In the example directory multi1, there is a command in the makefile
python -m cProfile -o /tmp/$(name).pro $(name).py

input python means use python2 interpreter, then raised ERROR
import yade File "/home/shguan/myyade/install/lib/x86_64-linux-gnu/yade/py/yade/__init__.py", line 75, in <module> from yade import boot ImportError: dynamic module does not define init function (initboot)

while python3 -m cProfile -o /tmp/$(name).pro $(name).py, the raised ERROR
File "multi1.py", line 11, in <module> import liboofem ImportError: dynamic module does not define module export function (PyInit_liboofem)

So how to solve this problem caused by the different version of python?

BEST WISHES

SH. GUAN
[email protected]

Dear Jan,
sorry to bother you again. I want to change the model in oofem, but i don't know how to run the software. I know it may be more suitable to consult the oofem forum, i tried but nobody answer me yet. So i have to bother you, the oofem is not very friendly to beginners. I hope you may provide some suggestions about learning the oofem.
Best regards.

Hi, Jan!
The surface coupling and multi-scale coupling in your coupling application examples are independent. One simulation problem I'm facing now is that an object A penetrates into another object B. First, I want to simulate the contact between the two objects by method of surface coupling. Second, when A penetrates B to a certain extent, some areas in B are simulated by RVE element, so that contact between A and RVE can be calculated, and then the stressed of RVE adjusted to the corresponding interagtion points of fininte element in B. Would you please to tell if the next two steps can be realized in the order of interface coupling and multi-scale coupling?

best regards,
Dez

Hi Jan,
I am trying to run your example: surf1
When I run the makefile, I get the following error:
I would appreciate you helping me out here.
Zoheir

~/FEMDEM/Installation/_build/install$ make -f makefile all

set usePolyhedra=True if poly option is set

use profiler or not

#python -m cProfile -o /tmp/surf1.pro surf1.py

reset _yade.py script after running

sed -i 's/^usePolyhedra =./usePolyhedra = False/' surf1_yade.py
python surf1_profile.py
Traceback (most recent call last):
File "surf1_profile.py", line 4, in
stats = StatsWrapper('/tmp/surf1.pro')
File "/home/zoheir/FEMDEM/Installation/_build/install/profiler.py", line 12, in init
self.stats = Stats(fName).stats
File "/usr/lib/python2.7/pstats.py", line 81, in init
self.init(arg)
File "/usr/lib/python2.7/pstats.py", line 95, in init
self.load_stats(arg)
File "/usr/lib/python2.7/pstats.py", line 109, in load_stats
f = open(arg, 'rb')
IOError: [Errno 2] No such file or directory: '/tmp/surf1.pro'
makefile:56: recipe for target 'profile' failed
make: *** [profile] Error 1

Thanks for your excellent work in this domain!

when runing the makefile in multi1, the error raised at "import liboofem

File "multi1.py", line 9, in import liboofem ImportError: /home/shguan/dem-fem-coupling-master/install/liboofem.so: undefined symbol: gc

could you help me about this problem?

sh. Guan
[email protected]

BEST WISHES

Hi Jan,

When running surf1 example, I get the following error:
I would appreciate your thoughts on this.
~/FEMDEM/Installation$ make -f makefile all

set usePolyhedra=True if poly option is set

use profiler or not

python -m cProfile -o /tmp/surf1.pro surf1.py
Traceback (most recent call last):
File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/usr/lib/python2.7/cProfile.py", line 200, in
main()
File "/usr/lib/python2.7/cProfile.py", line 193, in main
runctx(code, globs, None, options.outfile, options.sort)
File "/usr/lib/python2.7/cProfile.py", line 49, in runctx
prof = prof.runctx(statement, globals, locals)
File "/usr/lib/python2.7/cProfile.py", line 140, in runctx
exec cmd in globals, locals
File "surf1.py", line 9, in
import libyade
ImportError: dynamic module does not define init function (initlibyade)
makefile:41: recipe for target 'example' failed
make: *** [example] Error 1

Dear Jan
When i try to run the example of 'contact1' by 'make all' in Ubuntu18.4, it occurs a problem showing that no module named 'liboofem'. I have installed the yade and oofem in my system, and the file liboofem is located in ./usr/lib/liboofem.so. And then I try to specify an absolute path, but another problem occurs 'ImportError: Dynamic Module does not define Module export Function (PyInit_liboofem) '.

what should i do next?

Sincerely,
Tang
bug.txt

Hi Jan:
In line 728-733,
w1 = (cp-v1).cross(cp-v3).dot(cp-v2)
w2 = (cp-v1).cross(cp-v2).dot(cp-v4)
w3 = (cp-v1).cross(cp-v4).dot(cp-v3)
w4 = (cp-v2).cross(cp-v3).dot(cp-v4)
I don't really understand, maybe
w4 = (cp-v1).cross(cp-v3).dot(cp-v2)
w3 = (cp-v1).cross(cp-v2).dot(cp-v4)
w2 = (cp-v1).cross(cp-v4).dot(cp-v3)
w1 = (cp-v2).cross(cp-v3).dot(cp-v4)?
Yours,
Joe

Hi, Jan：
When I install fem-dem coupling, I use the make all command. Based on the answer in (#21), I installed python2 versions with the following code:

sudo apt install python-dev python-ipython python-numpy python-tk python-xlib python-pyqt5 python-minieigen python-pyqt5.qtwebkit python-gts

However I still got the following error:
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/oofem
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/yade
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/install
rm -rf /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig
wget http://www.oofem.org/cgi-bin/OOFEM/download.cgi?download=oofem-2.5.zip -O /home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip
--2021-07-13 13:54:40-- http://www.oofem.org/cgi-bin/OOFEM/download.cgi?download=oofem-2.5.zip
正在解析主机 www.oofem.org (www.oofem.org)... 147.32.130.71
正在连接 www.oofem.org (www.oofem.org)|147.32.130.71|:80... 已连接。
已发出 HTTP 请求，正在等待回应... 302 Found
位置：http://www.oofem.org/download/oofem-2.5.zip [跟随至新的 URL]
--2021-07-13 13:54:47-- http://www.oofem.org/download/oofem-2.5.zip
再次使用存在的到 www.oofem.org:80 的连接。
已发出 HTTP 请求，正在等待回应... 200 OK
长度： 14249792 (14M) [application/zip]
正在保存至: “/home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip”

/home/dadn/dem-fem- 100%[===================>] 13.59M 1.72MB/s 用时 14s

2021-07-13 13:55:02 (968 KB/s) - 已保存 “/home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip” [14249792/14249792])

unzip -q -o /home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip
mv oofem-2.5 /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig
rm -rf /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
cp -r /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
cd /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source &&
patch -s -p0 < /home/dadn/dem-fem-coupling-master/installation/oofem.diff
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/oofem/build
cd /home/dadn/dem-fem-coupling-master/installation/_build/oofem/build &&
cmake -DUSE_PYTHON_BINDINGS=ON /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
-- The CXX compiler identification is GNU 7.5.0
-- The C compiler identification is GNU 7.5.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.17", minimum required is "2.7")
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found suitable version "2.7.17", minimum required is "2.7")
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:567 (message):
Imported targets and dependency information not available for Boost version
(all versions older than 1.33)
Call Stack (most recent call first):
/usr/share/cmake-3.10/Modules/FindBoost.cmake:907 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:507 (find_package)

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
No header defined for python-py27; skipping header check
Call Stack (most recent call first):
CMakeLists.txt:507 (find_package)

CMake Error at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1947 (message):
Unable to find the requested Boost libraries.

Unable to find the Boost header files. Please set BOOST_ROOT to the root
directory containing Boost or BOOST_INCLUDEDIR to the directory containing
Boost's headers.
Call Stack (most recent call first):
CMakeLists.txt:507 (find_package)

-- Looking for C++ include unistd.h
-- Looking for C++ include unistd.h - found
-- Looking for C++ include execinfo.h
-- Looking for C++ include execinfo.h - found
-- Looking for access
-- Looking for access - found
-- Looking for cbrt
-- Looking for cbrt - found
-- Looking for isnan
-- Looking for isnan - not found
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
Boost_INCLUDE_DIR (ADVANCED)
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm

-- Configuring incomplete, errors occurred!
See also "/home/dadn/dem-fem-coupling-master/installation/_build/oofem/build/CMakeFiles/CMakeOutput.log".
See also "/home/dadn/dem-fem-coupling-master/installation/_build/oofem/build/CMakeFiles/CMakeError.log".
Makefile:119: recipe for target 'oofem-cmake' failed
make: *** [oofem-cmake] Error 1
I also got the CMakeOutput.log and CMakeError.log.

CMakeOutput.log
CMakeError.log

So，what should I do next ？
Thanks a lot！！
xue

Thank you Jan,
I was absent for a while for finding a job and did not conduct the research a period of time. Now i want to change the model for example like a slope. And first i want to try to increase the number of the DEM models. I change the nREVs=32 and stay the getIPs constant .But in the Paraview there is still just 2 DEM models.

I get the following error when running surf1 example:

set usePolyhedra=True if poly option is set

use profiler or not

#python -m cProfile -o /tmp/surf1.pro surf1.py

reset _yade.py script after running

sed -i 's/^usePolyhedra =./usePolyhedra = False/' surf1_yade.py
python surf1_profile.py
Traceback (most recent call last):
File "surf1_profile.py", line 5, in
tot = stats.getKeyByName('solveAt','demfemcoupling.py')
File "/home/zoheir/FEMDEM/Installation/_build/install/profiler.py", line 19, in getKeyByName
raise RuntimeError
RuntimeError
makefile:56: recipe for target 'profile' failed
make: *** [profile] Error 1

I would appreciate your thoughts

Cheers,
Zoheir

Hi,Jan

 When I install fem-dem coupling, I use the make all command. Based on the answer in (https://github.com/stranskyjan/dem-fem-coupling/issues/21), I installed python2 versions with the following code:
 sudo apt install python-dev python-ipython python-numpy python-tk python-xlib python-pyqt5 python-minieigen python-pyqt5.qtwebkit python-gts

//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
However I still got the following error:
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/oofem
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/yade
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/install
rm -rf /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig
wget http://www.oofem.org/cgi-bin/OOFEM/download.cgi?download=oofem-2.5.zip -O /home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip
--2021-07-13 13:54:40-- http://www.oofem.org/cgi-bin/OOFEM/download.cgi?download=oofem-2.5.zip
正在解析主机 www.oofem.org (www.oofem.org)... 147.32.130.71
正在连接 www.oofem.org (www.oofem.org)|147.32.130.71|:80... 已连接。
已发出 HTTP 请求，正在等待回应... 302 Found
位置：http://www.oofem.org/download/oofem-2.5.zip [跟随至新的 URL]
--2021-07-13 13:54:47-- http://www.oofem.org/download/oofem-2.5.zip
再次使用存在的到 www.oofem.org:80 的连接。
已发出 HTTP 请求，正在等待回应... 200 OK
长度： 14249792 (14M) [application/zip]
正在保存至: “/home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip”

/home/dadn/dem-fem- 100%[===================>] 13.59M 1.72MB/s 用时 14s

2021-07-13 13:55:02 (968 KB/s) - 已保存 “/home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip” [14249792/14249792])

unzip -q -o /home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip
mv oofem-2.5 /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig
rm -rf /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
cp -r /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
cd /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source &&
patch -s -p0 < /home/dadn/dem-fem-coupling-master/installation/oofem.diff
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/oofem/build
cd /home/dadn/dem-fem-coupling-master/installation/_build/oofem/build &&
cmake -DUSE_PYTHON_BINDINGS=ON /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
-- The CXX compiler identification is GNU 7.5.0
-- The C compiler identification is GNU 7.5.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
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//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
So，what should I do next ？
Thanks a lot！！
xue

Hi Jan,

Although I have "demfemcoupling.py" in the folder, I get the following error:

from yade._customConverters import *
Traceback (most recent call last):
File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/usr/lib/python2.7/cProfile.py", line 200, in
main()
File "/usr/lib/python2.7/cProfile.py", line 193, in main
runctx(code, globs, None, options.outfile, options.sort)
File "/usr/lib/python2.7/cProfile.py", line 49, in runctx
prof = prof.runctx(statement, globals, locals)
File "/usr/lib/python2.7/cProfile.py", line 140, in runctx
exec cmd in globals, locals
File "surf1.py", line 10, in
from demfemcoupling import OofemInterface,YadeInterface,OofemYadeMeshSurfaceMap,FemDemSurfaceCoupler,TimeStep
ImportError: No module named demfemcoupling
makefile:41: recipe for target 'example' failed
make: *** [example] Error 1

Should I re-install Yade and OOFEM?

Thanks,

Zoheir

Hi,

I cannot install oofem due to the website is down and I can't find the 2.5 release anywhere. Could you please add an alternative source for oofem?

Hi Jan:
In my model, I want to add constantSurfaceload to the element. But I don't know how to add surface load or edge load to it.
Now I use nodalload to model constant edge load. But when the normal vector of the element surface changed, the componentArray of nodalload will change, thus constant nodalload may not be suitable.
So how to add constantsurfaceload to element surface in the python module of oofem?
Yours,
Joe

Dear Jan,
Thank you very much for your sharing. I have tried to run the script by using python2.7 in Ubuntu , but it went wrong .

And I followed the “make” steps:

1. make
2. make all

what should i do next, and what is the potential problem?

Looking forward for your answer！

Sincerely,
Xu

Hi Jan,
sorry to bother you, i meet some problems, when i run the 'makefile' ,and print 'make all' command. The error is showen like this:
Segmentation fault (core dumped)
Makefile:105: recipe for target 'oofem-download' failed
make: *** [oofem-download] Error 139
how can i solve this problem?

Jan, i want to get the strain of the random region of FEM part, like node even the point on the edge of the fem element. And transport the strain to the DEM part at the same place. Can oofem monitor the strain at those place?

Hi, Jan~
I tried to post this question on the yadepad.
I want to add load on the certain nodes in FEM during the surface coupling of FEM/DEM, but something was wrong by the procedure with errror prompt as following:

Error:(/home/.../oofemlib/domain.C:353)
In Domain::giveload, number : 1:
cannot cast boundary condition 1 to Load class

Here was part of my script for FEM as following:
############
import liboofem
def readUnvFile111(fName):
...

read the mesh file of UNV and get the nodes

global Nodes4unv,Elems4unv111
Nodes4unv,Elems4unv111 = readUnvFile111('/tmp/membrane3Dtr12.unv')

read the nodes and elements

class Node:
def init(self,id,coords):
self.id = id
self.coords = list(coords)
self.bcs = [0,0,0]
def toOofem(self):
kw = dict(coords=self.coords)
if any(self.bcs):
kw["bc"] = self.bcs
return liboofem.node(self.id,domain,**kw)

def createOofemNodes():
nodes = [Node(-1,tuple(nodexyz)) for _, (nodexyz) in enumerate(Nodes4unv)]
for i,n in enumerate(nodes):
n.id = i+1
if n.coords[2] == 0.17:
n.bcs = [1,1,1]
elif n.coords[2] == 0.72:
n.bcs = [1,1,1]
return [n.toOofem() for n in nodes]

class Shell4tr:
def init(self,id,nodes):
self.id = id
self.nodes = list(nodes)
def toOofem(self):
return liboofem.element("LTRSpace",self.id, domain, nodes=self.nodes, mat=1, crossSect=1, nlgeo=1)

def createOofemElems():
elems = []
#for _, (NumId41) in enumerate(Elems4unv41):
#elems.append(Shell3tr(-1,(NumId41)))
for _, (NumId111) in enumerate(Elems4unv111):
elems.append(Shell4tr(-1,(NumId111)))
for i,e in enumerate(elems):
e.id = i+1
return [e.toOofem() for e in elems]

all above was get the mesh information from unv and built the geom of object in fem##

def sortNodes():
fxpNodes = []
fxnNodes = []
fypNodes = []
fynNodes = []
for i in xrange(domain.giveNumberOfDofManagers()):
a = domain.giveDofManager(i+1).giveCoordinates()
c = [a[j] for j in xrange(3)]
if abs(c[0]-0.04)<0.006:
fxpNodes.append(i+1)
if abs(c[0]-0.36)<0.006:
fxnNodes.append(i+1)
if abs(c[1]-0.04)<0.006:
fypNodes.append(i+1)
if abs(c[1]-0.36)<0.006:
fynNodes.append(i+1)
return fxpNodes,fxnNodes,fypNodes,fynNodes

according to the above, I extracted the nodes for loading##

def loadmembrane():
loadxp = liboofem.FloatArray()
loadxp.resize(3)
loadxp.zero()
loadxp[0] = 3 #x=0.045 & 0.035
loadxn = liboofem.FloatArray()
loadxn.resize(3)
loadxn.zero()
loadxn[0] = -3 #x=0.355 & 0.365
loadyp = liboofem.FloatArray()
loadyp.resize(3)
loadyp.zero()
loadyp[1] = 3 #x=0.045 & 0.035
loadyn = liboofem.FloatArray()
loadyn.resize(3)
loadyn.zero()
loadyn[1] = -3 #x=0.355 & 0.365
for ixp in fxpNodes:
lxp = domain.giveLoad(ixp)
axp = lxp.giveComponentArray()
axp.add(loadxp)
lxp.setComponentArray(axp)
for ixn in fxnNodes:
lxn = domain.giveLoad(ixn)
axn = lxn.giveComponentArray()
axn.add(loadxn)
lxn.setComponentArray(axn)
for iyp in fypNodes:
lyp = domain.giveLoad(iyp)
ayp = lyp.giveComponentArray()
ayp.add(loadyp)
lyp.setComponentArray(ayp)
for iyn in fynNodes:
lyn = domain.giveLoad(iyn)
ayn = lyn.giveComponentArray()
ayn.add(loadyn)
lyn.setComponentArray(ayn)

###and I apply the load on these nodes###

############################################################

engngModel

problem = liboofem.engngModel("nldeidynamic",1,nSteps=5,dumpCoef=.1,deltaT=10000,outFile="/tmp/membrane_oofem.out")

domain

domain = liboofem.domain(1, 1, problem, liboofem.domainType._3dMode, tstep_step=10000, dofman_all=True, element_all=True)
problem.setDomain(1, domain, True)

vtkxml

vtkxmlModule = liboofem.vtkxml(1,problem,tstep_step=10000,vars=[1,6],primvars=[1,4])
#vtkxmlModule = liboofem.vtkxml(1,problem,tstep_step=10000)
exportModuleManager = problem.giveExportModuleManager()
exportModuleManager.resizeModules(1)
exportModuleManager.setModule(1,vtkxmlModule)

boundary condition and time function

ltf = liboofem.loadTimeFunction("constantFunction",1,f_t=0)
bc = liboofem.boundaryCondition(1, domain, loadTimeFunction=1, prescribedValue=0.0)

nodes

nodes = createOofemNodes()

material and cross section

mat = liboofem.isoLE(1, domain, d=1200, E=1.2e7, n=0.48, tAlpha=0)
cs = liboofem.simpleCS(1, domain,)

elements

elems = createOofemElems()

add eveything to domain (resize container first)

domain.resizeDofManagers(len(nodes))
for n in nodes:
domain.setDofManager(n.number, n)
domain.resizeElements(len(elems))
for e in elems:
domain.setElement(e.number, e)
domain.resizeMaterials(1)
domain.setMaterial(1, mat)
domain.resizeCrossSectionModels(1)
domain.setCrossSection(1, cs)
domain.resizeBoundaryConditions(1)
domain.setBoundaryCondition(bc.number, bc)
domain.resizeFunctions(1)
domain.setFunction(ltf.number, ltf)

vtkxmlModule.initialize() # (!)

######################## extract the nodes and apply the load on them ###
fxpNodes,fxnNodes,fypNodes,fynNodes = sortNodes()
loadmembrane()
############### apply the load############

so did something wrong with the boundary or loading ?

Best regards,
Dez

Dear Jan,
i misunderstand my boss's demand. What he want is that turn the FEM element to DEM partical, after the FEM elemet is destroied. Is it possible to turn the FEM element to DEM partical? or it is another problem?

Dear Jan,

Many thanks for sharing with us your code and answering to our questions.
I have successfully installed your code

and then tried to run the contact1.py example and I am having this error:

The operating system is ubuntu 18.04

Thank you in advance.

With kind regards,
Kostas

Hey Jan, I have a quick question,

Is contact coupling only possible with polyhedrons or it also includes spheres?

If not, how simple is the implementation?

Hi Jan,
I am trying your surface coupler of DEM and FEM code and I tried to modify the material of fem by 'mat = liboofem.druckerprager(1, domain, tAlpha=0, d=1960, E=2e6, n=0.23, iys=2e4, alpha=0.23, alphasi=0.22)', but the error message showed that 'no module of 'druckerprager'', I tried other names like DruckerPrager, DP or druckerPrager, they didn't work. So did the liboofem lack the module of it? If so, how to invoke that material when I make the coupler of DEM and FEM?
Thanks,
De Zhang

Hi Jan:
I don't understand why there are 2 engines and 2 materials in the multi1_yade.py.
I saw the RVE generation file "prepareRVE.py" in trunk/example/FEM-DEM folder and found frictmat only and also only 1 engine was used.
I tried to delete cmpMat and its related engine, but it got error.
What are the differences of the 2 engines(material) and what are they used for?
Yours, Joe
BTW, did you compile the stuff on your new system? If so, I can attach my file here.

Hey Jan,

First of all thank you so much for uploading your codes. I really appreciate it. I have been using YADE for almost 6 months now and I want to start using the DEM FEM coupling. I installed the 'dem-fem-coupling-master' by going to dem-fem-coupling-master/installation and typing make all. The following is what I got when the installation was done:

Now everything should be compiled and prepared for use.
Try out some examples :-)
There is no need to run this script any more
If you want to run examples directly in this terminal, execute the
following command:
export PYTHONPATH=$PYTHONPATH:/home/nabid/Downloads/dem-fem-coupling-master/installation/_build/install:

Now I went to the examples/multi1 directory and typed make all. I got the following error:

python -m cProfile -o /tmp/multi1.pro multi1.py
/home/nabid/Downloads/dem-fem-coupling-master/installation/_build/yade/install/lib/x86_64-linux-gnu/yade/py/yade/system.py:9: RuntimeWarning: to-Python converter for std::vector<int, std::allocator > already registered; second conversion method ignored.
from yade._customConverters import *
/home/nabid/Downloads/dem-fem-coupling-master/installation/_build/yade/install/lib/x86_64-linux-gnu/yade/py/yade/system.py:9: RuntimeWarning: to-Python converter for std::vector<double, std::allocator > already registered; second conversion method ignored.
from yade._customConverters import *
Traceback (most recent call last):
File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/usr/lib/python2.7/cProfile.py", line 200, in
main()
File "/usr/lib/python2.7/cProfile.py", line 193, in main
runctx(code, globs, None, options.outfile, options.sort)
File "/usr/lib/python2.7/cProfile.py", line 49, in runctx
prof = prof.runctx(statement, globals, locals)
File "/usr/lib/python2.7/cProfile.py", line 140, in runctx
exec cmd in globals, locals
File "multi1.py", line 9, in
import libyade
File "/home/nabid/Downloads/dem-fem-coupling-master/installation/_build/install/libyade.py", line 260, in
import Xlib.display
ImportError: No module named Xlib.display
Makefile:41: recipe for target 'example' failed
make: *** [example] Error 1

I get the same error for all the examples that are provided. Any help? I am very new to this thing, so i might have missed an obvious thing.

Thank you so much for your help!

Best Regards,
Najm

Hi Jan:
I modified the loading time of your multi example:
1.I slowed down the loading speed in fem. I changed the loading time from 0.2s to 200s.(bcs are also changed)
2.I changed the dt from 2e-4 to 2e-2
3.In order to make sure the dem is stable, I changed the density in dem from 1e3 to 1e7 and set the gravity(0,0,0.0)

but it seems unstable, the strain seems relatively high(-0.0004 in step4).

Solving [Step number 0, Time 2.000000e-02]
('stress', Matrix3(-2.7232542208268342e-11,2.1607057838358735e-11,-7.565900182489134e-12, 2.1607057838358735e-11,-3.5733805174291325e-11,5.910176084244153e-12, -7.565900182489134e-12,5.910176084244153e-12,2.6839670851857137e-12))
('strain', Matrix3(0,0,0, 0,0,0, 0,0,0))
v:
Matrix3(0,0,0, 0,0,0, 0,0,0)

Solving [Step number 1, Time 4.000000e-02]
('stress', Matrix3(-1.083433491135522e-8,-1.3503776707434368e-8,1.7486952135573553e-8, -1.3503776707434368e-8,3.6347064127015305e-8,-2.926186112822691e-8, 1.7486952135573553e-8,-2.926186112822691e-8,8.99554151810844e-10))
('strain', Matrix3(0,0,0, 0,0,0, 0,0,0))
v:
Matrix3(0,0,0, 0,0,0, 0,0,0)

Solving [Step number 2, Time 6.000000e-02]
('stress', Matrix3(0.000015525172297319974,0.0000795526387192835,-0.00009283124932038486, 0.0000795526387192835,-0.0003630625371313257,0.0002590613138648092, -0.00009283124932038486,0.0002590613138648092,-0.00005720234018106285))
('strain', Matrix3(0.00005392650492956297,-1.7164899182052643e-18,-9.869235370759615e-6, -1.7164899182052643e-18,0.000053926504929562556,-9.869235370764533e-6, -9.869235370759615e-6,-9.869235370764533e-6,-0.00013675213675213405))
v:
Matrix3(0,1.3597608349867324e-16,2.353049132322896e-17, 1.3597608349867324e-16,0,6.850607918032826e-17, 2.353049132322896e-17,6.850607918032826e-17,0)

Solving [Step number 3, Time 8.000000e-02]
('stress', Matrix3(-11.3107674295793,1.7129703607246294,-2.787768422239802, 1.7129703607246294,-9.609769538283032,-0.23642769428808477, -2.787768422239802,-0.23642769428808477,-12.643860844491378))
('strain', Matrix3(0.00006091697779284176,4.488899208845239e-15,-0.000011148580698508899, 4.488899208845239e-15,0.00006091697779162887,-0.00001114858069311587, -0.000011148580698508899,-0.00001114858069311587,-0.0003103221564777195))
v:
Matrix3(1.2212453270876722e-13,1.1814561132037645e-13,1.6167065989061103e-13, 1.1814561132037645e-13,-1.6653345369377348e-14,-1.1915983548294906e-13, 1.6167065989061103e-13,-1.1915983548294906e-13,5.551115123125783e-14)

Solving [Step number 4, Time 1.000000e-01]
('stress', Matrix3(-7.308025222980424e8,9.503633740807763e7,-2.2945586023590547e8, 9.503633740807763e7,-9.180035574511294e8,1.3301196286263055e8, -2.2945586023590547e8,1.3301196286263055e8,-9.263253771518726e8))
('strain', Matrix3(0.000014233498104035896,-2.3639298424766302e-11,-2.6049070587392296e-6, -2.3639298424766302e-11,0.000014233512498104343,-2.6049467336185456e-6, -2.6049070587392296e-6,-2.6049467336185456e-6,-0.00045189774370015776))
v:
Matrix3(-5.176525874617255e-10,-1.0401586226850383e-9,-9.210391726013966e-10, -1.0401586226850383e-9,-1.3655188091377113e-10,5.564194956105476e-10, -9.210391726013966e-10,5.564194956105476e-10,-5.627942556429844e-10)

However, the loading speed must be slow in my example.
Is there any way to make dt a little larger?
I attached my multi_yade multi_oofem and multi.

multi_yade_oofem.zip

yours, Joe

Hi,Jan

When I install fem-dem coupling, I use the make all command. OOFEM can be installed normally, but there is a problem in the process of build Yade. I have installed Yade prerequisites[1], but when I installed FEM DEM coupling, Yade failed to install successfully.

best regards,
Jie

[1]https://yade-dem.org/doc/installation.html#compilation
The problems are as follows:
tar xfj /home/wj/dem-fem-coupling-master/installation/_build/yade/yade.tar.bz2
mv trunk-2019.01a /home/wj/dem-fem-coupling-master/installation/_build/yade/source-orig
rm -rf /home/wj/dem-fem-coupling-master/installation/_build/yade/source
cp -r /home/wj/dem-fem-coupling-master/installation/_build/yade/source-orig /home/wj/dem-fem-coupling-master/installation/_build/yade/source
cd /home/wj/dem-fem-coupling-master/installation/_build/yade/source &&
patch -s -p0 < /home/wj/dem-fem-coupling-master/installation/yade.diff
mkdir -p /home/wj/dem-fem-coupling-master/installation/_build/yade/build
cd /home/wj/dem-fem-coupling-master/installation/_build/yade/build &&
cmake
-DCMAKE_INSTALL_PREFIX=/home/wj/dem-fem-coupling-master/installation/_build/yade/install
-DENABLE_LINSOLV=OFF
-DENABLE_PFVFLOW=OFF
-DENABLE_LBMFLOW=OFF
-DENABLE_TWOPHASEFLOW=OFF
-DENABLE_GL2PS=OFF
-DNOSUFFIX=ON
/home/wj/dem-fem-coupling-master/installation/_build/yade/source
-- Found OpenMP_C: -fopenmp
-- Found OpenMP_CXX: -fopenmp
-- Found OpenMP: TRUE
qmake: could not exec '/usr/lib/x86_64-linux-gnu/qt4/bin/qmake': No such file or directory
-- Found unsuitable Qt version "" from NOTFOUND
-- Version is set to 2019.01a
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- python
-- thread
-- filesystem
-- iostreams
-- regex
-- serialization
-- system
-- date_time
-- chrono
-- atomic
-- Boost_VERSION: 106501
-- Boost_LIB_VERSION: 1_65_1
-- Boost_INCLUDE_DIRS: /usr/include
-- Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so/usr/lib/x86_64-linux-gnu/libpthread.so
-- Found Eigen3, version: 3.3.4
-- Disable vectorization
-- The imported target "vtkRenderingPythonTkWidgets" references the file
"/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so"
but this file does not exist. Possible reasons include:

• The file was deleted, renamed, or moved to another location.
• An install or uninstall procedure did not complete successfully.
• The installation package was faulty and contained
  "/usr/lib/cmake/vtk-6.3/VTKTargets.cmake"
  but not all the files it references.

-- The imported target "vtk" references the file
"/usr/bin/vtk"
but this file does not exist. Possible reasons include:

• The file was deleted, renamed, or moved to another location.
• An install or uninstall procedure did not complete successfully.
• The installation package was faulty and contained
  "/usr/lib/cmake/vtk-6.3/VTKTargets.cmake"
  but not all the files it references.

-- Found VTK
-- Found OpenMP_C: -fopenmp
-- Found OpenMP_CXX: -fopenmp
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GTS
-- USE QT5
-- Found GUI-Qt5-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
Yade will be installed to /home/wj/dem-fem-coupling-master/installation/_build/yade/install
-- Suffix is set to
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/wj/dem-fem-coupling-master/installation/_build/yade/install
-- Could NOT find gts (missing: PY_gts)
-- Use embedded version of gts. Please, consider installing the corresponding package
CMake Error at /usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find minieigen (missing: PY_minieigen)
Call Stack (most recent call first):
/usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
cMake/FindPythonModule.cmake:22 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
CMakeLists.txt:580 (find_python_module)

-- Configuring incomplete, errors occurred!
See also "/home/wj/dem-fem-coupling-master/installation/_build/yade/build/CMakeFiles/CMakeOutput.log".
See also "/home/wj/dem-fem-coupling-master/installation/_build/yade/build/CMakeFiles/CMakeError.log".
Makefile:149: recipe for target 'yade-cmake' failed
make: *** [yade-cmake] Error 1