Releases: martinzh/CollectiveDynamics.jl
First Release of the CollectiveDynamics.jl package
CollectiveDynamics.jl
A Julia language package of different models of collective motion of self-propelled particles and the theoretical study of their emergent properties and the dynamical effects of different kinds of interactions and environments.
Included Collective Motion Models
Simple Vicsek Model
Implementation of the Simple Vicsek Model within periodic boundaries condition introduced in Vicsek, T., Czirók, A., Ben-Jacob, E., Cohen, I. & Shochet, O. Novel type of phase transition in a system of self-driven particles. Phys. Rev. Lett. 75, 1226–1229 (1995). DOI 10.1103/physrevlett.75.1226. in 2D and 3D
Usage
Add module with using CollectiveDynamics.SVM2D for the 2D version and using CollectiveDynamics.SVM3D for the 3D version.
The scripts vicsek_2D_simulation.jl and vicsek_3D_simulation.jl in the Examples folder shows an example of using the module. Both scripts receive command line arguments, run them as: julia vicsek_2D_simulation.jl N rho eta T rep
- N: Number of particles
- rho: Density
- eta: Noise Intensity
- T: 10^T iterations
- rep: Ensemble index
The script will create a folder art_DATA/SVM_2D or art_DATA/SVM_3D and a folder structure within in the home directory were the files pos_rep.dat and vels_rep.dat with the positions and velocities of the particles will be saved. Both files are in binary format.
Behavioural Rules Model
Implementation of the Behavioural Rules Model introduced in Couzin, I.D., Krause, J., James, R., Ruxton, G.D. & Franks, N.R., (2002) Collective memory and spatial sorting in animal groups. Journal of Theoretical Biology 218, 1-11.
Usage
Add module with using CollectiveDynamics.BehaviouralRules
The script behavioural_rules_simulation.jl in the Examples folder shows an example of using the module. The script can be run in parallel and receives command line arguments, run it as: julia -p np behavioural_rules_simulation.jl N zoo zoa T rep init
- np: Number of processors
- N: Number of particles
- zoo: Size of the orientation zone relative to system size
- zoa: Size of the attraction zone relative to system size
- T: 10^T iterations
- rep: Ensemble index
- init: Initialization scheme, if
init = Rthen Random Initial Conditions ifinit = ARandom Initial Positions but aligned orientations.
The script will create a folder art_DATA/BEHAV_R_01_N_015 for the random initial conditions simulations and art_DATA/"BEHAV_R_01_N_015_AL for simulations starting from an ordered state and a folder structure within in the home directory were the files pos_rep.dat and vels_rep.dat with the positions and velocities of the particles will be saved. Both files are in binary format.
Extended Inertial Spin Model
Implementation of the Inertial Spin Model introduced in Cavagna, A. et al. Flocking and turning: a new model for self-organized collective motion. J. Stat. Phys. 158, 601–627 (2014). DOI 10.1007/s10955-014-1119-3. extended with long-range interactions.
Usage
Add module with using CollectiveDynamics.InertialSpin
The scripts inertial_spin_simulation.jl and inertial_spin_long_range_simulation.jl in the Examples folder show examples of using the module. The scripts receive command line arguments, run them as: julia inertial_spin_simulation.jl N eta T tau rep or julia inertial_spin_long_range_simulation.jl N eta T n_nl tau rep
- N: Number of particles
- eta: Dissipation term
- T: Temperature or noise
- n_nl: Average number of long-range interactions per particle
- tau: 10^tau iterations
- rep: Ensemble index
The script will create a folder art_DATA/INERTIAL_SPIN or art_DATA/EXTENDED_INERTIAL_SPIN and a folder structure within in the home directory were the files pos_rep.dat and vels_rep.dat with the positions and velocities of the particles will be saved. Both files are in binary format.
Collective Motion Model with Short and Long-range Interactions
A Collective Motion Model based on short and long-range alignment interactions between particles in open space. Short-range interactions can be defined either metric or topologically.
Usage
Add module with using CollectiveDynamics.ShortLongRange
The scripts SLR_metric_simulation.jl and SLR_top_simulation.jl in the Examples folder show examples of using the module for the case of metric or topological short-range interactions. The scripts can be run in parallel and receive command line arguments, run them as: julia -p np SLR_metric_simulation.jl N kappa omega eta Ti Tf rep or julia -p np SLR_top_simulation.jl N kappa omega eta Ti Tf rep
- np: Number of processors
- N: Number of particles
- kappa: Average long-range interactions per particle
- omega: Relative weight between short and long-range interactions in the system
- eta: Noise Intensity
- Ti: Start iterations at 10^Ti
- Tf: End iterations at 10^Tf
- rep: Ensemble index
The script will create a folder art_DATA/SLR_MET or art_DATA/SLR_TOP and a folder structure within in the home directory were the files pos_rep.dat and vels_rep.dat with the positions and velocities of the particles will be saved. Both files are in binary format.