whitetshirtxi/chlamymodel

Hydrodynamic calculation on microswimmers

Library and executable code can be used with python3.

install instructions

chlamymodel

The chlamymodel library relies on pre-calculated friction matrices that are saved in the python_internal pickle format. Those are provided in the folder install_data and have to be copied into your ${HOME} folder:

mkdir -p ~/.chlamymodel
cp install_data/*.pickle ~/.chlamymodel

friction matrix

The friction matrices themselves are created with a pre-compiled program utilizing the fast-multipole boundary element method. Executable files for Windows and Linux as well as two configuration files are installed as follows:

mkdir -p ~/.FMBEM
cp install_data/*.exe ~/.FMBEM
cp install_data/*.cnd ~/.FMBEM

data files

The sperm cell, analyzed by Ben:

cp -r install_data/sperm_data ~/.sperm_data

Chlamydomonas cell, measured by Christian, analyzed by myself:

cp -r install_data/chlamy_data ~/.chlamy_data

library usage

To use the python libraries, set the python path accordingly

export PYTHONPATH=${PYTHONPATH}:${this_install}

with ${this_install} being the folder in which this README file is saved.

example files

The folders example_* contain python files that can be executed when the files in install_data are copied to their appropriate places, see install intructions.

example_chlamymodel

example_computing_friction

example_sperm_swimming

create the documentation

A documentation web-page can be generated using sphinx. For this aim, install sphinx. Then execute sphinx-quickstart from within the doc folder. It is important, that you do not overwrite the file doc/index/rst. Also, make use of the autodoc feature. Then, execute from within the doc folder:

./apidoc-everything # creates the documentation files for the modules
make html           # generates html from them

Then, there should be a folder _build/html containing the file index.html, which is to be opened in a web browser.