jonaseichinger/bionetgen

Voronoi

Voronoi network generation algorithm extracted from the input generator

Building

$ mkdir build
$ cd build
$ cmake ..
$ make
$ cd ..

Usage

$ ./build/voronoi config.json

Configuration

Use the config.json file to set parameters for the algorithm.

The main operation mode can be selected by changing the values of generate and simulate in the config file. If only generate is true, a voronoi geometry will be generated and saved as the output. If simulate is also true, simulated annealing will additionally be performed before the geometry is saved to the output files. If only simulate is true, a previously saved geometry will be read from the input files, simulated annealing will be perfomed and the result will be saved to the output files.

Parameters

seed: The seed for the random number generator (can be any integer number)

particles: The number of Voronoi particles (can be any number greater 5)

input-prefix: The path prefix of the input files if simulated annealing is done on a previously generated geometry (relative to the working directory, optional)

output-prefix: The path prefix for the output files (relative to the working directory, not the )

generate: If a voronoi geometry should be generated (can be true or false)

simulate: If simulated annealing should be performed on a voronoi geometry (can be true or false)

box-size: The size of the box containing the voronoi geometry to be generated (must be an array of 3 positive values)

box-origin: The origin of the box (must be an array of 3 values)

simulated-annealing: Options for simulated annealing (if needed)

mode: Simulated annealing mode (can be 1, 2 or "both")

max-iter: Maximum number of iterations (can be any positive integer)

max-subiter: Maximum number of sub-iterations (can be any positive integer)

weight-line: Line weight (can be any positive value)

weight-cosine: Cosine weight (can be any positive value)

tolerance: Tolerance (can be any positive value)

temperature-initial: Initial temperature (can be any positive value)

temperature-decay-rate: Temperature decay rate (can be any positive value)

max-movement-frac: Maximum movement fraction (can be any value between 0 and 1)

screen-output-every: After how many iterations screen output is produced (can be any positive integer)

num-bins-length: Number of bins per length (can be any positive integer)

num-bins-cosine: Number of bins per cosine (can be any positive integer)

Acknowledgements

This project uses the library voro++ by Chris Rycroft from University of California, through Lawrence Berkeley National Laboratory, for the generation of the voronoi geometry, which can be downloaded from http://math.lbl.gov/voro%2B%2B/.