BASE PROJECT DELUXE

This project is a basic example of an hABM (agents + PDEs) simulation, where "good" cells scan a 2D-surface (defined by a planar mesh) using BPRW (see link), in search of "evil" cells. The good cells are guided by chemical signals (chemokines) released by evil cells.

Example of a simulation on a planar surface:

LIBRARIES & DEPENDENCIES

This project uses the following libraries:

• geometry-central for intrinsic geodesic agent motion and surface metrics
• gmsh to create meshes (using the Python wrapper)
• MFEM for solving PDEs
• ParaView for visualizing simulation outputs

INSTALLATION & RUNNING

(NOTE: The following steps are meant for Ubuntu 24, with an other OS you might have to build the libraries from the source)

Basic requirements:

sudo apt install git g++ cmake

Install gmsh:

sudo apt install gmsh libgmsh-dev

Install MFEM:

sudo apt install libmfem-dev

Install geometry-central dependencies:

sudo apt install libeigen3-dev libsuitesparse-dev

Install geometry-central from source:

git clone --recurse-submodules https://github.com/nmwsharp/geometry-central.git && cd geometry-central
mkdir build && cd build
cmake ..
make -j4
sudo make install #to install the library in /usr/local/include

Compile Base_Project_Deluxe:

git clone https://github.com/PiSimo/Base_Project_Deluxe.git && cd Base_Project_Deluxe
mkdir build && cd build
cmake ..
make -j4

Running:

./Base_Project_Deluxe

the output files will be saved in output/.

OVERVIEW

more details here.