Re: [DuMuX] Info tutorial

Wed, 19 Jul 2017 04:19:38 -0700 

Hi Claudia,
yes I checked and you need Dumux 2.8. I attached an install script and readme that should should set up everything for you. 

Best Timo


On 19.07.2017 13:05, claudia.bortolu...@uzh.ch wrote:

Dear Timo,


I have tried to remove the line that include the header  from the 
1dstokespropertydefaults.hh but I get others similar errors like:



/home/cborto/Software/dune-foamgrid-examples/dumux/freeflow/1dstokes/1dstokesvolumevariables.hh:31:62: 
fatal error: dumux/material/fluidstates/immisciblefluidstate.hh: No 
such file or directory


or


/home/cborto/Software/dune-foamgrid-examples/dumux/freeflow/1dstokes/1dstokesvolumevariables.hh:29:60: 
fatal error: dumux/implicit/common/implicitvolumevariables.hh: No such 
file or directory


I don't know if I can remove all the lines that include these headers.

Is it possible that to run this dune-foamgrid-examples I need an older 
version of dumux? i have installed version 2.11.0 of dumux.

Thank you.

Best Regards,

Claudia Bortolussi



-----Timo Koch <timo.k...@iws.uni-stuttgart.de 
<mailto:timo.k...@iws.uni-stuttgart.de>> wrote: -----

To: claudia.bortolu...@uzh.ch <mailto:claudia.bortolu...@uzh.ch>

From: Timo Koch <timo.k...@iws.uni-stuttgart.de 
<mailto:timo.k...@iws.uni-stuttgart.de>>

Date: 07/16/2017 08:31PM
Subject: Re: [DuMuX] Info tutorial

Hi Claudia,


try removing the line that includes this header from the 
1dstokespropertydefaults.hh it shouldn't be needed. Tell me if that 
works. If not I can check it again.


Timo


Am 14.07.2017 um 11:13 schrieb claudia.bortolu...@uzh.ch 
<mailto:claudia.bortolu...@uzh.ch>:



Dear Timo,

Thank you for your fast reply. I am trying to install the 
dune-foamgrid-examples as the other dune module: after cloning out 
dune-foamgrid-examples I use the command


./dune-common/bin/dunecontrol --only=dune-foamgrid-examples all

but I get this error:

-- Configuring done
-- Generating done

-- Build files have been written to: 
/home/cborto/Software/dune-foamgrid-examples/build-cmake

--- calling make for dune-foamgrid-examples ---
build directory: build-cmake
cmake --build . --

[ 16%] Building CXX object 
examples/bloodflow/CMakeFiles/bloodflow.dir/bloodflow.cc.o
In file included from 
/home/cborto/Software/dune-foamgrid-examples/dumux/freeflow/1dstokes2c/1dstokes2cproperties.hh:32:0,
                 from 
/home/cborto/Software/dune-foamgrid-examples/dumux/freeflow/1dstokes2c/1dstokes2cmodel.hh:30,
                 from 
/home/cborto/Software/dune-foamgrid-examples/examples/bloodflow/bloodflowproblem.hh:29,
                 from 
/home/cborto/Software/dune-foamgrid-examples/examples/bloodflow/bloodflow.cc:26 
<http://bloodflow.cc:26>:
/home/cborto/Software/dune-foamgrid-examples/dumux/freeflow/1dstokes/1dstokespropertydefaults.hh:30:47: 
fatal error: dumux/implicit/box/boxproperties.hh: No such file or 
directory

compilation terminated.

examples/bloodflow/CMakeFiles/bloodflow.dir/build.make:62: recipe for 
target 'examples/bloodflow/CMakeFiles/bloodflow.dir/bloodflow.cc.o' 
failed
make[2]: *** 
[examples/bloodflow/CMakeFiles/bloodflow.dir/bloodflow.cc.o] Error 1
CMakeFiles/Makefile2:1423: recipe for target 
'examples/bloodflow/CMakeFiles/bloodflow.dir/all' failed

make[1]: *** [examples/bloodflow/CMakeFiles/bloodflow.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
--- Failed to build dune-foamgrid-examples ---
Terminating dunecontrol due to previous errors!


The dumux/implicit/box folder is missing. Is there a way to fix this 
problem?


Best regards,

Claudia Bortolussi


-----Timo Koch <timo.k...@iws.uni-stuttgart.de 
<mailto:timo.k...@iws.uni-stuttgart.de>> wrote: -----
To: DuMuX User Forum <dumux@listserv.uni-stuttgart.de 
<mailto:dumux@listserv.uni-stuttgart.de>>, claudia.bortolu...@uzh.ch 
<mailto:claudia.bortolu...@uzh.ch>
From: Timo Koch <timo.k...@iws.uni-stuttgart.de 
<mailto:timo.k...@iws.uni-stuttgart.de>>

Date: 07/14/2017 09:16AM
Subject: Re: [DuMuX] Info tutorial

Hi Claudia,


you can find the examples described in the paper here for the moment: 
https://gitlab.dune-project.org/tkoch/dune-foamgrid-examples


Best wishes
Timo



Viele Grüße,
Timo

Am 13.07.2017 um 16:33 schrieb <claudia.bortolu...@uzh.ch 
<mailto:claudia.bortolu...@uzh.ch>> <claudia.bortolu...@uzh.ch 
<mailto:claudia.bortolu...@uzh.ch>>:



Dear all,


Is it possible to find a tutorial for Grid Adaptivity (Adaptive 
one-dimensional network grid embedded in three-dimensional space) 
and Root Water Uptake? I have read about them in "The Dune FoamGrid 
implementation for surface and network grids".

It would be very useful because I'm going to work on similar studies.
Thank you.

Best regards,

Claudia Bortolussi
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--
____________________________________________________________________

Timo Koch                      phone: +49 711 685 64676
IWS, Universität Stuttgart     fax:   +49 711 685 60430
Pfaffenwaldring 61             email: timo.k...@iws.uni-stuttgart.de
D-70569 Stuttgart              url:   www.hydrosys.uni-stuttgart.de
____________________________________________________________________


GXX_RELEASE_WARNING_OPTS=" \
    -Wall \
    -Wno-deprecated \
    -Wno-deprecated-declarations \
    -Wno-sign-compare"

GXX_RELEASE_OPTS=" \
    -fno-strict-aliasing \
    -fstrict-overflow \
    -fno-finite-math-only \
    -O3 \
    -march=native \
    -funroll-loops \
    -g0"

CMAKE_FLAGS="
-DCMAKE_C_COMPILER=/usr/bin/gcc
-DCMAKE_CXX_COMPILER=/usr/bin/g++
-DCMAKE_CXX_FLAGS_RELEASE='$GXX_RELEASE_OPTS $GXX_RELEASE_WARNING_OPTS'
-DCMAKE_CXX_FLAGS_DEBUG='-O0 -ggdb -Wall'
-DCMAKE_BUILD_TYPE=Release
"



Attachment:
install.sh

Description: application/shellscript


Installation guide dune-foamgrid
================================

You can set up foamgrid using the attached script install.sh.
You need to have the following requirements installed:
  * gcc >= 4.4
  * cmake >= 2.8.12
  * git
  * pkg-config
  * paraview (to visualize the results)
On debian-based system you can use this:
  $ apt-get install build-essential pkg-config cmake git paraview

Then, you can the execute the script and it will download the dune repositories
and build dune-foamgrid and dune-foamgrid-examples
  $ ./install.sh

This will clone the necessary repositories (in a subfolder 'dune'),
build all libaries and the example executables.
After running the script, please find the executables corresponding to the
examples in this paper in
'dune/dune-foamgrid-examples/build-cmake/examples/*'. You can run the 
executables,
modify parameters in the ini files, and inspect the result using e.g. paraview.

The dune core modules are also available as debian packages
(see http://www.dune-project.org/download.html#binary) where
the version 2.4 is required.

Running examples from paper
===========================

# example 1
  $ cd dune/dune-foamgrid-examples/build-cmake/examples/fractureflow
  $ ./fractureflow fractureflow.parset
  $ paraview "resultsfunc_..vtu"

note: Example 1 takes about half an hour to reproduce the results in the paper.
However stopping the simulation earlier (e.g. timestep 40 / 5min) already gives 
enough
idea on what is happening.

# example 2
  $ cd dune/dune-foamgrid-examples/build-cmake/examples/bloodflow
  $ ./bloodflow
  $ paraview brain.pvd

note: Example 2 should only take a few seconds to run

# example 3
  $ cd dune/dune-foamgrid-examples/build-cmake/examples/growth
  $ ./test_ccrootsystemgrowth
  $ paraview rootsystemtestcc.pvd

note: Example 3 should only take a few seconds to run

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