---
name: SIR_Script

system:
  - module: op_system
    spec:
      kind: expr
      state: [S, I, R]
      equations:
        S: -beta * S * I / sum_state()
        I: beta * S * I / sum_state() - gamma * I
        R: gamma * I
      initial_state:
        S: s0
        I: i0
        R: r0

engine:
  - module: op_engine
    state_change: flow
    config:
      method: heun
      adaptive: false
      strict: true
      rtol: 1.0e-6
      atol: 1.0e-9

simulate:
  demo:
    times: [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100]
  hires:
    times: 0.0:0.1:100.0

backend:
  - module: csv

process:
  plot_demo:
    module: shell
    command: python postprocessing/SIR_plot_op_engine.py
    args:
      - configs/config.yml
      - model_output/SIR_plot_op_engine.png

  r_plot:
    module: shell
    command: Rscript postprocessing/SIR_plot.R
    args:
      - configs/config.yml
      - model_output/SIR_plot.png

  notebook:
    module: ipynbrender
    file: postprocessing/SirPlot.ipynb
    output: model_output/SirPlot.html

parameter:
  beta: 0.3
  gamma: 0.1
  s0: 999
  i0: 1
  r0: 0