Adhesion. This code implements adhesive interaction for ContactMechanics.
The methods that are implemented in this code are described in the following papers:
The following badge should say build passing. This means that all automated tests completed successfully for the master branch.
You need Python 3 and FFTW3 to run Adhesion. All Python dependencies can be installed automatically by invoking
# install Adhesion
pip install Adhesion
The last command will install other dependencies including muFFT, NuMPI and runtests
Note: sometimes muFFT will not find the FFTW3 installation you expect.
You can specify the directory where you installed FFTW3
by setting the environment variable FFTWDIR
(e.g. to $USER/.local
)
If you cloned the repository. You can install the dependencies with
pip install [--user] numpy
pip install [--user] pylint
pip install [--user] cython
pip install [--user] mpi4py #optional
pip3 install [--user] -r requirements.txt
in the source directory. Adhesion can be installed by invoking
pip3 install [--user] .
in the source directoy. The command line parameter --user is optional and leads to a local installation in the current user's $HOME/.local
directory.
bicubic.cpp
is linked with lapack
, that is already available as a dependency of numpy
.
If during build, setup.py
fails to link to one of the lapack implementations
provided by numpy, as was experienced for mac, try providing following environment variables:
export LDFLAGS="-L/usr/local/opt/openblas/lib $LDFLAGS"
export CPPFLAGS="-I/usr/local/opt/openblas/include $CPPFLAGS"
export PKG_CONFIG_PATH="/usr/local/opt/openblas/lib/pkgconfig:$PKG_CONFIG_PATH"
export LDFLAGS="-L/usr/local/opt/lapack/lib $LDFLAGS"
export CPPFLAGS="-I/usr/local/opt/lapack/include $CPPFLAGS"
export PKG_CONFIG_PATH="/usr/local/opt/lapack/lib/pkgconfig:$PKG_CONFIG_PATH"
where the paths have probably to be adapted to your particular installation method (here it was an extra homebrew installation).
If you update Adhesion (whether with pip or git pull
if you cloned the repository),
you may need to uninstall NuMPI
, muSpectre
and or runtests
, so that the
newest version of them will be installed.
To run the automated tests, go to the main source directory and execute the following:
pytest
Tests that are parallelizable have to run with runtests
python run-tests.py
You can choose the number of processors with the option --mpirun="mpirun -np 4"
. For development purposes you can go beyond the number of processors of your computer using --mpirun="mpirun -np 10 --oversubscribe"
Other usefull flags:
--xterm
: one window per processor--xterm --pdb
: debugging
To use the code without installing it, e.g. for development purposes, use the env.sh
script to set the environment:
source /path/to/Adhesion/env.sh [python3]
Note that the parameter to env.sh
specifies the Python interpreter for which the environment is set up. Adhesion contains portions that need to be compiled, make sure to run
python setup.py build
whenever any of the Cython (.pyx) sources are modified.
Please read CONTRIBUTING if you plan to contribute to this code.
The code is documented via Python's documentation strings that can be accesses via the help
command or by appending a questions mark ?
in ipython/jupyter. There are two command line tools available that may be a good starting point. They are in the commandline
subdirectory:
soft_wall.py
: Command line front end for calculations with soft (possibly adhesive) interactions between rigid and elastic flat. This is a stub rather than a fully featured command line tool that can be used as a starting point for modified script. The present implementation is set up for a solution of Martin Müser's contact mechanics challenge.
- After changes to the Adhesion source, you have to build again:
python setup.py build
- Navigate into the docs folder:
cd docs/
- Automatically generate reStructuredText files from the source:
sphinx-apidoc -o source/ ../Adhesion
Do just once, or if you have added/removed classes or methods. In case of the latter, be sure to remove the previous source before:rm -rf source/
- Build html files:
make html
- The resulting html files can be found in the
Adhesion/docs/_build/html/
folder. Root isAdhesion/docs/_build/html/index.html
.
For convenience, all these steps are implemented in compile_doc.sh
.
Development of this project is funded by the European Research Council within Starting Grant 757343 and by the Deutsche Forschungsgemeinschaft within projects PA 2023/2 and EXC 2193.