ssa
A monte carlo engine for running Ising and Potts-model type simulations
Dependencies
The easiest way to ensure all dependencies are met is to use a Python distribution, such as Anaconda (https://store.continuum.io/cshop/anaconda/) or Canopy (https://www.enthought.com/products/canopy/)
Specifically, this code uses:
NumPy (1.9)
Matplotlib (1.4)
PyYaml (http://pyyaml.org)
Cython (http://cython.org)
Installation
After cloning, simply run: ''' ./setup.sh '''
Make sure you add [mcmc]/lib and [mcmc]/src to your PYTHONPATH environmental variable, where
'[mcmc]' points to the directory of the monte_carlo code.
You may also want to add mcmc/bin to your PATH
Simulation setup
Simulations require two (YAML formatted) configuration files:
System configuration file
Defines system and simulation run parameters:
- Run parameters (Run time, etc)
- Lattice grid setup (number of lattice sites, neighbor list location)
- Species definitions
Parameter configuration file
Defines parameters for the system defined in the system config file:
- System temperature
- Force field (determining pairwise interaction energies)
- (Optional) site-specific functions (for, e.g. background potentials or chemical potentials)
- initial state of system
See examples examples for more details:
sim.cfg - Simulation config
params.cfg - Parameter config
Running a simulation
ssa_init : Preprocess configuration files and initialize simulation
ssa_run : Run or continue simulation from state file
You can use either command with option '-h' or '--help' for more information