Adhesion

Adhesion. This code implements adhesive interaction for ContactMechanics.

The methods that are implemented in this code are described in the following papers:

• Pastewka, Robbins, PNAS 111, 3298 (2014)

Build status

The following badge should say build passing. This means that all automated tests completed successfully for the master branch.

Tests:

Building documentation:

Documentation

Computer-generated overview of code structure:

Sphinx built documentation

Installation

You need Python 3 and FFTW3 to run Adhesion. All Python dependencies can be installed automatically by invoking

Installation directly with pip

# 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)

Installation from source directory

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.

Installation problems with lapack and openblas

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).

Updating Adhesion

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.

Testing

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

Development

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.

Usage

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.

Compiling the documentation

• 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 is Adhesion/docs/_build/html/index.html.

For convenience, all these steps are implemented in compile_doc.sh.

Funding

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.