dumux merge requestshttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests2021-12-08T16:55:31Zhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2947Port 3p3c to new spatialparams2021-12-08T16:55:31ZBernd FlemischPort 3p3c to new spatialparams3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2946Port 3p to new spatialparams2021-12-08T16:25:30ZBernd FlemischPort 3p to new spatialparams3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2945Port richards to new spatialparams2021-12-08T12:01:50ZBernd FlemischPort richards to new spatialparams3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2939[readme] Add repo status badge2021-11-22T07:44:19ZTimo Kochtimokoch@math.uio.no[readme] Add repo status badge3.5Dennis GläserDennis Gläserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2934[python] Make bindings work with dune 2.92021-11-20T02:46:15ZTimo Kochtimokoch@math.uio.no[python] Make bindings work with dune 2.9This is a second attempt at !2912 to make Python work with dune 2.8 and dune 2.9. The two versions feature incompatible ways of setting up the Python bindings.This is a second attempt at !2912 to make Python work with dune 2.8 and dune 2.9. The two versions feature incompatible ways of setting up the Python bindings.3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2933[bin][parameter] Implement new parameter extraction scripts2021-11-19T09:19:31ZTimo Kochtimokoch@math.uio.no[bin][parameter] Implement new parameter extraction scriptsManual inputs are provided via a human-readable JSON file which is
under version control. The parameters.txt file is now completely
auto-generated and shouldn't be manually edited. All edits
happen to the JSON file. This makes sure forma...Manual inputs are provided via a human-readable JSON file which is
under version control. The parameters.txt file is now completely
auto-generated and shouldn't be manually edited. All edits
happen to the JSON file. This makes sure formatting and data
are separated properly and git changes are minimal.
Fixes #959.
The script `generate_parameterlist.py` extracts the parameters from header files. Per default header files in `test` and `examples` are excluded (user-defined parameters).
The file `parameters.json` in `doc/doxygen/extradoc` is used as the default input. The script will take the *explanation, default value, and param type* of a detected parameter from the input if given. Otherwise, it tries to automatically choose a value. Hence, if the automatic output is not good for some reason, write the best version into `parameters.json`. Only ever modify `parameters.json` since `parameters.txt` is auto-generated by the script.
In the JSON file, one can define multiple default values for certain parameters. In this case, all different values will be listed in the output file.
Parameters that are not found in code but exist in the input file will be added to the output.
Usage: `./generate_parameterlist.py` (`cwd = dumux/bin/doc`)
After the execution, information will be written in a log file such as
* the code where parameters can not be correctly extracted
* for the parameters with multi entries, all the values are listed. And the default value will be marked with source (input or code)
* added parameters, which may be manually added in the JSON file
* the list of parameters without explanations3.5Yue Wangyue.wang@iws.uni-stuttgart.deYue Wangyue.wang@iws.uni-stuttgart.dehttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2928Feature/initialize2021-11-10T17:25:58ZTimo Kochtimokoch@math.uio.noFeature/initializeAdd basic initialize (see !2909 for application with multithreading library Kokkos)
"Programmatic" version obtaining an additional parameter object to tune the initialization can be added later.Add basic initialize (see !2909 for application with multithreading library Kokkos)
"Programmatic" version obtaining an additional parameter object to tune the initialization can be added later.3.5Dennis GläserDennis Gläserhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2923[1d3d][avg] Skip point source if the circle stencil is empty (zero coupling t...2021-11-03T18:32:26ZTimo Kochtimokoch@math.uio.no[1d3d][avg] Skip point source if the circle stencil is empty (zero coupling term)In this case the integration element is zero anyways and there is no coupling but the pressure may
become NaN and makes the simulation crash due to NaN residuals.In this case the integration element is zero anyways and there is no coupling but the pressure may
become NaN and makes the simulation crash due to NaN residuals.3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2922Fix extractline data script to work with more pvpython versions2021-12-16T10:47:41ZHanchuan WuFix extractline data script to work with more pvpython versionsCloses #1086Closes #10863.5Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2921Dispersion2021-11-24T10:35:59ZNed ColtmanDispersionaddresses #320
Only existing dispersion test is on dumux-lecture (Henry Problem)
- [x] Implement compositional dispersion
- [x] Implement thermal dispersion
- [x] Scheidegger dispersion tensor
- [x] FullTensor dispersion tensor
- [x]...addresses #320
Only existing dispersion test is on dumux-lecture (Henry Problem)
- [x] Implement compositional dispersion
- [x] Implement thermal dispersion
- [x] Scheidegger dispersion tensor
- [x] FullTensor dispersion tensor
- [x] guard against multiphase and non-box methods
- [x] Add for tracer models compositional, and isothermal models
- [x] Add compiler time catches for missing properties, and add warnings
- [x] update dumux-lecture!170
- [x] Implement and test for TPFA constvelocity
- [x] Add changelog entry for this new feature
To test:
- [x] Thermal dispersion
- [x] Compositional dispersion flux
- [x] Scheidegger tensor from box velocity
- [x] Scheidegger tensor from tracer velocity (constant)
- [x] Open Tensor from input file vector
- [x] Open Tensor from input file scalar3.5Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2918Fix/epsilon 2d 2d intersections2021-11-02T23:29:00ZDennis GläserFix/epsilon 2d 2d intersections3.5Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2917Cleanup/dimless nums2021-11-01T18:04:41ZTimo Kochtimokoch@math.uio.noCleanup/dimless nums3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2916[readme] Order build badges by importance for users2021-11-01T17:03:02ZTimo Kochtimokoch@math.uio.no[readme] Order build badges by importance for users3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2914[box] Option to update all element volume variables when deflecting solution2022-02-24T15:11:14ZDmitry Pavlov[box] Option to update all element volume variables when deflecting solutionAllows for volume variables in the box scheme to depend on all dofs of the element.
Adds a 2p3c test with surfactant injection in porous medium (2p3c). The surfactant model is loosely based on the one described [here](https://www.sintef...Allows for volume variables in the box scheme to depend on all dofs of the element.
Adds a 2p3c test with surfactant injection in porous medium (2p3c). The surfactant model is loosely based on the one described [here](https://www.sintef.no/contentassets/0d97862cef164d1c965d268ce5e4e082/surfactant_model.pdf). (Also see [here](https://ntnuopen.ntnu.no/ntnu-xmlui/handle/11250/240038) for a longer version). This test will not work without the fix in this MR.
Fixes #8923.5Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2909Feature/multithreaded assembly using a coloring scheme2022-04-24T18:42:25ZTimo Kochtimokoch@math.uio.noFeature/multithreaded assembly using a coloring scheme* Multithreading backends and a default backend selection mechanism
* Backend can also manually selected by the user by setting `DUMUX_MULTITHREADING_BACKEND` via CMake
* Type of selected backend is reported by CMake on configure
* Backe...* Multithreading backends and a default backend selection mechanism
* Backend can also manually selected by the user by setting `DUMUX_MULTITHREADING_BACKEND` via CMake
* Type of selected backend is reported by CMake on configure
* Backend can also be changed "interactively" through `ccmake` by editing the cache
* Add a simple generic `Dumux::parallelFor` with one overload so far fully parallelizable loops over integer ranges
* Implements coloring for CCTPfa and Box to enable parallel assembly over colored subsets
* Enables parallel assembly per default if coloring is supported for disc method and a parallel backend is found
* `DUMUX_NUM_THREADS` can control the number of threads when TBB or OpenMP or Kokkos is the backend
* Support for backends `TBB`, `OpenMP`, `Cpp` (STL paralell algorithms), `Kokkos`, `Serial` (strictly serial execution)
* Bugfix in LoggingParamerTree which was not thread-safe (although the `const` interfaces implied so)
* Use Dumux::initialize in all tests which enables the `DUMUX_NUM_THREADS` control parameter
* Update examples
* Python bindings always use the Serial backend for now (the current implementation of the wrapper code is not thread-safe)3.5Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2908[cleanup] Remove code deprecated before release 3.42021-11-02T16:43:57ZRoman Winter[cleanup] Remove code deprecated before release 3.4Closes #1094Closes #10943.5Roman WinterRoman Winterhttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2905Deprecate the shell scripts2021-10-28T08:45:56ZFarid MohammadiDeprecate the shell scriptsCloses #883
TODO:
- [x] Deprecation warning in python for `bin/util/test_dumux.sh`
- [x] Deprecate the following scripts:
1. [compareparameters.sh](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/bin/doc/comp...Closes #883
TODO:
- [x] Deprecation warning in python for `bin/util/test_dumux.sh`
- [x] Deprecate the following scripts:
1. [compareparameters.sh](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/bin/doc/compareparameters.sh)
2. [replace_property_macros.sh](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/bin/util/replace_property_macros.sh)
- [x] Add changes in the `CHANGELOG.md`3.5Farid MohammadiFarid Mohammadihttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2903[cmake] Several smaller cleanups2021-10-26T16:20:45ZTimo Kochtimokoch@math.uio.no[cmake] Several smaller cleanupsMake CMake slightly less verbose and fix some warningsMake CMake slightly less verbose and fix some warnings3.5https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2902[md][embedded] Remove deprecation warning from extended source stencil interface2021-10-26T14:56:22ZTimo Kochtimokoch@math.uio.no[md][embedded] Remove deprecation warning from extended source stencil interfaceFixes #1089Fixes #10893.5Timo Kochtimokoch@math.uio.noTimo Kochtimokoch@math.uio.nohttps://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/merge_requests/2900Implement new mobility treatment for case of disconnected water columns2021-12-13T20:51:15ZLeopold StadlerImplement new mobility treatment for case of disconnected water columnsCloses #1088Closes #10883.5Leopold StadlerLeopold Stadler