dumux-repositories issues
https://git.iws.uni-stuttgart.de/groups/dumux-repositories/-/issues
2023-09-27T18:01:14Z
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1300
[porousmediumflow][2pnc][volvars] Correct comment for dynamic viscosity
2023-09-27T18:01:14Z
Anna Mareike Kostelecky
[porousmediumflow][2pnc][volvars] Correct comment for dynamic viscosity
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**Bug report**
@Simon Grether pointed out, that in [/dumux/porousmediumflow/2pnc/volumevariables.hh](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/porousmediumflow/2pnc/volumevariables.hh?ref_type=heads#L353) the comment for the viscosity says kinematic viscosity, but it's actually the **dynamic** viscosity.
This should be changed to avoid confusion.
3.8
Timo Koch
timokoch@math.uio.no
Timo Koch
timokoch@math.uio.no
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1296
Fix updateAfterGridAdaption() function call for multidomain assembler
2023-08-26T15:16:22Z
Ivan Buntic
Fix updateAfterGridAdaption() function call for multidomain assembler
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**What happened / Problem description**:
Calling the `updateAfterGridAdaption()` function of a [multidomain assembler](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/multidomain/fvassembler.hh#L323) results in compilation errors, as the called functions within expect arguments but these are not provided.
**How to reproduce it (as minimally and precisely as possible)**:
Call `updateAfterGridAdaption()` on a multidomain assembler.
3.8
Ivan Buntic
Ivan Buntic
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1295
Adjust extract porenetwork script - disconnected pores already include isolat...
2023-08-23T11:53:16Z
Anna Mareike Kostelecky
Adjust extract porenetwork script - disconnected pores already include isolated pores
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**Bug report**
**What happened / Problem description**:
Since the updating script [extract_pore_network_with_porespy.py](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/porenetwork/util/extract_pore_network_with_porespy.py) for the new openpnm version 3, isolated pores and pores in disconnected clusters are removed to avoid singularity. However, @mathis mentioned that isolated pores can't be removed anymore as they were already removed before by the pores in disconnected clusters.
Checking with the extraction script based on a OpenPNM version 2.X, "trim_pores" was used (see [OpenPNM version 2.8](https://github.com/PMEAL/OpenPNM/blob/v2.8.2/openpnm/utils/Project.py#L804)), which is equivilant to "disconnected_pores" in [OpenPNM version 3.X](https://github.com/PMEAL/OpenPNM/blob/dev/openpnm/utils/_health.py#L88).
**What you expected to happen**:
No error, when removing isolated pores or pores from disconnected clusters and no removed pores, which should not be.
**How to reproduce it (as minimally and precisely as possible)**:
<details><summary>Minimal Python example</summary>
A porenetwork is created and boundary throats are deleted such that it leaves a network with isolated pores at the corners (see plot).
It can be seen from the output, that isolated pores and pores in disconnected clusters are the same in this case. Hence, `disconnected_pores` also contains `isolated_pores`. After trimming the network with `disconnected_pores`, trimming with `isolated_pores` does not work any more/is unnecessary.
```python
import openpnm as op
import numpy as np
import matplotlib.pyplot as plt
import math
def plot_network_with_op(network):
print('\n------------------------------------------')
print('Plot network with openPNM visualization (using matplotlib)')
opMplStyle = True
if opMplStyle:
op.visualization.set_mpl_style()
fig = plt.figure(figsize=[20, 15])
ax = fig.add_subplot(111)
legend_labels = ['throat', 'pore']
ax = op.visualization.plot_connections(network, ax=ax, label = legend_labels[0])
ax = op.visualization.plot_coordinates(network, ax=ax, label = legend_labels[1])
plt.legend()
plt.show()
def calc_throat_center_coords(network):
pore_coords = network["pore.coords"]
throats = network["throat.conns"]
throat_centers = np.mean(pore_coords[throats], axis=1)
return throat_centers
def remove_boundary_throats(network):
eps = 1e-6
throat_centers = calc_throat_center_coords(network)
box_min = np.min(network['pore.coords'][:], axis=0)
box_max = np.max(network['pore.coords'][:], axis=0)
eps_array_2D = np.array([eps, eps, 0.0])
boundaryThroats = np.any((throat_centers < box_min + eps_array_2D) | (throat_centers > box_max - eps_array_2D), axis=1) #bool vector with True for throats at boundary
op.topotools.trim(network=network, throats=boundaryThroats)
N_x = 5
N_y = N_x
porenetwork = op.network.Cubic(shape=[N_x,N_y ])
# delete throats at boundary to create isolated pores in corners
remove_boundary_throats(porenetwork)
plot_network_with_op(porenetwork)
health = op.utils.check_network_health(porenetwork)
print("Pores in disconnected clusters: ", health["disconnected_pores"])
print("Isolated pores: ", health["isolated_pores"])
op.topotools.trim(network=porenetwork, pores=health["isolated_pores"])
op.topotools.trim(network=porenetwork, pores=health["disconnected_pores"])
```
</details>
**Sugdestion**:
Just use `disconnected_pores` to trim porenetwork as this is equivalent to the old script based on OpenPNM 2.X and it also contains the `isolated_pores`
**Environment**:
- Dune version:
- DuMux version:
- Others:
Anna Mareike Kostelecky
Anna Mareike Kostelecky
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/1024
Richards test do not converge
2021-05-06T08:56:37Z
Dennis Gläser
Richards test do not converge
It seems that after !2574, some richards tests don't converge anymore, causing all pipelines to fail: https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/pipelines/3789
I only checked one output log and saw that `test_richards_b...
It seems that after !2574, some richards tests don't converge anymore, causing all pipelines to fail: https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/pipelines/3789
I only checked one output log and saw that `test_richards_benchmark_infiltration_tpfa` fails due to timeout with poor newton convergence. There may be more tests affected.
In the MR I see that at the latest stage at least, there was no pipeline triggered. Did you test locally before merge @heck, @timok ?
3.4
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/955
Backport !2139 (RANS density) to 3.2
2020-10-31T09:57:01Z
Kilian Weishaupt
Backport !2139 (RANS density) to 3.2
!2139 could not be cherry-picked automatically. You need to do it by hand.
!2139 could not be cherry-picked automatically. You need to do it by hand.
Ned Coltman
Ned Coltman
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/844
Wrong dkrn_dswe analytical derivative in Brooks-Corey and Van Genuchten
2020-03-31T08:02:07Z
Theresa Schollenberger
Wrong dkrn_dswe analytical derivative in Brooks-Corey and Van Genuchten
The implementation of the analytical derivative dkrn_dswe in the Brooks-Corey law is not correct. This is also shown by a comparison with the numerical derivative.
Implemented derivative: $`\frac{d krn}{d swe} = 2 (swe -1) (1+\frac{1}{\...
The implementation of the analytical derivative dkrn_dswe in the Brooks-Corey law is not correct. This is also shown by a comparison with the numerical derivative.
Implemented derivative: $`\frac{d krn}{d swe} = 2 (swe -1) (1+\frac{1}{\lambda} \cdot swe^{\frac{2}{\lambda}} + \frac{1}{2} - (\frac{1}{2}+\frac{1}{\lambda}) \cdot swe)`$
Correct derivative: $`\frac{d krn}{d swe} = 2 (swe -1) (1+(\frac{1}{2} + \frac{1}{\lambda}) \cdot swe^{\frac{2}{\lambda}} - (\frac{3}{2}+\frac{1}{\lambda}) \cdot swe^{\frac{2}{\lambda}+1})`$
![dkrndSw](/uploads/6ae2e8e4116184f902d7d0a1a61858eb/dkrndSw.png)
Additionaly there is also an error in the analytical derivative dkrn_dswe in the Van Genuchten law.
Implemented derivative: $`\frac{d krn}{d swe} = -(1-swe)^{\gamma-1}\cdot(1-swe^{\frac{1}{m}})^{2m-1}\cdot (\gamma(1-swe^{\frac{1}{m}}) - 2\frac{1-swe}{swe} swe^{\frac{1}{m}})`$
Correct derivative: $`\frac{d krn}{d swe} = -(1-swe)^{\gamma-1}\cdot(1-swe^{\frac{1}{m}})^{2m-1}\cdot (\gamma(1-swe^{\frac{1}{m}}) \color{red}+ \color{black} 2\frac{1-swe}{swe} swe^{\frac{1}{m}})`$
![dkrndSw_vanGenuchten](/uploads/a5a6da85cf8b39c6d2c0aed9587edd3b/dkrndSw_vanGenuchten.png)
3.2
Theresa Schollenberger
Theresa Schollenberger
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/662
Wrong use of extrusion factors (freeflow)
2019-02-27T09:56:07Z
Kilian Weishaupt
Wrong use of extrusion factors (freeflow)
At certain points, the use of the extrusion factor is implemented wrong:
* fluxoversurface.hh lacks the factor for the calculation of the volume fluxes
* stokesdarcy/couplingdata.hh includes the factor in the calculation of diffusive fl...
At certain points, the use of the extrusion factor is implemented wrong:
* fluxoversurface.hh lacks the factor for the calculation of the volume fluxes
* stokesdarcy/couplingdata.hh includes the factor in the calculation of diffusive fluxes, however, those values
are then applied as Neuman-BCs where the factor is again applied
__TODO__ @heck What about the Maxwell-Stefan fluxes in the coupling data?
3.1
Kilian Weishaupt
Kilian Weishaupt
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/469
Compiler warnings
2018-10-31T15:52:12Z
Thomas Fetzer
Compiler warnings
We should fix or at least discuss whether we want to fix the following compiler warnings (I am aware that DUNE prints a lot of this warnings, too).
* [x] -Wshadow (shadowing of local variables, e.g. by lambda functions or if/for loops)
...
We should fix or at least discuss whether we want to fix the following compiler warnings (I am aware that DUNE prints a lot of this warnings, too).
* [x] -Wshadow (shadowing of local variables, e.g. by lambda functions or if/for loops)
* [x] -Wno-missing-braces -Wmissing-field-initializers (initiliazation, e.g. object({}) vs object{{}} )
* [x] -Wunused-result (e.g. #472)
* [x] -Wfloat-equal
3.0
Timo Koch
timokoch@math.uio.no
Timo Koch
timokoch@math.uio.no
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/364
Correct handling of diffusive fluxes
2018-07-26T11:46:43Z
Dennis Gläser
Correct handling of diffusive fluxes
In the seminar we came up with the following strategy:
- [x] When useMoles = false we will have to add the diffusive fluxes to the total mass balance equation (eqIdx = replaceCompIdx)
- [x] Fick's law will always be mole based (as in it...
In the seminar we came up with the following strategy:
- [x] When useMoles = false we will have to add the diffusive fluxes to the total mass balance equation (eqIdx = replaceCompIdx)
- [x] Fick's law will always be mole based (as in its derivation). However, the fluxes are transformed into mass fluxes if useMoles = false
- [x] Update documentation
- [x] Return vector of fluxes from fick's law and think about maxwell-stefan diffusion when implementing it
3.0
Katharina Heck
Katharina Heck
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/issues/474
[material][brine] Implement brine fluid system and brine pseudo component
2018-07-20T15:18:13Z
Timo Koch
timokoch@math.uio.no
[material][brine] Implement brine fluid system and brine pseudo component
Brine is currently a pseudo component but extends the interface to be able to have variable salinity. A mixture with variable salinity is however a fluid system. We should implement both interface (brine as fluidsystem and brine as pseud...
Brine is currently a pseudo component but extends the interface to be able to have variable salinity. A mixture with variable salinity is however a fluid system. We should implement both interface (brine as fluidsystem and brine as pseudocomponent with constant salinity) classes separately.
3.0