These minimal samples show how to run default-initialized simulations. Please see the provided .cpp files in the main directory and examples directory for more samples, or consult the documentation for more advanced usage.

Vertex.cpp

A simple interface that initializes and runs a simulation of the 2D vertex model. After being built with the included makefile, command line parameters can be passed in, controlling the number of cells, the number of initialization time steps, the number of production-run time steps, the time step size, the preferred cell energy and motility parameters, etc. This program can be used to reproduce the timing information in the cellGPU paper.

voronoi.cpp

The same thing, but for running the 2D Voronoi model

minimize.cpp

Provides an example of using the FIRE minimizer to minimize either a 2D Voronoi or AVM system.

runMakeDatabase.cpp

Provides an example of using the NetCDF database class to write snapshots of a simulation of the 2D Voronoi model, using either active cell or overdamped Brownian dynamics

tensions.cpp

Provides a simple example of adding line tension terms to a Voronoi model

vertexTensions.cpp

Provides a simple example of adding line tension terms to a 2D vertex model... see comments in this file for caveats

cellDivision.cpp

Provides a simple example of both vertex and voronoi models with cell division activated

cellDeath.cpp

Provides a simple example of both vertex and voronoi models with cell death activated... very similar to cellDivision, but particularly in the vertex model some extra care is needed

dynMat.cpp

Provides an example of computing the dynamical matrix of a minimized voronoi model and using the Eigen interface to diagonalize it.

nvtVoronoi.cpp

Example setting up and using the NoseHooverChainNVT integrator. Nothing special