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Commit 59cf9b32 authored by Santiago Ospina De Los Ríos's avatar Santiago Ospina De Los Ríos
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Merge branch '115-trim-changelog-entries' into 'master' 

Resolve "Trim Changelog entries"

Closes #115

See merge request !168
parents 9db650af e01bb17f
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CHANGELOG.md
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## Unreleased
### Added
* 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.
* New classes representing parameterizations. Every parameterization must now
derive from `RichardsParameterization`, and return function objects
representing parameterization functions.
* 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.
* Added an abstract base class
[`SimulationBase`](dune/dorie/common/simulation_base.hh)
that models the concept of simulation steps so that they
can be later coupled with other simulations.
* New classes representing parameterizations. Every parameterization must now
derive from `RichardsParameterization`, and return function objects
representing parameterization functions.
* 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.
* New class [`SimulationTransport`](dune/dorie/interface/transport_simulation.hh)
which solves the transport equation with a finite volume scheme for give
grid functions of water content and velocity.
* [`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
* Grid function container to store transient grid functions !115
* Infrastructure for the input of Miller scaling fields. !110
* Add logging framework 'spdlog' as submodule !106
* Logging framework [`spdlog`](https://github.com/gabime/spdlog) as
Git submodule for all terminal output !106
* Support input of boundary segmentations !119
* Reconstruction of continuous fluxes using RT finite elements !105
* Custom DG finite element map for simplices based on Pk polynomials !125
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* GitLab Description Templates for Releases !166
### Changed
* `Simulation` is renamed `RichardsSimulation` and moved to
[richards.hh](dune/dorie/model/richards/richards.hh).
* `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.
* 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.
* 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.
The old parameterization classes have been removed.
* `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
subdirectory
[dune/dorie/model/richards/adapters](dune/dorie/model/richards/adapters).
* `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`.
* `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).
* Swich to the stable release branch `releases/2.6` of `dune-testtools`.
* 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.
* Merge Python packages into single new package `dorie`.
* Executables and files of unit-tests and system-tests are now located in
[`dune/dorie/test/`](dune/dorie/test/) and [`test/`](test/) respectively.
* 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.
* Soil architecture and parameter input has been completely revised.
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).
* Improved and refurbished `Dorie::H5File`.
The source file was renamed to `dune/dorie/common/util_h5file.hh`. The
`read_dataset` function is now capable of directly opening dataset paths
that contain groups.
* The following changes were done in order to have a consistent API to support
different models:
* 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.
* The API has been updated to support several models: from now, categories
that target a specific model has to be preceded by a keyword
identifying the corresponding model (e.g. `richards.initial`,
`richards.output`, etc.), while common categories stay with no prefix
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
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.
* Use logging framework 'spdlog' for all terminal output !106
* DORiE now writes vertex data by default. #129
* 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
* Swich to the stable release branch `releases/2.6` of `dune-testtools` !97
* 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
* Extend run config file to contain data on multipe models !103
* DORiE now writes vertex data by default. !128
* Switch license from MIT to GPLv3 !135
* Specifying scaling field `extensions` and `offset` is now optional !133
* Generalized initial condition specification in config file !129
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* Deploy online documentation for each branch to private server !163
### Fixed
* Solver in `RichardsSimulation` was using the wrong time variable.
[!116](https://ts-gitlab.iup.uni-heidelberg.de/dorie/dorie/merge_requests/116)
* Allow meta-ini files for unit tests !101
* Solver in `RichardsSimulation` was using the wrong time variable !116
* Shape of input datasets was flipped when loading scaling factors !124
* `dune_add_system_test` requires target with location after bugfix !165
* `make all` would not build the solver application target `dorie` !167
### 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.
* The `adaptivity.useAdaptity` keyword is deprecated, please use the new keyword
`adaptivity.policy` (see the
[DORiE Configuration File Guide documentation](https://dorie-doc.netlify.com/quickstart-parameters.html#main-routine)
for details).
### Removed
* The class `H5File::AttributeReader` was completely removed.
* Boundary conditions `evaporation` and `limitedInflux` !120
## 1.1.1 (2018-08-21)
### Added
......
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