mirror of https://github.com/gsi-upm/soil
You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
104 lines
3.0 KiB
Python
104 lines
3.0 KiB
Python
# Verbatim copy from mesa
|
|
# https://github.com/projectmesa/mesa/blob/976ddfc8a1e5feaaf8007a7abaa9abc7093881a0/examples/virus_on_network/virus_on_network/model.py
|
|
import math
|
|
from enum import Enum
|
|
import networkx as nx
|
|
|
|
from soil import *
|
|
|
|
|
|
class State(Enum):
|
|
SUSCEPTIBLE = 0
|
|
INFECTED = 1
|
|
RESISTANT = 2
|
|
|
|
|
|
class VirusOnNetwork(Environment):
|
|
"""A virus model with some number of agents"""
|
|
num_nodes = 10
|
|
avg_node_degree = 3
|
|
initial_outbreak_size = 1
|
|
virus_spread_chance = 0.4
|
|
virus_check_frequency = 0.4
|
|
recovery_chance = 0
|
|
gain_resistance_chance = 0
|
|
|
|
def init(self):
|
|
prob = self.avg_node_degree / self.num_nodes
|
|
# Use internal seed with the networkx generator
|
|
self.create_network(generator=nx.erdos_renyi_graph, n=self.num_nodes, p=prob)
|
|
|
|
self.initial_outbreak_size = min(self.initial_outbreak_size, self.num_nodes)
|
|
self.populate_network(VirusAgent)
|
|
|
|
# Infect some nodes
|
|
infected_nodes = self.random.sample(list(self.G), self.initial_outbreak_size)
|
|
for a in self.agents(node_id=infected_nodes):
|
|
a.status = State.INFECTED
|
|
assert self.number_infected == self.initial_outbreak_size
|
|
|
|
@report
|
|
def resistant_susceptible_ratio(self):
|
|
try:
|
|
return self.number_resistant / self.number_susceptible
|
|
except ZeroDivisionError:
|
|
return math.inf
|
|
|
|
@report
|
|
@property
|
|
def number_infected(self):
|
|
return self.count_agents(status=State.INFECTED)
|
|
|
|
@report
|
|
@property
|
|
def number_susceptible(self):
|
|
return self.count_agents(status=State.SUSCEPTIBLE)
|
|
|
|
@report
|
|
@property
|
|
def number_resistant(self):
|
|
return self.count_agents(status=State.RESISTANT)
|
|
|
|
|
|
|
|
class VirusAgent(Agent):
|
|
status = State.SUSCEPTIBLE
|
|
virus_spread_chance = None # Inherit from model
|
|
virus_check_frequency = None # Inherit from model
|
|
recovery_chance = None # Inherit from model
|
|
gain_resistance_chance = None # Inherit from model
|
|
|
|
def try_to_infect_neighbors(self):
|
|
susceptible_neighbors = self.get_neighbors(status=State.SUSCEPTIBLE)
|
|
for a in susceptible_neighbors:
|
|
if self.prob(self.virus_spread_chance):
|
|
a.status = State.INFECTED
|
|
|
|
def try_gain_resistance(self):
|
|
if self.prob(self.gain_resistance_chance):
|
|
self.status = State.RESISTANT
|
|
return self.at(INFINITY)
|
|
|
|
def try_remove_infection(self):
|
|
# Try to remove
|
|
if self.prob(self.recovery_chance):
|
|
# Success
|
|
self.status = State.SUSCEPTIBLE
|
|
return self.try_gain_resistance()
|
|
|
|
def try_check_situation(self):
|
|
if self.prob(self.virus_check_frequency):
|
|
# Checking...
|
|
if self.status is State.INFECTED:
|
|
return self.try_remove_infection()
|
|
|
|
def step(self):
|
|
if self.status is State.INFECTED:
|
|
self.try_to_infect_neighbors()
|
|
return self.try_check_situation()
|
|
|
|
|
|
|
|
if __name__ == "__main__":
|
|
from _config import run_sim
|
|
run_sim(model=VirusOnNetwork) |