GitLab

Update default simulation config files

See merge request !183

Set default output paths and file names for both models

Resolve "Add DG local operator to the SimulationTransport class"

Closes #111

See merge request !112

Additionally, it updates documentation, targets, and factories related to the polynomial degree of the transport model.

Merge branch '171-negative-solute-concentrations-when-pulses-pass-through-soil-layer-interfaces' into 'master'

Resolve "Negative solute concentrations when pulses pass through soil layer interfaces"

Closes #171

See merge request !181

This introduces an option for a heuristic time step reduction scheme:
If the solution contains negative values, it is discarded, the
time step is reduced, and the computation is repeated.

Resolve "Follow-up from "Resolve "Add steady state as initial condition"""

Closes #173

See merge request !182

Resolve "CFL condition is based on water flux"

Closes #172

See merge request !180

* Pass water content grid function to CFL condition and calculate
  actual velocity together with flux.
* Read courant number once and throw error if it is negative.
* Print CFL condition result into trace log.

Resolve "Make CFL condition the upper limit for time steps in explicit transport solver"

Closes #170

See merge request !179

Suggesting a time step to the transport model now sets the end time in
the time step controller. This allows the CFL condition to increase the
time step while remaining inside the time interval limited by the
Richards model.

Resolve "Add steady state as initial condition"

Closes #156

See merge request !176

In the Richards model, add the IC type option 'stationary'. In this
mode, the stationary problem is solved by assembling a separate Newton
solver and applying it to the spatial grid operator only.

Resolve "Add XML version tags to config file parameter docs"

Closes #167

See merge request !175

Attributes are sorted by decreasing version.

Add new PVD Reader

See merge request !178

* Add a PVD file reader which stores a list of VTKReaders for each VTK
  file referenced in the PVD file. Store the times in the VTK readers.
* Add a unit test case to check the capabilities of the PVD reader.
* Expose grid bounds in the VTKReader as well as the VTKDataArray.

Explicitly use unsafe PyYAML loader

See merge request !177

This is required to load the OrderedDict instances written into the YAML files.

Resolve "Add CMake option to enable coverage on unit tests"

Closes #163

See merge request !172

Coverage compiler and linker flags are now appended to *all* targets
when the option is turned on. Use the option to enable coverage
reports in the CI pipeline. Adjust build job "needs" to make pipeline
run as fast as possible.

Merge branch '166-support-xml-tags-specifying-version-changes-of-config-file-parameters' into 'master'

Resolve "Support XML tags specifying version changes of config file parameters"

Closes #166

See merge request !171

* New attributes store version changes as dictionaries with version,
  description pairs.
* Adjust XML parser to parse values of new attributes.
* Update __str__ and __eq__ methods of Parameter.

Add tutorial for ParaView to user manual

See merge request !173

The tutorial contains the most commonly required ParaView features when
evaluating DORiE output files. Images are stored in the repository wiki.

Update README and Contribution Guide

See merge request !169

* Outline GitLab workflow.
* Add information on how to get an account.
* Mention Code of Conduct.

Resolve "Reformat config file parameter docs into list/objects"

Closes #165

See merge request !170

The RST writer now writes a single object per parameter instead of
merging all parameters of a category into a single table. This makes
the config file parameter documentation more flexible and readable.
The description input may contain paragraph breaks and indented list
which will be properly obeyed in the resulting RST output.

Fixes to user manual and GitLab description templates

See merge request !174

Manual:
* Update links to removed `.bcdat` files.
* Fix link in "Restart" cook book page.

Description Templates:
* Fix link to `CHANGELOG.md`.
* Add hint for MR assignee to check the squash commit message.

Resolve "New data structure for storing boundary conditions"

Closes #151, #136, #29, #126, and #125

See merge request !121

* Define classes of polymorphic boundary conditions and factory
* Only use enum in Operator namespace to discern types
* FlowBoundary now returns an entire boundary condition
* Adapt local operators (Richards only)
* Remove header 'util.hh'. Move functions to 'utility.hh', BaseTraits
  to 'typedefs.hh' and GFS helpers to 'gfs_helper.hh'
* Add setting for `horizontal_projection` of Neumann BC (only used in Richards model) #136 (comment 20384).
* Add setting for `concentration_type` of Dirichlet BC (only used in Transport model) #151.

Resolve "Trim Changelog entries"

Closes #115

See merge request !168

Make entries one-liners, where possible. Concatenate entries and refer
to MR for further information.

Update gitlab templates

Closes #79

See merge request !166

* Fix renamed ~Bug label
* Consistently format instructions in italic.
* Add squash commit requirement to MR checklist.

Cookbook: Infiltration in homogeneous medium

See merge request !157

Merge branch 'cookbook-infiltration-in-homogeneous-medium' of ssh://ts-gitlab.iup.uni-heidelberg.de:10022/dorie/dorie into cookbook-infiltration-in-homogeneous-medium