Kinteic Monte Carlo - Facilitation

Modified kinetic Monte Carlo (kMC) code for running simulation of elastically interacting excitations.

How to Use

To compile the program, you need a C compiler, such as gcc, clang, etc. Use the following command:

gcc kmcres.c gsd.c -o kmcres.exe -lm

Running the Program

The executable requires 5 command-line arguments:

kmcres.exe (L) (kappa) (betaJ) (filename) (gsd_mode)

• L: System size
• kappa: Interaction strength parameter
• betaJ: Inverse temperature parameter
• filename: Base name for output files
• gsd_mode: Set to on or off. If on, the program generates a GSD file for trajectory data.

Output Files

Note that this program will generates 4 files.

1. filename.log:

Contains:

• Number of timesteps
• Simulation time
• Bond-order correlation
• Self-intermediate scattering function
• Mean-squared displacement
• Persistence function
• Number of excitation
• Boolean flag indicating whether the threshold has been reached.

2. filename.bin Checkpoint file used for restarting simulations.

3. filename.fin An empty file created when the simulation ends normally. Useful as a completion flag.

4. filename.gsd (only if gsd_mode is on) Stores trajectory data in GSD format, which contains:

• particles/N: Total number of lattice sites
• particles/position: Positions of the lattice sites
• particles/diameter: Persistence variable of each site (0 or 1).
• particles/typid: Site type identifier -- 0 for type A and 1 for type B, where type B indicates an excited site.
• configuration/box: System size information.
• configuration/step: Current kinetic Monte Carlo step.

Notes

• Ensure the gsd.h and gsd.c files are included and properly linked.
• The program assumes a lattice-based system in 2 dimension with kinetic constraints.
• GSD files can be visualized using Ovito or analyzed with Python libraries such as gsd and hoomd.