Following up on my question on the precision error of my
boundary fluxes, I am trying to introduce the quad precision for my
multidomain problem with facets. For that, I have to use another
Linear Solver. Following the test case
in dumux/test/multidomain/facet/1p_1p/analytical, I tried to
use BlockDiagAMGBiCGSTABSolver, but the following error occurs:
Solve: M deltax^k = rNewton: Caught exception: "NumericalProblem
[solveLinearSystem:/home/analoyola/dumux/dumux/dumux/nonlinear/newtonsolver.hh:383]:
Linear solver did not converge"
Dune reported error: NumericalProblem
[.../dumux/dumux/dumux/nonlinear/newtonsolver.hh:260]: Newton solver
didn't converge after 0 iterations.
---> Abort!
When I try to run the test in
dumux/test/multidomain/facet/1p_1p/analytical for the box method, a
crash also occurs:
Solve: M deltax^k = rNewton: Caught exception: "SolverAbort
[apply:/home/analoyola/dumux3.4/dune-istl/dune/istl/solvers.hh:494]:
breakdown in BiCGSTAB - rho 0 <= EPSILON 1e-80 after 93.5 iterations"
terminate called after throwing an instance of 'Dumux::NumericalProblem'
what(): NumericalProblem
[.../dumux/dumux/nonlinear/newtonsolver.hh:397]: Newton solver didn't
converge after 0 iterations.
The same does not occur for the cell-centered schemes.
Any idea on what may be causing the crash and how to solve this ?
Thanks a lot
Ana
Em sex., 19 de nov. de 2021 às 00:02,
<[email protected]
<mailto:[email protected]>> escreveu:
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Today's Topics:
1. Re: Integration of boundary flux for upscaling: "errors"
(Christoph Gr?ninger)
2. Re: (no subject) (Pham, Vuong Van)
----------------------------------------------------------------------
Message: 1
Date: Thu, 18 Nov 2021 23:07:15 +0100
From: Christoph Gr?ninger <[email protected]
<mailto:[email protected]>>
To: [email protected]
<mailto:[email protected]>
Subject: Re: [DuMux] Integration of boundary flux for upscaling:
"errors"
Message-ID: <[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset=utf-8; format=flowed
Hi Ana,
I am not sure whether you are right that 1e-14 to 1e-16 should not be
considered as zero. It is the expected precision of a double. In
general, you cannot expect it to be better, just because in the
regular
case it by luck is actually better.
Maybe you can run your simulation with quad precision. That might
help
to get more knowledge regarding the limits of double precision.
Bye
Christoph
Am 17.11.21 um 11:31 schrieb Ana Carolina Loyola:
> Hello,
>
> I have been working on the?upscaling of the 2D permeability
tensor of
> fractured media with the Box Method using the multidomain module of
> Dumux 3.2. The code attached has worked well when compared to the
> analytical solutions of perpendicular and equally spaced fractures.
> I apply linear pressure boundary conditions and integrate flow
at the
> boundaries using the following equation*
> image.png
> And for that, I created a "boundary flux" function (at main.cc),
which
> calls the computeFlux function for all the faces that are
located at the
> boundary of the domain.
>
> The reason I send this message is that I have noticed some
precision
> errors that concern me when running another simple test case (one
> horizontal?and non-persistent fracture, meshes are attached).?
It is
> expected that I have kxy and kyx equal to 0, which seems to work
fine
> when I use a symmetric mesh (signalized with -sym in the .msh
files),
> since I get kxy and kyx in the order of < 1e-30 and net flux
balances in
> the order of <1e-28.
>
> But when I use non-symmetric meshes I get kxy in the order of
1e-17,
> which can not be considered to be 0, considering the matrix
> permeability, and boundary fluxes summation as high as 1e-14 when I
> apply the x gradient. The "error" does not seem to improve when
> refining?the mesh.
>
> So what I would like to ask here is if I am using the appropriate
> functions to integrate flow and if you would have any
> implementation-related suggestions to get past this issue.
>
> I am sorry for the long text; this may be more of a theoretical
issue
> than a code-related one, but I thought it was worth the shot
just?to see
> if I am missing something.
>
> *Equation used by Pouya and Fouch? (2009)
> Pouya, Amade & Fouch?, Olivier. (2009). Permeability of 3D
discontinuity
> networks: New tensors from boundary-conditioned homogenization.
Advances
> in Water Resources. 32. 303-314. 10.1016/j.advwatres.2008.08.004.
>
> Thanks
>
> Ana Loyola
>
> _______________________________________________
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<https://listserv.uni-stuttgart.de/mailman/listinfo/dumux>
>
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Lebe wie?im?Paradies,?womit hab' ich?das verdient?
Die Wahrheit?ist: Hab' ich nicht, ich bin nur reicher beschenkt
Als jemand in einem armen Land mit dem gleichen Talent
[frei nach Tua von Die Orsons - Oioioiropa]
------------------------------
Message: 2
Date: Thu, 18 Nov 2021 23:01:44 +0000
From: "Pham, Vuong Van" <[email protected]
<mailto:[email protected]>>
To: Timo Koch <[email protected]
<mailto:[email protected]>>, DuMux User Mailing List
<[email protected]
<mailto:[email protected]>>
Subject: Re: [DuMux] (no subject)
Message-ID:
<sn6pr01mb47029cf9172df257c3e86d95b6...@sn6pr01mb4702.prod.exchangelabs.com
<mailto:sn6pr01mb47029cf9172df257c3e86d95b6...@sn6pr01mb4702.prod.exchangelabs.com>>
Content-Type: text/plain; charset="utf-8"
Dear all,
Thanks for pointing that out, and so that is the issue I want to
address. My point is, I read the DuMuX course tutorial and came up
with this procedure, as follows (in order to use DuMuX):
Install DUNE and DuMuX -> build the source files
(i.e., CMakeLists.txt; problem.hh, params.input, etc) -> cmake
CMakeLists.txt -> execute DuMuX as ./?. params.input
Therefore, please assist me on the mistakes in my understanding
above (especially the meaning, use, and how-to-create such the
_build_ directory, or build-cmake)
I really appreciate your support. I am a beginner in DuMuX so I
hope that my questions are not that dumb.
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University
of Kansas
Email: [email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>
Phone: +1-(785)-979-2664
From: Timo Koch <[email protected] <mailto:[email protected]>>
Sent: Thursday, November 18, 2021 4:30 AM
To: DuMux User Mailing List <[email protected]
<mailto:[email protected]>>
Cc: Pham, Vuong Van <[email protected] <mailto:[email protected]>>
Subject: Re: [DuMux] (no subject)
Dear Vuong,
it looks like you ran cmake in the source directory. You have to
run ?make executable? in the _build_ directory. Per default
dumux/build-cmake/?
Timo
18. nov. 2021 kl. 08:19 skrev Kilian Weishaupt
<[email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>>:
?
Dear Vuong Van,
did you modify anything in your CMakeLists.txt file? You said the
test ran successfully so the executable in
dumux/dumux/build-cmake/test/porousmediumflow/1p" was build
successfully?
Best wishes
Kilian
On 18.11.21 07:53, Pham, Vuong Van wrote:
Dear Kilian,
Still following the Cmake command (i.e., make name_of_executable),
I attempted to do so in the Ubuntu command window, however I
received this error as attached:
<image001.png>
The picture indicated that for some reasons the command
?dune_symlink_to_source_files? is unknown to Cmake. Besides, what
I observed was that, the commands that are relevant to DUNE,
somehow are unknown by Cmake and cause incomplete configuration.
Please assist me on this error.
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University
of Kansas
Email: [email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>
Phone: +1-(785)-979-2664
From: Kilian Weishaupt <[email protected]
<mailto:[email protected]>><mailto:[email protected]
<mailto:[email protected]>>
Sent: Thursday, November 18, 2021 12:42 AM
To: Pham, Vuong Van <[email protected]
<mailto:[email protected]>><mailto:[email protected]
<mailto:[email protected]>>
Cc: DuMux User Mailing List <[email protected]
<mailto:[email protected]>><mailto:[email protected]
<mailto:[email protected]>>
Subject: Re: [DuMux] (no subject)
Dear Vuong Van,
I'm glad the installation worked now.
1.)
CMakeLists.txt is a configuration file read by CMake, a build
system generator. If configured correctly,
you compile your source code just by calling
make name_of_the_executable
If you make any changes to CMakeLists.txt, a simple
make
will update the build configuration.
Have a look at the tests or at our course exercises here
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-course/-/tree/master/exercises/exercise-basic
<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-course/-/tree/master/exercises/exercise-basic><https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux-course%2F-%2Ftree%2Fmaster%2Fexercises%2Fexercise-basic&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092917187%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=zdHLOvKbHWQHW7G17zW1GN1%2Bq5Vj%2FajNuTGk0LVx8F4%3D&reserved=0
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to get more information
on how to properly use CMakeLists.txt
2.) You may either just use a simple text editor such as Atom or
notepad++ or you can try setting up VS Code (an IDE) which
however, is a little bit more involved to configure. Note that you
can either edit your files under Windows (as shown in the windows
explorer) or using the Ubuntu subsytem. Whatever works better for you.
See Point 3 in our wiki on how to get VS Code
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/wikis/Windows-Subsystem-for-DuMux
<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/wikis/Windows-Subsystem-for-DuMux><https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fwikis%2FWindows-Subsystem-for-DuMux&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092927180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=gLWMDVj2UyWQPUESnsfD2QvorfIAifDLjJefjt%2BTzX0%3D&reserved=0
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PS: Please always respond to the mailing list
([email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>, I also forgot to do
that in my first mail) such that others can profit from our
discussion, too.
Best wishes
Kilian
On 17.11.21 20:56, Pham, Vuong Van wrote:
Dear Kilian,
I am glad to receive your swift response. Following the use of
DuMuX (at this point I installed all folders and ran the test
successfully), I have the concerns listed as below:
1. The core structure of a ?DuMux? job contains files as the
attached figure. I believe that I have to compile the
?CMakeLists.txt? using CMake prior to any further execution. May
you assist me how to compile such that ?CMakeLists.txt? properly?
<image002.png>
2. By far, I only know how to modify contents in a file
(within Ubuntu subsystem) using Vim editor. However, I may need
either Python/C++ later to modify such files. May you suggest me
an IDE to use with C++ in Ubuntu subsystem?
I hope that my concerns are appropriate.
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University
of Kansas
Email: [email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>
Phone: +1-(785)-979-2664
From: Kilian Weishaupt <[email protected]
<mailto:[email protected]>><mailto:[email protected]
<mailto:[email protected]>>
Sent: Wednesday, November 17, 2021 10:28 AM
To: Pham, Vuong Van <[email protected]
<mailto:[email protected]>><mailto:[email protected]
<mailto:[email protected]>>
Subject: Re: [DuMux] (no subject)
Dear Vuong Van,
we recently updated our wiki for installing Dumux under Windows 10.
There seems to be an issue with git clone which can be fixed as
described in the wiki.
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/wikis/Windows-Subsystem-for-DuMux
<https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/wikis/Windows-Subsystem-for-DuMux><https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fwikis%2FWindows-Subsystem-for-DuMux&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092927180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=gLWMDVj2UyWQPUESnsfD2QvorfIAifDLjJefjt%2BTzX0%3D&reserved=0
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Best wishes
Kilian
On 12.11.21 01:39, Pham, Vuong Van wrote:
To the DuMux development team,
My name is VUONG VAN PHAM and I am an interested DuMux user for my
research purpose. When I was tempted to install the simulator
using installdumux.py, the installation was paused and the .log
file is attached.
Please assist me on how to install DuMux correctly. Also please
note that I was tempted to install in ubuntu subsystem within
Windows 10 (I do not know whether that impacts the installation
process, however, I inform that fact just in case).
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University
of Kansas
Email: [email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>
Phone: +1-(785)-979-2664
_______________________________________________
DuMux mailing list
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--
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Kilian Weishaupt
Institut f?r Wasser- und Umweltsystemmodellierung (IWS)
Lehrstuhl f?r Hydromechanik und Hydrosystemmodellierung
Universit?t Stuttgart, Pfaffenwaldring 61, 70569 Stuttgart
Email: [email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>
Telefon: 0049 711 685-60461 ** fax: 0049-711-685-60430
http://www.hydrosys.uni-stuttgart.de
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Kilian Weishaupt
Institut f?r Wasser- und Umweltsystemmodellierung (IWS)
Lehrstuhl f?r Hydromechanik und Hydrosystemmodellierung
Universit?t Stuttgart, Pfaffenwaldring 61, 70569 Stuttgart
Email: [email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>
Telefon: 0049 711 685-60461 ** fax: 0049-711-685-60430
http://www.hydrosys.uni-stuttgart.de
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Kilian Weishaupt
Institut f?r Wasser- und Umweltsystemmodellierung (IWS)
Lehrstuhl f?r Hydromechanik und Hydrosystemmodellierung
Universit?t Stuttgart, Pfaffenwaldring 61, 70569 Stuttgart
Email: [email protected]
<mailto:[email protected]><mailto:[email protected]
<mailto:[email protected]>>
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End of DuMux Digest, Vol 128, Issue 12
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