dumux issues
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues
2024-02-28T10:42:39Z
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1346
[doc] fix as much typos as possible unto next release
2024-02-28T10:42:39Z
Kai Wendel
[doc] fix as much typos as possible unto next release
**Description**
when one reads through the DuMux core codes comments and other documentation, one can find sometimes comments that are obviously not correctly describing the underlining code, or there are typos. It would be worth to try...
**Description**
when one reads through the DuMux core codes comments and other documentation, one can find sometimes comments that are obviously not correctly describing the underlining code, or there are typos. It would be worth to try keeping this as tidy as we could as typos and incorrect comments are limiting the readability.
It is worth the effort, to fix as much obvious (and possbibly also some less obvious) typos or inconsistencies until the upcoming release.
Branch, that focuses on the `freeflow` part: [cleanup/smallCleanups](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/tree/cleanup/smallCleanups?ref_type=heads). The changes are currently all limited to `freeflow`
Branch focusing on fluidsystems: [cleanup/fluidsAndFluidsystems](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/tree/cleanup/fluidsAndFluidsystems?ref_type=heads)
Kai Wendel
Kai Wendel
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1338
Parameter group and documentation
2024-01-30T14:53:03Z
Timo Koch
timokoch@math.uio.no
Parameter group and documentation
In https://dumux.org/docs/doxygen/master/runtime-parameters.html add a description about the parameter model when dealing with multiple instances of the same class and a global parameter tree. We use group prefixes then to set different ...
In https://dumux.org/docs/doxygen/master/runtime-parameters.html add a description about the parameter model when dealing with multiple instances of the same class and a global parameter tree. We use group prefixes then to set different parameters for the different instances. This could be more transparent for most classes but definitely needs to be documented in the doc page.
We should also think about flexibility and better design to pass param groups. It would be good if the parameter group could be changed after construction. Or maybe we could think about some factory pattern that allows to set the parameter group of a class instance and use this pattern everywhere. Maybe parameterized classes could provide constructor overloads that take the param group as the first parameter (using some named type).
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1337
[doxygen] Erroneous processing of installation doc
2024-01-09T09:00:28Z
Maziar Veyskarami
[doxygen] Erroneous processing of installation doc
It seems that the script for cloning the DUNE modules on the website is displayed wrongly. It is
`for module in common geometry grid localfunctions istl; do
git clone -b releases/2.9 https://gitlab.dune-project.org/core/dune-\f$module...
It seems that the script for cloning the DUNE modules on the website is displayed wrongly. It is
`for module in common geometry grid localfunctions istl; do
git clone -b releases/2.9 https://gitlab.dune-project.org/core/dune-\f$module.git
done`
It should be
`for module in common geometry grid localfunctions istl; do
git clone -b releases/2.9 https://gitlab.dune-project.org/core/dune-$module.git
done`
that means \f in front of $module is not necessary.
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1323
[doc] Large number of uncategorized files in Fluidmatrixinteractions group
2024-03-25T10:37:27Z
Lars Kaiser
[doc] Large number of uncategorized files in Fluidmatrixinteractions group
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**Feature request**
I propose to add more subgroups to the Fluidmatrixinteractions group to make it easier to see what kind of constitutive relations are contained in this group.
**What does this feature / why does DuMux need it**:
Currently, there is a large number of files directly in the Fluidmatrixinteractions group and it is hard to get an overview of what is available. Introducing the subgroups will also bring the organization of the documentation closer to the internal folder structure of Dumux, where the files are already grouped.
Lars Kaiser
Lars Kaiser
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1314
[doc][doxygen][pm] Effective diffusion
2023-12-17T18:41:34Z
Timo Koch
timokoch@math.uio.no
[doc][doxygen][pm] Effective diffusion
The models with diffusion should explain that the diffusion coefficient is effective and refer to other places in the documentation that explains what type of laws are available. I think there could be a dedicated small page / doxygen gr...
The models with diffusion should explain that the diffusion coefficient is effective and refer to other places in the documentation that explains what type of laws are available. I think there could be a dedicated small page / doxygen group for effective diffusion laws (take them out of the generic fluidmatrixinteraction)
3.9
Lars Kaiser
Lars Kaiser
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1313
[doc][doxygen][pm] Time-dependent porosity
2023-11-01T13:26:37Z
Timo Koch
timokoch@math.uio.no
[doc][doxygen][pm] Time-dependent porosity
The porous medium models are capable of handling evolving porosity. This should be reflected in the doxygen formulas.
The porous medium models are capable of handling evolving porosity. This should be reflected in the doxygen formulas.
3.9
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1312
Better name for DualNetwork FancyFactor
2023-10-30T15:06:50Z
Timo Koch
timokoch@math.uio.no
Better name for DualNetwork FancyFactor
There is a type of heat conduction law called FancyFactor. We should find a better name.
Maybe HeatConductionWeighted or name it after the paper.
See !3682
There is a type of heat conduction law called FancyFactor. We should find a better name.
Maybe HeatConductionWeighted or name it after the paper.
See !3682
3.8
Anna Mareike Kostelecky
Anna Mareike Kostelecky
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1310
Symbolic representation of div and grad
2023-10-27T19:01:34Z
Ivan Buntic
Symbolic representation of div and grad
In our doxygen documentation, we use a written form of `grad` and `div`. Instead, symbolic representation of these operators would be nicer to look at. See [this equation](https://dumux.org/docs/doxygen/master/group___one_p_model.html) a...
In our doxygen documentation, we use a written form of `grad` and `div`. Instead, symbolic representation of these operators would be nicer to look at. See [this equation](https://dumux.org/docs/doxygen/master/group___one_p_model.html) as an example.
!3675
3.8
Leon Keim
Leon Keim
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1307
Update doxygen to 3.8
2023-10-27T20:40:04Z
Timo Koch
timokoch@math.uio.no
Update doxygen to 3.8
For example, the installation instructions are now in doxygen and need updating:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/doc/doxygen/pages/installation.md?ref_type=heads
For example, the installation instructions are now in doxygen and need updating:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/doc/doxygen/pages/installation.md?ref_type=heads
3.8
Ivan Buntic
Ivan Buntic
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1306
Add variables description in equations
2023-10-27T11:38:34Z
Yue Wang
yue.wang@iws.uni-stuttgart.de
Add variables description in equations
see !3670
see !3670
3.8
Yue Wang
yue.wang@iws.uni-stuttgart.de
Yue Wang
yue.wang@iws.uni-stuttgart.de
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1238
Merge handbook into doxygen
2023-06-28T23:07:28Z
Timo Koch
timokoch@math.uio.no
Merge handbook into doxygen
In order to have all documentation in one place, I suggest to merge the handbook into doxygen. This also allows to easily view everything online and improve searchability and cross-linking capabilities.
As far as I can see the handbook ...
In order to have all documentation in one place, I suggest to merge the handbook into doxygen. This also allows to easily view everything online and improve searchability and cross-linking capabilities.
As far as I can see the handbook content is up-to-date and useful documentation. Currently, we have some sections doubled like the installation instructions. But also the advanced topic make sense for me in the doxygen documentation in the respective group, linked from the high-level documentation.
In case some people prefer PDF it is also possible to look into generating PDFs which doxygen from which the class docs could be excluded. Another possibility since all doc will be in markdown is to generate latex from selected markdown documents via pandoc. That way the sources are not doubled and the documentation will be easier to maintain and find.
3.8
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1223
Remove solver deprecation warnings
2023-03-20T21:05:52Z
Timo Koch
timokoch@math.uio.no
Remove solver deprecation warnings
* [ ] After merging !3386 there are deprecation warnings concerning the solvers for many test. The solvers should be updated to use the new IstlSolverBackend.
* [ ] After merging !3386 there are deprecation warnings concerning the solvers for many test. The solvers should be updated to use the new IstlSolverBackend.
3.7
Timo Koch
timokoch@math.uio.no
Timo Koch
timokoch@math.uio.no
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1212
License text
2023-02-19T16:36:58Z
Timo Koch
timokoch@math.uio.no
License text
Our default header license text mentions COPYING but that file has been removed. We should also clearly state how to reuse DUmux files, i.e. what text needs to be provided
I think the license headaer should refer to Authors and say some...
Our default header license text mentions COPYING but that file has been removed. We should also clearly state how to reuse DUmux files, i.e. what text needs to be provided
I think the license headaer should refer to Authors and say something like copyright "the dumux developers". (And in Authors there should be a headline "the dumux developers")
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1204
OpenSSF Best Practices
2022-12-13T10:59:37Z
Bernd Flemisch
OpenSSF Best Practices
I added DuMux to OpenSSF Best practices: https://bestpractices.coreinfrastructure.org/en/projects/6768
Things look already quite good, but I didn't feel competent enough to address the criteria "Security" and "Analysis". We should
- [x...
I added DuMux to OpenSSF Best practices: https://bestpractices.coreinfrastructure.org/en/projects/6768
Things look already quite good, but I didn't feel competent enough to address the criteria "Security" and "Analysis". We should
- [x] complete the evaluation form
- [x] add the badge to the repo
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1197
CodeMeta Data: Authors/contributors?
2023-10-26T11:16:22Z
Timo Koch
timokoch@math.uio.no
CodeMeta Data: Authors/contributors?
The following discussion from !3101 should be addressed:
- [ ] @bernd started a [discussion](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/3101#note_75683): (+5 comments)
> The most relevant open quest...
The following discussion from !3101 should be addressed:
- [ ] @bernd started a [discussion](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/3101#note_75683): (+5 comments)
> The most relevant open questions concern authorship. CodeMeta distinguishes between "authors" and "contributors". Should we also distinguish? Who will be included? (How) do we automate the update of the file?
Add generic author (Dumux development team / Dumux developers) and list of contributors
3.9
Bernd Flemisch
Bernd Flemisch
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1194
[examples] Review and improve new Example 9: Embedded network 1D-3D model
2023-03-16T17:32:28Z
Timo Koch
timokoch@math.uio.no
[examples] Review and improve new Example 9: Embedded network 1D-3D model
Several sections are not super well documentation and some code snippets are fairly long. Not all files are documented (but this might be fine to not loose the focus on the main thing). The initial merge request has been merged without r...
Several sections are not super well documentation and some code snippets are fairly long. Not all files are documented (but this might be fine to not loose the focus on the main thing). The initial merge request has been merged without review !3339 to make it immediately available. This issue is a reminder to complete the review.
3.7
Dennis Gläser
Dennis Gläser
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1184
Improve doc of Riemann solver
2023-12-13T11:13:10Z
Timo Koch
timokoch@math.uio.no
Improve doc of Riemann solver
There are some variables which use abbreviations. This might be justified to have it close to how the algorithm is described in a text book. But then all variablenames that are not self-explanatory shoild be documented for better maintai...
There are some variables which use abbreviations. This might be justified to have it close to how the algorithm is described in a text book. But then all variablenames that are not self-explanatory shoild be documented for better maintainability of the code.
In case there is no correspondence to the textbook renaiming to self-explantory name is preferred (style guide)
Leopold Stadler
Leopold Stadler
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1181
Make doc on master fails
2022-07-31T13:07:08Z
David Werner
Make doc on master fails
**Bug report**
Running ``make doc`` to build the documentation fails.
**Problem description**:
The CI for building of the website failed, unfortunately I did not see any artifacts there,
which should be fixed too. I tried then subsequ...
**Bug report**
Running ``make doc`` to build the documentation fails.
**Problem description**:
The CI for building of the website failed, unfortunately I did not see any artifacts there,
which should be fixed too. I tried then subsequently the build_documentation.sh from the CI in my local environment and
also manually ``make doc`` and also ``pdflatex`` direct onto ``0_dumux-handbook.tex`` in the ``dumux/doc/handbook`` directory.
**What you expected to happen**:
The pdf-file of the handbook should be build without errors. The return status of 'make doc' and 'pdflatex' should be 0.
For the ``make doc`` the process for building the doxygen-docs should be started after a clean build of the ``doc/handbook/0_dumux-handbook.pdf``.
**How to reproduce it**:
Checkout first appropriate dune-modules together with dumux master.
Do
```
./dune-common/bin/dunecontrol --opts=dumux/cmake.opts configure
cd dumux/build-cmake
make doc
echo $? # show the status of the last command in your shell.
```
Or a shortcut to see directly the latex problem do:
```
git clone https://git.iws.uni-stuttgart.de/dumux-repositories/dumux
cd dumux/doc/handbook
pdflatex 0_dumux-handbook.tex
```
**Anything else we need to know?**:
It looks like that ``dumux/build-cmake/doc/handbook/0_dumux-handbook.log`` indicates that there are latex-errors in
``dumux/doc/handbook/5_scripts.tex``. One can comment out the last section of this file and the 'make doc' succeeds to start doxygen.
**Environment**:
- Dune version: 2.8
- DuMux version: 81767483f9ed98b0468358d02c6ddbc0387c4095 (master from 2022-07-30)
- Others:
'pdfTeX 3.141592653-2.6-1.40.24 (TeX Live 2022/Arch Linux)'
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1160
Prototypical math models for testing and as examples
2023-09-23T18:14:28Z
Timo Koch
timokoch@math.uio.no
Prototypical math models for testing and as examples
__Proposed feature__:
Many models in Dumux are relatively general and support many variations. This can also often be distracting both when understanding the code and when thinking about general concepts and structure. I propose (someth...
__Proposed feature__:
Many models in Dumux are relatively general and support many variations. This can also often be distracting both when understanding the code and when thinking about general concepts and structure. I propose (something similar has been proposed in dumux-repositories/dumux-course#17) to add some models with simple structure. For example:
* Poisson's equation
* Heat equation / Diffusion equation
* Wave equation
* Burger's equation
* Cahn-Hillard equation(s)
* (Multidomain) Incompressible Stokes equations
These prototypical models have the advantage that we can mostly assume scalar constant parameters (no need for fluid systems and so on), a small number of primary variables (e.g. 1 scalar), and simple local residual. Parameter names could be generic and not imply specific physics.
__The goal would be to use such models__
* to demonstrate (to users and developers) what the essential and minimal ingredients of a new model are
* to use them as starting point for new models
* to test if our software components work well in isolation and are small enough (testing). If they turn out not to be these models should be good candidates to think about better abstractions (development).
* to have simple demonstrators for teaching/outreach
* to use them directly as tools/components
__Open questions:__
* In which folder would such models go?
* Do we even want to hard-code some models for one spatial discretization scheme to further simplify?
_Examples where a procedure like this helped to improve the code:_
* #867
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1154
Add high-level documentation on the main concepts in Dumux
2024-03-25T10:09:45Z
Dennis Gläser
Add high-level documentation on the main concepts in Dumux
I propose a new structure for the High-Level-Design Document (HLDD).
[HLD_Proposal.md](/uploads/613c0e4e889894693fbe5f2611d6538c/HLD_Proposal.md)
After reviewing more sources, I think we mixed here High-Level and Architecture and genera...
I propose a new structure for the High-Level-Design Document (HLDD).
[HLD_Proposal.md](/uploads/613c0e4e889894693fbe5f2611d6538c/HLD_Proposal.md)
After reviewing more sources, I think we mixed here High-Level and Architecture and general Documentation. This could lower the pain of potential double documentation.
One could take the old HLD Branches/MR and:
1. Filter for HLDD
2. Take architectural parts such as interfaces and use this for Architectural Documentation
3. If something is now left behind and interesting think about adding it to the normal Documentation
It was decided to use the diagram added in !3755 as a starting point.
Each class here gets two to three sentences. Not more.
----
#### From here on the old Issue.
----
On Dumux Day, 25th of May, we said that it could be good to have such high-level docu somewhere (e.g. in the handbook?). This could describe generic concepts like grid geometry (is actually nicely described in the last Dumux paper), grid variables, etc...
Current status of this issue is related to !3406 <br>
If you want to work on the high_level_documentation: <br>
For each file you are working on: <br>
- Create a branch from !3406
- Create a MR to !3406
- When you are happy with the description of the class merge that branch in !3406 and tick of the box here. Afterwards tag yourself.Also include the MR number. <br>
Thank you in advance! <br>
Main problem that needs to be resolved: <br>
Doxygen move everything that is included in a group to that group.
One needs to find a way to have high-level docu in the groups while still having a monolithic one source high-level docu.
General approach to tackle this:
1st Describe entities that are modular
- In easy words, possible usage and interface to other entities
- Is this entity necessary to run a simulation
2nd Describe non modular entities
- In easy words, possible usage and interface to other entities
- Is this entity necessary to run a simulation
- Highlight dependencies and why they are necessary
3rd Find out and show how they are interconnected
- Highlight if this entity is necessary (i.e., green vs. red)
The following entities should be modular:
- [ ] Grid @IvBu !3621
- [ ] GridManager @IvBu (review: @DennisGlaeser) !3623
- [ ] Discretization Method
- [ ] GridGeometry @IvBu !3645
- [ ] GridView @kaiw
- [ ] FVElementGeometry
- [ ] VtkOutputModule @kaiw
- [ ] IOFields @kaiw !3587
- [ ] Solver @nedc (review: @leonidas) !3588
- [ ] NonLinearSolver @nedc
- [ ] NewtonLoop @nedc
- [ ] linearPDEsolver @nedc
- [ ] LinearSolver @nedc
- [ ] TimeLoop @kaiw
- [ ] LocalResidual @leonidas @mathis @kaiw
The following entities are not modular:
- [ ] Problem @kaiw
- [ ] BoundaryTypes
- [ ] PrimaryVariables
- [ ] Indices
- [ ] SolutionVector @kaiw
- [ ] NumEqVector
- [ ] GridVariables @leonidas @DennisGlaeser
- [ ] GridVolumeVariables @leonidas @DennisGlaeser
- [ ] Assembler @leonidas @mathis @kaiw
- [ ] localAssembler @leonidas @mathis @kaiw
- [ ] CouplingManager
- [ ] FluidSystem @leonidas
- [ ] FluidState @leonidas
- [ ] FluidMatrix ?
- [ ] SpatialParams @kaiw
General remarks and details about accessing data
- [ ] VolumeVariables @leonidas
- [ ] FluxVariablesCache @leonidas
- [ ] Element
- [ ] GlobalPosition
- [ ] ElementVolumeVariables @leonidas @DennisGlaeser
- [ ] ElementFaceVariables @leonidas
- [ ] ElementFluxVariablesCache @leonidas
- [ ] ControlVolume
- [ ] ControlVolumeFace
- [ ] SubControlVolume
- [ ] SubControlVolumeFace
General remarks on property system
- [ ] TypeTag
- [ ] Traits
- [ ] Model @kaiw !358
3.9
Leon Keim
Leon Keim