Celadro: Cells as active droplets

Phase-field modelling of epithelial cells using finite-difference integrator.
Example movie 1 Example movie 2

Publications

This code has served as a basis for the simulations included in the following papers:

Active Inter-cellular Forces in Collective Cell Motility
G Zhang, R Mueller, A Doostmohammadi, JM Yeomans
arXiv preprint arXiv:2005.13087, 2020
Emergence of active nematic behavior in monolayers of isotropic cells
R Mueller, JM Yeomans, A Doostmohammadi
Physical review letters 122 (4), 048004
Movie 1 Movie 1
Sustained oscillations of epithelial cell sheets
G Peyret, R Mueller, J d'Alessandro, et al.
Biophysical journal 117 (3), 464-478

Building

We use cmake. Typically you would type:

mkdir build
cd build
cmake ..
make

We rely on the boost::program_options which must be installed prior to building the program. We also use modern C++ features, such that you will require a modern compiler (tested with g++-4.9).

Running

The code is run from the command line and a runcard must always be given as the first argument:

./celadro runcard.dat [options]

A runcard is a simple file providing the parameters for the run. Example runcards can be found in the example/ directory. Every option can also be given to the program using the command line as ./celadro runcard.dat --option=arg. A complete list of available options can be obtained by typing ./celadro -h.

By default the program writes output files in the current directory. This can be changed using --output=dir/ or -o dir/, where dir/ is the target directory. The program also supports compressed (using zip) output with the option flag --compression or -c. Typical usage is ./celadro runcard.dat -fco output/

Type ./celadro -h for a list of available options.

Examples

Examples runs and ploting scripts can be found in the example directory. Try to run bash make_all_movies.sh and have a look at the results.

Multi-threading and CUDA

WARNING !!! this feature is currently unmaintained and can not be used for now (2020) !!!

The code supports both multi-threading and CUDA. The CUDA-enabled version of the code can be built using

mkdir build-cuda
cd build-cuda
cmake ..
make celadro-cuda

Troubleshooting

Hard to solve linking problems with `boost::program_options`

On some platforms the compiler might be unable to link to the boost library properly which results in undefined reference errors. This can be due to the installed boost libraries using a different ABI than the code when it is compiled with a recent compiler. In order to solve this problem, either switch back to an older compiler (e.g. gcc-4.9) or uncomment the line

add_definitions(-D_GLIBCXX_USE_CXX11_ABI=0)

in CMakeLists.txt.

rhomu/celadro