Re: [DuMux] Distribution of spatial parameters

[Martin Schneider]

Dear Suzon,

could you please report what you had to do to solve your issue, at least 
if this might be relevant for other users to solve similar issues.


You can use gstat to generate permeability or porosity data, see for 
example the tests

https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/test/porousmediumflow/1p/isothermal/

You can also attach data to your grid file, see for example
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/tree/master/test/porousmediumflow/co2

Best,
Martin

On 17.09.24 12:22, Suzon Jammes wrote:

Hi all,

I was able to solve my problem and to import my grid file in my new 
model. Thanks for your suggestion and help.


I would like now to use an input file to control the distribution of 
the spatial parameters (i.e porosity and permeability). Do you know if 
there is somewhere an example doing something similar ?


Thank you for your help

Suzon


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Re: [DuMux] Problem with importing grid files

[Martin Schneider]

Hi Suzon,

this error message is not really helpful to me, it is probably related 
to your system.


You said that it seems to be related to the grid.
Then you could set up a minimal test case where you just read-in the 
grid, and you should be able to reproduce this error.

Then send all the files of this minimal example here to the mailing list.

Best,
Martin

On 09.09.24 17:47, Suzon Jammes wrote:

Hi Martin,

I am still getting the same error message.

Suzon


==20909== Memcheck, a memory error detector
==20909== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==20909== Using Valgrind-3.15.0 and LibVEX; rerun with -h for 
copyright info

==20909== Command: ./NewDTest2PNCNI_Test_fractures params.input
==20909==
vex amd64->IR: unhandled instruction bytes: 0x62 0xF1 0xFD 0x28 0x6F 
0x5 0x82 0x61 0x2A 0x0

vex amd64->IR:   REX=0 REX.W=0 REX.R=0 REX.X=0 REX.B=0
vex amd64->IR:   VEX=0 VEX.L=0 VEX.n=0x0 ESC=NONE
vex amd64->IR:   PFX.66=0 PFX.F2=0 PFX.F3=0
==20909== valgrind: Unrecognised instruction at address 0x39e214.
==20909==    at 0x39E214: 
ALUGrid::Gitter::Geometric::Tetra::initEdgesNotOnFace() (in 
/home/suzon/CODE_NUMERIQUES/dumux/dumux-Suzon/build-cmake/NewDTest2PNCNI_Test/NewDTest2PNCNI_Test_fractures)
==20909==    by 0x1682A6: _GLOBAL__sub_I_gitter_geo.cc (in 
/home/suzon/CODE_NUMERIQUES/dumux/dumux-Suzon/build-cmake/NewDTest2PNCNI_Test/NewDTest2PNCNI_Test_fractures)
==20909==    by 0x56FA4C: __libc_csu_init (in 
/home/suzon/CODE_NUMERIQUES/dumux/dumux-Suzon/build-cmake/NewDTest2PNCNI_Test/NewDTest2PNCNI_Test_fractures)

==20909==    by 0x4E7F00F: (below main) (libc-start.c:264)
==20909== Your program just tried to execute an instruction that Valgrind
==20909== did not recognise.  There are two possible reasons for this.
==20909== 1. Your program has a bug and erroneously jumped to a non-code
==20909==    location.  If you are running Memcheck and you just saw a
==20909==    warning about a bad jump, it's probably your program's 
fault.
==20909== 2. The instruction is legitimate but Valgrind doesn't handle 
it,
==20909==    i.e. it's Valgrind's fault.  If you think this is the 
case or
==20909==    you are not sure, please let us know and we'll try to fix 
it.

==20909== Either way, Valgrind will now raise a SIGILL signal which will
==20909== probably kill your program.
==20909==
==20909== Process terminating with default action of signal 4 (SIGILL)
==20909==  Illegal opcode at address 0x39E214
==20909==    at 0x39E214: 
ALUGrid::Gitter::Geometric::Tetra::initEdgesNotOnFace() (in 
/home/suzon/CODE_NUMERIQUES/dumux/dumux-Suzon/build-cmake/NewDTest2PNCNI_Test/NewDTest2PNCNI_Test_fractures)
==20909==    by 0x1682A6: _GLOBAL__sub_I_gitter_geo.cc (in 
/home/suzon/CODE_NUMERIQUES/dumux/dumux-Suzon/build-cmake/NewDTest2PNCNI_Test/NewDTest2PNCNI_Test_fractures)
==20909==    by 0x56FA4C: __libc_csu_init (in 
/home/suzon/CODE_NUMERIQUES/dumux/dumux-Suzon/build-cmake/NewDTest2PNCNI_Test/NewDTest2PNCNI_Test_fractures)

==20909==    by 0x4E7F00F: (below main) (libc-start.c:264)
==20909==
==20909== HEAP SUMMARY:
==20909== in use at exit: 5,672 bytes in 25 blocks
==20909==   total heap usage: 31 allocs, 6 frees, 119,332 bytes allocated
==20909==
==20909== LEAK SUMMARY:
==20909==    definitely lost: 0 bytes in 0 blocks
==20909==    indirectly lost: 0 bytes in 0 blocks
==20909==  possibly lost: 0 bytes in 0 blocks
==20909==    still reachable: 5,672 bytes in 25 blocks
==20909== suppressed: 0 bytes in 0 blocks
==20909== Rerun with --leak-check=full to see details of leaked memory
==20909==
==20909== For lists of detected and suppressed errors, rerun with: -s
==20909== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
Illegal instruction (core dumped)

On 09/09/2024 15:46, Martin Schneider wrote:

Dear Suzon,

did you compile your code with Debug opts?
You find some details about this in 
https://dumux.org/docs/handbook/releases/3.7/dumux-handbook.pdf


As written there, you simply need to add the following line
set(CMAKE_BUILD_TYPE Debug)
to you CMakeLists.txt of your test case. Then again compile your code.

Afterwards, you hopefully get more information from valgrind.
Please send the new output then to the Mailinglist.

Best,
Martin

On 09.09.24 15:39, Suzon Jammes wrote:

Hi,

I am not familiar with valgrind but I got this message with it.

Does it help ?

Thanks Suzon

==17785== Memcheck, a memory error detector
==17785== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward 
et al.
==17785== Using Valgrind-3.15.0 and LibVEX; rerun with -h for 
copyright info

==17785== Command: ./NewDTest2PNCNI_Test_fractures params.input
==17785==
vex amd64->IR: unhandled instruction bytes: 0x62 0xF1 0xFD 0x28 0x6F 
0x5 0x92 0x85 0x26 0x0

vex amd64->IR:   REX=0 REX.W=0 REX.R=0 REX.X=0 REX.B=0
vex amd64->IR:   VEX=0 VEX.L=0 VEX.n=0x0 ESC=NONE
vex amd64->IR:   PFX.66=0 PFX.F2=0 PFX.F3=0
==17785== valgrin

Re: [DuMux] Problem with importing grid files

[Martin Schneider]

Hi Suzon,

I tried to read-in your grid and I don't see any issues, so I guess it 
is related to your test case.
I would again suggest to use some tool to get more details where the 
error is thrown.


Best,
Martin

On 09.09.24 14:54, Suzon Jammes wrote:

Hi martin,

I am using a code that was working before. I just changed the input 
file to read the new grid. The problem seems to be coming from the 
mesh file but I don't understand why.


Suzon

On 09/09/2024 13:32, Martin Schneider wrote:

Dear Suzon,

did you try to use some debugger / valgrind to see at which line in 
your code the error is thrown.

It seems that the size of some of your vectors is not large enough.

Best,
Martin


On 09.09.24 11:19, Suzon Jammes wrote:

Hi all,

I am still working on the fracture problem.

With Matlab and gmsh I created a grid setup that I would like to use 
for my models.


The msh file seems to be ok (see files attached) but when I try to 
use it in a simulation I get the following error message :


Invalid MIT-MAGIC-COOKIE-1 keyReading parameters from file 
params.input.
WARNING (ignored): Could not open file 'alugrid.cfg', using default 
values!
ALUGrid-LB values: 0 < [balance] < 1.2, partitioning method 
'ALUGRID_SpaceFillingCurve(9)'.


You are using DUNE-ALUGrid, please don't forget to cite the paper:
Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.

Created parallel ALUGrid<2,2,simplex> (conforming) from input stream.

Computed bounding box tree with 11087 nodes for 5544 grid entities 
in 0.0022099 seconds.

terminate called after throwing an instance of 'std::length_error'
  what():  vector::reserve
[suzon-Precision-7920:07449] *** Process received signal ***
[suzon-Precision-7920:07449] Signal: Aborted (6)
[suzon-Precision-7920:07449] Signal code:  (-6)
[suzon-Precision-7920:07449] [ 0] 
/lib/x86_64-linux-gnu/libpthread.so.0(+0x14420)[0x7f1969e46420]
[suzon-Precision-7920:07449] [ 1] 
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcb)[0x7f196976300b]
[suzon-Precision-7920:07449] [ 2] 
/lib/x86_64-linux-gnu/libc.so.6(abort+0x12b)[0x7f1969742859]
[suzon-Precision-7920:07449] [ 3] 
/lib/x86_64-linux-gnu/libstdc++.so.6(+0x9e8d1)[0x7f1969b1a8d1]
[suzon-Precision-7920:07449] [ 4] 
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa37c)[0x7f1969b2637c]
[suzon-Precision-7920:07449] [ 5] 
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa3e7)[0x7f1969b263e7]
[suzon-Precision-7920:07449] [ 6] 
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa699)[0x7f1969b26699]
[suzon-Precision-7920:07449] [ 7] 
/lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt20__throw_length_errorPKc+0x41)[0x7f1969b1d2e4]
[suzon-Precision-7920:07449] [ 8] 
./NewDTest2PNCNI_Test_fractures(+0x1a3e9c)[0x55e8b88d2e9c]
[suzon-Precision-7920:07449] [ 9] 
./NewDTest2PNCNI_Test_fractures(+0x1a5d85)[0x55e8b88d4d85]
[suzon-Precision-7920:07449] [10] 
./NewDTest2PNCNI_Test_fractures(+0x1a6272)[0x55e8b88d5272]
[suzon-Precision-7920:07449] [11] 
./NewDTest2PNCNI_Test_fractures(+0x5c57a)[0x55e8b878b57a]
[suzon-Precision-7920:07449] [12] 
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f1969744083]
[suzon-Precision-7920:07449] [13] 
./NewDTest2PNCNI_Test_fractures(+0x5f91e)[0x55e8b878e91e]

[suzon-Precision-7920:07449] *** End of error message ***
Aborted (core dumped)

Do you have any ideas what could be the problem ? I must have forget 
something but I can't figure out what it is so far.


Thank you for your help,

Suzon



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Re: [DuMux] Problem with importing grid files

[Martin Schneider]

Dear Suzon,

did you try to use some debugger / valgrind to see at which line in your 
code the error is thrown.

It seems that the size of some of your vectors is not large enough.

Best,
Martin


On 09.09.24 11:19, Suzon Jammes wrote:

Hi all,

I am still working on the fracture problem.

With Matlab and gmsh I created a grid setup that I would like to use 
for my models.


The msh file seems to be ok (see files attached) but when I try to use 
it in a simulation I get the following error message :


Invalid MIT-MAGIC-COOKIE-1 keyReading parameters from file params.input.
WARNING (ignored): Could not open file 'alugrid.cfg', using default 
values!
ALUGrid-LB values: 0 < [balance] < 1.2, partitioning method 
'ALUGRID_SpaceFillingCurve(9)'.


You are using DUNE-ALUGrid, please don't forget to cite the paper:
Alkaemper, Dedner, Kloefkorn, Nolte. The DUNE-ALUGrid Module, 2016.

Created parallel ALUGrid<2,2,simplex> (conforming) from input stream.

Computed bounding box tree with 11087 nodes for 5544 grid entities in 
0.0022099 seconds.

terminate called after throwing an instance of 'std::length_error'
  what():  vector::reserve
[suzon-Precision-7920:07449] *** Process received signal ***
[suzon-Precision-7920:07449] Signal: Aborted (6)
[suzon-Precision-7920:07449] Signal code:  (-6)
[suzon-Precision-7920:07449] [ 0] 
/lib/x86_64-linux-gnu/libpthread.so.0(+0x14420)[0x7f1969e46420]
[suzon-Precision-7920:07449] [ 1] 
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcb)[0x7f196976300b]
[suzon-Precision-7920:07449] [ 2] 
/lib/x86_64-linux-gnu/libc.so.6(abort+0x12b)[0x7f1969742859]
[suzon-Precision-7920:07449] [ 3] 
/lib/x86_64-linux-gnu/libstdc++.so.6(+0x9e8d1)[0x7f1969b1a8d1]
[suzon-Precision-7920:07449] [ 4] 
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa37c)[0x7f1969b2637c]
[suzon-Precision-7920:07449] [ 5] 
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa3e7)[0x7f1969b263e7]
[suzon-Precision-7920:07449] [ 6] 
/lib/x86_64-linux-gnu/libstdc++.so.6(+0xaa699)[0x7f1969b26699]
[suzon-Precision-7920:07449] [ 7] 
/lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt20__throw_length_errorPKc+0x41)[0x7f1969b1d2e4]
[suzon-Precision-7920:07449] [ 8] 
./NewDTest2PNCNI_Test_fractures(+0x1a3e9c)[0x55e8b88d2e9c]
[suzon-Precision-7920:07449] [ 9] 
./NewDTest2PNCNI_Test_fractures(+0x1a5d85)[0x55e8b88d4d85]
[suzon-Precision-7920:07449] [10] 
./NewDTest2PNCNI_Test_fractures(+0x1a6272)[0x55e8b88d5272]
[suzon-Precision-7920:07449] [11] 
./NewDTest2PNCNI_Test_fractures(+0x5c57a)[0x55e8b878b57a]
[suzon-Precision-7920:07449] [12] 
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f1969744083]
[suzon-Precision-7920:07449] [13] 
./NewDTest2PNCNI_Test_fractures(+0x5f91e)[0x55e8b878e91e]

[suzon-Precision-7920:07449] *** End of error message ***
Aborted (core dumped)

Do you have any ideas what could be the problem ? I must have forget 
something but I can't figure out what it is so far.


Thank you for your help,

Suzon



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Re: [DuMux] Boundary condition setting for two-phase flow problem

[Martin Schneider]

Dear Jianwen,

- exactly you can use the capillary pressure-saturation relationship.

- Why do you think that you can't set set the boundary as you initially 
planned? A Neumann condition is not related to a primary variable but to 
one of you phase balances.
Which discretization method do you want to use? For the Box method you 
can directly set mixed conditions.


- 1pnc, n=2 -> 1p2c :); You can have n components in this model.

Best,
Martin

On 05.06.24 10:20, Jianwen Du wrote:

Hi Martin,

Thank you for your helpful suggestions.

Okay, I see. So for my first question, I will calculate the 
saturation of one phase based on the two phases' pressure using the 
capillary pressure-saturation relationship.


For my second question, I intend to set a Dirichlet boundary condition 
for one phase's pressure and a Neumann boundary condition for another 
phase's flux. If the primary variables should include one phase's 
pressure and one phase's saturation, I think I cannot set the boundary 
as I initially planned. Do you have any suggestions?


Besides, I'm afraid that I could only find 
"dumux/dumux/porousmediumflow/1pnc", which doesn't contain the 
subfolder 1p2c.


Thanks again for your help!

Sincerely,
Jianwen

--

Ph.D. student

Hydrology and Atmospheric Sciences

University of Arizona

janewe...@arizona.edu


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Re: [DuMux] Error Installing Dumux with DFM Oil-Water Model

[Martin Schneider]

Dear Jianwen,

the compiler tells you what the error is "error: ‘matrixDomainId’ is not 
a constant expression".
You can have a look at the other facet tests, there you typically define 
constexpr auto bulkDomainId = Dune::index_constant<0>();


Best,
Martin

On 05.06.24 04:33, Jianwen Du wrote:

Hi Nikolai and Christoph.

Thanks for your help. I corrected my installation of UMFPack. Now it 
has a new error see attached file. Could you be able to help check 
this issue when you have time? Thank you so much for offering help!


Sincerely,
Jianwen
--

Ph.D. student

Hydrology and Atmospheric Sciences

University of Arizona

janewe...@arizona.edu


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Re: [DuMux] Boundary condition setting for two-phase flow problem

[Martin Schneider]

Dear Jianwen,

we don't have the option to choose both pressures as primary variables. 
But instead pressure + saturation. But you can calculate a saturation 
from the inverse capillary-pressure-saturation relation sw = 
pc^-1(pn-pw) where you specify pn and pw.


When using the Box discretization scheme you can use mixed boundary 
conditions. For the cell-centered schemes you need to realize this by 
using solution-dependent Neumann conditions, see for example the 
following test "porousmediumflow/1pnc/1p2c/isothermal/problem.hh"


Best,
Martin

On 05.06.24 05:59, Jianwen Du wrote:

Dear DuMux developers,

Please forgive me for having some basic questions.

I wonder if DuMux allows setting the boundary condition for a 
two-phase flow problem by specifying the pressure of both phases. From 
the example models I've seen, it seems that only one phase's pressure 
and one phase's saturation are applied. Additionally, I think it 
should be possible to use a mixed boundary condition, where the 
Dirichlet boundary is set for one phase and the Neumann boundary for 
another phase. Would you be able to tell me where I can find some 
examples or guidance available for these?


Sincerely,
Jianwen
--

Ph.D. student

Hydrology and Atmospheric Sciences

University of Arizona

janewe...@arizona.edu


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Re: [DuMux] inqury about Navier Stokes Equation

[Martin Schneider]

Dear Junqiang Wang,

currently there is unfortunately no multiphase Navier-Stokes solver 
implemented.


Best,
Martin

On 18.04.24 06:57, 王俊强（ Junqiang Wang ） wrote:

Dear Dumux Community,

I've been doing multiphase flow simulations lately. Can Dumux perform 
multi-phase navier stokes equation simulations?


Best regards;

Junqiang Wang


王俊强
junqiangwang_...@163.com

 



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Re: [DuMux] Non isothermal coupled exercise

[Martin Schneider]

Hi Suzon,

line 324 in porousmediumsubproblem.hh is incorrect. You have defined 
values before. So when writing
*auto values = 
couplingManager().couplingData().massCouplingCondition(element, 
fvGeometry, elemVolVars, scvf);*
you declare it within the if statement. This is exactly what the 
compiler tells you.


Did you also check if the massCouplingCondition also implements the 
energy coupling condition?


Best,
Martin


On 05.04.24 17:08, Suzon Jammes wrote:


Hi Edward,


Thank you for you answer, it did help. The code is now compiling (with 
a warning-> porousmediumsubproblem.hh:324:19: warning: variable 
‘values’ set but not used [-Wunused-but-set-variable]) but doesn't run 
:-(!


The linear solver doesn't converge so there is still a problem somewhere.


To keep it simple, I just added a constant temperature in the 
initialAtPos function in the porousmediumsubproblem and a 
freeflowsubproblem but it doesn't work. Any idea why it doesn't 
converge ?


I am attaching the .hh files that I am using that are a slightly 
modified version of the exercises/exercise-coupling-ff-pm/models.



Thank you for your help,


Suzon





On 02/04/2024 16:25, Coltman, Edward wrote:


Hello Suzon,


I'm not sure if this is really where you are working, but assuming:

- the error you are working on is coming from the 
"evaluateInterfaceFluxes" function,


- in porousmediumsubproblem.hh header file,

- and you have added a call to evaluate the face-wise flux at 
somepoint that looks like this:



>

NumEqVector flux = 
couplingManager().couplingData().massCouplingCondition(element, 
fvGeometry, elemVolVars, scvf)
                                   * scvf.area() * 
elemVolVars[scvf.insideScvIdx()].extrusionFactor() * 
FluidSystem::molarMass(1) * -1.0 * 86400.0;

> (taken from the exercise solution)


Then there will be a compatibility problem between the call to the 
"massCouplingCondition(...)" function, and the type NumEqVector.



NumEqVector will have three entries (FieldVector<[...],3>, including 
the added temperature), and the returned vector from the 
massCouplingCondition(...) function will only have two entries 
(FieldVector<[...],2>, only evaluating the mass fluxes).



To fix this, you can use the correct type (for this I would recommend 
to simply use the auto type).


If this is not where your error is coming from, it would be very 
helpful if you could send us a bit more output from the compiler 
error. This is just a best guess based on the line number and error 
you have mentioned.


Best,
Ned


*From:* DuMux  on behalf of 
Suzon Jammes 

*Sent:* Tuesday, April 2, 2024 4:01 PM
*To:* DuMux User Mailing List
*Subject:* Re: [DuMux] Non isothermal coupled exercise
Hi Christoph,

I was able to use non isothermal condition with another example using 
TwoPNCNI model so I guess that the problem comes from the coupling part.
I assume that indeed the temperature should be taken into at the 
coupling interface but I am not sure how to do that.

Should I modify something in the couplingManager ?
Thanks for your help,

—
Suzon Jammes
Researcher & Consultant

M&U sas, Geology by Research
www.mandu-geology.fr
su...@mandu-geology.fr / +33(0)768692934



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avertir immédiatement l'expéditeur ou par email 
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On 30 Mar 2024, at 16:23, Christoph Grüninger  
wrote:


Hi Suzon,
I did not look into the code, so I might guess wrong.

I suspect that by adding temperature, you got a third primary 
variable. The error points out that you are using a vector with two 
entries (representing two primary variables) at a place where you 
should use a vector with three entries (for all three primary vars).


I hope this helps you figuring out what went wrong.

Bye
Christoph


Am 29.03.24 um 11:14 schrieb Suzon Jammes:

Hi all,
I am now working from the coupled exercise 
(exercises/exercise-coupling-ff-pm/models) with a 2pnc model. I 
wanted to make it non-isothermal so I change TwoPNC by TwoPNCNI and 
NavierStockesNC by NavierStockesNCNI in the properties file but I 
get the following error :
error: conversion from ‘FieldVector<[...],2>’ to non-scalar type 
‘FieldVector<[...],3>’ requested
  263 | elemVolVars[scvf.insideSc

Re: [DuMux] Exercice-fractures

[Martin Schneider]

Dear Suzon,

did you change the the model in properties.hh?
If you want to include nonisothermal effects you have to use the TwoPNI 
model instead of the TwoP model.


Best,
Martin

On 19.03.24 17:36, Suzon Jammes wrote:

Dear users,

To learn how to use dumux I am trying to modify a bit the exercise 
about fractures 
(https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-course/-/blob/master/exercises/exercise-fractures). 
Today I wanted to make it nonisothermal as explained in exercice-basic 
but I am getting the following error :


error: ‘temperatureIdx’ is not a member of 
‘Dumux::MatrixSubProblem::Indices’ 
{aka ‘Dumux::TwoPIndices’}


Is there anybody who knows how to solve this error ?

Thank you for your help,

Suzon


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Re: [DuMux] About modifying the output path

[Martin Schneider]

Dear Yiqun,

you could realize this by simply using some bash or python script.
Please have, for example, a look at the "run_and_plot_m21.py" script:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/test/porousmediumflow/richards/benchmarks/run_and_plot_m21.py?ref_type=heads

Best regards,
Martin

On 13.10.23 05:12, Yiqun Ma wrote:

Dear DuMux,

I want to modify some data for testing and output each result to a 
different folder, but I didn't find the relevant instructions. How 
could I modify the location of the file after running it?


Kind regards,

Yiqun

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Re: [DuMux] Report ERROE for dumux install

[Martin Schneider]

Dear Renzhi WANG,

in the output you can find the error message which tells you that "a 
package named like python-dev package or python3-devel" is needed.

So could you please check if these packages are properly installed?

Best,
Martin


On 08.09.23 16:45, Renzhi Wang wrote:

Dear dumux officers,

I am a PhD student from the University of Strasbourg. It is my first 
time to install dumux in Ubuntu.


I have followed the line: 
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-course to 
install and it comes to error. I have installed: wget gcc git cmake 
pkg-config mpich mpich-doc libmpich-dev zlib1g zlib1g-dev 
gmsh libdune-istl-dev libdune-grid-dev libdune-iggrid-dev clang.


After that I use the installdumux.py. It comes with the information 
"-- ERROR: The command ./dune-common/bin/dunecontrol 
--opts=dumux/cmake.opts all returned with non-zero exit code.". The 
log of error has been attached behind.


Could you help me to fix the problem? Thank you!


Best regards
Renzhi WANG

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Re: [DuMux] About installing opm using scripts

[Martin Schneider]

Dear Yiqun,

in the script it is mentioned that you need additional packages (here it 
says that Boost is missing).

You can find these information here:
https://opm-project.org/?page_id=239

Best,
Martin

On 12.09.23 04:08, Yiqun Ma wrote:

Dear Sir/Madam,

I'm having problems installing Dumux components using ssh connection 
to NCI (0. Welcome to Gadi - NCI Help - Opus - NCI Confluence 
).


When I go through the steps at DuMux: Installation 
 to 
install opm, after executing the command

. /dune-common/bin/dunecontrol --opts=. /dumux/cmake.opts all
I get the following error


Attached is the file and the module I loaded


Looking forward to your reply and thanks for your help.

All the best,

Yiqun


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Re: [DuMux] Gradients of solution vector with TPFA

[Martin Schneider]

Dear Helena,

if I understand you correctly, you want to calculate spatial gradients 
of your primary variables?
This is not straight-forward for CCTPFA, at least if you have 
heterogeneous data.
If you need the pressure gradient, you could recalculate it from the 
darcy velocity and simply use the existing
velocity calculation in dumux 
(https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/porousmediumflow/velocity.hh). 



There is also a more generic way to calculate gradients by using for 
example equation (39) in

https://ogst.ifpenergiesnouvelles.fr/articles/ogst/pdf/2018/01/ogst180050.pdf
There, K denotes the control volume (element) for which you want to 
calculate the gradient of some primary variable u and u_\sigma is some 
approximation of your solution on face \sigma (in Dumux denoted as scvf).
For CCTPFA u_\sigma can be calculated as the harmonic average of 
neighboring solution values with corresponding transmissibilities. If 
you have homogeneous data this would be simply some distance average.


We are currently working on a generic way to interpolate variables and 
to calculate gradients, however, this is not yet available.


I hope this helps.

Best regards,
Martin


On 09.02.23 20:06, Helena Kschidock wrote:

Hi all,

I am currently implementing a cell problem in DuMuX and am using an 
adapted 1p model/Darcy Problem with CCTPFA discretization to do so. 
After obtaining the solution vector, I need to obtain the gradients of 
the solution which I will then use to calculate my upscaled 
conductivities through integration.


In the exchange with Dimitry Pavlov in the mailing list archive (see 
2020q2 "How to implement MaterialLawParams that depend on pressure 
gradient"), Timo suggested using the Jacobian to obtain the gradients 
(which I could easily make available in my case, as the step is done 
AFTER solving the cell problem). However I am slightly confused - 
isn't the Jacobian the partial derivative of the residual with respect 
to the solution (instead of the partial residual of the solution with 
respect to the dimension)? At least this is what the handbook seems to 
imply.


Thanks for any help,
Helena

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Re: [DuMux] Reading entry pressure from the grid file

[Martin Schneider]

Dear Kenza,

if you are using the dgf files you can have a look at the following test:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/test/porousmediumflow/co2/spatialparams.hh
which shows how to add parameters to grid files and use them in the 
spatialparams.


For other grid file formats you can have a look at the tests related to 
grid io:

https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/test/io/gridmanager/

I hope this helps.

Best regards,
Martin



On 17.01.23 01:36, kenza bouznari wrote:

Dear Dumux Users,

I can't figure out how to implement a feature in the code that would 
allow it to read entry pressure values from the grid file. I am using 
"2p2c/chemicalnonequilibrium" test (of dumux3.4).


Any help and guidance in this regard would be greatly appreciated.

Best regards,
--Kenza

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Re: [DuMux] Printing Fluxes in VTK Files

[Martin Schneider]

Dear Mohammad Hodroj,

couldn't you find related topics in the mail archive, as Timo suggested?

Anyhow, I'll try to give you some hints:

- The 2ptracer test case shows how fluxes can be calculated for each 
scvf. Have a look at

https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/test/porousmediumflow/tracer/2ptracer/main.cc
This should also work for your test case

- Writing out fluxes is not straightforward since they are face related 
and can't be assigned to cells/elements.
For this you could use the "Dumux::PointCloudVtkWriter", where you could 
write fluxes at face centers (points) or have a look at 
ConformingIntersectionWriter

where data can be directly assigned to faces.

I hope this helps to solve your issues.

Best regards,
Martin

On 14.12.22 11:01, Mohammad Hodroj (Student) wrote:

Dear DuMux Community,

I hope this email finds you well.

I am writing to ask for your support in the following:

a) I am working on 2p flow - porous medium
b) I am using cctpfa
c) I am using the Neuman boundary conditions for the domain.
d) Gas is injected from the bottom
e) no water flow
f) at time = 0 , Sg = 0 and Sw = 0.2.
g) I am using fvGridGeometry

*Help:*

How can I print the gas fluxes on VTK files? and Should I write the 
code of the flux in the injection2pproblem.hh and 2pmain.cc?


*Note:*

I read Rafael's script, but it seems his problem is different.

Could you please guide me on this matter or attach a sample code.

Thanks for your help.

Best Regards,
Mohammad Hodroj



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Re: [DuMux] End gas injection in AddPointSource function

[Martin Schneider]

Dear Kenza,

you can't do it like this, because you set-up the point sources 
initially and then you don't call this function in every time step.


However, you can pass a lambda function instead which is then evaluated 
in each time step.

You can find an example of how this works in
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/test/porousmediumflow/richardsnc/problem.hh
Here, the point source value can be chosen time-dependent.

Alternatively, you can do it as indicated in the test
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/test/porousmediumflow/solidenergy/problem.hh
where you implement the additional *pointSource *function to update the 
source value.


Best regards,
Martin

On 02.05.22 13:24, kenza bouznari wrote:

Hello Dumux users,

I have tried to impose a time to end gas injection in my domain.
To inject the gas, I use addPointSource and so in this function I add 
the condition of the time I want as follows:

     void addPointSources(std::vector& pointSources) const.
     {
         if ( time_ < injectionFin_)
       {
         pointSources.push_back(PointSource({30.00, 0.00}, {0, 
InjectionRate_})) ;

        }
     }
The injection continues even after the simulation has reached the 
"injectionFin_" time!


P.S.: I use the "2p2c / injection" test. I have attached the following 
files:

parms.input; problem.hh and main.cc

Any help will be appreciated. Thanks in advance for your time!

Best regards,

Kenza

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Re: [DuMux] Heterogeneous cornerpoint grid - Pressure drop/increase in scattered cells

[Martin Schneider]

Dear Sebastian,

you can't use everywhere Neumann when solving an incompressible 1p 
problem, because then

your pressure solution is only defined up to some constant.

Why didn't you set everywhere Dirichlet according to your initial 
conditions?


Best regards,
Martin


On 14.09.21 09:32, Alexander Sebastian Hogeweg wrote:


Dear Martin,

Attached you can find the corresponding files. Additionally, I forgot 
to tell you that I am now using Neumann no-flow boundaries at all 
boundaries.


Thank you in advance and if you need further data, just let me know.

Best Regards

Sebastian

*Von:*Martin Schneider 
*Gesendet:* Dienstag, 14. September 2021 09:15
*An:* Alexander Sebastian Hogeweg 
; 
dumux@listserv.uni-stuttgart.de
*Betreff:* Re: AW: AW: [DuMux] Heterogeneous cornerpoint grid - 
Pressure drop/increase in scattered cells


Dear Sebastian,

could you please also provide the header files of your test case.
It would help to see the boundary conditions, etc.

Best regards,
Martin

On 14.09.21 08:36, Alexander Sebastian Hogeweg wrote:

Dear Martin,

First of all, thank you again for your time. Now, I built a 1p
(liquid) cornerpoint model to find the origin of the problem.
However, now I am observing a pressure change in the complete
structure. The attached images represent the pressure initially
and after the first timestep (100s). The initialization is done
using the hydrostatic pressure (simpleH2O):

values[0] = globalPos[2] * 1000 * gravity()[2];

The petrophysical properties are defined as homogeneous (k=1mD,
phi = 0.2). The structure's thickness is approximately 190m which
should induce a pressure difference of ca. 19 bar along with the
structure. After the first time step, the pressure difference
increases to 66bar, which I do not understand. Do you have any
ideas about what is causing this problem?

Thank you in advance.

Best regards,

Sebastian

    *Von:*Martin Schneider 
<mailto:martin.schnei...@iws.uni-stuttgart.de>
*Gesendet:* Freitag, 3. September 2021 11:43
*An:* Alexander Sebastian Hogeweg

<mailto:alexander.sebastian.hoge...@tu-clausthal.de>;
dumux@listserv.uni-stuttgart.de
<mailto:dumux@listserv.uni-stuttgart.de>
*Betreff:* Re: AW: [DuMux] Heterogeneous cornerpoint grid -
Pressure drop/increase in scattered cells

Dear Sebastian,

I just checked the tpfa darcylaw:

https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh

<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh>
and it seems that you can't use my previous suggestion and simply
use absolute values in the functions of

https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh

<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh>
because there in the darcylaw we calculate the transbissibility
t_j related to the neighboring element as:
-1.0*computeTpfaTransmissibility()

Did you try to change

https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh

<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh>
such that all transmissibilities for the flux calculation are
positive.

Maybe you could also start setting up a 1p problem and try if it
works there.

Best regards,
Martin

On 03.09.21 11:11, Alexander Sebastian Hogeweg wrote:

Dear Martin,

thank you for the fast response. I followed your
recommendations and changed the cell center location based on
the arithmetic mean (|HACK_CELL_CENTROIDS)|. Here, I am still
facing negative values for the grid block transmissibilities (ti).

Additionally, I use the absolute value for the
transmissibilities leading to positive values. However, the
pressure drop/increase in some cells is still observable.

Do you have other ideas, which could cause this behavior?
Thank you in advance.

    Best regards,

Sebastian

*Von:*Martin Schneider 
<mailto:martin.schnei...@iws.uni-stuttgart.de>
*Gesendet:* Freitag, 3. September 2021 09:37
*An:* DuMux User Mailing List

<mailto:dumux@listserv.uni-stuttgart.de>; Alexander Sebastian
Hogeweg 
<mailto:alexander.sebastian.hoge...@tu-clausthal.de>
*Betreff:* Re: [DuMux] Heterogeneous cornerpoint grid -
Pressure drop/increase in scattered cells

Dear Sebastian,

for CP-grids it might happen that the centroid is located out
of the cell such that the 

Re: [DuMux] Heterogeneous cornerpoint grid - Pressure drop/increase in scattered cells

[Martin Schneider]

Dear Sebastian,

could you please also provide the header files of your test case.
It would help to see the boundary conditions, etc.

Best regards,
Martin

On 14.09.21 08:36, Alexander Sebastian Hogeweg wrote:


Dear Martin,

First of all, thank you again for your time. Now, I built a 1p 
(liquid) cornerpoint model to find the origin of the problem. However, 
now I am observing a pressure change in the complete structure. The 
attached images represent the pressure initially and after the first 
timestep (100s). The initialization is done using the hydrostatic 
pressure (simpleH2O):


values[0] = globalPos[2] * 1000 * gravity()[2];

The petrophysical properties are defined as homogeneous (k=1mD, phi = 
0.2). The structure's thickness is approximately 190m which should 
induce a pressure difference of ca. 19 bar along with the structure. 
After the first time step, the pressure difference increases to 66bar, 
which I do not understand. Do you have any ideas about what is causing 
this problem?


Thank you in advance.

Best regards,

Sebastian

*Von:*Martin Schneider 
*Gesendet:* Freitag, 3. September 2021 11:43
*An:* Alexander Sebastian Hogeweg 
; 
dumux@listserv.uni-stuttgart.de
*Betreff:* Re: AW: [DuMux] Heterogeneous cornerpoint grid - Pressure 
drop/increase in scattered cells


Dear Sebastian,

I just checked the tpfa darcylaw:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh 
<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh>
and it seems that you can't use my previous suggestion and simply use 
absolute values in the functions of
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh 
<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh>
because there in the darcylaw we calculate the transbissibility t_j 
related to the neighboring element as:

-1.0*computeTpfaTransmissibility()

Did you try to change 
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh 
<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh>

such that all transmissibilities for the flux calculation are positive.

Maybe you could also start setting up a 1p problem and try if it works 
there.


Best regards,
Martin

On 03.09.21 11:11, Alexander Sebastian Hogeweg wrote:

Dear Martin,

thank you for the fast response. I followed your recommendations
and changed the cell center location based on the arithmetic mean
(|HACK_CELL_CENTROIDS)|. Here, I am still facing negative values
for the grid block transmissibilities (ti).

Additionally, I use the absolute value for the transmissibilities
leading to positive values. However, the pressure drop/increase in
some cells is still observable.

Do you have other ideas, which could cause this behavior? Thank
you in advance.

Best regards,

    Sebastian

*Von:*Martin Schneider 
<mailto:martin.schnei...@iws.uni-stuttgart.de>
*Gesendet:* Freitag, 3. September 2021 09:37
*An:* DuMux User Mailing List 
<mailto:dumux@listserv.uni-stuttgart.de>; Alexander Sebastian
Hogeweg 
<mailto:alexander.sebastian.hoge...@tu-clausthal.de>
*Betreff:* Re: [DuMux] Heterogeneous cornerpoint grid - Pressure
drop/increase in scattered cells

Dear Sebastian,

for CP-grids it might happen that the centroid is located out of
the cell such that the currently implemented
transmissibility calculation yields negative values.

Did you check if all the transmissibility calculated with the
functions in the following header

https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh

<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh>
are positive?

I guess you will observe negative values. There are two solutions
to overcome this
1. Try to use another cell center instead of the centroid.
2. Try to use the absolute value of the transmissibility
(corresponds to switching the normal vector of the corresponding face)

I hope this solves your problem.

Best regards,
Martin


On 02.09.21 18:15, Alexander Sebastian Hogeweg wrote:

Hello everyone,

I am facing a problem during the simulation of an underground
gas storage scenario. The used grid is a cornerpoint-grid with
a heterogeneous distribution of permeability and porosity.
Additionally, the structure contains a fault connecting a
lower part of the formation. The used fluid model is 2pnc
 

Re: [DuMux] Heterogeneous cornerpoint grid - Pressure drop/increase in scattered cells

[Martin Schneider]

Dear Sebastian,

I just checked the tpfa darcylaw:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh
and it seems that you can't use my previous suggestion and simply use 
absolute values in the functions of
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh 
<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh>
because there in the darcylaw we calculate the transbissibility t_j 
related to the neighboring element as:

|-1.0*computeTpfaTransmissibility()

Did you try to change 
||https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/flux/cctpfa/darcyslaw.hh

such that all transmissibilities for the flux calculation are positive.
|
Maybe you could also start setting up a 1p problem and try if it works 
there.


Best regards,
Martin

On 03.09.21 11:11, Alexander Sebastian Hogeweg wrote:


Dear Martin,

thank you for the fast response. I followed your recommendations and 
changed the cell center location based on the arithmetic mean 
(|HACK_CELL_CENTROIDS)|. Here, I am still facing negative values for 
the grid block transmissibilities (ti).


Additionally, I use the absolute value for the transmissibilities 
leading to positive values. However, the pressure drop/increase in 
some cells is still observable.


Do you have other ideas, which could cause this behavior? Thank you in 
advance.


Best regards,

Sebastian

*Von:*Martin Schneider 
*Gesendet:* Freitag, 3. September 2021 09:37
*An:* DuMux User Mailing List ; 
Alexander Sebastian Hogeweg 
*Betreff:* Re: [DuMux] Heterogeneous cornerpoint grid - Pressure 
drop/increase in scattered cells


Dear Sebastian,

for CP-grids it might happen that the centroid is located out of the 
cell such that the currently implemented

transmissibility calculation yields negative values.

Did you check if all the transmissibility calculated with the 
functions in the following header
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh 
<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh>

are positive?

I guess you will observe negative values. There are two solutions to 
overcome this

1. Try to use another cell center instead of the centroid.
2. Try to use the absolute value of the transmissibility (corresponds 
to switching the normal vector of the corresponding face)


I hope this solves your problem.

Best regards,
Martin


On 02.09.21 18:15, Alexander Sebastian Hogeweg wrote:

Hello everyone,

I am facing a problem during the simulation of an underground gas
storage scenario. The used grid is a cornerpoint-grid with a
heterogeneous distribution of permeability and porosity.
Additionally, the structure contains a fault connecting a lower
part of the formation. The used fluid model is 2pnc (h2on2o2), and
the initialization is based on the example 2p_cornerpoint
(hydrostatic pressure and pores fully water-saturated). At the top
and bottom of the structure, Neumann (no-flow) boundaries are
defined (Dirichlet at the sides with initial). In the present
status, the molecular diffusion is deactivated, and additionally,
the centroid cell center location is used.

After the initialization (looks all right), the pressure in some
cells of the lower part increases while neighboring grid blocks
show a lower pressure. Attached you can find some images showing
the problem (Image 1 and 3: t=0; Image 2 and 4: t =6000s (timestep
8) and the problem file.  Other (more conforming)
cornerpoint-grids do not show this behavior.

Overall, I would like to know if somebody else observed a similar
situation and could help me with the problem.

I appreciate any help you can provide, and please let me know if
you need further information.

Best Regards,

Sebastian

Dumux Version: 3.4

Model: 2pnc

Grid type: Cornerpoint

Fluid system: h2on2o2.hh



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Re: [DuMux] Heterogeneous cornerpoint grid - Pressure drop/increase in scattered cells

[Martin Schneider]

Dear Sebastian,

for CP-grids it might happen that the centroid is located out of the 
cell such that the currently implemented

transmissibility calculation yields negative values.

Did you check if all the transmissibility calculated with the functions 
in the following header

https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/dumux/discretization/cellcentered/tpfa/computetransmissibility.hh
are positive?

I guess you will observe negative values. There are two solutions to 
overcome this

1. Try to use another cell center instead of the centroid.
2. Try to use the absolute value of the transmissibility (corresponds to 
switching the normal vector of the corresponding face)


I hope this solves your problem.

Best regards,
Martin


On 02.09.21 18:15, Alexander Sebastian Hogeweg wrote:


Hello everyone,

I am facing a problem during the simulation of an underground gas 
storage scenario. The used grid is a cornerpoint-grid with a 
heterogeneous distribution of permeability and porosity. Additionally, 
the structure contains a fault connecting a lower part of the 
formation. The used fluid model is 2pnc (h2on2o2), and the 
initialization is based on the example 2p_cornerpoint (hydrostatic 
pressure and pores fully water-saturated). At the top and bottom of 
the structure, Neumann (no-flow) boundaries are defined (Dirichlet at 
the sides with initial). In the present status, the molecular 
diffusion is deactivated, and additionally, the centroid cell center 
location is used.


After the initialization (looks all right), the pressure in some cells 
of the lower part increases while neighboring grid blocks show a lower 
pressure. Attached you can find some images showing the problem (Image 
1 and 3: t=0; Image 2 and 4: t =6000s (timestep 8) and the problem 
file.  Other (more conforming) cornerpoint-grids do not show this 
behavior.


Overall, I would like to know if somebody else observed a similar 
situation and could help me with the problem.


I appreciate any help you can provide, and please let me know if you 
need further information.


Best Regards,

Sebastian

Dumux Version: 3.4

Model: 2pnc

Grid type: Cornerpoint

Fluid system: h2on2o2.hh


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Re: [DuMux] Error building a new module (dumux-trial)

[Martin Schneider]

Dear Mahmoud Atef,

did you change something in the src/CMakeLists.txt file?
Could you please also send the files of the src folder in your module.

Regards,
Martin

On 03.03.21 04:04, Mahmoud Atef Mahmoud Mohamed Aboelseoud S277151 wrote:

Hello Dumux Team,

I hope all is well. I'm an absolute beginner and all new to dumux and 
the programming world. I am actually currently trying to use dumux for 
my master thesis in petroleum engineering. After installing dumux, I'm 
having an error when trying to build a new module called (dumux-trial) 
as I'm getting the following error:
CMake Error at 
/home/mahmoud/dumux/dune-common/cmake/modules/DuneMacros.cmake:991 
(target_link_libraries):

  The "debug" argument must be followed by a library.
Call Stack (most recent call first):
  src/CMakeLists.txt:2 (target_link_dune_default_libraries)


-- Configuring incomplete, errors occurred!
See also 
"/home/mahmoud/dumux/dumux-trial/build-cmake/CMakeFiles/CMakeOutput.log".
See also 
"/home/mahmoud/dumux/dumux-trial/build-cmake/CMakeFiles/CMakeError.log".

--- Failed to build dumux-trial ---

I cannot figure out the problem and would really appreciate your 
guidance as I'm really new to all of this. I'm attaching to this 
e-mail a word file containing the lines in the terminal starting from 
the command: ./dune-common/bin/dunecontrol --opts=dumux/cmake.opts 
--only=dumux-trial all


Thanks in advance & Best Regards

Mahmoud Atef

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Re: [DuMux] upwind mobility (2p) at boundary

[Martin Schneider]

Dear Gergely,

when using the Box method, this is not straightforward, because 
calculating fluxes for faces at the boundary
will not result in the expected value, because Dirichlet conditions are 
not weakly enforced.


Therefore, elemVolVars[scvf.insideScvIdx()] will return the volVars 
which are calculated from the boundary values.

Since in your case Sn=0, the mobility will also be 0.

Instead, you could calculate fluxes over interior scvfs such that 
scvf.outsideScvIdx() is related to your boundary DOF

but scvf.insideScvIdx() is not located at the boundary.

I hope this helps.

Best regards,
Martin


On 16.02.21 16:22, Gergely Schmidt wrote:

Dear Dumux community,

I'd like to calculate the the volumetric fluxes through a Dirichlet 
boundary. Does somebody know, how I can access the upwind mobility of 
an outflowing phase? 
elemVolVars[scvf.insideScvIdx()].mobility(phaseIdx) gives me the 
downwind value.


As an illustration, I can get the advective fluxes in a postTimeStep 
function acc. to box/darcyslaw.hh for a porousmediumflow/2p test 
problem, which looks like this:

    Noflow BC
 
    |    |
Dirichlet BC for Sn = 0 |    | Neumann BC <- gas 
inflow

    ||

--> x    Noflow BC

Left-side gas outflow must equal right inflow here, but the calculated 
volumetric flux is always 0 m/s with 
elemVolVars[scvf.insideScvIdx()].mobility(phaseIdx).


Thank you and best regards,
Gergely



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Re: [DuMux] Radial symmetry

[Martin Schneider]

Dear Dmitry,

yes, this is possible. You can find an example at
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/tree/master/examples/1protationsymmetry

Best regards,
Martin

On 02.02.21 09:21, Dmitry Pavlov wrote:

Hello,

I was wondering whether it is possible in DuMux to model a 2D porous 
flow problem in polar coordinates but without dependency on the angle, 
so it is essentially a 1D problem.


Imagine, for instance, a radial porous flow from a vertical injection 
well, and a task to calculate s(r, t), where s is the water 
saturation, r is the distance from the injection well, and t is time.


Best regards,

Dmitry


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Re: [DuMux] Dumux and Eclipse - errors which are not errors

[Martin Schneider]

Dear Markus,

to my knowledge it is not so easy to find some IDE that can resolve all 
your errors when using templates.
I am using Visual Studio Code and there it seems that the error handling 
also causes some problems  (see for example 
https://github.com/Microsoft/vscode-cpptools/issues/1014).
In the past I also used eclipse and I simply disabled some of the error 
messages, because I also haven't been able to resolve all of them.



Best regards,
Martin

On 10.09.20 12:38, Markus M. Knodel wrote:


and Kate does not have such problems to mark correct code as error (as 
Eclipse has it), Kate finds the corresponding sources for the expressions?



or is it similar to the case of Eclipse?


Kind regards

  Markus




Am 10.09.20 um 11:48 schrieb Flemisch, Bernd:


Ok, sorry, I was mislead by the "TYPETAG" mentioned in your Email.


I personally use Kate, but probably there are people using Eclipse 
out there that could comment.



Kind regards

Bernd


--
_

Bernd Flemisch
IWS, Universität Stuttgart               phone: +49 711 685 69162
Pfaffenwaldring 61              email: be...@iws.uni-stuttgart.de
D-70569 Stuttgart           url: www.iws.uni-stuttgart.de/en/lh2/ 


_

*Von:* DuMux  im Auftrag von 
Markus M. Knodel 

*Gesendet:* Donnerstag, 10. September 2020 11:37:09
*An:* dumux@listserv.uni-stuttgart.de
*Betreff:* Re: [DuMux] Dumux and Eclipse - errors which are not errors

Hi Bernd, hi Christoph

thank you very much for your kind answers.

I am already using the present git master which to my understanding 
corresponds to Dumux 3.3 git, anyhow Eclipse seems to be - to use a 
German word - "überfordert", i.e. overstrained. Maybe in future we 
might solve this problem, from time to time I will try to consider 
this question again. Which IDE do you use for DuMux?


Best wishes

    Markus



Am 10.09.20 um 09:04 schrieb Flemisch, Bernd:


Hi Markus,


in any case, I would recommend to move to DuMux 3.0 or newer. You 
can use the property system without macros by now, which might also 
help the Eclipse IDE.



Kind regards

Bernd


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_

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IWS, Universität Stuttgart               phone: +49 711 685 69162
Pfaffenwaldring 61              email: be...@iws.uni-stuttgart.de
D-70569 Stuttgart           url: www.iws.uni-stuttgart.de/en/lh2/ 


_

*Von:* DuMux  im Auftrag 
von Christoph Grüninger 

*Gesendet:* Mittwoch, 9. September 2020 22:46:57
*An:* dumux@listserv.uni-stuttgart.de
*Betreff:* Re: [DuMux] Dumux and Eclipse - errors which are not errors
Hi Markus,
probably CDT's parser is not good enough to work all his way through the
TypeTag magic DuMuX piles up. There are no additional files you could
include. With Eclipse, I see no way to achieve more.

Clangd could be useful, but as far as I know it is not supported in
Eclipse's CDT. The idea is already at least three years old:
https://www.eclipse.org/community/eclipse_newsletter/2017/april/article5.php

Bye
Christoph

--
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Re: [DuMuX] Dumux Digest, Vol 112, Issue 10

[Martin Schneider]

Dear Kai,

after you have executed
*srun -n 6 --pty /bin/bash**
*you have reserved 6 slots such that you can directly run
*mpirun -n 6 REMEDIATION_3D_cake*

Does this help?

Best regards,
Martin

On 16.06.20 12:37, Kai Wendel wrote:

Hello Kilian,

I tried this and the error message did not occur. Another strange 
thing is, that it seems to be slower with mpirun than without.


Regards
Kai

Am Di., 16. Juni 2020 um 12:00 Uhr schrieb 
<mailto:dumux-requ...@listserv.uni-stuttgart.de>>:


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Today's Topics:

   1. Re: Problem when using mpirun on a cluster (Kilian Weishaupt)


--

Message: 1
Date: Tue, 16 Jun 2020 07:49:40 +0200
From: Kilian Weishaupt mailto:kilian.weisha...@iws.uni-stuttgart.de>>
To: dumux@listserv.uni-stuttgart.de
<mailto:dumux@listserv.uni-stuttgart.de>
Subject: Re: [DuMuX] Problem when using mpirun on a cluster
Message-ID:
        <1d292a35-199a-37bd-fd9e-a23da952c...@iws.uni-stuttgart.de
<mailto:1d292a35-199a-37bd-fd9e-a23da952c...@iws.uni-stuttgart.de>>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hi Kai,

do you get the same error if you try to run the simulation locally on
your computer, using e.g. only two cores?

Regards
Kilian

Am 15.06.20 um 11:28 schrieb Kai Wendel:
> Hello,
>
> when trying to run a parallel? simulation on a cluster by using
> mpirun, I get the following error message:
> Dune reported error: Dune::IOError
>
[VectorP0VTKFunction:/temp/kaiw/DUMUX/dumux/dumux/io/vtkfunction.hh:99]:

> VectorP0VTKFunction: size mismatch between field process rank
(32160)
> and mapper (17952) ---> Abort!
>
> I tried also to actualize all versions, but the problem remains.
> I did the following commands:
>
> srun -n 6 --pty /bin/bash
> srun mpirun -n 6 ?REMEDIATION_3D_cake
>
> Greetings
> Kai Wendel
>
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-- 


Kilian Weishaupt M.Sc.
Institut f?r Wasser- und Umweltsystemmodellierung (IWS)
Lehrstuhl f?r Hydromechanik und Hydrosystemmodellierung
Universit?t Stuttgart, Pfaffenwaldring 61, 70569 Stuttgart
Email: kilian.weisha...@iws.uni-stuttgart.de
<mailto:kilian.weisha...@iws.uni-stuttgart.de>
Telefon: 0049 711 685-60461 ** fax: 0049-711-685-60430
http://www.hydrosys.uni-stuttgart.de


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University of Stuttgart
Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
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Re: [DuMuX] Cornerpoint in DuMuX: problem to install opm-grid

[Martin Schneider]

Dear Etienne,

did you install opm by using the dumux installexternal.sh script and did 
you build opm by using dunecontrol?


Best regards,
Martin

On 10.06.20 10:37, Etienne Ahusborde wrote:


Dear DuMuX users,

I would like to use a mesh in the grdecl format using the version 3.1.

So I tried to execute the test 
dumux/test/porousmediumflow/2p/implicit/cornerpoint


I loaded the modules opm-grid and opm-common but when I compiled 
everything, I had the following error during the compilation of opm


Boost version: 1.65.1
-- Found the following Boost libraries:
--   date_time
--   system
--   unit_test_framework
-- A library with BLAS API found.
-- A library with BLAS API found.
*CMake Error at /usr/share/cmake-3.10/Modules/FindLAPACK.cmake:361 
(message):*
  A required library with LAPACK API not found.  Please specify 
library location


I don't understand because I think that  I have installed all the 
package required by lapack using the command:


sudo apt install liblapack*

Using the command whereis lapack, I obtain:

lapack: /usr/lib/x86_64-linux-gnu/lapack /usr/share/man/man3/lapack.3.gz

Maybe I have to specify in the option file the exact path to find the 
lapack library. I had the same problem with blas but after the 
installation, the blas library was automatically found.


Can you help me please?

Best regards

Etienne



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Re: [DuMuX] What is dofIndex?

[Martin Schneider]

Dear Dmitry,

the *dofIndex()* is related to the corresponding *dofPosition().*
For the box method, the degrees of freedom are located at the grid vertices*
*and not at the centers of a subcontrolvolume, i.e. scv.center().*
*
Best regards,
Martin

On 25.05.20 17:15, Dmitry Pavlov wrote:


Hello,

I am writing my own local residual for porous medium flow with the Box 
method with my own addFluxDerivatives and all. I have a quick question.


When iterating over sub-control volumes (scvs), I supposed that they 
are indexed in the Jacobian by their dofIndex(). I see that there are 
as many different dofIndex-es as there are scvs in the grid.


I supposed that scv.dofIndex() has one-to-one mapping to scv.center(), 
in one assembly, anyway. But I did some debug printing and I see that 
I was wrong. In different addFluxDerivatives() calls, during one 
assembly, the same dofIndex is assigned to different scvs.


The grid, if it matters, is 2D (actually 1D) 4x1, dimensions 150x800.

Assemble: r(x^k) = dS/dt + div F - q;   M = grad r
addFluxDerivatives called for face at [9.375 400]
  scv at [9.375 200] has dofIndex = 0
  scv at [28.125 200] has dofIndex = 1
  scv at [9.375 600] has dofIndex = 5
  scv at [28.125 600] has dofIndex = 6

addFluxDerivatives called for face at [28.125 400]
  scv at [9.375 200] has dofIndex = 0
  scv at [28.125 200] has dofIndex = 1
  scv at [9.375 600] has dofIndex = 5
  scv at [28.125 600] has dofIndex = 6

addFluxDerivatives called for face at [18.75 200]
  scv at [9.375 200] has dofIndex = 0
  scv at [28.125 200] has dofIndex = 1
  scv at [9.375 600] has dofIndex = 5
  scv at [28.125 600] has dofIndex = 6

addFluxDerivatives called for face at [18.75 600]
  scv at [9.375 200] has dofIndex = 0
  scv at [28.125 200] has dofIndex = 1
  scv at [9.375 600] has dofIndex = 5
  scv at [28.125 600] has dofIndex = 6

addFluxDerivatives called for face at [46.875 400]
*  scv at [46.875 200] has dofIndex = 1*
  scv at [65.625 200] has dofIndex = 2
*  scv at [46.875 600] has dofIndex = 6*
  scv at [65.625 600] has dofIndex = 7

You see that as soon as we got to the faces in the second grid cell, 
the dofIndex-es 1 and 6 are assigned to different scvs than they were 
in the first grid cell. Only four dofIndex-es, out of ten, always map 
to the same scvs: 0, 4, 5, 9.



At this point I am wondering whether I misunderstand something about 
how the Jacobian should be built and maybe the trouble that I am 
having with the convergence may come from it.



Best regards,

Dmitry




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Re: [DuMuX] TPFA, MPFA and BOX -- grid issues

[Martin Schneider]

Dear Lorenzo,

did you check if all the permeability values are unequal to zero?
You could also use the direct solver UMFPack and see if the matrix is 
singular.


Regards,
Martin


Am 23.04.20 um 12:22 schrieb lk:

Dear community,

I'm trying to run a 2D five spot test case with 1p2c model on 
unstructured grid (like the one attached). More details are in the 
source, but everything is very standard except the random permeability 
which anyway does not create any problem.


My issue, is related to the fact that when I run with BOX scheme, the 
simulation goes as expected but with MPFA and TPFA schemes, it raises 
an error reported in the log file.


I see that running TPFA with unstructured grid may be not a good idea, 
but I guess anyway it should work and MPFA as well.



Changing grid handlers (UGGRID, ALUGRID, YASP) doesn't help, as well, 
linear solvers ...


Do I miss something?

Thank you,

Kind regards,

Lorenzo



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Re: [DuMuX] Implicit problem of 2p immiscible fluid

[Martin Schneider]

Dear Dmitry,

but then I don't see the point why you want to use a compositional model.
Couldn't you simply use the dumux/porousmediumflow/2p model?

Best regards,
Martin

On 25.03.20 18:02, Dmitry Pavlov wrote:


Dear Martin,

Thank you for a quick reply. I am currently dealing with a two-phase 
two-component Darcy flow of water and oil. Both liquids are 
incompressible and have constant viscosity. Gravity, thermal transfer 
and diffusion are not considered. Custom functions are provided for 
capillary pressure, relative permeability for water, and relative 
permeability for oil. Is more information needed?


Initially, I wrote my program basing on the example 
test/porousmediumflow/2p/sequential/test_mpfa2p, and it worked; now I 
am exploring the implicit method option.


Best regards,
Dmitry


On 25.03.2020 19:50, Martin Schneider wrote:

Dear Dmitry,

the compositional models in Dumux take into account diffusion effects 
between the different fluid phases,

which is why you can't use an immiscible fluidsystem.

Could you maybe send some more details about your equations you want 
to solve

and about the phases and components that are involved.

Best regards,
Martin

On 25.03.20 17:36, Dmitry Pavlov wrote:


Dear Martin,

Following your advice, I decided to try an implicit model of my 
problem, namely a PorousMediumFlowProblem, following the example in 
tests/porousmediumflow/2pnc/implicit/diffusion.


I managed to compile it, but am getting a runtime error upon the 
start and, honestly, have no idea what to do about it. I will 
appreciate any pointers.


For convenience, I will describe my task again. I am trying to 
simulate a two-phase two-component flow on a 2D rectangular area 
with one border being the influx and the opposite one being the 
outflow (setOutflow()). Two other two borders are walls, of course, 
with setAllNeumann().


The fluid system is realized as a TwoPImmiscible of two 
OnePLiquid-s. The first of the liquids is the wetting phase, the 
second is the nonwetting phase.


Now, the error that I am getting is

Dune reported error: Dune::InvalidStateException 
[binaryDiffusionCoefficient:.../dumux/dumux/material/fluidsystems/2pimmiscible.hh:462]: 
Binary diffusion coefficients of components are meaningless if 
immiscibility is assumed


I never any "binary diffusion coefficients" directly in my files, so 
it comes from the method.


I have doubts about the following line of my program

    values.setState(Indices::bothPhases);

which is present in dirichletAtPos(), neumannAtPos(), and 
initialAtPos() implementation. I do not really understand what does 
this setState() setting mean, so I kind of guessed.



Am I on the right path at all here? I can provide more details, of 
course, if that helps to understand what is going on.


Best regards,

Dmitry


On 23.03.2020 20:59, Martin Schneider wrote:

Dear Dmitry,

most of the Dumux users are using the fully-coupled (implicit) models.
The sequential methods have not really been further developed (at 
least the discretization schemes)

over the last few years.

However, if you want to use the MPFA-L method you have to use the 
sequential method.

The implicit models only support the MPFA-O scheme.

Best regards,
Martin

On 23.03.20 18:53, Dmitry Pavlov wrote:


Dear Martin,

I guess not, I took the first one that worked, after numerous 
failed attempts with other methods taken from random examples, 
though the said attempts might have failed because of me being a 
non-experienced user, and not because of the nature of the 
methods. Would you suggest to use an implicit method instead?


Best regards,

Dmitry

On 23.03.2020 20:48, Martin Schneider wrote:

Dear Dmitry,

if I remember correctly, the sequential MPFA-L scheme requires 
that each vertex is surrounded by 4 quadrilaterals (in 2D).
If this is not the case, the construction of interaction volumes 
fails.


Is there any reason why you are using the sequential method?

Best regards,
Martin

On 23.03.20 18:42, Dmitry Pavlov wrote:


Dear Kilian,


1.) You should be able to use more recent versions of gmsh if you go to File -> 
Export. If you name your grid *.msh

there will be an option to chose the older Version II ASCII format, readable by 
Dumux.

Thank you!

2.) Have you tried an unstructured grid with quadrilaterals? According to the 
header where the error comes from,
only quadrilaterals are supported (at least, this is what some comments in the 
code suggest). You can force gmsh to
use only quads (also unstructured ones).


I just tried an unstructured quad grid and got the same error. 
However, a gmsh-generated structured quad grid went fine, which 
means that there is no trouble with gmsh itself.


Good news: using FVPressureTwoPAdaptive instead of 
FvMpfaL2dPressureTwoP allowed me to use an gmsh-generated 
unstructured grid (both triangular and quadrilateral). I am 
wondering whether MPFA-L in DuMux "officially" requires a 
structur

Re: [DuMuX] Implicit problem of 2p immiscible fluid

[Martin Schneider]

Dear Dmitry,

the compositional models in Dumux take into account diffusion effects 
between the different fluid phases,

which is why you can't use an immiscible fluidsystem.

Could you maybe send some more details about your equations you want to 
solve

and about the phases and components that are involved.

Best regards,
Martin

On 25.03.20 17:36, Dmitry Pavlov wrote:


Dear Martin,

Following your advice, I decided to try an implicit model of my 
problem, namely a PorousMediumFlowProblem, following the example in 
tests/porousmediumflow/2pnc/implicit/diffusion.


I managed to compile it, but am getting a runtime error upon the start 
and, honestly, have no idea what to do about it. I will appreciate any 
pointers.


For convenience, I will describe my task again. I am trying to 
simulate a two-phase two-component flow on a 2D rectangular area with 
one border being the influx and the opposite one being the outflow 
(setOutflow()). Two other two borders are walls, of course, with 
setAllNeumann().


The fluid system is realized as a TwoPImmiscible of two OnePLiquid-s. 
The first of the liquids is the wetting phase, the second is the 
nonwetting phase.


Now, the error that I am getting is

Dune reported error: Dune::InvalidStateException 
[binaryDiffusionCoefficient:.../dumux/dumux/material/fluidsystems/2pimmiscible.hh:462]: 
Binary diffusion coefficients of components are meaningless if 
immiscibility is assumed


I never any "binary diffusion coefficients" directly in my files, so 
it comes from the method.


I have doubts about the following line of my program

    values.setState(Indices::bothPhases);

which is present in dirichletAtPos(), neumannAtPos(), and 
initialAtPos() implementation. I do not really understand what does 
this setState() setting mean, so I kind of guessed.



Am I on the right path at all here? I can provide more details, of 
course, if that helps to understand what is going on.


Best regards,

Dmitry


On 23.03.2020 20:59, Martin Schneider wrote:

Dear Dmitry,

most of the Dumux users are using the fully-coupled (implicit) models.
The sequential methods have not really been further developed (at 
least the discretization schemes)

over the last few years.

However, if you want to use the MPFA-L method you have to use the 
sequential method.

The implicit models only support the MPFA-O scheme.

Best regards,
Martin

On 23.03.20 18:53, Dmitry Pavlov wrote:


Dear Martin,

I guess not, I took the first one that worked, after numerous failed 
attempts with other methods taken from random examples, though the 
said attempts might have failed because of me being a 
non-experienced user, and not because of the nature of the methods. 
Would you suggest to use an implicit method instead?


Best regards,

Dmitry

On 23.03.2020 20:48, Martin Schneider wrote:

Dear Dmitry,

if I remember correctly, the sequential MPFA-L scheme requires that 
each vertex is surrounded by 4 quadrilaterals (in 2D).

If this is not the case, the construction of interaction volumes fails.

Is there any reason why you are using the sequential method?

Best regards,
Martin

On 23.03.20 18:42, Dmitry Pavlov wrote:


Dear Kilian,


1.) You should be able to use more recent versions of gmsh if you go to File -> 
Export. If you name your grid *.msh

there will be an option to chose the older Version II ASCII format, readable by 
Dumux.

Thank you!

2.) Have you tried an unstructured grid with quadrilaterals? According to the 
header where the error comes from,
only quadrilaterals are supported (at least, this is what some comments in the 
code suggest). You can force gmsh to
use only quads (also unstructured ones).


I just tried an unstructured quad grid and got the same error. 
However, a gmsh-generated structured quad grid went fine, which 
means that there is no trouble with gmsh itself.


Good news: using FVPressureTwoPAdaptive instead of 
FvMpfaL2dPressureTwoP allowed me to use an gmsh-generated 
unstructured grid (both triangular and quadrilateral). I am 
wondering whether MPFA-L in DuMux "officially" requires a 
structured quad grid.



Best regards,

Dmitry









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Re: [DuMuX] grid adaptation for 1p2c model

[Martin Schneider]

Dear Lorenzo Campoli,

if you want to use grid adaptation for the 1p2c model,
you have to implement your own *griddatatransfer* and *gridadaptindicator*
classes, so you have to implement the interfaces by yourself.

Best regards,
Martin

On 24.03.20 12:08, lk wrote:

Dear Dumux community,

I'd like to ask in the last Dumux version, is it possible to use grid 
adaptation for 1p, specifically, 1p2c model?


Moreover, if yes, is it possible for which kind of grid, both 
structured and unstructured?


I cannot find any example for 1pnc, maybe I can do something similar 
to what it is shown for 2p? But what about the following lines?


#include 
#include 

TwoPGridAdaptIndicator indicator(gridGeometry);
TwoPGridDataTransfer ...

I cannot find any interface for 1pnc models.


Thanks for your help,

Lorenzo Campoli





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Re: [DuMuX] "boundary shape not available as interaction volume shape" with gmsh-made grid

[Martin Schneider]

Dear Dmitry,

most of the Dumux users are using the fully-coupled (implicit) models.
The sequential methods have not really been further developed (at least 
the discretization schemes)

over the last few years.

However, if you want to use the MPFA-L method you have to use the 
sequential method.

The implicit models only support the MPFA-O scheme.

Best regards,
Martin

On 23.03.20 18:53, Dmitry Pavlov wrote:


Dear Martin,

I guess not, I took the first one that worked, after numerous failed 
attempts with other methods taken from random examples, though the 
said attempts might have failed because of me being a non-experienced 
user, and not because of the nature of the methods. Would you suggest 
to use an implicit method instead?


Best regards,

Dmitry

On 23.03.2020 20:48, Martin Schneider wrote:

Dear Dmitry,

if I remember correctly, the sequential MPFA-L scheme requires that 
each vertex is surrounded by 4 quadrilaterals (in 2D).

If this is not the case, the construction of interaction volumes fails.

Is there any reason why you are using the sequential method?

Best regards,
Martin

On 23.03.20 18:42, Dmitry Pavlov wrote:


Dear Kilian,


1.) You should be able to use more recent versions of gmsh if you go to File -> 
Export. If you name your grid *.msh

there will be an option to chose the older Version II ASCII format, readable by 
Dumux.

Thank you!

2.) Have you tried an unstructured grid with quadrilaterals? According to the 
header where the error comes from,
only quadrilaterals are supported (at least, this is what some comments in the 
code suggest). You can force gmsh to
use only quads (also unstructured ones).


I just tried an unstructured quad grid and got the same error. 
However, a gmsh-generated structured quad grid went fine, which 
means that there is no trouble with gmsh itself.


Good news: using FVPressureTwoPAdaptive instead of 
FvMpfaL2dPressureTwoP allowed me to use an gmsh-generated 
unstructured grid (both triangular and quadrilateral). I am 
wondering whether MPFA-L in DuMux "officially" requires a structured 
quad grid.



Best regards,

Dmitry







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Re: [DuMuX] "boundary shape not available as interaction volume shape" with gmsh-made grid

[Martin Schneider]

Dear Dmitry,

if I remember correctly, the sequential MPFA-L scheme requires that each 
vertex is surrounded by 4 quadrilaterals (in 2D).

If this is not the case, the construction of interaction volumes fails.

Is there any reason why you are using the sequential method?

Best regards,
Martin

On 23.03.20 18:42, Dmitry Pavlov wrote:


Dear Kilian,


1.) You should be able to use more recent versions of gmsh if you go to File -> 
Export. If you name your grid *.msh

there will be an option to chose the older Version II ASCII format, readable by 
Dumux.

Thank you!

2.) Have you tried an unstructured grid with quadrilaterals? According to the 
header where the error comes from,
only quadrilaterals are supported (at least, this is what some comments in the 
code suggest). You can force gmsh to
use only quads (also unstructured ones).


I just tried an unstructured quad grid and got the same error. 
However, a gmsh-generated structured quad grid went fine, which means 
that there is no trouble with gmsh itself.


Good news: using FVPressureTwoPAdaptive instead of 
FvMpfaL2dPressureTwoP allowed me to use an gmsh-generated unstructured 
grid (both triangular and quadrilateral). I am wondering whether 
MPFA-L in DuMux "officially" requires a structured quad grid.



Best regards,

Dmitry



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Re: [DuMuX] Dumux Digest, Vol 108, Issue 10

[Martin Schneider]

Dear Kenza,

okay, so as I already mentioned, your Constructor in your spatialParams 
file is wrong.


Instead of
*HeterogeneousSpatialParams(std::shared_ptr 
fvGeometry)

*you have to use*
HeterogeneousSpatialParams(const GridView &gridView)

*I also can't see the point why you want to pass the *FVElementGeometry 
*to the constructor

because it doesn't provide the functions you are using there.

Furthermore, is there any reason why you are using Dumux 2.8?
The newest version offers you more flexibility.

Best regards,
Martin*
**


*
Am 28.02.20 um 15:09 schrieb kenza bouznari:

Dear Martin,

Thank you for your reply. Please find attached the main file and I am 
using DuMux 2.8.


Best regards,

Kenza

Le ven. 28 févr. 2020 à 06:00, 
<mailto:dumux-requ...@listserv.uni-stuttgart.de>> a écrit :


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Today's Topics:

   1. Re: Error - Random field distribution (Martin Schneider)


--

    Message: 1
    Date: Fri, 28 Feb 2020 09:27:04 +0100
From: Martin Schneider mailto:martin.schnei...@iws.uni-stuttgart.de>>
To: DuMuX User Forum mailto:dumux@listserv.uni-stuttgart.de>>, kenza bouznari
        mailto:bouznari.ke...@gmail.com>>
Subject: Re: [DuMuX] Error - Random field distribution
Message-ID:
        <538738a5-89ce-2b23-9589-b6b686715...@iws.uni-stuttgart.de
<mailto:538738a5-89ce-2b23-9589-b6b686715...@iws.uni-stuttgart.de>>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Dear Kenza,

it seems that you are passing the wrong arguments to the
Constructor of
your SpatialParams File*.
*
Could you also send us your main File and let us know which Dumux
version you are using,
because it seems that you are using an old one.

In older Dumux versions you had to pass the *gridView* to the
spatialParams,
but you are passing the *std::shared_ptr
fvGeometry.*
*
*Best regards,
Martin*
***


Am 28.02.20 um 00:09 schrieb kenza bouznari:
> Hello,
>
> I'm trying to implement a random distribution of K in my domain. I
> followed the example of 1p provided in DuMux-test. But I am
having the
> following error :
>

//home/ggl/dumux/dumux/test/porousmediumflow/co2/implicit/test_boxco2.cc:79:58:

> ? required from here
> /usr/include/c++/7/ext/new_allocator.h:136:4: error: no matching
> function for call to
>

?Dumux::HeterogeneousSpatialParams::HeterogeneousSpatialParams(const

> Dune::GridView (Dune::ALUGridElementType)1, (Dune::ALUGridRefinementType)1>,
> (Dune::PartitionIteratorType)4> >&)?
> ? { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }/
>
> Do you have any suggestions on how can I fixe it.
> PS : Please find attached the problem and spatialparameters files.
> Regards,
>
> Kenza
>
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Re: [DuMuX] Error - Random field distribution

[Martin Schneider]

Dear Kenza,

it seems that you are passing the wrong arguments to the Constructor of 
your SpatialParams File*.

*
Could you also send us your main File and let us know which Dumux 
version you are using,

because it seems that you are using an old one.

In older Dumux versions you had to pass the *gridView* to the spatialParams,
but you are passing the *std::shared_ptr 
fvGeometry.*

*
*Best regards,
Martin*
***


Am 28.02.20 um 00:09 schrieb kenza bouznari:

Hello,

I'm trying to implement a random distribution of K in my domain. I 
followed the example of 1p provided in DuMux-test. But I am having the 
following error :
//home/ggl/dumux/dumux/test/porousmediumflow/co2/implicit/test_boxco2.cc:79:58: 
  required from here
/usr/include/c++/7/ext/new_allocator.h:136:4: error: no matching 
function for call to 
‘Dumux::HeterogeneousSpatialParams::HeterogeneousSpatialParams(const 
Dune::GridView(Dune::ALUGridElementType)1, (Dune::ALUGridRefinementType)1>, 
(Dune::PartitionIteratorType)4> >&)’

  { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }/

Do you have any suggestions on how can I fixe it.
PS : Please find attached the problem and spatialparameters files.
Regards,

Kenza

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Re: [DuMuX] adsorption/desorption term

[Martin Schneider]

Dear Lorenzo,

after having a quick look at your localresidual, it seems that you did 
not incorporate Dennis' suggestion

because you still use
*Scalar SolidDensity = getParam("Solid.Density");*
in the *computeStorage *function, which is quite costly.

So you should define it as
*static const Scalar SolidDensity = getParam("Solid.Density");*

Regards,
Martin

Am 19.02.20 um 14:09 schrieb lc:

Hello,


On 19.02.2020 14:07, Flemisch, Bernd wrote:
What exactly is slower: the whole simulation, one assembly step, one 
solution step...? 
Well, the simulation and each step printed on screen. At the moment, 
is not the main concern.

How does your local residual look like exactly?


Actually, I do not know how to see the residual.


I composed a minimal reproducible test (maybe some include paths 
should be changed).


Testcase: I am trying to simulate a 1p2c fluidsytem where water and 
polymer are the components of the liquid phase in an horizontal domain.


I would like to perform:

    1) water injection into polymer-saturated reservoir

    2) polymer injection into water-saturated reservoir

About this, my first doubt is about BCs and ICs. I should impose, 
Dirichlet on pressure and polymer at inlet (left) and Dirichlet on 
pressure at outlet (right) and Neuman or Outflow (kind of) on the 
component. No-flow elswhere.


The fluidsystem should be the same, right? How to switch from 1) to 2) 
Just in the assignment of the BC and IC?


Secondly, I'd like to add adsorption and viscosity depending on 
polymer saturation. I followed the implementation of Nikolai Andrianov 
(https://git.iws.uni-stuttgart.de/andrian/dumux/tree/master/dfm-ow3c) 
for the adsorption part and your previous guideline for viscosity.


Nevertheless, I think that I did some mistake, probably in the 
dimensions.



Any comment is welcomed!

Thank you,

Lorenzo Campoli



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Re: [DuMuX] BCs for five spot pattern

[Martin Schneider]

Dear Lorenzo,

"oil people" usually apply a well model, e.g. Peaceman well model.
This can be done in DuMuX by using a solution-dependent source term.

Therefore, I would recommend to first read some papers about well modeling.

You can also have a look at a previous discussion we had on this mailing 
list, based on

an old Dumux version:
https://www.mail-archive.com/dumux@listserv.uni-stuttgart.de/msg01757.html


Best regards,
Martin


Am 18.11.19 um 15:31 schrieb lc:

Dear Dumux team,

I'm studying the traditional five spot pattern, as shown in the 
attached mesh, where the central hole is the unique injection well.



I'd like to ask, which boundary conditions to apply to each well and 
if needed at walls.



As I understand, in the physical world, oil people apply a Delta P 
among the wells, so I would be tempted to apply something like a 
Dirichlet BC:


values[pwIdx] = +/- 10e5 (depending on the well) and treating the wall 
with no-flow Neuman BC.



In doing so, nothing happens in the flowfield.

Is it wrong?


Thank you,

Lorenzo



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Re: [DuMuX] liquidDiffusionCoefficient

[Martin Schneider]

Dear Deepanshu Khare,

it is only used in
*dumux/material/binarycoefficients/h2o_constant.hh*
within the function
*static Scalar liquidDiffCoeff(Scalar temperature, Scalar pressure)
*which in turn is called by**the fluidsystems

In linux you can use the command *grep command
*to find the files where it is used.

I hope this answers your question?

Kind regards,
Martin


Am 23.10.19 um 16:05 schrieb Khare, Deepanshu:

Dear Dumux community,

I was trying to understand richardsnc problem given in
test/porousmediumflow/richardsnc/implicit. There is a parameter:
liquidDiffusionCoefficient. I am not able to exactly find where this
parameter is used in the code? I found one was used in
dumux/material/binarycoefficients, but is there any other file as well
where it is used?

--
Best Regards,
Deepanshu Khare,
Institute of Bio-and Geosciences: Agrosphere (IBG-3)
Forschungszentrum Jülich GmbH,
52425 Jülich
Germany
Telephone: +49-(0)2461-618606
Email: d.kh...@fz-juelich.de





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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Re: [DuMuX] Cornerpointgrid with ccmpfa

[Martin Schneider]

Hello Gion,

no this is not possible because the MPFA scheme needs to construct 
interaction regions

which are quite hard to construct for general cp grids.

Furthermore, the opm-grid module has not all of the functionality needed 
for the construction,

e.g. calling the corners() function for an intersection returns 0.

Regards,
Martin


Am 11.07.19 um 11:03 schrieb Gion Joel Strobel:


Hello,

is it possible to run a cornerpoint-grid with the 
ccmpfa discretization? I tried to use it with the model 
2p/Cornerpoint, but it shows the error while initialization:



/Dune reported error: Dune::NotImplemented 
[computeScvfCornersOnIntersection:/home/ite/workspace/DuMux/DumuxJune2019/DUMUX/dumux/dumux/discretization/cellcentered/mpfa/helper.hh:406]: 
Mpfa scvf corners for dim = 3, dimWorld = 3, corners = 0 ---> Abort!/



Best regards,

*
*

*Gion*




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Re: [DuMuX] 2pncNIMin & Box Method

[Martin Schneider]

Dear Joan,

I think you can ignore it. It tells you that the phase state might not 
be set for

the *PrimaryVariable* in the *evalSolution* function.

However, after having a quick look at the function, it seems that the 
state is set (at least per default).


Best regards,
Martin

Am 04.07.19 um 15:05 schrieb Joan Delort Ylla:


Dear DuMuX community,

I am running DuMuX release/3.0.

*I switched* an app using the 2pncNIMin model *from CCTpfa* spatial 
disctretization method *to the Box* discretization *method*.


The application runs fine, but I always get this *warning* at compile 
time :


*Scanning dependencies of target ccs_biofilm*
[ 50%] Building CXX object
ccs_biofilm/CMakeFiles/ccs_biofilm.dir/ccs_biofilm.cc.o
In file included from
/path/to/dumuxfolder/dumux/dumux/porousmediumflow/2pnc/model.hh:98:0,
 from
/path/to/dumuxfolder/dumux/dumux/porousmediumflow/2pncmin/model.hh:94,
 from
/path/to/dumuxfolder/mymodule/app/ccs_biofilm.hh:35,
 from
/path/to/dumuxfolder/mymodule/app/ccs_biofilm.cc:54:

path/to/dumuxfolder/dumux/dumux/porousmediumflow/compositional/switchableprimaryvariables.hh:
In function ‘PrimaryVariables Dumux::evalSolution(const Element&,
const typename Element::Geometry&, const
Dumux::BoxElementSolution&,
const typename Element::Geometry::GlobalCoordinate&, bool) [with
Element = Dune::Entity<0, 3, const Dune::YaspGrid<3,
Dune::TensorProductCoordinates >, Dune::YaspEntity>;
FVElementGeometry =
Dumux::BoxFVElementGeometry > > >,
true,

Dumux::BoxDefaultGridGeometryTraits > > >,

Dumux::DefaultMapperTraits > > >,

Dune::MultipleCodimMultipleGeomTypeMapper > > >,
Dune::Impl::MCMGFailLayout>,

Dune::MultipleCodimMultipleGeomTypeMapper > > >,
Dune::Impl::MCMGFailLayout> > > >, true>; PrimaryVariables =
Dumux::SwitchablePrimaryVariables,
int>]’:

path/to/dumuxfolder/dumux/dumux/porousmediumflow/compositional/switchableprimaryvariables.hh:37:7:
*warning: *‘*((void*)& result +48)’ may be used uninitialized in
this function [*-Wmaybe-uninitialized*]
 class *SwitchablePrimaryVariables* : public PrimaryVariables
   ^~
In file included from
/path/to/dumuxfolder/mymodule/app/ccs_biofilm.hh:41:0,
 from
/path/to/dumuxfolder/mymodule/app/ccs_biofilm.cc:54:
/path/to/dumuxfolder/dumux/dumux/discretization/evalsolution.hh:193:26:
*note:* ‘*((void*)& result +48)’ was declared here
 PrimaryVariables *result(0.0)*;
  ^~
[100%] *Linking CXX executable ccs_biofilm*
[100%] Built target ccs_biofilm

Note that /path/to/dumuxfolder/mymodule/app/ccs_biofilm.cc:54 is :

#include "ccs_biofilm.hh"

And /path/to/dumuxfolder/mymodule/app/ccs_biofilm.hh:35 is :

#include 

And /path/to/dumuxfolder/mymodule/app/ccs_biofilm.hh:41:0 is :

#include 

I tried to look around in the files but this is probably too technical 
for me.


Is this warning somehow familiar to you ? Can I ignore it without any 
problem or should I try to solve that ?


Best regards,

Joan


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Re: [DuMuX] Fluidmatrix interactionlaws - partial derivatives

[Martin Schneider]

Dear Felix,

just an additional comment.
In the file
porousmediumflow/2p/incompressiblelocalresidual.hh
these functions are called and this residual is used for the calculation of
an analytical Jacobian, as Bernd already mentioned.

Best regards,
Martin

Am 17.06.19 um 15:42 schrieb Flemisch, Bernd:


Hi Felix,


the derivatives are currently only used inside the laws themselves, 
particularly for the regularization. See for example the pc function 
in regularizedvangenuchten.hh. There, the function 
VanGenuchten::dpc_dswe is called to determine the correct slope of the 
regularized curve.



If you implement your own law, you don't need the derivative functions 
since they are never called from outside.



One could use the derivative functions to calculate analytical 
derivatives for the Jacobian matrix, but this hasn't been done so far. 
Maybe a clean approach for the future would be to remove these 
functions from the interface.



Kind regards

Bernd


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*Von:* Dumux  im Auftrag von 
Felix Feldmann 

*Gesendet:* Montag, 17. Juni 2019 15:18:16
*An:* DuMuX User Forum
*Betreff:* [DuMuX] Fluidmatrix interactionlaws - partial derivatives

Dear DuMux developer,

Looking at the fluidmatrixinteractionlaws, I do find the 
implementation of several partial derivatives.


For example, in case of the BrooksCorey model:

•    The derivative of the relative permeability for the 
non-wetting phase in regard to the wetting saturation  dkrn_dswe()


•    The derivative of the relative permeability for the 
wetting phase with regard to the wetting saturation  dkrw_dswe()


•    The partial derivative of the capillary pressure w.r.t. 
the effective saturation dpc_dswe()


•    The partial derivative of the effective saturation w.r.t. 
the capillary pressure dswe_dpc()


I don’t really understand the purpose of the derivatives. In case I 
remove them, my code is still running fine and is given me the 
identical result. However, since I am currently implementing a 
modified fluidmatrixinteractionlaw, I would like to understand the 
purpose of the derivatives. Unfortunately, in this case, the DuMux 
Handbook as well as the online documentation provides quite limited 
information.


Best regards,

Felix

**

*Felix Feldmann*

Research Assistant

cid:image001.png@01D3DFD3.27E5A010

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P O Box 2533, Petroleum Institute

Abu Dhabi, UAE
M +971 565624402

felix.feldm...@ku.ac.ae 


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Re: [DuMuX] random permeability field

[Martin Schneider]

Dear Lorenzo,

there are tests where random permeability values are assigned to the 
cells. See for example

*/test/porousmediumflow/1p/implicit/isothermal/spatialparams.hh*
where gstat ist used to generate a random field which is physically 
meaningful.


Regards,
Martin

On 4/22/19 5:33 PM, lc wrote:

Dear Dumux developers,


how can I assign a random permeability value for each cell?

I asa thinking something like this but I need to loop over all cell ...

Scalar RandPerm = 0.;
    for (int i = 0; i < dim; i++) {
    RandPerm = rand() % 5 + 98;
    RandPerm *= 9.86923266716E-16;
    K_[i][i] = RandPerm;
    std::cout << K_[i][i] << std::endl;

Kind regards,

Lorenzo

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Re: [DuMuX] How to get intersections from scvf and element?

[Martin Schneider]

Hi Samuel,

maybe I am wrong but the scvf.boundaryFlag() returns the boundaryId
of AluGrid which is only properly defined if you are using a DGF grid file.
The CO2 test uses such a DGF file, which is why it works there.

Maybe having a look at the tests in test/io/gridmanager helps.

Best regards,
Martin


On 08.04.19 19:34, Samuel Scherrer wrote:

Hi Timo, Hi Bernd,

thanks a lot for your help.
I'm compiling the dune modules with the cmake.opts in the dumux
repository, which contains "-
DDUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS:BOOL=True" in "CMAKE_FLAGS", so
I assume that I don't need any additional changes.

The problem file in co2/implicit looks like what I need. However, when
using scvf.boundaryFlag() I always get the same value, 1, but when I
instead loop over all interfaces of the current element and use the
'getBoundaryDomainMarker'-function I do get the values I expect.

I'm using the gmsh mesh-format version 2.2 and ALUGrid. Do you know
what might be going wrong here?

Best regards,
Samuel



On Mon, 2019-04-08 at 18:09 +0200, Timo Koch wrote:

Hi Samuel,

as an addition to Bernd's answer, you might have to set
DUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS:BOOL=TRUE
for compiling dune-grid and the grid modules. I'm not sure if this is
still required.

Best wishes
Timo

On 08.04.19 17:37, Flemisch, Bernd wrote:

Hi Samuel,

I think that it is given by scvf.boundaryFlag(). Have a look at


https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/blob/master/test/porousmediumflow/co2/implicit/problem.hh

Kind regards
Bernd



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Von: Dumux  im Auftrag von
Samuel Scherrer 
Gesendet: Montag, 8. April 2019 17:30:26
An: dumux@listserv.uni-stuttgart.de
Betreff: [DuMuX] How to get intersections from scvf and element?
  
Hi Dumux people,


I'm currently trying to use a grid generated with gmsh and would
like
to set the boundaries based on BoundaryDomainMarkers.
I found that it's possible to access the boundary domain markers
via
the function 'getBoundaryDomainMarkers', which accepts either a
Intersection or a boundary segment index as argument.

How do I now get the intersection/boundary segment index when I
have a
given element and scvf, e.g. inside the 'neumann' function
(solution
dependent neumann boundary)?

Best regards,
Samuel

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Re: [DuMuX] Invoke spatial depending parameter in fluidmatrixinteraction

[Martin Schneider]

Dear Felix,

I think you should either write
*Scalar  salinity_test= salinity();
*or
**Scalar  salinity_test= salinity_;

**Because salinity is the name of the function defined in the 
VolumeVariables you sent me.


I hope this helps. Best regards,
Martin

On 04/02/2019 05:26 PM, Felix Feldmann wrote:


Dear Martin,

Thank you very much for your answer.

Yes, I am using DuMux 2.12.

As you suggested, I wrote a new MaterialLaw which is a function of two 
parameters: Effective water saturation and salinity.


My problem is however caused by volumevariables file, in which the 
capillary pressure is invoked (2PMINC):


*static void completeFluidState(const PrimaryVariables& priVars,*

*const Problem& problem,*

*const Element& element,*

*const FVElementGeometry& fvGeometry,*

* int scvIdx,*

*FluidState& fluidState,*

*bool isOldSol = false)*

   { ….

// calculate capillary pressure

    const MaterialLawParams &materialParams = 
problem.spatialParams().materialLawParams(element, fvGeometry, scvIdx);


    Scalar pc = MaterialLaw::pc(materialParams, 1 - Sg, 1 ); // 
(material params, saturation, salinity)


….}

The MaterialLaw is working fine as long as I define a number for the 
salinity. The corresponding output file displays the expected 
(correct) capillary pressure values.


However, as I exchange the random number by salinity, I obtain the 
below listed error.


{….

// calculate capillary pressure

    const MaterialLawParams &materialParams = 
problem.spatialParams().materialLawParams(element, fvGeometry, scvIdx);


    Scalar pc = MaterialLaw::pc(materialParams, 1 - Sg, salinity );

….}

error: cannot convert 
‘Dumux::TwoPNCMinVolumeVariables::salinity’ 
from type 
‘Dumux::TwoPNCMinVolumeVariables::Scalar 
(Dumux::TwoPNCMinVolumeVariables::)() 
const {aka double 
(Dumux::TwoPNCMinVolumeVariables::)() 
const}’ to type 
‘Dumux::TwoPNCMinVolumeVariables::Scalar 
{aka double}’


 Scalar  salinity_test= salinity;

I attached my volumevariables file for an better understanding. Do you 
have any idea how to solve this problem?


Thank you and best regards,

Felix

*From:*Martin Schneider [mailto:martin.schnei...@iws.uni-stuttgart.de]
*Sent:* Thursday, March 28, 2019 2:20 PM
*To:* DuMuX User Forum ; Felix 
Feldmann 
*Subject:* Re: [DuMuX] Invoke spatial depending parameter in 
fluidmatrixinteraction


Dear Felix,

you are using DuMuX 2.12, if I remember correctly. In DuMuX 2.12, you 
could
overwrite the *preTimeStep()* method in your problem file, see for 
example *2p/implicit/lensproblem.hh.*
In this method,  you could call some*updateLaws(args) *function from 
the spatialParams class.
This function gets all arguments *args*, e.g. time, problem, etc., 
that are needed to calculate your parameters.


I hope this helps.

Best regards,
Martin




On 03/28/2019 07:50 AM, Felix Feldmann wrote:

Dear DuMux community,

Thank you very much again for helping me on my “GravityAtPosition”
problem earlier this year. Unfortunately, I am facing a new problem.

I am trying to invoke a value inside my
fluidmatrixinteraction.file which is defined by my
problemspatialparams.file

*_Dumux provides several examples in which this is done for
(constant) Scalar values. For example:_*

const MaterialLawParams& materialLawParams(const Element &element,
const FVElementGeometry &fvGeometry, const int scvIdx) const

    {   const GlobalPosition &globalPos =
fvGeometry.subContVol[scvIdx].global;

    if (isOutletMaterial_(globalPos))

 return outletMaterialParams_;

    else

   return coreMaterialParams_;   }

*_Where the parameters can be defined as following_*

CorefloodProblemSpatialParams(const GridView &gridView)

    : ParentType(gridView)

    {

outletMaterialParams_.settest(1);

coreMaterialParams_.settest(2);

    }

This is quite clear to me - However, I am wondering if this also
possible for properties which change in time and spatial
orientation? In my very specific case, I would like to invoke a
fluid component concentration inside my fluidmatrixinteraction.

Do you have any suggestions?

Thank you and best regards,

Felix




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Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
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E-Mail: martin.schnei...@iws.uni-stuttgart.de 
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_

Re: [DuMuX] Invoke spatial depending parameter in fluidmatrixinteraction

[Martin Schneider]

Dear Felix,

you are using DuMuX 2.12, if I remember correctly. In DuMuX 2.12, you could
overwrite the *preTimeStep()* method in your problem file, see for 
example *2p/implicit/lensproblem.hh.*
In this method,  you could call some*updateLaws(args) *function from the 
spatialParams class.
This function gets all arguments *args*, e.g. time, problem, etc., that 
are needed to calculate your parameters.


I hope this helps.

Best regards,
Martin




On 03/28/2019 07:50 AM, Felix Feldmann wrote:


Dear DuMux community,

Thank you very much again for helping me on my “GravityAtPosition” 
problem earlier this year. Unfortunately, I am facing a new problem.


I am trying to invoke a value inside my fluidmatrixinteraction.file 
which is defined by my problemspatialparams.file


*_Dumux provides several examples in which this is done for (constant) 
Scalar values. For example:_*


const MaterialLawParams& materialLawParams(const Element &element, 
const FVElementGeometry &fvGeometry, const int scvIdx) const


    {   const GlobalPosition &globalPos = 
fvGeometry.subContVol[scvIdx].global;


    if (isOutletMaterial_(globalPos))

 return outletMaterialParams_;

    else

   return coreMaterialParams_; }

*_Where the parameters can be defined as following_*

CorefloodProblemSpatialParams(const GridView &gridView)

    : ParentType(gridView)

    {

   outletMaterialParams_.settest(1);

   coreMaterialParams_.settest(2);

    }

This is quite clear to me - However, I am wondering if this also 
possible for properties which change in time and spatial orientation? 
In my very specific case, I would liketo invoke a fluid component 
concentration inside my fluidmatrixinteraction.


Do you have any suggestions?

Thank you and best regards,

Felix



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Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
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Re: [DuMuX] (no subject)

[Martin Schneider]

Hello Elena,

no, that is not possible. The Richards model is a specialisation of the 
2p model.

You can have a look at the documentation
https://dumux.org/doxygen/master/a01860.html

Why do you not just use the 3p model?

Best regards,
Martin


Am 19.01.2019 um 10:43 schrieb Elena Shaporenko:

Good day all!
Can I use Richards for 3p calculations?
Best regard,
Elena

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Re: [DuMuX] gravity dependency on global postion

[Martin Schneider]

Dear Felix,

you have to implement the following function
*    const GravityVector &gravityAtPos(const GlobalPosition &pos) const
*in your own problem file.
This overwrites the function from/dumux/porousmediumflow/problem.hh

I hope this helps.

Regards,
Martin

On 12/19/2018 03:43 PM, Felix Feldmann wrote:


Dear DuMux community,

Is there any method to define gravity dependency 
<https://www.dict.cc/englisch-deutsch/dependency.html> on the global 
position? Or in other words, is it possible to define a specific 
gravity value for each node?


Best regards,

Felix




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Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
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Re: [DuMuX] on IMPES, grid adaptation and BCs

[Martin Schneider]

Hello Lorenzo,

1) -The IMPES algorithm itself is sequential, so I do not understand the 
question since it is sequential per definition.
 -You could for example use Brooks-Corey and set the entry pressure 
to zero.


2) You can find adaptive tests in
 dumux/test/porousmediumflow/2p/sequential

3) What about asking google about "outflow and Neumann" boundary conditions?
 I am sure you will find a lot of explanations about it.

Regards,
Martin

On 12/03/2018 12:37 PM, lc wrote:

Hello,

I have the following questions:

1) Is it possible to run IMPES algorithm in sequential (not implicit) 
mode without considering capillarity forces (pressure)?


2) Is it possible to do some sort of grid adaptation, for example 
locally refine the (unstructrured) mesh where the water saturation 
front becomes steeper? If yes, how, is there any example?


3) What actually the Outflow BC does? What is the difference with 
Neumann?



Thank you very much!

Kind regards,

Lorenzo

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Department of Hydromechanics and Modelling of Hydrosystems
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D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
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Re: [DuMuX] dumux: change constitutive relations

[Martin Schneider]

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Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
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Re: [DuMuX] Dumux 2.12.0, dune 2.6.0 and opm 2017.10 compatibility

[Martin Schneider]

Dear Felix,

probably the *array *should be replaced by***std::array.
*However, I would recommend you to use the opm release 2017.04 and ert 
by installing it using the

installexternal.sh script from the dumux 2.12 release:
*https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/blob/releases/2.12/bin/installexternal.sh*

You should also think about using the Dumux master branch (which will be 
released soon)

which works with the opm 2018.04 release.

I hope this helps. Best regards,
Martin

**On 10/23/2018 12:53 PM, Felix Feldmann wrote:


Dear All,

I am currently running some 2D simulations using Dumux 2.12.0 and Dune 
2.6.0. However, I would like to additionally compute cornerpoint 
(“petrel grids”) problems.


According to 
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/blob/master/CHANGELOG.md, 
this should be possible by combining Dumux 2.12.0, Dune 2.6.0 as well 
as OPM 2017.10.


Dumux 2.12.0 and Dune 2.6.0 are running fine, while the OPM 
installation is causing problems: Considering the OPM hierarchy, I am 
able to successfully install the first three OPM modules:


1)Libecl

2)Opm-common

3)Opm-material

However, as I try to add opm-grid, I do receive an error message (the 
shortened message is listed below). Do you think, that Dumux 2.12.0, 
Dune 2.6.0 and Opm 2017.10 are compatible? Did you experience similar 
problems during the installation of Dumux, Dune and Opm-grid (former 
cornerpoint)?


Best regards,
Felix

*Felix Feldmann*

Research Assistant

cid:image001.png@01D3DFD3.27E5A010

SAN Campus

P O Box 2533, Petroleum Institute

Abu Dhabi, UAE
M +971 565624402

felix.feldm...@ku.ac.ae <mailto:felix.feldm...@ku.ac.ae>

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/home/felix/workspace/dune/opm-grid-release-2017.10/dune/grid/cpgrid/CpGridData.hpp:347:29: 
error: template argument 1 is invalid


 std::vector< array >   cell_to_point_;

 ^

/home/felix/workspace/dune/opm-grid-release-2017.10/dune/grid/cpgrid/CpGridData.hpp:347:29: 
error: template argument 2 is invalid


/home/felix/workspace/dune/opm-grid-release-2017.10/dune/grid/cpgrid/CpGridData.hpp:347:31: 
error: expected unqualified-id before ‘>’ token


 std::vector< array >   cell_to_point_;



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Department of Hydromechanics and Modelling of Hydrosystems
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Re: [DuMuX] dgf error in 1D combustionproblem

[Martin Schneider]

Dear Max,

I had a look at the test case and I got the same message.
The problem is that the grids folder is missing in your build-cmake 
directory

where you run your tests.

This can be easily fixed by putting the following command into your 
*CMakeLists.txt* file (in the directory *porousmediumflow/mpnc/implicit/*):

*dune_symlink_to_source_files(FILES grids)*

After you have added this command you have to type *make* in your 
build-cmake folder

such that a link to your grid files is added.

Thanks for reporting this issue. It will be fixed soon.

I hope this helps. Best regards,
Martin

On 10/19/2018 04:36 PM, Maximilian Johannes Lueftner wrote:



Dear DuMuX experts,

i try to calculate the simulation from the test folder 
„porousmediumflow/mpnc/implicit/test_boxmpncthermalnonequil.cc" and 
get the following error message:



DGF exception thrown (DGFException 
[BasicBlock:/home/max/dumux3/dumux/dune-grid/dune/grid/io/file/dgfparser/blocks/basic.cc:28]: 
file not found in BasicBlock::BasicBlock). Most likely, the DGF file 
name is wrong or the DGF file is corrupted, e.g. missing hash at end 
of file or wrong number (dimensions) of entries. ---> Abort!


Could you please help me to solve this problem? I tried it myself 
several times but was not successful until now.


Thank you in advance and best regards,

Max


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Re: [DuMuX] dumux: about capillarity

[Martin Schneider]

Dear Lorenzo,

for the water oil system that is stated in the handbook 2.12, you have 
the relationship
that p_o = p_c + p_w. Therefore, inserting this relationship into 
equation (3.2) you end up
in the same equations you sent. Therefore, you can easily transform the 
equations into your formulation.


Please not that in Dumux capillary pressure is included by default.

Regards,
Martin

On 10/17/2018 03:43 PM, lc wrote:

Dear developers and users,

looking at equations 3.1 and 3.2 of the handbook 2.12 it seems that no 
capillarity effect is taken into account.


Indeed, I would expect something like the equations reported in the 
attachment. Nevertheless,


values for capillarity pressure are loaded in the example. So, are 
they taken into account? Which equations are solved?


If they are not taken into account, what should modify to include them?


Kind regards,

Lorenzo




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Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
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Re: [DuMuX] Parallel / Grid (cake piece)

[Martin Schneider]

Hi Anwar,

having a look at your files, it seems that you do not call
*gridManager.init();
*in your *test_1pfv.cc *file*.

*If this does not help, please also run your test case without using mpirun,
i.e. simply execute ./test_1pbox ./test_1pfv.input

You should also have a look at the grid that is generated for your 
parameters,

for example by using the test "*test_gridmanager_cake" *
*(in the folder dumux/test/io/gridmanager) *

Furthermore, you could also try to use UGGrid instead of ALUGrid.
***
*Regards,
Martin*
*


On 10/08/2018 02:09 PM, Anwar Al Assadi wrote:

Hi Martin, Hi all,
thanks for your answer, but i tried now both schems, and i'm still 
getting the same error message.

Best,
Anwar
**

mpirun -np 1  ./test_1pbox ./test_1pfv.input

###         #   #        # #

#  #  #  #  ## ##  #  #   #

#  #  #  #  # # #  #  #  # #

###    ##   #   #   ##

Dune for Multi-{ Phase,

                 Component,

                 Scale,

                 Physics,

                 ...} flow and transport in porous media

[eu-login-10-ng:03667] *** Process received signal ***

[eu-login-10-ng:03667] Signal: Segmentation fault (11)

[eu-login-10-ng:03667] Signal code: Address not mapped (1)

[eu-login-10-ng:03667] Failing at address: 0x80

[eu-login-10-ng:03667] [ 0] 
/lib64/libpthread.so.0(+0xf6d0)[0x2b2e51a706d0]


[eu-login-10-ng:03667] [ 1] 
./test_1pbox(_ZNK4Dune9ALU3dGridILi3ELi3ELNS_20ALU3dGridElementTypeE7ENS_14ALUGridMPICommEE12leafIndexSetEv+0x0)[0x678aa0]


[eu-login-10-ng:03667] [ 2] 
./test_1pbox(_ZN4Dune35MultipleCodimMultipleGeomTypeMapperINS_8GridViewINS_23ALU3dLeafGridViewTraitsIKNS_7ALUGridILi3ELi3ELNS_18ALUGridElementTypeE1ELNS_21ALUGridRefinementTypeE1ENS_14ALUGridMPICommEEELNS_21PartitionIteratorTypeE4ENS_4Impl14MCMGFailLayoutEEC1ERKSB_RKSt8functionIFmNS_12GeometryTypeEiEE+0x25)[0x67aa35]


[eu-login-10-ng:03667] [ 3] 
./test_1pbox(_ZN5Dumux18BaseFVGridGeometryINS_17BoxFVGridGeometryIdN4Dune8GridViewINS2_23ALU3dLeafGridViewTraitsIKNS2_7ALUGridILi3ELi3ELNS2_18ALUGridElementTypeE1ELNS2_21ALUGridRefinementTypeE1ENS2_14ALUGridMPICommEEELNS2_21PartitionIteratorTypeE4ELb0ENS_28BoxDefaultGridGeometryTraitsISD_NS_19DefaultMapperTraitsISD_NS2_35MultipleCodimMultipleGeomTypeMapperISD_NS2_4Impl14MCMGFailLayoutEEESJ_EESD_SL_EC1ERKSD_+0x48)[0x67ece8]


[eu-login-10-ng:03667] [ 4] ./test_1pbox(main+0x19f)[0x5d175f]

[eu-login-10-ng:03667] [ 5] 
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b2e51c9f445]


[eu-login-10-ng:03667] [ 6] ./test_1pbox[0x5d5bb6]

[eu-login-10-ng:03667] *** End of error message ***

---

Primary job  terminated normally, but 1 process returned

a non-zero exit code. Per user-direction, the job has been aborted.

---

--

mpirun noticed that process rank 0 with PID 0 on node eu-login-10-ng 
exited on signal 11 (Segmentation fault).**


*Gesendet:* Freitag, 05. Oktober 2018 um 13:32 Uhr
*Von:* "Martin Schneider" 
*An:* "DuMuX User Forum" , "Anwar Al 
Assadi" 

*Betreff:* Re: [DuMuX] Parallel / Grid (cake piece)
Dear Anwar,

do you get the same problem for the box scheme and for the 
cell-centered (TPFA) scheme,

or did you only try it with the Box scheme?

Regards,
Martin

On 10/05/2018 11:00 AM, Anwar Al Assadi wrote:

Hello everyone,
I'm trying to run my code on a cluster, but I got a segmentation
fault. I already ran the test_1pcctpfa problem parallel, but now
after changing the grid to 3 d (cake piece, with the cake creator)
something seems wrong. Did someone already have this problem? or
do you have a hint for me? I attached my code and the error message.
Thanks a lot!
Best,
Anwar
DuMux : dumux-course-2018

"""""""""
mpirun -np 1  ./test_1pcctpfa ./test_1pfv.input


You idiot! You signed the order to destroy Earth!

 - Douglas Adams, HGttG


[eu-login-13-ng:15924] *** Process received signal ***

[eu-login-13-ng:15924] Signal: Segmentation fault (11)

[eu-login-13-ng:15924] Signal code: Address not mapped (1)

[eu-login-13-ng:15924] Failing at address: 0x80

[eu-login-13-ng:15924] [ 0]
/lib64/libpthread.so.0(+0xf6d0)[0x2b69fa3006d0]

[eu-login-13-ng:15924] [ 1]

./test_1pcctpfa(_ZNK4Dune9ALU3dGridILi3ELi3ELNS_20ALU3dGridElementTypeE7ENS_14ALUGridMPICommEE12leafIndexSetEv+0x0)[0x609c90]

[eu-login-13-ng:15924] [ 2]

./test_1pcctpfa(_ZN4Dune35MultipleCodimMultipleGeomTypeMapperINS_8GridViewINS_23ALU3dLeafGridViewTraitsIKNS_7ALUGridILi3ELi3ELNS_18ALUGridElementTypeE1ELNS_21ALUGridRefinementTypeE1ENS_14ALUGridMPICommEEELNS_21PartitionIteratorTypeE4ENS_4Impl14MCMGFailLayoutEEC1ERKSB_RKSt8functio

Re: [DuMuX] Parallel / Grid (cake piece)

[Martin Schneider]

Dear Anwar,

do you get the same problem for the box scheme and for the cell-centered 
(TPFA) scheme,

or did you only try it with the Box scheme?

Regards,
Martin

On 10/05/2018 11:00 AM, Anwar Al Assadi wrote:

Hello everyone,
I'm trying to run my code on a cluster, but I got a segmentation 
fault. I already ran the test_1pcctpfa problem parallel, but now after 
changing the grid to 3 d (cake piece, with the cake creator) something 
seems wrong. Did someone already have this problem? or do you have a 
hint for me? I attached my code and the error message.

Thanks a lot!
Best,
Anwar
DuMux : dumux-course-2018

"""""""""
mpirun -np 1  ./test_1pcctpfa ./test_1pfv.input


You idiot! You signed the order to destroy Earth!

 - Douglas Adams, HGttG


[eu-login-13-ng:15924] *** Process received signal ***

[eu-login-13-ng:15924] Signal: Segmentation fault (11)

[eu-login-13-ng:15924] Signal code: Address not mapped (1)

[eu-login-13-ng:15924] Failing at address: 0x80

[eu-login-13-ng:15924] [ 0] 
/lib64/libpthread.so.0(+0xf6d0)[0x2b69fa3006d0]


[eu-login-13-ng:15924] [ 1] 
./test_1pcctpfa(_ZNK4Dune9ALU3dGridILi3ELi3ELNS_20ALU3dGridElementTypeE7ENS_14ALUGridMPICommEE12leafIndexSetEv+0x0)[0x609c90]


[eu-login-13-ng:15924] [ 2] 
./test_1pcctpfa(_ZN4Dune35MultipleCodimMultipleGeomTypeMapperINS_8GridViewINS_23ALU3dLeafGridViewTraitsIKNS_7ALUGridILi3ELi3ELNS_18ALUGridElementTypeE1ELNS_21ALUGridRefinementTypeE1ENS_14ALUGridMPICommEEELNS_21PartitionIteratorTypeE4ENS_4Impl14MCMGFailLayoutEEC1ERKSB_RKSt8functionIFmNS_12GeometryTypeEiEE+0x25)[0x60bc25]


[eu-login-13-ng:15924] [ 3] 
./test_1pcctpfa(_ZN5Dumux20CCTpfaFVGridGeometryIN4Dune8GridViewINS1_23ALU3dLeafGridViewTraitsIKNS1_7ALUGridILi3ELi3ELNS1_18ALUGridElementTypeE1ELNS1_21ALUGridRefinementTypeE1ENS1_14ALUGridMPICommEEELNS1_21PartitionIteratorTypeE4ELb0ENS_31CCTpfaDefaultGridGeometryTraitsISC_NS_19DefaultMapperTraitsISC_NS1_35MultipleCodimMultipleGeomTypeMapperISC_NS1_4Impl14MCMGFailLayoutEEESI_EC2ERKSC_+0x54)[0x61b8f4]


[eu-login-13-ng:15924] [ 4] ./test_1pcctpfa(main+0x19b)[0x56f48b]

[eu-login-13-ng:15924] [ 5] 
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b69fa52f445]


[eu-login-13-ng:15924] [ 6] ./test_1pcctpfa[0x573ae6]

[eu-login-13-ng:15924] *** End of error message ***

---

Primary job  terminated normally, but 1 process returned

a non-zero exit code. Per user-direction, the job has been aborted.

---

--

mpirun noticed that process rank 0 with PID 0 on node eu-login-13-ng 
exited on signal 11 (Segmentation fault)."""""""""""""""""""""""



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University of Stuttgart
Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
E-Mail: martin.schnei...@iws.uni-stuttgart.de

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Re: [DuMuX] Newton solver did not converge error

[Martin Schneider]

Hi Ranjeet,

I agree with Dennis, for an incompressible test case you can't use 
Neumann boundary conditions

everywhere (at least for solution-independent source/sink terms).

Instead of using a Dirichlet boundary condition you could also
implement some well model as a solution dependent source term. This 
allows you

to set Neumann boundary conditions on the whole domain boundary.

Best regards,
Martin

On 09/18/2018 09:04 AM, Dennis Gläser wrote:


Hi Ranjeet,

to me the problem seems to be that you do not specify Dirichlet 
boundary conditions anywhere. You must have a Dirichlet boundary 
somewhere for the system to be defined properly and that is why it 
works when you use the original boundaryTypes() function.


Best wishes,
Dennis


On 18.09.2018 07:58, Ranjeet Singh wrote:
Hi, I am implementing the 2P PorousmediumFlowProblem with cornerpoint 
spe9 grid. Boundary conditions are no flow along all boundary and 
injection source at one corner (0th element) and production source at 
another opposite corner. Boundary and Initial condition are set as 
follows:


//problem.hh
    BoundaryTypes boundaryTypesAtPos(const GlobalPosition& globalPos) 
const

    {
    BoundaryTypes bcTypes;
    bcTypes.setAllNeumann();
    return bcTypes;
    }

    NumEqVector source(const Element &element,
   const FVElementGeometry& fvGeometry,
   const ElementVolumeVariables& elemVolVars,
   const SubControlVolume &scv) const
    {
    NumEqVector values(0.0);

    int eIdx = 
this->fvGridGeometry().gridView().indexSet().index(element);

    if (eIdx == injectionElement_)
    values[FluidSystem::phase1Idx] = 
injectionRate_/element.geometry().volume();


    if (eIdx == productionElement_)
    values[FluidSystem::phase0Idx] = 
-productionRate_/element.geometry().volume();


    return values;
    }

    PrimaryVariables initialAtPos(const GlobalPosition &globalPos) const
    {
    PrimaryVariables values;

    // hydrostatic pressure
    Scalar densityW = 1000;
    values[Indices::pressureIdx] = 5e5 + 
densityW*(this->gravity()*globalPos);  // inital pw

    values[Indices::saturationIdx] = 0.0; // initial sn

    return values;
    }
I guess I am doing something wrong with boundary condition. In the 
cornerpoint test problem, the boundary condition is implemented as,

    BoundaryTypes boundaryTypes(const Element &element,
    const SubControlVolumeFace &scvf) const
    {
    BoundaryTypes bcTypes;
    // set no-flux on top and bottom, hydrostatic on the rest
    // use the scvf normal to decide
    const auto& normal = scvf.unitOuterNormal();
    using std::abs;
    if (abs(normal[dimWorld-1]) > 0.5)
    bcTypes.setAllNeumann();
    else
    bcTypes.setAllDirichlet();

    return bcTypes;
    }
when I implement the same BC, then solution gets converged. Could you 
please explain what I am doing wrong and also, in 
abs(normal[dimwold-1])> 0.5

, why it is compared with 0.5, not 0?

Thank you!

Regards,
Ranjeet


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University of Stuttgart
Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
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Re: [DuMuX] Formulation used in darcyslaw.hh

[Martin Schneider]

Hi Nikolai,

maybe the easiest way is to also implement an priVarFormulation() function*
*in your TwoP volVars, as it is for example done for the 2p2c volVars.

Then you can access the formulation using 
ElementVolumeVariables::VolumeVariables::priVarFormulation()

in your darcyslaw.

I guess this is related to the previous discussion where you mentioned 
that you had to change

darcyslaw as follows:

*    if (!scvf.boundary()) {**

**    // Inside the domain calculate the phase flux using 
phase pressures (with pn = pw + pc)**

**        pInside = insideVolVars.pressure(phaseIdx);**
**        pOutside = outsideVolVars.pressure(phaseIdx);**
**    }**
**    else {**
**        // Do not include the contributions from capillary 
forces for boundary fluxes**
//static_assert( (VolumeVariables::priVarFormulation() == 
TwoPFormulation::p0s1), "darcyslaw.hh: BC implemented for p0s1 
formulation only!");       // uncommenting this yields an error**

**    // WARNING: implemented for p1s0 formulation only!**
**        pInside = insideVolVars.pressure(1);**
**        pOutside = outsideVolVars.pressure(1);**
**    }*

Which means that you do not want to have a capillary flux over your 
domain boundary.
I think the easier alternative would be to use a solution-dependent 
Neumann condition in your problem


*    NumEqVector neumann(const Element& element,**
**    const FVElementGeometry& fvGeometry,**
**    const ElementVolumeVariables& elemVolVars,**
**    const SubControlVolumeFace& scvf) const

*where you can get the nonwetting phase pressure of the boundary cell 
via the *elemVolVars*,
and the fluxes can then be calculated in this function similar to 
darcyslaw but now you can specify

that pc=0 for your boundary fluxes (i.e. pw = pn).

Kind regards,
Martin

On 08/24/2018 09:34 AM, Nikolai Andrianov wrote:


Hi Martin,


I would like to know from within 
dumux/discretization/cellcentered/tpfa/darcyslaw.hh if 
TwoPFormulation::p0s1 or TwoPFormulation::p1s0 is used.



Thanks,

Nikolai

--------
*From:* Martin Schneider 
*Sent:* Thursday, August 23, 2018 4:26:20 PM
*To:* DuMuX User Forum; Nikolai Andrianov
*Subject:* Re: [DuMuX] Formulation used in darcyslaw.hh
Dear Nikolai,

could you please specify what you mean with "formulation".
Do you mean which implementation of CCTpfaDarcysLaw?

Thanks,
Martin

On 08/23/2018 03:39 PM, Nikolai Andrianov wrote:


Dear DuMuX experts,


Please advise how can I identify, which formulation is used in 
dumux/discretization/cellcentered/tpfa/darcyslaw.hh.



Thanks,

Nikolai



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Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
E-Mail:martin.schnei...@iws.uni-stuttgart.de



--
M.Sc. Martin Schneider
University of Stuttgart
Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
E-Mail: martin.schnei...@iws.uni-stuttgart.de

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Re: [DuMuX] Formulation used in darcyslaw.hh

[Martin Schneider]

Dear Nikolai,

could you please specify what you mean with "formulation".
Do you mean which implementation of CCTpfaDarcysLaw?

Thanks,
Martin

On 08/23/2018 03:39 PM, Nikolai Andrianov wrote:


Dear DuMuX experts,


Please advise how can I identify, which formulation is used in 
dumux/discretization/cellcentered/tpfa/darcyslaw.hh.



Thanks,

Nikolai



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University of Stuttgart
Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
E-Mail: martin.schnei...@iws.uni-stuttgart.de

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Re: [DuMuX] How to implement Peaceman well model in DuMuX?

[Martin Schneider]

Dear Birger,

thanks for this comment, you are right.

You can directly use *scv.volume()* to get the volume.

Regards,
Martin


On 08/22/2018 10:38 AM, Birger Hagemann wrote:


Dear Martin,

The unit for the well index is m³. Consequently the unit for your 
expression for values[contiWEEqIdx] is kg/s. However, the source term 
has the unit kg/m³/s. I think you have to divide by the cell volume:


*values[contiWEqIdx] = densityW/viscosityW * WI *(pbh - 
pw)/fvGeometry.subContVol[scvIdx].volume;*


**

Am I wrong?

Regards Birger

*Von:*Dumux [mailto:dumux-boun...@listserv.uni-stuttgart.de] *Im 
Auftrag von *Martin Schneider

*Gesendet:* Mittwoch, 22. August 2018 10:03
*An:* DuMuX User Forum ; Ranjeet 
Singh 

*Betreff:* Re: [DuMuX] How to implement Peaceman well model in DuMuX?

Dear Ranjeet,

you can implement the Peaceman well model as a solution-dependent source,
using the following function in your problem file

*NumEqVector source(const Element &element,
           const FVElementGeometry& 
fvGeometry,
                       const ElementVolumeVariables& 
elemVolVars,

                       const SubControlVolume &scv) const*

(see for example porousmediumflow/2pnc/implicit/fuelcellproblem.hh)

With the *elemVolVars *you have access to the pressure, density, etc.:
*const auto& volVars = elemVolVars[scv];
Scalar pw = volVars.pressure(wPhaseIdx);
Scalar densityW = volVars.density(wPhaseIdx);
Scalar viscosityW = volVars.viscosity(wPhaseIdx);
*
Such that the source term looks as follows (if you inject water and 
neglect gravity)

*NumEqVector values(0.0);*
*values[contiWEqIdx] = densityW/viscosityW * WI *(pbh - pw);

*where *WI *is the well index (see the Peaceman well model); *pbh* the 
bottom hole pressure, etc.

If gravity is included you have to use the phase potentials.

Kind regards,
Martin*

*
On 08/09/2018 04:03 AM, Ranjeet Singh wrote:

Hi,

  I want use Peaceman well model in DuMuX?.  Could you please some
information (or any example if already implemented) so that I can
implement the well model?

Thank you!

Regards,

Ranjeet




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--
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University of Stuttgart
Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
E-Mail:martin.schnei...@iws.uni-stuttgart.de 
<mailto:martin.schnei...@iws.uni-stuttgart.de>



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--
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University of Stuttgart
Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
E-Mail: martin.schnei...@iws.uni-stuttgart.de

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Re: [DuMuX] How to implement Peaceman well model in DuMuX?

[Martin Schneider]

Dear Ranjeet,

you can implement the Peaceman well model as a solution-dependent source,
using the following function in your problem file

*NumEqVector source(const Element &element,**
**           const FVElementGeometry& 
fvGeometry,**
**                       const ElementVolumeVariables& 
elemVolVars,**

**                       const SubControlVolume &scv) const*

(see for example porousmediumflow/2pnc/implicit/fuelcellproblem.hh)

With the *elemVolVars *you have access to the pressure, density, etc.:
*const auto& volVars = elemVolVars[scv];
Scalar pw = volVars.pressure(wPhaseIdx);
Scalar densityW = volVars.density(wPhaseIdx);
Scalar viscosityW = volVars.viscosity(wPhaseIdx);
*
Such that the source term looks as follows (if you inject water and 
neglect gravity)

*NumEqVector values(0.0);*
*values[contiWEqIdx] = densityW/viscosityW * WI *(pbh - pw);

*where *WI *is the well index (see the Peaceman well model); *pbh* the 
bottom hole pressure, etc.

If gravity is included you have to use the phase potentials.

Kind regards,
Martin*

*
On 08/09/2018 04:03 AM, Ranjeet Singh wrote:

Hi,
  I want use Peaceman well model in DuMuX?.  Could you please some 
information (or any example if already implemented) so that I can 
implement the well model?



Thank you!


Regards,
Ranjeet




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Re: [DuMuX] Separate folders for debug builds

[Martin Schneider]

Dear Nikolai,

you can specify the name by using */--builddir=build-cmake-debug /*when 
you run dunecontrol:


/*./dune-common/bin/dunecontrol --opts=./dumux/debug.opts 
--builddir=*//**/build-cmake-debug/* all*/


Further information can be found by executing

/*./dune-common/bin/dunecontrol --help*/

Regards,
Martin

Am 26.07.2018 um 21:16 schrieb Nikolai Andrianov:


Dear DuMuX experts,

Please advise how can I set up separate folders for debug builds 
(i.e., get something like ./dune-common/build-cmake-debug etc), 
depending on the settings in cmake.opts (e.g. as a function of 
-DCMAKE_BUILD_TYPE=Debug).


Many thanks,

Nikolai



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Re: [DuMuX] Newton scheme in Dumux

[Martin Schneider]

Dear Georg,

what do you mean with "an exact Newton-scheme formulated and then 
discretized".
The PDEs that you want to solve are discretized using the residual 
formulations, where
the discrete solution is obtained by solving the nonlinear system of 
equations R(x) = 0,
and x is the unknown discrete solution that you want to solve. So 
Newton's method is applied

to your discretized equations.

To solve these nonlinear systems of equations, the Jacobian matrix of R
is usually calculated numerically (i.e. it is not exact).

Regards,
Martin


On 08/01/2018 10:24 AM, georg.fut...@dlr.de wrote:


Hello Dumuxers,

I have a question concerning the Newton-scheme in Dumux:

Is discretization done first and the Newton-scheme is applied 
subsequently *OR*  is an exact Newton-scheme formulated and then 
discretized?


Best regards

Georg Futter

——

*German Aerospace Center *(DLR)

Institute of Engineering Thermodynamics | Computational 
Electrochemistry | Pfaffenwaldring 38-40 | 70569 Stuttgart


Dipl.-Ing. *Georg Futter* | Ph.D. student

Telefon 0711/6862-8135 | georg.fut...@dlr.de <mailto:georg.fut...@dlr.de>

www.DLR.de <http://www.dlr.de/>



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Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
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Fax: (+49) 0711/ 685-60430
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Re: [DuMuX] Debugging DuMuX using gdb

[Martin Schneider]

Dear Nikolai,

which opts-file did you use for dunecontrol?
Did you also change the *CMAKE_BUILD_TYPE *to *Debug* for the fracture 
test?


It might help to delete all build-folders, including those of your dune 
modules, and rerun dunecontrol

with *debug.opts.*

Regards,
Martin

On 07/27/2018 06:44 PM, Nikolai Andrianov wrote:


Dear DuMuX experts,

I am trying to debug DuMuX using gdb, but for some reason I cannot get 
into the main() of 
dumux-course/exercises/exercise-fractures/exercise_fractures.cc. The 
debugger starts at 
./dune-alugrid/dune/alugrid/impl/serial/gitter_geo.cc, exits to a 
library, and then executes the code of the exercise without stepping 
into it.


Debugging other examples (e.g. exercise-basic and 
exercise-fluidsystem) gets into corresponding main()’s without problem.


Is there still a way to get into main() of exercise_fractures.cc using 
gdb?


 Dear Nikolai,

which ops-file did you use when executing dunecontrol?
Did you also change the *CMAKE_BUILD_TYPE *to Debug

Many thanks,

Nikolai



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Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
Tel: (+49) 0711/ 685-69159
Fax: (+49) 0711/ 685-60430
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Re: [DuMuX] Separate folders for debug builds

[Martin Schneider]

Dear Nikolai,

you can specify the name by using */--builddir=build-cmake-debug /*when 
you run dunecontrol:


/*./dune-common/bin/dunecontrol --opts=./dumux/debug.opts 
--builddir=*//**/build-cmake-debug/* all*/


Further information can be found by executing

/*./dune-common/bin/dunecontrol --help*/

Regards,
Martin

On 07/26/2018 09:16 PM, Nikolai Andrianov wrote:


Dear DuMuX experts,

Please advise how can I set up separate folders for debug builds 
(i.e., get something like ./dune-common/build-cmake-debug etc), 
depending on the settings in cmake.opts (e.g. as a function of 
-DCMAKE_BUILD_TYPE=Debug).


Many thanks,

Nikolai



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Re: [DuMuX] Memory Problem with AMG in parallel computation in version 2.10

[Martin Schneider]

Hi Mustapha,

did you try to also change the CoarsenCriterion? You could try to 
replace "Dune::Amg::SymmetricCriterion" with
"Dune::Amg::UnSymmetricCriterion".  There might be some reason why a 
symmetric preconditioner SSOR

is used for for the case of a symmetric CoarsenCriterion.

Regards,
Martin

On 02/08/2017 09:56 AM, Mustapha El Ossmani wrote:


Hi Christoph,

Thank you for your reply. Here are some precisions

* Do see this problem only in parallel or also in sequential code? 
Only with AMG or also with GMRES and ILU?


We have this problem in both case (sequential and parrallel code) 
*only*when we compile with *MPI* and only with *AMG* solver and 
Dune::*SeqILU0* as Preconditioner. Contrariwise this problem does not 
occur with SSOR as Preconditionner.


* Analyze the problem with Valgrind or AddressSanitizer. Having it 
reduced might be beneficial.


We have run a simple test (co2 model in DUMUX)in some iterations with 
valgrind and we obtained the messages that can be found in the 
enclosed filewhich confirms that there is a loss of memory.


Have you ever met this issue ?

Best regards

M. El Ossmani


Le 07/02/2017 à 06:22, Christoph Grüninger a écrit :

Hi Mustapha,
I have never seen such problems but I am no solver expert. What you 
can do:


* Do see this problem only in parallel or also in sequential code? 
Only with AMG or also with GMRES and ILU?
* Reduce the problem as much as you can. The best would be a minimal 
piece of software that only depends on Dune-istl that reads in your 
matrix and repeatedly solves your linear system with the seen 
undesired memory consumption. Not sure whether this is possible and 
whether such minimal setup would still have the problem at all. When 
you reduce your current problem, the problem might vanish, too. This 
can help to find the cause of your issue.
* Analyze the problem with Valgrind or AddressSanitizer. Having it 
reduced might be beneficial.
* Turning on all compiler warnings and carefully evaluating them 
might help. But there are false positives but it can help.
* Maybe its worth repeating your question at the Dune mailing list 
d...@dune-project.org  as there are 
more Users and developers of istl.


Bye,
Christoph

Am 03.02.2017 um 11:14 schrieb Mustapha El Ossmani 
mailto:m.elossm...@ensam.umi.ac.ma>>:




Dear DuMu^X developers,

We are performing parallel computation with AMG solver. Due to 
problems of convergence in the newton's method,  in amgproperties.hh 
we  set  the Preconditioner from Dune::SeqSSOR to Dune::SeqILU0 :


typedef 
Dune::BlockPreconditionerVType> > Smoother;
 // typedef 
Dune::BlockPreconditionerVType> > Smoother;


It seems that there is some problems of memory loss with ILU0 
preconditionner. Indeed we can see that the memory of computation is 
continually


increasing, until the computation stops with the following error 
message :


Solve: M deltax^k = rslurmstepd: Job 936902 exceeded memory limit 
(41146808 > 41058304), being killed

slurmstepd: Exceeded job memory limit

We can notice that this problem does not occur with SSOR as 
Preconditionner.


Have you ever met this issue ?

Best regards

M. El Ossmani

University of Pau

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Re: [DuMuX] Boundary conditions in decoupled problem

[Martin Schneider]

ution, io have the 
folowing error:


 ./tutorial_decoupled

Wherever he saw a hole he always wanted to know the depth of it. To 
him this was important.

 - Jules Verne, A journey to the center of the earth

Rank 0: No parameter file given. Defaulting to 
'./tutorial_decoupled.input' for input file.

Initializing problem 'tutorial_decoupled'
Dune reported error: ISTLError 
[apply:/home/latifa/Dumux_2.6.0/dune-istl-2.3.1/dune/istl/solvers.hh:679]: 
h=0 in BiCGSTAB


So please, where os the problem in my definition of the boundary 
conditions? An how i can arrange it?

Best regards.



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Department of Hydromechanics and Modelling of Hydrosystems
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Fax: (+49) 0711/ 685-60430
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Re: [DuMuX] Parallel run of 2p2c decoupled model

[Martin Schneider]

Hi Tri Dat,

probably the MPFA L method has problems with the grid you are using. 
There are some grid restrictions for the implemented MPFA methods.

Could you please send us your grid file.

You could try to run the test with the Mimetic discretization instead, 
by executing

test_2p3d  -ModelType Mimetic

Kind regards,
Martin

Am 22.05.2015 um 10:59 schrieb Tri Dat NGO:

Hi Bernd,

Thank you so much for your help.
Please let me know if you have any progress on the decouple 2p2c in 
parallel.


Concerning 2p decoupled  adaptive + parallel simulations, your 
comments lead me to run /test_3d2p/ in /dumux/test/decoupled/2p/ in 
parallel and I obtained the following error message:


##
No model type specified
Default to finite volume MPFA l-method model
Dune reported error: Dune::NotImplemented 
[storeBoundaryInteractionVolume:../../../dumux/decoupled/2p/diffusion/fvmpfa/lmethod/fvmpfal3dinteractionvolumecontainer.hh:2031]: 
Boundary shape not implemented

##

It seems that there is a problem when storing the boundary interaction 
volumes in the /mpfa-lmethod///. My test domain dimension is 10x10x10 
[m x m x m] with the grid 20x20x20, all boundaries have id 1. I 
haven't tested yet decoupled 2p - 3d parallel + adaptive using 
/mpfa-omethod/tpfa method/. Please let me know if you have any 
additional suggestions.


Kind regards,
Tri Dat

2015-05-21 12:40 GMT+02:00 Bernd Flemisch >:


Hi Tri Dat,

I just tried to run test_dec2p2c in parallel and it seems that at
least the output is wrong. While the pvd-file contains pointers to
correct parallel pvtu-file names, only sequential vtu-files are
written. I will investigate this further.

In any case, to run in parallel, you need to switch the
LinearSolver to the AMGBackend in your problem file by adding

#include 

and adding/changing something like

SET_TYPE_PROP(TestDecTwoPTwoCProblem, LinearSolver,
Dumux::AMGBackend);


Decoupled 2p adaptive and parallel is possible as far as I know.
However the 2p adaptive stuff only works with ALUGrid and that
means that one has to use a 3d test case because 2d ALUGrid is not
parallel. I will try to set up a corresponding case.

I assume that decoupled 2p2c adaptive and parallel is a larger
task. Since we would also like to have it, we can put it on our
to-do list, but it is hard to estimate when we actually can do it.

Kind regards
Bernd



On 05/21/2015 11:51 AM, Tri Dat NGO wrote:

Dear DuMuX,

I would like to know whether there is any test case of 2p2c
decoupled model which works correctly in parallel mode?
I tried to run the parallel simulations of all examples in
/dumux_v2.6/test/decoupled/2p2c with mpirun but I obtained always
the results of sequential simulations.

Another question always on parallel simulation but concerning the
adaptive grid refinement, can we implement the adaptive grid
method with 2p/2p2c model in parallel mode?

Thank you in advance for your reply.

Kind regards,
Tri Dat


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[DuMuX] DuMuX 2.5 release

[Martin Schneider]

Dear DuMuXers,

today is another important day in the history of DuMuX. We are happy to
announce, that the 2.5 version of DuMuX is now available.
Hopefully you profit from the changes. We recommend to change to the current 
version.

You can download the tarball from
http://www.dumux.org/download/dumux-2.5.0.tar.gz

Alternatively, and particularly if you want to develop within the
DuMuX module directory, you can svn-checkout the release branch:
svn checkout --username=anonymous --password=''
svn://svn.iws.uni-stuttgart.de/DUMUX/dumux/branches/release-2.5 dumux

Below you find the most important changes.

Notable Differences Between DuMuX 2.4 and DuMuX 2.5

Note: For the detailed description of changes in the DuMuX-2.5 release please
see the CHANGELOG.

   - The three-dimensional implementation of the MPFA L-method is made
 available for the decoupled compositional 2p2c models. It also allows
 for simulation on an adaptive grid.

   - Coupling of 2c2p with stokesnc and 2p2cNI with Stokesncni was
 added. The stokes2c and stokes2cni are now DEPRICATED and will be kicked
 out by the next release. Instead generalized stokesnc and stokesncni
 models are introduced. Unlike 2c models the transport equations in
 the nc models are capable of using both mass and mole fractions.
 NOTE: For coupling test examples be aware of the harsh version
 restrictions mentioned in dumux/test/modelcoupling/README.



Have a lot of fun and best regards,
Martin Schneider (DuMuX 2.5 Release Manager)

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***

M.Sc. Martin Schneider
University of Stuttgart 
Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
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[DuMuX] DuMuX hard freeze

[Martin Schneider]

Dear DuMuXers,

I want to remind you, that the DuMuX hard freeze was last Friday. That 
means that we should discuss all major fixes you want to commit!

Thank you and cheers,
Martin

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Institute for Modelling Hydraulic and Environmental Systems
Department of Hydromechanics and Modelling of Hydrosystems
Pfaffenwaldring 61
D-70569 Stuttgart
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[DuMuX] DuMuX 2.5 release timetable

[Martin Schneider]

Dear DuMuX,

I am pleased to announce that we prepare a 2.5 release of DuMuX.
Consider following dates in your development / commit strategy:

== Soft feature freeze: 7. March 2014 ==
- All major changes that should be included and are not yet commited
should be announced. Add comment to FS#219 describing the feature and
areas affected by the change.
- Major changes not announced will be rejected after the soft freeze.
- Reports from the management representatives about remaining tasks.

== Hard feature freeze: 21. March 2014 ==
- All major changes must be committed before the hard feature freeze.
- Invasive fixes which might break other code are only accepted after
consultation with the release manager, small fixes are ok.
- Try to get your bugs fixed, your tests included and your documentation
written before the hard feature freeze.
- Final reports from the management representatives what is finished and
what must be dropped.

== Final testing: 31. March 2014 ==
- No commits are allowed except these which are done by the release
manager or which are explicitly authorization by the release manager.
- Release candidate packages will be provided.
- Tests on the various systems, compilers, with different settings are run.

== DuMuX 2.5 release: 4. April 2014 ==
- celebrate, I will bring something to drink!

All commits violating this plan will be reverted without further comment...

Looking forward to a good release,
Martin
(Release manager DuMuX 2.5)

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[DuMuX] next dumux meeting

[Martin Schneider]

Dear DuMuXers,

the next DuMuX meeting will take place on Fri 7.3 at 10:00h in the MML.

best regards
Martin

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