CHANGELOG.md 12.3 KB
Newer Older
Lukas Riedel's avatar
Lukas Riedel committed
1 2
# DORiE Changelog

Lukas Riedel's avatar
Lukas Riedel committed
3

Lukas Riedel's avatar
Lukas Riedel committed
4 5
## Unreleased

Lukas Riedel's avatar
Lukas Riedel committed
6
### Added
Lukas Riedel's avatar
Lukas Riedel committed
7 8
* DORiE now depends on [`yaml-cpp`](https://github.com/jbeder/yaml-cpp/), a
    library for reading YAML files. The version required is >=5.2.0.
Lukas Riedel's avatar
Lukas Riedel committed
9 10 11
* New classes representing parameterizations. Every parameterization must now
    derive from `RichardsParameterization`, and return function objects
    representing parameterization functions.
Santiago Ospina's avatar
Santiago Ospina committed
12 13 14
* Added a abstract base class [`SimulationBase`](dune/dorie/interface/base_simulation.hh) 
    that models the concept of simulation steps so that they 
    can be later coupled with other simulations.
Lukas Riedel's avatar
Lukas Riedel committed
15
* Added an abstract base class
16
    [`SimulationBase`](dune/dorie/common/simulation_base.hh)
Santiago Ospina's avatar
Santiago Ospina committed
17 18
    that models the concept of simulation steps so that they 
    can be later coupled with other simulations.
Lukas Riedel's avatar
Lukas Riedel committed
19 20 21
* New classes representing parameterizations. Every parameterization must now
    derive from `RichardsParameterization`, and return function objects
    representing parameterization functions.
Lukas Riedel's avatar
Lukas Riedel committed
22 23 24 25 26 27 28
* CMake module `DorieTesting.cmake`. The module contains multiple functions
    which facilitate registering tests in the two new testing categories:
    System tests and Unit tests. Unit tests are compiled with appropriate flags
    for code coverage reports.
* Code coverage reports for unit tests. Detailed reports can be retrieved from
    the artifacts of the `test:unit-tests` test in the folder
    `build-cmake/test/coverage`. The total coverage is reported to GitLab.
29
* New class [`SimulationTransport`](dune/dorie/interface/transport_simulation.hh)
30
    which solves the transport equation with a finite volume scheme for give
31
    grid functions of water content and velocity.
Lukas Riedel's avatar
Lukas Riedel committed
32
* Grid function container to store transient grid functions !115
Lukas Riedel's avatar
Lukas Riedel committed
33
* Infrastructure for the input of Miller scaling fields. !110
Lukas Riedel's avatar
Lukas Riedel committed
34
* Add logging framework 'spdlog' as submodule !106
Lukas Riedel's avatar
Lukas Riedel committed
35
* Support input of boundary segmentations !119
Lukas Riedel's avatar
Lukas Riedel committed
36
* Reconstruction of continuous fluxes using RT finite elements !105
Lukas Riedel's avatar
Lukas Riedel committed
37
* Custom DG finite element map for simplices based on Pk polynomials !125
Lukas Riedel's avatar
Lukas Riedel committed
38 39
* Initial conditions expressed as analytic functions using
    [muparser](http://beltoforion.de/article.php?a=muparser) !131
Lukas Riedel's avatar
Lukas Riedel committed
40
* Coupling between transient models for water flow and solute transport !96
Lukas Riedel's avatar
Lukas Riedel committed
41
* Initial conditions generated from H5 input data !130
Lukas Riedel's avatar
Lukas Riedel committed
42
* Generic Python VTK file reader !143
Lukas Riedel's avatar
Lukas Riedel committed
43
* Parameterizations for hydrodynamic dispersion in solute transport !141
Lukas Riedel's avatar
Lukas Riedel committed
44
* Generic Python VTK file reader !143, !150
Lukas Riedel's avatar
Lukas Riedel committed
45 46

### Changed
Lukas Riedel's avatar
Lukas Riedel committed
47
* `Simulation` is renamed `RichardsSimulation` and moved to 
48
	[richards.hh](dune/dorie/model/richards/richards.hh).
Lukas Riedel's avatar
Lukas Riedel committed
49 50 51
* `RichardsSimulation` now has its own `RichardsSimulationTraits` derived from
    `BaseTraits`, which defines all its member types. `BaseTraits` now have
    reduced content and are intended to be shared between models/simulations.
Lukas Riedel's avatar
Lukas Riedel committed
52 53 54 55 56 57 58 59 60 61 62 63 64
* Data structures for storing and accessing parameters. The new class
    `FlowParameters` maps parameter sets and scaling factors to every grid cell
    on the coarsest grid level, and only stores one set of parameters for
    each soil layer. Before querying the parameterization functions, users need
    to call `FlowParameters::bind` with a grid entity to cache the appropriate
    data. All classes and functions querying parameter data have been updated.
    
    The old parameterization classes located in
    [`param_base.hh`](dune/dorie/solver/param_base.hh),
    [`param_factory.hh`](dune/dorie/solver/param_factory.hh), and
    [`param_van_genuchten.hh`](dune/dorie/solver/param_van_genuchten.hh)
    are still used for reading in data for the new storage scheme.
    The respective objects are freed once a simulation commences.
65 66 67
* Grid adaptation now is done in two steps: (1) mark entities of the grid to 
    refine/coarse and (2) adapt the grid and project the degrees of freedom on 
    the new grid.
Lukas Riedel's avatar
Lukas Riedel committed
68
    The old parameterization classes have been removed.
Lukas Riedel's avatar
Lukas Riedel committed
69 70 71 72 73 74
* `RichardsSimulation` now uses one vector of coefficients instead of two, which
    now is a `shared_ptr` instead a `unique_ptr`.
* Every `VTKAdapter` is now able to be used as `GridFunctionAdapter` of the
    solution vector.
* `GradientFluxAdapter` was reimplemented and renamed `WaterFluxAdapter`.
* Every grid function adapter has its own file and are gathered in the 
75 76
    subdirectory
    [dune/dorie/model/richards/adapters](dune/dorie/model/richards/adapters).
Lukas Riedel's avatar
Lukas Riedel committed
77 78 79 80
* `VTKAdapters` are now managed with `shared_ptr` instead of references.
* `OutputWriter` class is deprecated in favor of an minimal extension of the 
    usual `VTKSequenceWriter` for grid functions called
    `GridFunctionVTKSequenceWriter`.
81 82 83 84 85 86 87 88
* `RichardsSimulation` now models the `SimulationBase` class (See details in
    https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/issues/94). For this, 
    several methods were renamed with basically no change in behaviour.
* `RichardsSimulation` and `TimeController` are able to receive a suggestion for
    the next timestep.
* Static const `bool`s for adaptivity and output writing in `BaseTraits` were 
    removed in favor of run-time policies (See details in
    https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/issues/94).
89
* Swich to the stable release branch `releases/2.6` of `dune-testtools`.
Lukas Riedel's avatar
Lukas Riedel committed
90 91 92
* The `build` CI stage now explicitly builds system tests and unit tests. The
    job `build:main` has been removed. The `build:debug` jobs now build the
    unit test targets.
Lukas Riedel's avatar
Lukas Riedel committed
93
* Merge Python packages into single new package `dorie`.
94
* Executables and files of unit-tests and system-tests are now located in 
95
    [`dune/dorie/test/`](dune/dorie/test/) and [`test/`](test/) respectively.
Lukas Riedel's avatar
Lukas Riedel committed
96 97 98
* The `dorie` CLI has been moved into the DORiE Python package. It can now only
    be invoked after activating the DUNE virtual environment. The usage
    instructions in docs and `README.md` have been updated accordingly.
Lukas Riedel's avatar
Lukas Riedel committed
99
* Soil architecture and parameter input has been completely revised.
Lukas Riedel's avatar
Lukas Riedel committed
100

Lukas Riedel's avatar
Lukas Riedel committed
101 102 103 104 105 106 107 108 109 110 111 112 113 114 115
    DORiE now expects a YAML file containing parameterization data and separate
    domain mapping data which can be supplied through the input GMSH file, or as
    H5 dataset. See the documentation for more information. Several keys in the
    main routine config file have been changed.

    See [#86](https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/issues/86).

* The Parameter Field Generator (PFG) module has been revised and does not
    write parameterization data anymore.
    
    It can be used to create mappings for heterogeneous media through the
    binary converter, or continuous scaling fields (feature pending).
    Several keys in the PFG config file have been changed.

    See [#86](https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/issues/86).
Lukas Riedel's avatar
Lukas Riedel committed
116

Lukas Riedel's avatar
Lukas Riedel committed
117 118
* Improved and refurbished `Dorie::H5File`.

119
    The source file was renamed to `dune/dorie/common/util_h5file.hh`. The
Lukas Riedel's avatar
Lukas Riedel committed
120 121
    `read_dataset` function is now capable of directly opening dataset paths
    that contain groups.
Lukas Riedel's avatar
Lukas Riedel committed
122

123 124 125
* The following changes were done in order to have a consistent API to support 
    different models:

126 127 128
    * Folder structure has changed to a model based structure: in the main
        [C++ source directory](dune/dorie/) there now is a `common` folder, and
        a folder for `model` containing the source files for each model.
129 130 131

    * The API has been updated to support several models: from now, categories 
        that  target a specific model has to be preceded by a keyword 
132 133
        identifying the  corresponding model (e.g. `richards.initial`,
        `richards.output`, etc.), while common categories stay with no prefix
134 135 136 137
        at all (e.g. `grid`, `adaptivity`, etc.).

    * The parameter scraper now accepts the argument `--model <model>` which
        adds the prefix `<model>.` to every category in the scraper. This helps
138 139 140
        to be able to use the method `sub()` from the `ParameterTree` object.
        It dumps its data into a YAML file which is then loaded for writing
        the default configuration files and the cheat sheet.
141

Lukas Riedel's avatar
Lukas Riedel committed
142
* Use logging framework 'spdlog' for all terminal output !106
143
* DORiE now writes vertex data by default. #129
Lukas Riedel's avatar
Lukas Riedel committed
144
* Switch license from MIT to GPLv3 !135
Lukas Riedel's avatar
Lukas Riedel committed
145
* Specifying scaling field `extensions` and `offset` is now optional !133
Lukas Riedel's avatar
Lukas Riedel committed
146
* Generalized initial condition specification in config file !129
Lukas Riedel's avatar
Lukas Riedel committed
147
* Structure and setup of Sphinx user docs !126
148
* Switch to stable `dune-randomfield` release branch !151
Lukas Riedel's avatar
Lukas Riedel committed
149

150 151 152
### Fixed
* Solver in `RichardsSimulation` was using the wrong time variable.
   [!116](https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/merge_requests/116)
Lukas Riedel's avatar
Lukas Riedel committed
153
* Shape of input datasets was flipped when loading scaling factors !124
154

Lukas Riedel's avatar
Lukas Riedel committed
155 156 157 158
### Deprecated
* The configuration file key `[parameters.interpolation]` is deprecated due to
    the new scheme for storing parameterization data. DORiE now only supports 
    nearest-neighbor interpolation of parameters and scaling factors.
Lukas Riedel's avatar
Lukas Riedel committed
159

160
* The `adaptivity.useAdaptity` keyword is deprecated, please use the new keyword
161 162
     `adaptivity.policy` (see the 
    [DORiE Configuration File Guide documentation](https://dorie-doc.netlify.com/quickstart-parameters.html#main-routine)
163 164
     for details).

Lukas Riedel's avatar
Lukas Riedel committed
165 166
### Removed
* The class `H5File::AttributeReader` was completely removed.
Lukas Riedel's avatar
Lukas Riedel committed
167
* Boundary conditions `evaporation` and `limitedInflux` !120
Lukas Riedel's avatar
Lukas Riedel committed
168 169 170 171 172 173 174 175 176 177

## 1.1.1 (2018-08-21)

### Added
* Documentation of Docker images and their usage in the CI/CD pipeline.

### Changed
* Rebuilds of the DUNE environment Docker image are now triggered by setting the
    CI variable `REBUILD_BASE_IMAGE` to a non-empty value. Previously, the
    builds in stage `setup` where triggered by any manual pipeline run.
Lukas Riedel's avatar
Lukas Riedel committed
178
* The test system folder was renamed from `testing` to [`test`](test).
179 180
* File `operator_DG.hh` is renamed  
    [`richards_operator_DG.hh`](dune/dorie/solver/richards_operator_DG.hh)
Lukas Riedel's avatar
Lukas Riedel committed
181

Lukas Riedel's avatar
Lukas Riedel committed
182 183 184 185
### Fixed
* Removed VTK output from `dorie_mass_conservation` executable, which would
    cause the corresponding test to fail if the designated output directory did
    not exist.
Lukas Riedel's avatar
Lukas Riedel committed
186
* Removed CI artifacts of `test` stage from `deploy` jobs.
Lukas Riedel's avatar
Lukas Riedel committed
187 188 189
* Correctly estimate the number of row entries in the matrix backend based on
    the DG discretization and proper static blocking. This can lead to a
    performance improvement for large problems.
Lukas Riedel's avatar
Lukas Riedel committed
190 191 192
* VTK output is now written _before_ the grid is adapted. Previously, the output
    displayed the adapted grid and not the one the solution was computed on.
* Grid adaptation is skipped after computing the final solution.
Lukas Riedel's avatar
Lukas Riedel committed
193 194
* Path to Pipeline artifacts for `test` stage. The artifacts are now correctly
    captured and can be viewed and downloaded from the GitLab web interface.
Lukas Riedel's avatar
Lukas Riedel committed
195 196
* Fix a bug in the boundary condition evaluation where an `end()` iterator
    was dereferenced without error.
Lukas Riedel's avatar
Lukas Riedel committed
197 198
* Re-introduced deployment of the documentation which can now be found online
    at https://dorie-doc.netlify.com/.
Lukas Riedel's avatar
Lukas Riedel committed
199

Lukas Riedel's avatar
Lukas Riedel committed
200

Lukas Riedel's avatar
Lukas Riedel committed
201
## 1.1.0 (2018-07-27)
Lukas Riedel's avatar
Lukas Riedel committed
202

Lukas Riedel's avatar
Lukas Riedel committed
203
### Added
Lukas Riedel's avatar
Lukas Riedel committed
204 205
* DORiE now employs a `SubsamplingVTKWriter` for higher output precision.
    Subsampling levels are controlled via the new key `output.subsamplingLevel`.
Santiago Ospina's avatar
Santiago Ospina committed
206 207 208
* Automatic deployment of `devel` and stable DORiE Docker Images to Docker Hub.
* Automatic update of the DUNE environment Docker Image for `master` builds.
* CI pipeline now also compiles a Debug build with the LLVM Clang compiler.
Lukas Riedel's avatar
Lukas Riedel committed
209
* Add `.gitattributes` for `CHANGELOG.md` to reduce merge conflicts with
Santiago Ospina's avatar
Santiago Ospina committed
210
    `merge=union`.
Lukas Riedel's avatar
Lukas Riedel committed
211
* Public API definition in documentation.
Lukas Riedel's avatar
Lukas Riedel committed
212

Lukas Riedel's avatar
Lukas Riedel committed
213
### Changed
Santiago Ospina's avatar
Santiago Ospina committed
214
* Update code base to *DUNE v2.6*.
Lukas Riedel's avatar
Lukas Riedel committed
215
* Raise software requirements to versions available on Ubuntu 18.04 LTS
Santiago Ospina's avatar
Santiago Ospina committed
216 217
    (Bionic Beaver).
* Switch VTK output from conforming to non-conforming.
Lukas Riedel's avatar
Lukas Riedel committed
218
* Use `multicore` build tag only for `test:parallel` build because the current
Santiago Ospina's avatar
Santiago Ospina committed
219
    GitLab Runner cannot handle the load.
Lukas Riedel's avatar
Lukas Riedel committed
220 221
* Use the `OVLP_AMG_4_DG` linear solver for all computations, including
    sequential ones. This significantly improves performance for large problems.
Lukas Riedel's avatar
Lukas Riedel committed
222
* Change compilation order which reduces RAM usage when compiling in parallel.
Santiago Ospina's avatar
Santiago Ospina committed
223
* Decentralization of the header system so that in most of the header files are 
Santiago Ospina's avatar
Santiago Ospina committed
224
	independent of each other.
Lukas Riedel's avatar
Lukas Riedel committed
225 226 227 228 229

### Deprecated
* `output.subsamplingLevel` is optional and defaults to 0 if not given
    explicitly in the config file. The key will become mandatory in future
    versions.
Lukas Riedel's avatar
Lukas Riedel committed
230

Lukas Riedel's avatar
Lukas Riedel committed
231 232
### Removed
* Complete doxygen documentation from Sphinx docs.
Lukas Riedel's avatar
Lukas Riedel committed
233

Lukas Riedel's avatar
Lukas Riedel committed
234
### Fixed
Lukas Riedel's avatar
Lukas Riedel committed
235 236
* The source code is now compatible to the Clang LLVM compiler.
    DORiE can now be compiled with the onboard compiler on macOS.
Lukas Riedel's avatar
Lukas Riedel committed
237 238
* Fix finite element map used for simplex grids. The old one did not implement
    a discontinuous function space.
Lukas Riedel's avatar
Lukas Riedel committed
239
* Allow warnings on ParMETIS not being available for parallel computations.
Lukas Riedel's avatar
Lukas Riedel committed
240 241


Lukas Riedel's avatar
Lukas Riedel committed
242 243
## 1.0.0 (2018-03-28)

244
First stable version.