CellGPU
0.8.0
GPUaccelerated simulations of cells

These minimal samples show how to run defaultinitialized 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.
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 productionrun 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.
The same thing, but for running the 2D Voronoi model
Provides an example of using the FIRE minimizer to minimize either a 2D Voronoi or AVM system.
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
Provides a simple example of adding line tension terms to a Voronoi model
Provides a simple example of adding line tension terms to a 2D vertex model... see comments in this file for caveats
Provides a simple example of both vertex and voronoi models with cell division activated
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
Provides an example of computing the dynamical matrix of a minimized voronoi model and using the Eigen interface to diagonalize it.
Example setting up and using the NoseHooverChainNVT integrator. Nothing special