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# DORiE Changelog

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## Unreleased

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### Added
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* [`yaml-cpp`](https://github.com/jbeder/yaml-cpp/) v5.2.0 or greater as
    dependency !81
* Abstract base class for Models !87
* Finite volume solver for passive transport model !93 !88
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* Grid function container to store transient grid functions !115
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* Infrastructure for the input of Miller scaling fields. !110
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* Logging framework [`spdlog`](https://github.com/gabime/spdlog) as
    Git submodule for all terminal output !106
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* Support input of boundary segmentations !119
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* Reconstruction of continuous fluxes using RT finite elements !105
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* Custom DG finite element map for simplices based on Pk polynomials !125
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* Initial conditions expressed as analytic functions using
    [muparser](http://beltoforion.de/article.php?a=muparser) !131
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* Coupling between transient models for water flow and solute transport !96
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* Initial conditions generated from H5 input data !130
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* Linear interpolator for initial conditions and scaling fields !145, !156
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* Parameterizations for hydrodynamic dispersion in solute transport !141
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* Generic Python VTK file reader !143, !150, !178
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* Define compile-time settings via CPP macros !144
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* [Google Test](https://github.com/google/googletest) unit test framework
    as Git Submodule !159
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* Upwinding options for Richards finite volume local operator !161
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* Cookbook tutorial on infiltration into homogeneous sand !157
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* GitLab Description Templates for Releases !166
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* ParaView tutorial for analyzing DORiE output files !173
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* Parameter XML files support tags for version changes !171
* Unit test for Parameter XML file parser !171
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* CMake option to enable code coverage flags on all targets !172
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* Changes to config file parameters listed per version in user docs !175
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### Changed
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* Data structures for storing and accessing parameter information !55
* Split unit tests into separate CI job with coverage reports !98
* Split grid adaptivity process into marking and actual adaptation !91
* Rework VTK adapters and VTK output writer !64
* `RichardsSimulation` now implements the abstract simulation base class !89
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* Switch to the stable release branch `releases/2.6` of `dune-testtools` !97
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* Merge Python packages into single new package `dorie` !100
* Move `dorie` Command Line Interface script into Python package !102
* Parameterization data input via YAML and H5 files !82
* Simplify H5 reader to only read datasets !109
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* Extend run config file to contain data on multiple models !103
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* DORiE now writes vertex data by default. !128
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* Switch license from MIT to GPLv3 !135
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* Specifying scaling field `extensions` and `offset` is now optional !133
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* Generalized initial condition specification in config file !129
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* Structure and setup of Sphinx user docs !126
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* Switch to stable `dune-randomfield` release branch !151, !153
* System tests for executing `dorie pfg` module !153
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* Finite volume solver for the Richards equation !132
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* Build independent library and executable for each compile-time setting !144
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* `SimulationBase` unit test now uses Google Test !159
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* Deploy online documentation for each branch to private server !163
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* Use YAML (instead of muPhi `.bcdat`) files for specifying BCs !121
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* Unit and system tests report code coverage separately !172
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### Fixed
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* Allow meta-ini files for unit tests !101
* Solver in `RichardsSimulation` was using the wrong time variable !116
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* Shape of input datasets was flipped when loading scaling factors !124
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* `dune_add_system_test` requires target with location after bugfix !165
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* `make all` would not build the solver application target `dorie` !167
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* Allow Neumman BC to be applied on a different direction other than gravity !121
* Transport model option `dirichletMode` was not working properly !121
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* Use unsafe loader of PyYAML v5.2 for loading parameter scraper data !177
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### Deprecated
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### Removed
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* Boundary conditions `evaporation` and `limitedInflux` !120
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## 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.
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* The test system folder was renamed from `testing` to [`test`](test).
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* File `operator_DG.hh` is renamed  
    [`richards_operator_DG.hh`](dune/dorie/solver/richards_operator_DG.hh)
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### 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.
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* Removed CI artifacts of `test` stage from `deploy` jobs.
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* 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.
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* 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.
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* Path to Pipeline artifacts for `test` stage. The artifacts are now correctly
    captured and can be viewed and downloaded from the GitLab web interface.
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* Fix a bug in the boundary condition evaluation where an `end()` iterator
    was dereferenced without error.
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* Re-introduced deployment of the documentation which can now be found online
    at https://dorie-doc.netlify.com/.
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## 1.1.0 (2018-07-27)
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### Added
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* DORiE now employs a `SubsamplingVTKWriter` for higher output precision.
    Subsampling levels are controlled via the new key `output.subsamplingLevel`.
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* 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.
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* Add `.gitattributes` for `CHANGELOG.md` to reduce merge conflicts with
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    `merge=union`.
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* Public API definition in documentation.
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### Changed
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* Update code base to *DUNE v2.6*.
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* Raise software requirements to versions available on Ubuntu 18.04 LTS
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    (Bionic Beaver).
* Switch VTK output from conforming to non-conforming.
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* Use `multicore` build tag only for `test:parallel` build because the current
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    GitLab Runner cannot handle the load.
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* Use the `OVLP_AMG_4_DG` linear solver for all computations, including
    sequential ones. This significantly improves performance for large problems.
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* Change compilation order which reduces RAM usage when compiling in parallel.
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* Decentralization of the header system so that in most of the header files are 
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	independent of each other.
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### 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.
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### Removed
* Complete doxygen documentation from Sphinx docs.
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### Fixed
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* The source code is now compatible to the Clang LLVM compiler.
    DORiE can now be compiled with the onboard compiler on macOS.
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* Fix finite element map used for simplex grids. The old one did not implement
    a discontinuous function space.
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* Allow warnings on ParMETIS not being available for parallel computations.
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## 1.0.0 (2018-03-28)

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First stable version.