing only the first deviation from the reference solution, it now
    prints the maximum deviation in each field/variable.

1047
* DEPRECATED BUILD SYSTEM: DuMu<sup>x</sup> 2.7 will be the last release which can be built
1048
    with the Autotools based build system. It is deprecated and will be removed
1049
    for DuMu<sup>x</sup> 2.8. We encourage the change towards CMake, especially with the
1050
1051
1052
    upcoming DUNE 2.4.
    The warning can be suppressed with --disable-dumux-deprecated-autotools

Bernd Flemisch's avatar
Bernd Flemisch committed
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
* IMMEDIATE INTERFACE CHANGES not allowing/requiring a deprecation period:
  - Before, the "heatCapacity" function in the spatial parameters and volume
    variables of the implicit nonisothermal models was a misnomer, since it
    returned an effective quantity, namely,
    heatCapacity*density*(1 - porosity) in [J/(K m^3)].
    Except for mpnc, which resulted in an additional inconsistency.
    Corresponding to the decision documented in FS#216, the function has been
    renamed to "solidHeatCapacity" and returns always the "true" (non-effective)
    heat capacity in [J/(kg K)]. This requires an additional function
    "solidDensity" which returns the mass density of the porous matrix.
    Moreover, the functions "thermalConductivitySolid/Fluid" are renamed to
    "solid/fluidThermalConductivity". The decision to prepend with "solid/fluid"
    rather than to append is motivated by consistency with components and fluid
    systems, where "gas" and "liquid" are always prepended to the corresponding
    function names.
    Therefore, it might be necessary to adapt your thermal solid parameters in
    the spatialparams file such that they offer functions "solidHeatCapacity",
    "solidDensity" and "solidThermalConductivity". See
    test/implicit/2p2c/injectionspatialparams.hh for an example.

Bernd Flemisch's avatar
Bernd Flemisch committed
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
  - Due to the change in the Newton terminology (see above), there exist two
    backward-compatibility breakages:
    . If a model re-implements the function "relativeErrorDof", it has to be
      renamed to "relativeShiftAtDof". See dumux/implicit/implicitmodel.hh for
      an example.

    . If a NewtonController re-implements the function "newtonUpdateRelError",
      it has to be renamed to "newtonUpdateShift". See
      dumux/nonlinear/newtoncontroller.hh for an example.

1083
1084
1085
  - The properties "AMGPDELabBackend" and "AMGLocalFemMap" have been unified to
    "AmgTraits".

Bernd Flemisch's avatar
Bernd Flemisch committed
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
* Deprecated PROPERTY and PARAMETER NAMES, to be removed after 2.7: BEWARE: The
  compiler will not print any warning if a deprecated property or parameter name
  is used. However, a run-time warning should appear in the summary lines after
  the corresponding run.
  - Corresponding to the improved Newton terminology, the following properties
    (prepended with "Newton") and parameters (in the group "Newton") are
    renamed:
    AbsTolerance -> ResidualReduction
    EnableAbsoluteCriterion -> EnableResidualCriterion
    RelTolerance -> MaxRelativeShift
    EnableRelativeCriterion -> EnableShiftCriterion
    SatisfyAbsAndRel -> SatisfyResidualAndShiftCriterion

Bernd Flemisch's avatar
Bernd Flemisch committed
1099
* Deprecated CLASSES/FILES, to be removed after 2.7:
1100
1101
1102
1103
1104
  - SeqAMGBackend and ScaledSeqAMGBackend, replaced by AMGBackend.

  - P0LocalFiniteElementMap.

  - CellData2P2Cmultiphysics, replaced by CellData2P2CMultiPhysics.
1105

1106
1107
  - BoxLocalOperator from dumux/multidomain/common/pdelablocaloperator.hh.

Bernd Flemisch's avatar
Bernd Flemisch committed
1108
1109
1110
1111
1112
1113
1114
* Deprecated MEMBER FUNCTIONS, to be removed after 2.7:
  - The functions "heatCapacity", "densitySolid" (mpnc only) and
    "thermalConductivitySolid/Fluid" in the VolumeVariables of the nonisothermal
    implicit porous-media models: use "solidHeatCapacity", "solidDensity" and
    "solid/fluidThermalConductivity" instead. See also the immediate interface
    changes above.

Bernd Flemisch's avatar
Bernd Flemisch committed
1115
1116
1117
1118
1119
1120
1121
1122
1123
  - In dumux/implicit/common/implicitmodel.hh and
    dumux/geomechanics/el2p/elp2basemodel.hh:
    "relativeErrorDof" -> "relativeShiftAtDof"

  - In dumux/nonlinear/newtoncontroller.hh:
    "setRelTolerance" -> "setMaxRelativeShift"
    "setAbsTolerance" -> "setResidualReduction"
    "newtonUpdateRelError" -> "newtonUpdateShift"

1124
1125
1126
1127
  - The 1p2c volume variables no longer use the method tortuosity() from
    spatial params class, the value is now calculated within the effective
    diffusivity model. Thus the method is deprecated in the spacial params
    classes FVSpatialParamsOneP and ImplicitSpatialParamsOneP.
Bernd Flemisch's avatar
Bernd Flemisch committed
1128

Bernd Flemisch's avatar
Bernd Flemisch committed
1129
* Deprecated protected MEMBER VARIABLES, to be removed after 2.7: BEWARE: Older
1130
  compilers will not print any warning if a deprecated protected member variable
Bernd Flemisch's avatar
Bernd Flemisch committed
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
  is used.
  - In dumux/nonlinear/newtoncontroller.hh:
    "error_" -> "shift_"
    "lastError_" -> "lastShift_"
    "tolerance_" -> "shiftTolerance_"
    "absoluteError_" -> "reduction_"
    "lastAbsoluteError_" -> "lastReduction_"
    "initialAbsoluteError_" -> "initialResidual_"
    "absoluteTolerance_" -> "reductionTolerance_"
    "enableRelativeCriterion_" -> "enableShiftCriterion_"
    "enableAbsoluteCriterion_" -> "enableResidualCriterion_"
    "satisfyAbsAndRel_" -> "satisfyResidualAndShiftCriterion_"

Bernd Flemisch's avatar
Bernd Flemisch committed
1144
* DELETED classes/files, property names, constants/enums,
1145
  member functions, which have been deprecated in DuMu<sup>x</sup> 2.6:
Bernd Flemisch's avatar
Bernd Flemisch committed
1146
1147
1148
  Everything listed as deprecated below has been removed.


1149
Differences Between DuMu<sup>x</sup> 2.5 and DuMu<sup>x</sup> 2.6
1150
1151
1152
===================================================

* IMPROVEMENTS and ENHANCEMENTS:
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
  - For the non-isothermal porous media models, the energy equation is
    implemented in a more generic way for all models in
    dumux/implicit/nonisothermal. The existing TypeTag names like TwoPNI stay
    the same. If a new non-isothermal model should be used, it is important
    to NOT include anything from the old model-specific implementation like
    from dumux/implicit/2pni, but to include from the model folder without the
    "ni". See test/implicit/2pni for details. In principle, any isothermal
    porous media model can be enhanced with the energy equation. Ideally, only
    the corresponding property files have to be augmented. See
    dumux/implicit/2p/2ppropert*.hh for details. The 1p2c model already has
    been enhanced, the remaining models will follow in 2.7.

  - The AMG backend is based directly on dune-istl now. No PDELab is required
    anymore. The tests so far exhibit an improved robustness. Thanks to Markus
    Blatt for the work.

  - The multidomain models can now be used with the 2.3 release versions of the
    DUNE core modules and dune-multidomaingrid, and the 2.0 release versions
    of dune-pdelab and dune-multidomain. See test/multidomain/README for
    details.

  - In the fully implicit mpnc model, a further specialization allows now to
    describe two-phase flow with two energy equations.

  - The free flow models now include the component enthalpy fluxes transported
    by diffusion processes (h^k D grad x), which was not considered before.

  - UMFPack is a new direct linear solver and can be use as a drop-in
    replacement for SuperLU. Some users claim a speed-up up to a factor of
    seven. We know cases where it was 10% slower, so please measure for your
    problems.
1184
1185

* IMMEDIATE INTERFACE CHANGES not allowing/requiring a deprecation period:
1186
1187
1188
1189
1190
1191
1192
1193
1194
  - The 3p3cni model now also uses an effective thermal conductivity model
    (ETCM). The ETCM is easily exchangeable. The default one is
    ThermalConductivitySomerton, which is implemented in
    dumux/material/fluidmatrixinteractions/3p. The ETCM requires that 3p3cni
    spatial parameters provide a function thermalConductivitySolid instead of
    matrixHeatFlux. See test/implicit/3p3cni/columnxylolspatialparams.hh for
    details. Moreover, the employed fluid system has to actually implement the
    function thermalConductivity. See
    dumux/material/fluidsystems/h2oairxylenefluidsystem.hh for details.
1195

1196
1197
1198
1199
1200
1201
1202
1203
1204
  - The non-isothermal flux variables call the effective thermal conductivity
    models (ETCM) in a different way. If you used a self-written ETCM and want
    to use a new non-isothermal model, the ETCM has to be adapted. See
    material/fluidmatrixinteractions/2p/thermalconductivitysomerton.hh for
    details.

  - Fully implicit mpnc model: in order to account for the possibility of using
    two energy equations, the boolean property EnableKineticEnergy has been
    changed to the integer property NumEnergyEquations.
1205

1206
1207
1208
* Deprecated way of setting command line parameters, to be removed after 2.6:
  - To set paramaters from the command line, the notation --parameterFile=NAME
    is deprecated. Use from now on -ParameterFile NAME.
1209

1210
1211
1212
* Deprecated CLASSES/FILES, to be removed after 2.6:
  - The old non-isothermal porous media models are deprecated. Technically,
    including a ..niproperties.hh file triggers a deprecation warning.
1213

1214
1215
1216
1217
1218
  - FVPressure2P2CAdaptive, use dimension-specific implementations
    FV2dPressure2P2CAdaptive and FV3dPressure2P2CAdaptive instead.

  - FVTransport2P2CAdaptive, use dimension-specific implementations
    FV2dTransport2P2CAdaptive and FV3dTransport2P2CAdaptive instead.
1219
1220

* Deprecated MEMBER FUNCTIONS, to be removed after 2.6:
1221
1222
1223
1224
1225
  - In the Stokes flux variables, the method eddyViscosity() is deprecated, use
    dynamicEddyViscosity() instead.

  - In the Stokes non-isothermal flux variables, the method eddyConductivity()
    is deprecated, use thermalEddyConductivity() instead.
1226

1227
1228
1229
  - Already in 2.5, the following member functions of MultiDomainModel/Problem
    have been deprecated: subProblemX, subModelX, subIDX, gridViewX with X=1,2.
    They are replaced by sdProblemX, sdModelX, sdIDX, sdGridViewX.
1230

1231
* DELETED classes/files, property names, constants/enums,
1232
  member functions, which have been deprecated in DuMu<sup>x</sup> 2.5:
1233
1234
1235
  Everything listed as deprecated below has been removed.


1236
Differences Between DuMu<sup>x</sup> 2.4 and DuMu<sup>x</sup> 2.5
1237
1238
1239
===================================================

* IMPROVEMENTS and ENHANCEMENTS:
1240
  - The three-dimensional implementation of the MPFA L-method is made
1241
    available for the decoupled compositional 2p2c models. It also allows
1242
    for simulation on an adaptive grid.
1243
  - Coupling of 2c2p with stokesnc and 2p2cNI with Stokesncni was
1244
1245
1246
    added. The stokes2c and stokes2cni are now DEPRECATED and will be kicked
    out by the next release. Instead generalized stokesnc and stokesncni
    models are introduced. Unlike 2c models the transport equations in
1247
    the nc models are capapable of using both mass and mole fractions.
1248
    NOTE: For coupling test examples be aware of the harsh version
1249
    restrictions mentioned in dumux/test/modelcoupling/README.
1250

1251
* IMMEDIATE INTERFACE CHANGES not allowing/requiring a deprecation period:
1252
  - Dropped support for PDELab 1.0.1, PDELab 1.1 is required.
1253
1254

* Deprecated CLASSES/FILES, to be removed after 2.5:
1255
1256
  - Stokes2cModel was replaced by StokesNCModel, similar for more
    Stokes2c* classes.
1257

1258
* DELETED classes/files, property names, constants/enums,
1259
  member functions, which have been deprecated in DuMu<sup>x</sup> 2.4:
1260
1261
1262
  Everything listed as deprecated below has been removed.


1263
Differences Between DuMu<sup>x</sup> 2.3 and DuMu<sup>x</sup> 2.4
1264
1265
===================================================

1266
1267
1268
1269
1270
1271
1272
* IMPORTANT NOTES:
  - If the current trunk version of DUNE (2.3) is used, the co2 and co2ni tests
    require that the DUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS flag is set. This
    flag is needed in order to be able to use the function boundaryId(). An
    error is thrown during compilation if the flag is not set. For reference see
    the commented part in optim.opts and debug.opts.

1273
1274
  - All two-component models (1p2c, 2p2c, 2p2cni, co2, co2ni) can now be used
    with either mole or mass fractions. The property useMoles has to be set in
1275
    the problem file and the boundary conditions have to be choosen accordingly.
1276
1277
1278
    . 1p2c, 2p2c, 2p2cni use MOLE fractions by default.
    . co2, co2ni use MASS fractions by default.
    . For completeness: 3p3c, 3p3cni and mpnc use MOLE fractions only.
1279

1280
* IMPROVEMENTS and ENHANCEMENTS:
1281
1282
1283
1284
1285
1286
1287
1288
1289
  - Three geomechanics models have been added, thanks to the previous PhD work
    of Melanie Darcis. The models are located in dumux/geomechanics, a test for
    each model is provided in test/geomechanics:
    . elastic: linear elasticity equations that account only for the solid
               mechanics.
    . el1p2c:  poroelasticity equations for one solid and one fluid phase, where
               the fluid phase is admitted to consist of two components.
    . el2p:    poroelasticity equations for one solid phase and two immiscible
               fluid phases.
1290

1291
1292
1293
  - A three-dimensional implementation of the MPFA L-method is added and made
    available for the decoupled 2p models. It also allows for simulation on
    an adaptive grid.
1294

Bernd Flemisch's avatar
Bernd Flemisch committed
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
  - The MPNC model now allows to drop the assumptions of local thermal and/or
    chemical equilibrium. Dropping the local chemical equilibrium assumption
    leads to mole fractions in different phases that are not determined via
    equilibrium relations. If the local thermal equilibrium assumption is
    dropped, phases (fluids and solid) are locally allowed to have different
    temperatures. See test/implicit/mpnc/test_boxmpnckinetic for an example.

  - A fully-implicit three-phase immiscible model has been added. The headers
    are contained in dumux/implicit/3p, tests are provided in test/implicit/3p.

1305
1306
1307
1308
1309
1310
  - The handling of Dirichlet boundary conditions for the fully-implicit cell-
    centered models has been improved. Now, the conditions are evaluated at the
    centers of the corresponding boundary faces. In general, they are
    incorporated into the local residual in a weak sense. Only for mixed
    Dirichlet/Neumann conditions and for the MPNC model, they still are
    incorporated in a strong sense.
1311

1312
1313
1314
  - The sequential models can use a sub-timestepping in the transport scheme, if
    the property "SubCFLFactor" is chosen smaller than "CFLFactor", which in
    that case specifies the CFL factor used in the pressure equation.
1315
1316
1317

  - All fully-implicit porous-media models now provide the possibility to write
    the velocities to the VTK output. This can be achieved by setting the
1318
    parameter "AddVelocity" of the group "Vtk" or the corresponding property
1319
1320
    "VtkAddVelocity." See test/implicit/1p2c for an example.

1321
1322
1323
  - The CMake build system support uses the experimental mechanisms from DUNE.
    Recent versions of Dune 2.3-svn or newer are required to use CMake.

1324
1325
1326
1327
1328
1329
1330
1331
1332
  - Our naming rules have been refined and enforced for member functions and
    variables. Many inconsistencies could be removed, especially the special
    status of the capitalized "S" indicating saturation. See the deprecation
    listings below or FS#180 for details.

  - Misleading names in the fully-implicit models that still contained "b/Box"
    have been replaced by more generic ones. See the deprecation listings below
    or FS#194 for details.

1333
  - The ...FVElementGeometry classes have been cleaned up a bit. See the
1334
    deprecation listings below or FS#192 for details.
1335

1336
1337
  - Added compiler support for Clang 3.2, Clang 3.3, and GCC 4.8.

1338
* Deprecated CLASSES/FILES, to be removed after 2.4:
1339
  - OnePBoxModel, OnePTwoCBoxModel -> OnePModel, OnePTwoCModel
1340

Bernd Flemisch's avatar
Bernd Flemisch committed
1341
  - Headers containing capitalized letters are replaced by their non-capitalized
1342
1343
    analogs.
    In dumux/decoupled: 1p/cellData1p.hh, 1p/fluxData1p.hh,
Bernd Flemisch's avatar
Bernd Flemisch committed
1344
1345
1346
1347
1348
1349
    2p/cellData2padaptive.hh, 2p/fluxData2p.hh, 2p/cellData2p.hh,
    2p2c/cellData2p2c.hh, 2p2c/cellData2p2cadaptive.hh, 2p2c/fluxData2p2c.hh,
    2p2c/cellData2p2cmultiphysics.hh.
    In dumux/material/fluidmatrixinteractions/3p: parkerVanGen3p.hh,
    parkerVanGen3pparams.hh.

1350
* Deprecated CONSTANTS/ENUMS, to be removed after 2.4: BEWARE: Older compilers
1351
  will not print any warning if a deprecated constant/enum is used.
1352
  - saturation indices: S0Idx, SnIdx, SnOrXIdx, SOrX1Idx, SOrX2Idx, SwIdx,