Simulation Workflow#

  1. Load configuration

  2. Initialize patches and initial conditions

  3. Load network adjacency matrix

  4. Flatten patch-compartment states into a single vector

  5. Construct the ODE right-hand side

  6. Solve using scipy.integrate.odeint

  7. Reshape results per patch

  8. Generate plots and outputs

All simulation logic is deterministic and continuous-time.