dumux issueshttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues2019-08-28T11:24:39Zhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/378[doc] Differentiate between test, tutorial/documented, tutorial/undocumented2019-08-28T11:24:39ZTimo Kochtimokoch@math.uio.no[doc] Differentiate between test, tutorial/documented, tutorial/undocumentedCurrently we have two general "getting started tutorials", however many of our _tests_ are also thought of tutorials as they demonstrate a certain model.
I suggest to distinguish between _tests_ in the _test_ -folder that are specifical...Currently we have two general "getting started tutorials", however many of our _tests_ are also thought of tutorials as they demonstrate a certain model.
I suggest to distinguish between _tests_ in the _test_ -folder that are specifically designed to test certain features and are small/run rather fast, and _tutorials_ in the _tutorial_-folder that are designed to show a certain feature, e.g. how to use the tensor grid factory in a Richards model to refine towards the soil top. I further suggest to create two new subfolders _documented_ and _undocumented_ where all _documented tutorials_ have a detailed latex/markdown problem and feature description. In the future, a number of maybe 10 such documented tutorials would be nice. All tutorials in undocumented can potentially become documented in the future.
Of course tutorials should also tested by the automated build system.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/347Doxygen pages and handbook of Dumux-2.10 not online yet2017-04-26T08:57:59ZThomas FetzerDoxygen pages and handbook of Dumux-2.10 not online yethttp://www.dumux.org/documentation.phphttp://www.dumux.org/documentation.phpBernd FlemischBernd Flemischhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/315FS#315 "using" command interferes with doxygen2017-05-25T05:10:35ZMartin BeckFS#315 "using" command interferes with doxygen# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Martin Beck (martin.beck@iws.uni-stuttgart.de) |
| Reported at | Feb 24, 2016 10:35 |
| Type | DuMuX day |
| V...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Martin Beck (martin.beck@iws.uni-stuttgart.de) |
| Reported at | Feb 24, 2016 10:35 |
| Type | DuMuX day |
| Version | Git |
| Last edited by | Johannes Hommel (johannes.hommel@iws.uni-stuttgart.de) |
| Last edited at | Jul 27, 2016 07:08 |
| Closed by | Johannes Hommel (johannes.hommel@iws.uni-stuttgart.de) |
| Closed at | Jul 27, 2016 07:08 |
| Closed in version | unknown (Id=0) |
| Resolution | Implemented |
# Description
While working on an update for the description of some functions of the fluidsystems, I noticed that my changes do not appear in the doxygen. After a bit of investigation, I found out that the "using" command is to be blamed. Apparently, it copies the description of the function, to which the "using" command refers to and ignores the description of the actual function.
One example: For the enthalpy function of the brine-air fluid system, the description of the base fluid systems shows up instead of the specific description where some references are provided. So this information is lost and one becomes only aware of if one goes through the source code.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/397[doc] Tutorial structure2017-12-21T07:40:07ZTimo Kochtimokoch@math.uio.no[doc] Tutorial structureThe diff solution files seem to be outdated.
Anyway: What do we do with the old implicit and sequential tutorials?The diff solution files seem to be outdated.
Anyway: What do we do with the old implicit and sequential tutorials?Johannes HommelJohannes Hommelhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/348Link the user survey on the Dumux website2018-07-11T10:11:44ZTimo Kochtimokoch@math.uio.noLink the user survey on the Dumux websiteThere is a new DuMuX user survey on ILIAS
https://ilias3.uni-stuttgart.de/goto_Uni_Stuttgart_svy_1148632.html?lang=en
After being tested and if necessary adjusted it should be linked on the website and publicly announced on the mai...There is a new DuMuX user survey on ILIAS
https://ilias3.uni-stuttgart.de/goto_Uni_Stuttgart_svy_1148632.html?lang=en
After being tested and if necessary adjusted it should be linked on the website and publicly announced on the mailing list.
One the questions are publicly announced and the first participated we can't change single questions anymore. So we should be sure they are answering what we want.3.0https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/433Initial porosity and permeability in respective laws2018-04-25T08:30:50ZJohannes HommelInitial porosity and permeability in respective lawsCurrently, the initial porosity and permeability values in the respective laws for the mineralization model are treated as values of the clean, unreactive porous medium without any initial precipitates. However, there are many cases, jus...Currently, the initial porosity and permeability values in the respective laws for the mineralization model are treated as values of the clean, unreactive porous medium without any initial precipitates. However, there are many cases, just as in the 2pncmin test, where there is some dissolving mineral present initially. In such cases, the initial porosity and permeability as implemented now are misleading, as the initial porosity and permeability in the calculations will not be the input value, but those updated by the effect of the initial mineral volume fraction.
I think a good way to improve this would be to rename initialPorosity(...) and initialPermeability(...). But I do not yet have good suggestion except for maybe cleanP.(...), unreactiveP.(...), or referenceP.(...). Further, the values for referenceP.(...) should be calculated in the initialization of the spatial parameters based on the actual initial porosity and permeability values: referencePorosity_= initialPorosity_-sum(precipitateVolumeFractions); and accordingly for referencePermeability_ with the respective permeability law used.
Whatever we decide to do, we should be more clear about what the reference parameters (currently initialPorosity(...) and initialPermeability(...)) for the porosity and permeability laws really are. Are they the "clean-porous-medium" values or the "initial" values or some arbitrary reference?. In my opinion, the "initial" is too misleading as it is used right now.
* [X] update 1pncmin and 2pncmin to use referenceXY(), as the already define reference and not initial values
3.0https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/462Changelog for 3.02018-12-17T12:13:26ZTimo Kochtimokoch@math.uio.noChangelog for 3.0This is supposed to be a collection of things that changed in version 3.0. We also planned to write a little guide on the newly introduced things concerning implementers of problem/spatialparams/mainfile/materiallaws.This is supposed to be a collection of things that changed in version 3.0. We also planned to write a little guide on the newly introduced things concerning implementers of problem/spatialparams/mainfile/materiallaws.3.0Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/317FS#317 More use of copydoc in material2018-07-11T10:08:46ZAlexander KissingerFS#317 More use of copydoc in material# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Reported at | Mar 8, 2016 08:57 |
| Type | ...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Reported at | Mar 8, 2016 08:57 |
| Type | DuMuX day |
| Version | Git |
| Last edited by | Bernd Flemisch (bernd@iws.uni-stuttgart.de) |
| Last edited at | Jul 26, 2016 08:26 |
# Description
There is still some duplicate doxygen documentation in the material folder, for example the FluidState set-functions all have the same documentation.
This could be a task for an upcoming Dumux day or a Hiwi.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/214FS#214 Implement naming rules for class names2023-12-13T11:13:07ZBernd FlemischFS#214 Implement naming rules for class names# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | General |
| Reported by | Bernd Flemisch (bernd@iws.uni-stuttgart.de) |
| Reported at | Nov 4, 2013 09:34 |
| Type | Feature Request |
| Versi...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | General |
| Reported by | Bernd Flemisch (bernd@iws.uni-stuttgart.de) |
| Reported at | Nov 4, 2013 09:34 |
| Type | Feature Request |
| Version | Git |
| Last edited by | Kilian Weishaupt (kilian.weishaupt@iws.uni-stuttgart.de) |
| Last edited at | Jan 22, 2016 10:18 |
# Description
From 2.3 to 2.4, all member functions and enums have been adapted to our naming conventions. We want to evaluate how we want to do this for class names. Currently, we have inconsistencies like TwoPTwoCNI and Stokes2cni. We discuss in particular the issue about digits in class names.
Newer compilers should provide easier deprecation possibilities. An example will follow.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/346[doc] Linear solver description2018-04-18T12:43:27ZTimo Kochtimokoch@math.uio.no[doc] Linear solver descriptionMany users - including me -- don't know the advantages, disadvantages, requirements to matrix of all the solvers and preconditioners we support.
Can we add some hints to the Solver Backend classes?Many users - including me -- don't know the advantages, disadvantages, requirements to matrix of all the solvers and preconditioners we support.
Can we add some hints to the Solver Backend classes?Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/297FS#297 Bibliography in doxygen2018-04-18T12:43:28ZThomas FetzerFS#297 Bibliography in doxygen# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Reported at | Sep 30, 2015 07:30 |
| Type | Hiwi Job |
...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Reported at | Sep 30, 2015 07:30 |
| Type | Hiwi Job |
| Version | Git |
| Last edited by | Kilian Weishaupt (kilian.weishaupt@iws.uni-stuttgart.de) |
| Last edited at | Jan 12, 2016 16:49 |
| Closed by | Kilian Weishaupt (kilian.weishaupt@iws.uni-stuttgart.de) |
| Closed at | Jan 12, 2016 16:49 |
| Closed in version | unknown (Id=0) |
| Resolution | Implemented |
# Description
To further emphasize the scientific background of dumux we could think about adding a reference list in doxygen (e.g. for fluid properties, etc.). Generally doxygen offers the possibility to cite literature with the latex command \cite and to extract the papers from a bib file.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/289FS#289 Fluid Framework Description inside the Handbook2018-04-18T12:43:28ZThomas FetzerFS#289 Fluid Framework Description inside the Handbook# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Reported at | Sep 1, 2015 14:07 |
| Type | Feature Requ...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Reported at | Sep 1, 2015 14:07 |
| Type | Feature Request |
| Version | Git |
| Last edited by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Last edited at | Mar 8, 2016 08:39 |
| Closed by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Closed at | Mar 8, 2016 08:39 |
| Closed in version | 2.9 |
| Resolution | Implemented |
# Description
```
Currently we have a quite large section about the fluid system and fluid state inside the handbook. This is good and comprehensive but things like function descriptions should be treated in doxygen. The disadvantage of the current state is.
1) the functions/variables might not be up-to-date
2) the list of available fluidstates/fluidsystem is _not_ up-to-date
Therefore the handbook group decided to move this section out of the handbook. In which kind and if this makes sense has to be discussed. One option is to create base classes which contain all respective functions and from which all subclasses inherits from (e.g. compositionalfluidstate would then inherit from basefluidstate). In the handbook we would then refer to the doxygen pages created from this file.
```https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/484Bring handbook up to date2018-12-18T19:36:05ZBeatrix BeckerBring handbook up to dateThere are a few larger TODOs in the handbook:
* [x] Check and update chapter 2 Getting started (@hommel): maybe split in two chapters ("Getting started" including the quick guide and something else...) or rename chapter, add grids (@kw...There are a few larger TODOs in the handbook:
* [x] Check and update chapter 2 Getting started (@hommel): maybe split in two chapters ("Getting started" including the quick guide and something else...) or rename chapter, add grids (@kweis), delete mentioning of dumux-devel
* [x] Check and update chapter 3 Tutorial (@nedc): explain check out of dumux-course with the dumux-course tag, mention that dumux-course will be updated soon to work with 3.0 release and that examples will be added in 3.1 release, delete tutorial
* [x] Update chapter 4.1, 4.2, 4.3 plus change file for naming conventions to md-file (@kweis)
* [x] Update chapter 5.4 Restart (@timok)
* [x] Add Input/Output chapter with paraview, gmsh... Move 5.5 Grid Handling to this chapter (@leopold.stadler, @utz)
* [x] Write subsection on grid (e.g., cornerpoint, @martins) in 5_grids.tex
* [x] Write subsubsection on temporal discretization in 5_models.tex (@felixw, with help from @holle)
* [x] Write subsubsection on MPFA (@martins) in 5_spatialdiscretizations.tex
* [x] Revise subsubsection on Staggered grid (@melaniel) in 5_spatialdiscretizations.tex
* [x] Revise section about implementation structure and revise figure in 5_stepsofasimulation.tex (link to main file from course) (@melaniel)
* [x] Check and update 5.4 Property System (@seitz)
* [x] Check and update 5.5 Grid Handling (@nedc): ICEM raus
* [x] Write section on how to use DuMuX in parallel (@leopold.stadler, @utz): mpirun, only AMG, Multidomain and freeflow not in parallel, depends on grid (dune)
* [x] Add section on gas mixing laws
* ~~[ ] Add chapter on physics of porous media flow (e.g. pc-sw curves) (@holle)~~
* [x] Link to wiki about changes from 2.12 to 3.0 (@becker)3.0Martin SchneiderMartin Schneiderhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/497Contribution and style guide2018-07-25T12:34:00ZTimo Kochtimokoch@math.uio.noContribution and style guideWe should have a contribution guide (how to format commits, what we expect, e.g. that a new feature is tested),
and a style guide (naming conventions and formatting conventions).
GitLab recognized a `CONTRIBUTING.md` file and others can...We should have a contribution guide (how to format commits, what we expect, e.g. that a new feature is tested),
and a style guide (naming conventions and formatting conventions).
GitLab recognized a `CONTRIBUTING.md` file and others can be linked in there. See !992.
We should extend !992 so that we have basic guidelines which can be extended.3.0https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/202FS#202 Explain important svn commands in handbook2018-08-15T10:05:17ZAlexander KissingerFS#202 Explain important svn commands in handbook# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Reported at | Aug 13, 2013 06:40 |
| Type |...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Reported at | Aug 13, 2013 06:40 |
| Type | Feature Request |
| Version | Git |
| Last edited by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Last edited at | Sep 26, 2013 15:26 |
| Closed by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Closed at | Sep 26, 2013 15:26 |
| Closed in version | 2.4 |
| Resolution | Implemented |
# Description
Committing problems in dumux for example for a thesis or visiting phd student requires some basic knowledge of svn (what is a repository, why do we need it?) and some basic commands (update, add, commit, revert, mv etc). I think giving some basic explanations here for example in the Section \\\\\\\"Setup a new folder\\\\\\\" (where svn ignore is also explained) could save the supervisor a lot of time.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/596Bring Doxygen up to date2018-12-19T12:01:32ZSimon EmmertBring Doxygen up to dateI had a quick lock at Doxygen today.
The question that we should discuss is:
**What do we (not) want to document in Doxygen?**
Under **Modules** we currently have a list of available `models` and `discretization schemes`.
This seem...I had a quick lock at Doxygen today.
The question that we should discuss is:
**What do we (not) want to document in Doxygen?**
Under **Modules** we currently have a list of available `models` and `discretization schemes`.
This seems good to me and maybe could get a small update.
The newly established `Multidomain simulations` part should also be in there in my opinion.
We also list our `Material/Fluid Framework`, which looks good to me.
Then we have `Benchmarks and Tests,` which is not really a module in my opinion and could be replaced by our examples in the near future (3.1). **So we could get rid of this.**
And then there is `Adaptive`
`Assembly`
`Common`
`Input Output`
`Linear`
`Nonlinear`
`Parallel`
where I am not sure if we could combine them maybe.
**We used to have a feature list and a parameter list.**
**Do we want to have them also in 3.0? And if so, in which detail level?**
The last time I tried this, we opted more towards a general feature/parameter list without listing all the possible combinations and variations.
Comments?3.0https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/635Proofread handbook2018-12-20T16:11:08ZTimo Kochtimokoch@math.uio.noProofread handbook* [x] Throw out/improve stuff that is not correct
* [x] Run spell-checker
* [x] Shorten gnuplot section and remove stuff that is not general* [x] Throw out/improve stuff that is not correct
* [x] Run spell-checker
* [x] Shorten gnuplot section and remove stuff that is not general3.0https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/697[shallowwater] Complete the doxygen documentation2019-05-13T14:33:48ZMartin Utz[shallowwater] Complete the doxygen documentationThe doxygen documentation for the shallow water part does not work properly, because the modules.txt is not updated. After fixing that, in general the shallowwater doxygen documentation shall be tested.
* [x] Add entry in modules.txt fo...The doxygen documentation for the shallow water part does not work properly, because the modules.txt is not updated. After fixing that, in general the shallowwater doxygen documentation shall be tested.
* [x] Add entry in modules.txt for ShallowWater
* [x] Check that all classes and functions have a docstring
* [x] Document ShallowWaterFlux classMartin UtzMartin Utzhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/769[doxygen] warnings2019-10-02T13:17:05ZBeatrix Becker[doxygen] warningsI encountered a few warnings running doxygen that I couldn't make disappear. This is the doxyerr.log file as it is produced on the branch feature/doxygen-warnings-part-1: [doxyerr.log](/uploads/b0c3ca48b8fef6a41355e9981f88a8d7/doxyerr.lo...I encountered a few warnings running doxygen that I couldn't make disappear. This is the doxyerr.log file as it is produced on the branch feature/doxygen-warnings-part-1: [doxyerr.log](/uploads/b0c3ca48b8fef6a41355e9981f88a8d7/doxyerr.log)
**Lines 1-15** were already there last time and according to @emmert they had something to do with forward declarations, but that he couldn't solve the problem either. Does anyone have an idea now? If not, we can probably live with this.
**Lines 17-30** are problems associated with staggeredcouplingmanager and **lines 32-end** problems associated with the base fluidsystem. In either cases, doxygen complains that a parameter is not in the argument list of the function, although it is. Doxygen just looks in the wrong place. For the staggeredcouplingmanager, doxygen looks at Dumux::StokesDarcyCouplingManager and for the base fluidsystem, it looks at functions in Dumux::FluidSystems::Brine, which is obviously wrong. But I don't know how to make doxygen look in the right place. This is probably an easy one... @bernd @timok any hints?3.1https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/770[doxygen on website] Latex is not rendered correctly2020-03-16T20:47:20ZBeatrix Becker[doxygen on website] Latex is not rendered correctlyAlso there is nothing under "Description" (jump to that is possible with the "More..."-link, see [example](https://dumux.org/doxygen/master/a01972.html) and [another example](https://dumux.org/doxygen/master/a18158.html)). The locally bu...Also there is nothing under "Description" (jump to that is possible with the "More..."-link, see [example](https://dumux.org/doxygen/master/a01972.html) and [another example](https://dumux.org/doxygen/master/a18158.html)). The locally build version works however!3.2David WernerDavid Wernerhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/775Example main page should contain title and abstracts2019-10-09T08:12:50ZTimo Kochtimokoch@math.uio.noExample main page should contain title and abstractsThe example main readme page does not look very inviting. I would be nice to describe the model/application with a brief title and add a brief description of the example below. Would be also good to number them in the intro page so peopl...The example main readme page does not look very inviting. I would be nice to describe the model/application with a brief title and add a brief description of the example below. Would be also good to number them in the intro page so people can refer to them as Example 1, etc.3.1Katharina HeckKatharina Heckhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/785[handbook][parallel] Mention that the AMG only works properly with direct coa...2019-12-17T14:30:40ZTimo Kochtimokoch@math.uio.no[handbook][parallel] Mention that the AMG only works properly with direct coarse grid solver3.2Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/793[examples] Allow to exclude/fold code in the example README.md2020-01-29T16:08:01ZTimo Kochtimokoch@math.uio.no[examples] Allow to exclude/fold code in the example README.mdFor long files and class with a lot of boilerplate code it might be good to be able to exclude stuff from the automatically generated doc. This is probably possible by defining a keyword like
```c++
//[begin exclude]
...
//[end exclude]...For long files and class with a lot of boilerplate code it might be good to be able to exclude stuff from the automatically generated doc. This is probably possible by defining a keyword like
```c++
//[begin exclude]
...
//[end exclude]
```
Another idea would be (as an alternative or additionally to the suggestion above) to allow collapsible code snippet as demonstrated here:
<details>
<summary>Click to expand code snippet</summary>
```c++
class Class {
using Boilerplate = Code;
using Boilerplate = Code;
using Boilerplate = Code;
using Boilerplate = Code;
using Boilerplate = Code;
};
```
</details>
This could be also achieved with a keyword like
```c++
//[begin fold]
...
//[end fold]
```
Related MRs: !1682 3.2Melanie LippMelanie Lipphttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/815New folder "properties"2020-03-03T16:34:17ZTimo Kochtimokoch@math.uio.noNew folder "properties"For the sake if isolating the property system and making it easier to find stuff in Dumux, I believe it might be helpful to create a new top level folder `properties` that contains
```
properties
|- properties.hh
|- propertysystem.hh
|-...For the sake if isolating the property system and making it easier to find stuff in Dumux, I believe it might be helpful to create a new top level folder `properties` that contains
```
properties
|- properties.hh
|- propertysystem.hh
|- base.hh
|- grid.hh
|- discretization
|- box.hh
|- cctpfa.hh
...
```
i.e. all files that are concerned with setting basic properties. The question is what to do with the `model.hh` headers but I suggest that they remain part of the respective model folder, and only the "base"-property headers are separately structured.3.2https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/824[doc] Automate examples doc creation2020-03-17T08:08:07ZTimo Kochtimokoch@math.uio.no[doc] Automate examples doc creationThe example READMEs currently have to be created with the `bin/merge_cpp_and_md.sh` script AFAIK.
To execute the script you need to correct files and the correct file order. However I couldn't find the specific command for each example b...The example READMEs currently have to be created with the `bin/merge_cpp_and_md.sh` script AFAIK.
To execute the script you need to correct files and the correct file order. However I couldn't find the specific command for each example being documented anywhere.
Maybe we could create something like a `.doc_config` that lists this information for each example?
Then it would be also easy to create a script that builds all examples docs3.2Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/827Dune 2.6 and Dune 2.7 compatible with dumux 3.2?2020-05-04T15:56:23ZNed ColtmanDune 2.6 and Dune 2.7 compatible with dumux 3.2?For the 3.2 release, we want to be dependent on dune 2.7, correct?
This should be mentioned in:
* change log with reasons why.
* all install scripts
* website under installation instructions
TODOs
* [x] After release 3.2 add note...For the 3.2 release, we want to be dependent on dune 2.7, correct?
This should be mentioned in:
* change log with reasons why.
* all install scripts
* website under installation instructions
TODOs
* [x] After release 3.2 add note to the change log that 2.12 is no longer supported and
* [x] Write email to users about above.
* [x] After release 3.2 increase dependency to Dune 2.7
Current proposal for the testing plan during and after release 3.2 (as soon as a release branch is created)
| Dune version --> | 2.5 | 2.6 | 2.7 | master |
| ------ | ------ | ------ | ------ |------ |
| Dumux master | | | x | x |
| Dumux 3 (latest release 3.2) | | x | x | |
| ~~Dumux 2 (latest release 2.12)~~ | | | | |3.2Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/831[examples] Better structure and overview by subfolders2020-04-03T11:34:33ZTimo Kochtimokoch@math.uio.no[examples] Better structure and overview by subfoldersHere are some ideas for a better structure in the examples:
Especially if they are large (see !1784 for an extreme case).
We could
* add separate `.md` files in the `doc` folder that are linked from the main document rather than inclu...Here are some ideas for a better structure in the examples:
Especially if they are large (see !1784 for an extreme case).
We could
* add separate `.md` files in the `doc` folder that are linked from the main document rather than included into the main document
* we could have a separate starting page that explains the setup and the layout, folder and file structure in the example and provides links to the documentation of each file or a group of files
* automate the script to look for `.doc_config` in all subfolder recursively so that for every subfolder we could have an extra autogenerated `README.md` if wanted. That `README.md` can be linked from the main document.
* Remove header guards from the doc
* Improve figure formatting by using HTML
```html
<figure>
<img src="dumux_logo" alt="Dumux logo" style="width:50%">
<figcaption><b>Figure 1 -</b> This is the figure caption for the Dumux logo</figcaption>
</figure>
```
<figure>
<img src="https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/doc/logo/dumux_logo_small.png" alt="Dumux logo">
<figcaption><b>Figure 1 -</b> This is the figure caption for the Dumux logo</figcaption>
</figure>
* see #811 3.2https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/842Link new Dumux paper in Readme2020-03-26T21:41:35ZTimo Kochtimokoch@math.uio.noLink new Dumux paper in Readme3.2Ned ColtmanNed Coltmanhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/882Use mathjax to render formulas in doxygen2020-05-27T14:31:48ZMelanie LippUse mathjax to render formulas in doxygenGoal: Make formulas look nicer in doxygen.
* [x] Add doc/doxygen/Doxylocal `+USE_MATHJAX = YES`
* [x] Get rid of `\textup`, `\textbf` and `\bf` as they are not properly parsed by mathjax and should not be used in the formulas anyway
*...Goal: Make formulas look nicer in doxygen.
* [x] Add doc/doxygen/Doxylocal `+USE_MATHJAX = YES`
* [x] Get rid of `\textup`, `\textbf` and `\bf` as they are not properly parsed by mathjax and should not be used in the formulas anyway
* [x] See if further commands are not parsed properly
Spin-off of the discussion in !19643.3https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/887[doxygen] Exclude tests from doxygen?2020-05-27T11:13:44ZTimo Kochtimokoch@math.uio.no[doxygen] Exclude tests from doxygen?There is a number of arguments for simply removing the tests and all files in the test directory from doxygen
* The is a large amount of classes and files that distract from the actual classes and files in the Dumux core
* The code doc ...There is a number of arguments for simply removing the tests and all files in the test directory from doxygen
* The is a large amount of classes and files that distract from the actual classes and files in the Dumux core
* The code doc of the tests is poorly structured and doesn't help much
* Unclear which information gain we get from inclusion
* Our doxygen takes very long to compile and is quite large. This would help reducing it a bit (all dumux source files in the `dumux` folder are `231,172` lines total, all source files (`.hh`,`.cc`) in the `test` folder are `90,691` lines total; using `find . -name '*.hh' -o -name '*.cc' | xargs wc -l`)
* Much of the doc is not very good (while that is a problem in itself and the doc comments in the tests should actually be of high quality too, this is in the current stage really distracting). Even if it would be better the other points remain.
I navigated through the test docs in the online class documentation a bit. I didn't find anything useful in the `Test & Benchmarks` section. Any other opinions and arguments for keeping it?https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/905Flux functions for law in dumux/flux not documented2020-08-28T09:18:36ZTimo Kochtimokoch@math.uio.noFlux functions for law in dumux/flux not documentedAt least the `flux` function for box Fick's law is not documented: https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/box/fickslaw.hh#L86.
There should be documentation indicating what is returned and in w...At least the `flux` function for box Fick's law is not documented: https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/box/fickslaw.hh#L86.
There should be documentation indicating what is returned and in which unit.3.3https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/956Update parameterlist.txt2020-11-05T16:06:21ZKilian WeishauptUpdate parameterlist.txt`parameterlist.txt` should be updated using the new python script (!2334)
I think @melaniel is already on this, I'm just opening this issue so we don't forget.`parameterlist.txt` should be updated using the new python script (!2334)
I think @melaniel is already on this, I'm just opening this issue so we don't forget.3.3Melanie LippMelanie Lipphttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/958[doc] Document the tests2020-11-04T18:17:59ZFarid Mohammadi[doc] Document the testsIn the old version (<=3.2) of the handbook, it was pointed out that the available test cases had been documented:
```tex
An overview over the available test cases can be found in the class documentation \url{http://www.dumux.org/document...In the old version (<=3.2) of the handbook, it was pointed out that the available test cases had been documented:
```tex
An overview over the available test cases can be found in the class documentation \url{http://www.dumux.org/documentation.php}.
```
Apparently, that is not the case. Let's document the test cases.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/959[getparamlist.py] Keep old parameter descriptions2021-11-18T19:21:09ZKilian Weishaupt[getparamlist.py] Keep old parameter descriptionsWe should modify the script such that it extracts the parameter descriptions given in `parameterlist.txt`
and automatically uses them for the overwritten file.We should modify the script such that it extracts the parameter descriptions given in `parameterlist.txt`
and automatically uses them for the overwritten file.3.5Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/142FS#142 Improve layout of handbook2013-08-13T10:14:07ZDavid WernerFS#142 Improve layout of handbook# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | David Werner (david.werner@iws.uni-stuttgart.de) |
| Reported at | Mar 8, 2012 14:07 |
| Type | Feature Reques...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | David Werner (david.werner@iws.uni-stuttgart.de) |
| Reported at | Mar 8, 2012 14:07 |
| Type | Feature Request |
| Version | Git |
| Last edited by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Last edited at | Aug 13, 2013 10:14 |
| Closed by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Closed at | Aug 13, 2013 10:14 |
| Closed in version | 2.4 |
| Resolution | Implemented |
# Description
Dumux handbook appears as generated from different sources.
Make graphics appear more coherent through the text, especially used colors in them.
Improve the latex writing of String DuMuX that it appears more like the logo on web site.
Write C++ with smaller +. If not exists write, a style guidefor content and layout. Add a glossary. Add documentation as own category in flyspray.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/163FS#163 Improve content of handbook - brainstorm2012-10-12T07:59:39ZAlexander KissingerFS#163 Improve content of handbook - brainstorm# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Reported at | Jul 16, 2012 14:42 |
| Type |...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Alexander Kissinger (alexander.kissinger@iws.uni-stuttgart.de) |
| Reported at | Jul 16, 2012 14:42 |
| Type | Feature Request |
| Version | Git |
| Last edited by | Christoph Grüninger (gruenich@iws.uni-stuttgart.de) |
| Last edited at | Oct 12, 2012 07:59 |
| Closed by | Christoph Grüninger (gruenich@iws.uni-stuttgart.de) |
| Closed at | Oct 12, 2012 07:59 |
| Closed in version | 2.2 |
| Resolution | Fixed |
# Description
```
What content needs to be added or changed to the handbook for the Dumux 2.2 release?
- New model descriptions which are introduced in the stable (eg CO2, CO2ni)
- Tutorial improvement (ask Hiwis and Newcomers where they face problems?)
- etc.
Any suggestions?
```https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/179FS#179 extend \\\\\\\"how to add a folder\\\\\\\" in docu2013-02-25T17:54:13ZNicolas SchwenckFS#179 extend \\\\\\\"how to add a folder\\\\\\\" in docu# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Nicolas Schwenck (nicolas.schwenck@iws.uni-stuttgart.de) |
| Reported at | Jan 23, 2013 12:09 |
| Type | Featu...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Nicolas Schwenck (nicolas.schwenck@iws.uni-stuttgart.de) |
| Reported at | Jan 23, 2013 12:09 |
| Type | Feature Request |
| Version | Git |
| Last edited by | Christoph Grüninger (gruenich@iws.uni-stuttgart.de) |
| Last edited at | Feb 25, 2013 17:54 |
| Closed by | Christoph Grüninger (gruenich@iws.uni-stuttgart.de) |
| Closed at | Feb 25, 2013 17:54 |
| Closed in version | 2.3 |
| Resolution | Implemented |
# Description
```
as discussed in the coffee break, I propose to extend the docu by adding:
* svn:ignore attributes
and open this flyspray task to ask for further suggestions (Christoph?).
I propose to add this also as a dependency for the 2.3 release.
```https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/209FS#209 Improve Doxygen documentation2014-03-07T09:32:22ZThomas FetzerFS#209 Improve Doxygen documentation# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Reported at | Oct 16, 2013 05:21 |
| Type | Bug Report ...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Reported at | Oct 16, 2013 05:21 |
| Type | Bug Report |
| Version | Git |
| Last edited by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Last edited at | Mar 7, 2014 09:32 |
| Closed by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Closed at | Mar 7, 2014 09:32 |
| Closed in version | 2.5 |
| Resolution | Implemented |
# Description
```
Preparing the doxygen documentation for the 2.4 release we noticed some points, which could be improved for the next release.
1) Comment all public functions.
2) Update misleading/ wrong description functions. (e.g. intrinsic permeability in spatialparameters).
2) Doxygen groups still named \\\"*Box*\\\" (skip or replace by \\\"Implicit\\\").
Therefore we thought about creating one model description (e.g. the 1p files), where one can see how to document the code. The use of \\\\tparam, \\\\param and \\\\return can be also discussed in this scope.
This task shall be used for announcing possible improvements for the doxygen documentation, so that we could discuss in the next meeting.
```https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/220FS#220 Some Doxygen comments are ignored2016-01-22T10:17:51ZThomas FetzerFS#220 Some Doxygen comments are ignored# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Reported at | Feb 10, 2014 16:24 |
| Type | Bug Report ...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Thomas Fetzer (thomas.fetzer@iws.uni-stuttgart.de) |
| Reported at | Feb 10, 2014 16:24 |
| Type | Bug Report |
| Version | Git |
| Last edited by | Kilian Weishaupt (kilian.weishaupt@iws.uni-stuttgart.de) |
| Last edited at | Jan 22, 2016 10:17 |
| Closed by | Kilian Weishaupt (kilian.weishaupt@iws.uni-stuttgart.de) |
| Closed at | Jan 22, 2016 10:17 |
| Closed in version | 2.9 |
| Resolution | Fixed |
# Description
For example in dumux/dumux/freeflow/stokes/stokesproperties.hh:
//! Returns whether gravity is considered in the problem
NEW_PROP_TAG(ProblemEnableGravity);
Will not show up in the documentation, regardless whether the comment is put above (as shown) or behind the statement (using //!<).
This only affects certain properties but it is not clear yet, why.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/239FS#239 update parameterlist File Reference2015-01-15T10:15:12ZChristoph GrüningerFS#239 update parameterlist File Reference# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Christoph Grüninger (gruenich@iws.uni-stuttgart.de) |
| Reported at | Sep 29, 2014 08:11 |
| Type | Bug Report...# Metadata
| Property | Value |
| -------- | ----- |
| Project | dumux |
| Category | Documentation |
| Reported by | Christoph Grüninger (gruenich@iws.uni-stuttgart.de) |
| Reported at | Sep 29, 2014 08:11 |
| Type | Bug Report |
| Version | 2.5 |
| Last edited by | Bernd Flemisch (bernd@iws.uni-stuttgart.de) |
| Last edited at | Jan 15, 2015 10:15 |
| Closed by | Bernd Flemisch (bernd@iws.uni-stuttgart.de) |
| Closed at | Jan 15, 2015 10:15 |
| Closed in version | 2.7 |
| Resolution | Implemented |
# Description
The parameterlist File Reference seems to be outdated. We need to update the list.
We should think about a way to generate the list and keep it updated for every release.
Online link for 2.5:
http://www.dumux.org/doxygen-stable/html-2.5/a01097.phphttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/994dumux listens on TCP-Ports2021-08-20T19:41:18ZDavid Wernerdumux listens on TCP-PortsHaving opened TCP ports which are not needed is a security risk. A possible attack can be to inject buffers with arbitrary content. So this should not happen if not otherwise configured.
The ports are open on all IPv4-Adresses.
I see c...Having opened TCP ports which are not needed is a security risk. A possible attack can be to inject buffers with arbitrary content. So this should not happen if not otherwise configured.
The ports are open on all IPv4-Adresses.
I see currently two jobs on hal which have opened TCP Ports 1027 and 1028 for whatever reasons:
```
root@hal:/var/log# lsof -nP -iTCP -sTCP:LISTEN |grep 1027
test_pnm_ 608139 maziar 15u IPv4 2121895 0t0 TCP *:1027 (LISTEN)
root@hal:/var/log# lsof -nP -iTCP -sTCP:LISTEN |grep 1028
test_darc 771895 nepal 16u IPv4 2944280 0t0 TCP *:1028 (LISTEN)
```
Process of maziar looks in tool `pstree -u`
```
slurm_script(608134)───mpirun(608135)─┬─test_pnm_drop_s(608139)─┬─{test_pnm_drop_s}(608140)
│ └─{test_pnm_drop_s}(608141)
├─{mpirun}(608136)
├─{mpirun}(608137)
└─{mpirun}(608138)
```
And with `ps auxww | grep 608139`
```
maziar 608139 98.8 9.7 11601160 6429192 ? Rl Feb18 7995:05 ./test_pnm_drop_stokes_1p
```
Process of nepal looks like:
```
root@hal:/var/log# pstree -u nepal -p
slurm_script(771894)───test_darcy(771895)─┬─orted(771896)─┬─{orted}(771897)
│ ├─{orted}(771898)
│ └─{orted}(771899)
├─{test_darcy}(771900)
└─{test_darcy}(771901)
root@hal:/var/log# ps auxww |grep 771895
nepal 771895 99.9 0.0 238064 29196 ? Rl Feb22 2154:57 ./test_darcy test_darcy.input
```
It would be interesting to stop this and/or document at least its cause.
I have no idea of cause, it can be openmpi related but other things might be possible.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1007Add changelog entry for gasviscosity update2021-04-06T14:07:34ZTimo Kochtimokoch@math.uio.noAdd changelog entry for gasviscosity updateIt slightly changes results so we should mention this in the changelog, maybe with a remark in which ranges we expect a better approximation now.It slightly changes results so we should mention this in the changelog, maybe with a remark in which ranges we expect a better approximation now.3.4https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1019Add section on the scripts to the handbook2021-05-07T09:33:15ZBernd FlemischAdd section on the scripts to the handbook3.4Ned ColtmanNed Coltmanhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1020Complete CHANGELOG for 3.42021-05-07T13:04:31ZBernd FlemischComplete CHANGELOG for 3.4The following merged MRs are worth to be considered for mentioning in the changelog for 3.4. Please have a look and add their content in a few words if necessary, and then mark it in the checkbox.
- [x] !2408
- [x] !2569
- [x] !2296
- ...The following merged MRs are worth to be considered for mentioning in the changelog for 3.4. Please have a look and add their content in a few words if necessary, and then mark it in the checkbox.
- [x] !2408
- [x] !2569
- [x] !2296
- [x] !2507
- [x] ~~!2285~~ (We want to include this new grid variable concept after this can be really used instead of still in namespace 'Experimental')
- [x] !2521
- [x] !2510
- [x] !2509
- [x] !2505
- [x] !2243
- [x] !2239 The `LinearPDESolver` can reuse the matrix and thus avoid unnecessary reassembly. See `test/porousmediumflow/tracer/constvel/main.cc` for an example.
- [x] !2414
- [x] !2454
- [x] !2421
- [x] !2457
- [x] !2422
- [x] !2419 : This MR is mentioned in the changelog for 3.3. Please check if this is correct.
- [x] !2425
- [x] ~~!2282~~ (This was not merged into `master`but into the new staggered dev branch)
- [x] !24173.4https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1023Message warning about suboptimal performance of AMG in case no direct solver ...2021-05-09T12:17:02ZTimo Kochtimokoch@math.uio.noMessage warning about suboptimal performance of AMG in case no direct solver is availableIf no direct solver (UMFPack, SuperLU) is found (both are optional dependencies),
the coarse grid solver in the AMG is a `BiCGSTABSolver` hard-coded to a tolerance of 1e-2 (see https://gitlab.dune-project.org/core/dune-istl/-/blob/master...If no direct solver (UMFPack, SuperLU) is found (both are optional dependencies),
the coarse grid solver in the AMG is a `BiCGSTABSolver` hard-coded to a tolerance of 1e-2 (see https://gitlab.dune-project.org/core/dune-istl/-/blob/master/dune/istl/paamg/amg.hh#L771) which
may not be precise enough depending on the application.
I suggest to print a warning if an AMG-based solver is instantiated and neither UMFPack or SuperLU is found.
We have a patch in dumux that can be applied to decrease the tolerance (https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/patches/istl-2.6.patch)3.4Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1033Update list of contributors2021-05-19T08:37:06ZTimo Kochtimokoch@math.uio.noUpdate list of contributorsLICENSE.md for release 3.4LICENSE.md for release 3.43.4Hanchuan WuHanchuan Wuhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1057Document Python generator classes2023-12-13T11:13:09ZTimo Kochtimokoch@math.uio.noDocument Python generator classesFollow-up from "Feature/python main file"
The following discussion from !2681 should be addressed:
- [ ] @timok started a [discussion](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2681#note_62023):
> ...Follow-up from "Feature/python main file"
The following discussion from !2681 should be addressed:
- [ ] @timok started a [discussion](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2681#note_62023):
> we have to document these generators very well because it's the interface used from the Python side. But I think that's a separate task for when the bindings are a bit more stable...https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1095Pore network model needs dune-foamgrid to work2021-11-02T17:17:19ZMaziar VeyskaramiPore network model needs dune-foamgrid to workAdd dune-foamgrid to the dune-module list which needs to be installed in the [Dumux webpage](https://dumux.org/installation/) or mention it separately that to use pore network model you need to install dune-foamgrid.Add dune-foamgrid to the dune-module list which needs to be installed in the [Dumux webpage](https://dumux.org/installation/) or mention it separately that to use pore network model you need to install dune-foamgrid.3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1100Add documentation on website on how to install external dependencies so that ...2022-02-23T18:20:51ZTimo Kochtimokoch@math.uio.noAdd documentation on website on how to install external dependencies so that Dune finds themSome explanations on build system, how to work with dunecontrol, on the website would be nice.Some explanations on build system, how to work with dunecontrol, on the website would be nice.3.5Leopold StadlerLeopold Stadlerhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1101Update parameterlist2022-06-01T11:42:34ZTimo Kochtimokoch@math.uio.noUpdate parameterlistThe parameter list is now generated by a new script !2933. The script still reports several errors that should be fixed. Some of these result from wrong configuration in the new input file. Some of them are related to old parameter which...The parameter list is now generated by a new script !2933. The script still reports several errors that should be fixed. Some of these result from wrong configuration in the new input file. Some of them are related to old parameter which have been removed. Some of them are related to new parameters.
The script can be run by
```
python3 bin/doc/generate_parameterlist.py
```
This creates a log file with all info in the current directory.
Debug output can be added to the log file by running
```
DUMUX_DEBUG_LEVEL=Debug python3 bin/doc/generate_parameterlist.py
```3.5Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1102[python] Add doc for Python with Dune 2.92022-06-02T17:27:11ZTimo Kochtimokoch@math.uio.no[python] Add doc for Python with Dune 2.93.6https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1106[test][cleanup] Remove test description above problem/spatialparams/main (in-...2022-04-07T12:50:35ZTimo Kochtimokoch@math.uio.no[test][cleanup] Remove test description above problem/spatialparams/main (in-code doc)In many (system-)tests, we have a description of the scenario on top of the problem and sometimes running instructions. Such a description is only required for documented examples. In the test folder, it tends to easily become outdated o...In many (system-)tests, we have a description of the scenario on top of the problem and sometimes running instructions. Such a description is only required for documented examples. In the test folder, it tends to easily become outdated or it's often wrong in the first place due to copy and paste. Running the test is already documented by CMakeLists.txt and should be done through CTest anyways. The description easily becomes outdated if the test is extended or changes.
This suggests removing any such "documentation" in the test folder.3.5Mathis KelmMathis Kelmhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1119Improve documentation of pore-network grid creator parameters2023-12-13T11:13:09ZKilian WeishauptImprove documentation of pore-network grid creator parametersThe generic pore-network grid creator comes with a lot of parameters which are not quite clear immediately.
We should document those properly.
See also !2996
Should this go into the generic `Parameters` documentation table? Not sure...The generic pore-network grid creator comes with a lot of parameters which are not quite clear immediately.
We should document those properly.
See also !2996
Should this go into the generic `Parameters` documentation table? Not sure if this is enough because they would probably be scattered all over the table. Maybe we also need a wiki entry for summary?
Just a brief explanation how the `StructuredLatticeGridCreator` works (based on https://link.springer.com/article/10.1007/s11242-009-9412-3):
1.) Create a regular, axis-parallel 2D or 3D host grid using YaspGrid (can also have grading)
2.) All 2D/3D element edges are considered as throats, connecting the pores located on the bulk element vertices
3.) Add additional throats by connecting the element vertices diagonally
4.) From this "fully-connected" network, delete throats by specifying a certain `DeletionProbability` for each spatial direction (x,y,z and diagonals). This allows to generate anisotropy.
When setting a value of one to the diagonals, a regular axis-aligned lattice grid is created.
5.) Run a sanitation algorithm to remove potential isolated clusters
6.) Assign parameters like `PoreInscribedRadius` to the remaining entities
__Collection of parameters for StructuredLatticeGridCreator__
* `Grid.RemoveThroatsOnBoundary`: Takes list of integers for specifying the side of a cubic domain (0 = xMin, 1 = xMax, 2 = yMin, 3 = yMax, 4 = zMin, 5 = zMax). Removes throats lying on the given sides, i.e. remove throats whose center touches the sides.
* `Grid.DeletionRandomNumberSeed`: Random number seed used when randomly deleting throats from the fully connected lattice. Needed for reproducibility.
* `Grid.RegularLattice`: When set to `true`, a regular axis-aligned lattice grid without any diagonal throats is created. Corresponds to setting `Grid.DeletionProbability`to `1.0` for all diagonal directions.
* `Grid.DeletionProbability` Takes list of doubles corresponding to the deletion probability of throats for each possible spatial direction.
The directions in 2D are : (1, 0), (0, 1), (1, 1) (1, -1)
Example: 0.0, 0.5, 1.0 , 1.0 will delete all diagonal throats and 50% of all throats in y-direction.
The directions in 3D are (1, 0, 0), (0, 1, 0), (0, 0, 1), (1, 1, 0), (1, -1, 0), (1, 0, 1), (1, 0, -1), (0, 1, 1), (0, 1, -1), (1, 1, 1), (1, 1, -1), (-1, 1, 1), (-1, -1, 1)
* `Grid.Positions`: The host grid positions when using tensor grid coordinates.
* `Grid.LowerLeft`: The host grid lower left
* `Grid.UpperRight`: The host grid upper right
* `Grid.NumPores`: The number of pores in each directions (equals hostGridElements + 1)
* `Grid.Grading`: The host grid grading when using tensor grid coordinates.
* `Grid.AllowIntersectingDiagonals`. If set `true`, diagonal throats in an host grid element may intersect. Default is `true`.
__Collection of parameters for ParametersForGeneratedGrid__
* `Grid.SubregionX.LowerLeft`: The lower left of a network subregion, for which individual parameters may be set. X is the subregion id (int).
* `Grid.SubregionX.UpperRight`: The upper right of a network subregion, for which individual parameters may be set. X is the subregion id (int).
* `Grid.PoreInscribedRadius`: Sets a fixed inscribed radius for all pores.
* `Grid.PoreVolume`. Sets a fixed volume for all pores. If not set, the value will be calculated automatically based on the pore geometry and inscribed radius.
* `Grid.ThroatInscribedRadius`. Sets a fixed inscribed radius for all throats. If not set, the value will be calculated automatically based on the throat length and the adjacent pore body radii.
* `Grid.ThroatLength`: Sets a fixed length for all throat. If not set the value will be calculated automatically based on the adjacent pore body centers and radii.
* `Grid.PriorityList`: Takes list of integers for specifying the side of a cubic domain (0 = xMin, 1 = xMax, 2 = yMin, 3 = yMax, 4 = zMin, 5 = zMax). Need to avoid ambiguities when setting the boundary pore labels for pores on corners. The order within the lists determines the precedence of labels.
* `Grid.BoundaryFaceMarker`: Takes a list of integers to specifiy the pore label at each boundary.
2D example: `Grid.BoundaryFaceMarker = 1 2 0 0` results in label(xMin) = 1, label(xMax) = 2, label(yMin) = 0, label(yMax) = 0
* `Grid.CapPoreRadii`. If set `true` (default), pore body inscribed radii are capped such that the pores do not intersect.
* `Grid.MinThroatLength`. Sets a minimum throat length (default 1e-9) in case pores are capped.
* `Grid.PoreLabelsToSetFixedRadius`. Takes a list of pore labels at which a certain fixed radius shall be set. Should probably be removed as we have `SubRegions`. Those could also be set based on labels instead of locations.
* `Grid.PoreLabelsToApplyFactorForRadius` Takes a list of pore labels at which the given pore radius shall be multiplied by a given factor. Should probably be removed as we have `SubRegions`. Those could also be set based on labels instead of locations.
* Grid.FixedPoreRadiusForLabel
* Grid.PoreRadiusFactorForLabel
* `Grid.ParameterRandomNumberSeed`: Random number seed for setting randomly generated parameter. Needed for reproducibility.
* `Grid.ParameterType (uniform / lognormal)`: Specifies the type of random number distribution for setting parameters.
* `Grid.PoreGeometry`: Sets the pore body geometry for all pores.
* `Grid.CapPoresOnBoundaries`: If set `true` pores on boundaries will be cut in half (affects volume).
* `Grid.PoreHeight`: Parameter needed if cylindrical or non-cubic/non-spherical pores are considered.
* `Grid.SubstractRadiiFromThroatLength`: If set true, the pore body inscribed radii will be subtracted from the throat length (which is the Euclidean distance between pore body centers). TODO: fix typo and deprecate!
* `Grid.MeanPoreInscribedRadius`: Sets the mean inscribed pore radius for random parameters.
* `Grid.StandardDeviationPoreInscribedRadius`: Sets the standard deviation of the inscribed pore radius for random parameters.
__Collection of parameters for GridManager__
* `Grid.File`: The grid file.
* `Grid.Sanitize`: If set `true`, isolated network clusters will be found and removed.
* `Grid.SanitationMode`: Options are `KeepLargestCluster` (default) and `UsePoreLabels` keeps all pores connected to a list of labels (`PruningSeedIndices`).
* `Grid.PruningSeedIndices` See `SanitationMode`. Default is (1)
__Collection of parameters for GridData__
* `Grid.NumSubregions`. The number of network subregions. Default is zero.https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1131Doxygen for 3.52022-03-02T08:05:39ZMelanie LippDoxygen for 3.5Todos:
* [x] empty doxyerr.log as much as possible
* [x] Anything interesting to fix in doxygen.log?
There is a warning "warning: Tag 'COLS_IN_ALPHA_INDEX' at line 114 of file 'Doxyfile' has become obsolete." However, this concerns dune-...Todos:
* [x] empty doxyerr.log as much as possible
* [x] Anything interesting to fix in doxygen.log?
There is a warning "warning: Tag 'COLS_IN_ALPHA_INDEX' at line 114 of file 'Doxyfile' has become obsolete." However, this concerns dune-common/doc/doxygen/Doxystyle, not dumux.
* [x] does doc/doxygen/modules.txt match the folder structure?
* [x] Check for missing ingroup
* [x] Check for wrong ingroup
* [x] check correct display of the equations
* [x] correct linking of the sites (see sanitizelinks.sh for previous fixes)
* [x] does work on the dumux website as well?
* [x] under Namespaces - Namespace List spot some undocumented classes
* [x] does the documentation make sense? spot mistakenly made copy& paste?
For possible reference of a future doxygen dude:
The documentation is built by running make doc in the dumux build folder.
One way to switch doxygen versions is to:
* download the doxygen git repository from https://github.com/doxygen/doxygen.git
* checkout the branch you want, e.g. Release_1_8_17
* the first time do: mkdir build, cd build, cmake -G "Unix Makefiles" ..
* always do in the doxygen build directory: make, sudo make install
* the first time do: export PATH=/usr/local/bin/doxygen:$PATH
* delete the dumux build folder and rerun dunecontrol for dumux ./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts --only=dumux all
After Changes in scr/doxygen.cpp delete the build folder an recreate it.
Related MRs: !3027, !30293.5Melanie LippMelanie Lipphttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1139Geomechanics documentation is missing the equation overview2022-04-26T11:20:37ZTimo Kochtimokoch@math.uio.noGeomechanics documentation is missing the equation overviewThe current geomechanics models don't state the implemented equations in doxygen.The current geomechanics models don't state the implemented equations in doxygen.3.5Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1140Improve documentation of shallow water model2022-04-19T14:51:54ZMartin UtzImprove documentation of shallow water modelThe documentation of the shallow water model (https://dumux.org/docs/doxygen/master/a18412.html) should be improved in the following points:
- [x] Add the viscous term to the documentation.
- [x] Improve the documentation of the source t...The documentation of the shallow water model (https://dumux.org/docs/doxygen/master/a18412.html) should be improved in the following points:
- [x] Add the viscous term to the documentation.
- [x] Improve the documentation of the source terms. Add units and explain the bottom friction term more comprehensively.3.5Martin UtzMartin Utzhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1142Fix doxygen modules formatting2022-04-20T08:23:47ZMartin UtzFix doxygen modules formattingIn the doxygen documentation of the modules there is often a blank line missing between the `\brief` description and the rest of the description e.g.:
![Doxygen_modules](/uploads/e05205edfacf61396b7af220dcd66853/Doxygen_modules.PNG)
Wi...In the doxygen documentation of the modules there is often a blank line missing between the `\brief` description and the rest of the description e.g.:
![Doxygen_modules](/uploads/e05205edfacf61396b7af220dcd66853/Doxygen_modules.PNG)
Without the blank line doxygen takes the whole model description as `\brief`, which causes a duplication of the description and a missing full stop between the `\brief` description and the rest of the description:
![Doxygen](/uploads/870f463762d1829c2d753b7900228c20/Doxygen.PNG)3.5Martin UtzMartin Utzhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1144Cleanup model documentation2022-04-26T11:19:52ZTimo Kochtimokoch@math.uio.noCleanup model documentationThe doxygen model documentation (the part with the equations) shouldn't talk about discretization (or at least not a single discretization) because the discretization aspect is separate. If another discretization method becomes available...The doxygen model documentation (the part with the equations) shouldn't talk about discretization (or at least not a single discretization) because the discretization aspect is separate. If another discretization method becomes available updating the documentation is easily forgotten.
The following discussion from !3046 should be addressed:
- [ ] @timok started a [discussion](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/3046#note_74400): (+4 comments)
> ```suggestion:-0+0
> ```
> This is strictly speaking not part of the model, right?3.5Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1149Documentation for flux headers2022-10-06T09:48:50ZTimo Kochtimokoch@math.uio.noDocumentation for flux headersAdd "physics" documentation (discretization-agnostic) for the fluxes (e.g. Darcy's law / Fick's law / ...).
This can then be referenced by the model documentation.
Todo:
- [x] Darcys law (!3177)
- [x] Ficks law (@leonidas, !3267 )
- [x]...Add "physics" documentation (discretization-agnostic) for the fluxes (e.g. Darcy's law / Fick's law / ...).
This can then be referenced by the model documentation.
Todo:
- [x] Darcys law (!3177)
- [x] Ficks law (@leonidas, !3267 )
- [x] Forchheimers law (@leonidas, !3231 )
- [x] Fouriers law (@leonidas, !3269 )
- [x] Hooks law (@leonidas, !3270 )
- [x] Maxwell Stefans law (@stefaniekiemle, !3297)
- [x] dispersion (@stefaniekiemle, !3299)
- [x] effective stress law (@leonidas, !3229 )
- [x] Shallowwater (@leopold.stadler , !3301 )
- [x] Shallowwaterviscous (@utz , !3301)
- [x] Fourierslaw non equilibrium (@stefaniekiemle, !3314 )3.6Theresa SchollenbergerTheresa Schollenbergerhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1181Make doc on master fails2022-07-31T13:07:08ZDavid WernerMake 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/1184Improve doc of Riemann solver2023-12-13T11:13:10ZTimo Kochtimokoch@math.uio.noImprove doc of Riemann solverThere 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 StadlerLeopold Stadlerhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1194[examples] Review and improve new Example 9: Embedded network 1D-3D model2023-03-16T17:32:28ZTimo Kochtimokoch@math.uio.no[examples] Review and improve new Example 9: Embedded network 1D-3D modelSeveral 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.3.7Dennis GläserDennis Gläserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1204OpenSSF Best Practices2022-12-13T10:59:37ZBernd FlemischOpenSSF Best PracticesI 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 repohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1223Remove solver deprecation warnings2023-03-20T21:05:52ZTimo Kochtimokoch@math.uio.noRemove 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.3.7Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1238Merge handbook into doxygen2023-06-28T23:07:28ZTimo Kochtimokoch@math.uio.noMerge handbook into doxygenIn 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.3.8https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1306Add variables description in equations2023-10-27T11:38:34ZYue Wangyue.wang@iws.uni-stuttgart.deAdd variables description in equationssee !3670see !36703.8Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1307Update doxygen to 3.82023-10-27T20:40:04ZTimo Kochtimokoch@math.uio.noUpdate doxygen to 3.8For 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=headsFor 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=heads3.8Ivan BunticIvan Buntichttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1310Symbolic representation of div and grad2023-10-27T19:01:34ZIvan BunticSymbolic representation of div and gradIn 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.
!36753.8Leon KeimLeon Keimhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1312Better name for DualNetwork FancyFactor2023-10-30T15:06:50ZTimo Kochtimokoch@math.uio.noBetter name for DualNetwork FancyFactorThere is a type of heat conduction law called FancyFactor. We should find a better name.
Maybe HeatConductionWeighted or name it after the paper.
See !3682There is a type of heat conduction law called FancyFactor. We should find a better name.
Maybe HeatConductionWeighted or name it after the paper.
See !36823.8Anna Mareike KosteleckyAnna Mareike Kosteleckyhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1313[doc][doxygen][pm] Time-dependent porosity2023-11-01T13:26:37ZTimo Kochtimokoch@math.uio.no[doc][doxygen][pm] Time-dependent porosityThe 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.3.9https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1314[doc][doxygen][pm] Effective diffusion2023-12-17T18:41:34ZTimo Kochtimokoch@math.uio.no[doc][doxygen][pm] Effective diffusionThe 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)3.9Lars KaiserLars Kaiserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1337[doxygen] Erroneous processing of installation doc2024-01-09T09:00:28ZMaziar Veyskarami[doxygen] Erroneous processing of installation docIt 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/1346[doc] fix as much typos as possible unto next release2024-02-28T10:42:39ZKai 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 WendelKai Wendel