def run_simulator(seed, num_days):
"""
Runs the simulator once.
Configures the num_days and seed parameter of the simulator.
:param seed for the random number generator, used by the simulator
:param num_days the number of days (steps) the simulator needs to run.
"""
simulator = Simulation()
simulator.loadRunConfig("../config/run_default_nolog.xml")
set_influenza(simulator)
simulator.runConfig.setParameter("rng_seed", seed)
simulator.run()
def runBaseline():
"""
Execute the baseline case.
"""
sim = Simulation()
# Set parameters
sim.runConfig.setParameter("output_prefix", "Baseline")
sim.runConfig.setParameter("num_days", 60)
sim.runConfig.setParameter("disease_config_file",
"data/disease_measles.xml")
sim.runConfig.setParameter("r0", 11)
sim.runConfig.setParameter("seeding_rate", 0)
sim.runConfig.setParameter("seeding_age_min", 1)
sim.runConfig.setParameter("seeding_age_max", 99)
sim.runConfig.setParameter("population_file", "data/pop_flanders600.csv")
sim.runConfig.setParameter("output_persons", "false")
sim.runConfig.setParameter("num_participants_survey", 10000)
sim.runConfig.setParameter("age_contact_matrix_file",
"data/contact_matrix_flanders_subpop.xml")
sim.runConfig.setParameter("log_level", "SusceptibleContacts")
sim.runConfig.setParameter("start_date", "2017-01-01")
sim.runConfig.setParameter("holidays_file", "data/holidays_none.json")
# immunity_profile
# vaccine_profile
# vaccine_link_probability
# immunity_rate
# vaccine_rate
sim.runConfig.setParameter("local_information_policy",
"NoLocalInformation")
sim.runConfig.setParameter("global_information_policy",
"NoGlobalInformation")
sim.runConfig.setParameter("belief_policy/name", "NoBelief")
sim.runConfig.setParameter("behaviour_policy", "NoBehaviour")
sim.runConfig.setParameter("rng_seed", 1)
# Register callbacks
sim.RegisterCallback(measureSusceptiblesClustering)
sim.RegisterCallback(seedInfection)
# TODO run forks with varying parameters (itertools.product(...))
# Run simulation
sim.run()
from pystride.Simulation import Simulation
if not len(sys.argv) == 2:
sys.exit(
"Please add the amount of runs as an argument: \npython3 runExperimentsBatchRuns.py 100"
)
t_start = time.perf_counter()
try:
amount_of_runs = int(sys.argv[1])
except ValueError:
sys.exit("amount of runs is not a number.")
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_batchruntests1.xml")
simulation.runConfig.setParameter("output_prefix", "BatchRunsTesting")
# Create forks with different values for RNG
RNG_values = []
for i in range(amount_of_runs):
RNG_values.append(random.randint(0, 4294967294))
for rng in RNG_values:
# Create fork
fork = simulation.fork("rng_" + str(rng))
fork.runConfig.setParameter("rng_seed", rng)
# Run all forks
simulation.runForks()
import pystride
from pystride.Simulation import Simulation
pystride.workspace = "simulations"
def checkFinished(sim, timestep):
pop = sim.GetSimulator().GetPopulation()
infected = pop.GetInfectedCount()
print("Amount infected: ", infected)
if infected >= 4000:
sim.Stop()
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
simulation.runConfig.setParameter("generate_person_file", 0)
simulation.registerCallback(checkFinished)
simulation.run()
import itertools
import pystride
from pystride.Simulation import Simulation
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
simulation.runConfig.setParameter("num_days", 10)
# Create forks with varying parameters
for b0, ir in list(itertools.product([14, 10, 5], [0.2, 0.4, 0.6])):
# Create fork
fork = simulation.fork("b0_" + str(b0) + "-ir_" + str(ir))
fork.diseaseConfig.setParameter("transmission/b0", b0)
fork.runConfig.setParameter("immunity_rate", ir)
fork.runConfig.setParameter("r0", 15)
# Run all forks
simulation.runForks()
import random
import csv
import pystride
from pystride.Simulation import Simulation
# RNG types to test
# Note: Default (mrg2) -- See results from previous test
RNG_TYPES = ["lcg64", "yarn2", "lcg64_shift", "mrg3", "yarn3"]
# Amount of random values to test
amount_of_runs = 1
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_batch_measles.xml")
simulation.runConfig.setParameter("output_prefix", "BatchRngTypeTesting")
# Initialize the random values
rng_values = []
for i in range(amount_of_runs)):
rng_values.append(random.randint(0, 4294967294))
## Create Forks
for rng_type in RNG_TYPES:
for rng_value in rng_values:
# measles_16
fork16 = simulation.fork("measles_16_" + rng_type + "_" + str(rng_value))
fork16.runConfig.setParameter("r0", 16)
fork16.runConfig.setParameter("rng_type", rng_type)
fork16.runConfig.setParameter("rng_seed", rng_value)
from pystride.Simulation import Simulation
# Load run configuration
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
# Run the simulation
simulation.run()
if not len(sys.argv) == 2:
sys.exit(
"Please add the amount of runs as an argument: \npython3 runThreads_influenza.py 100"
)
try:
amount_of_runs = int(sys.argv[1])
except ValueError:
sys.exit("amount of runs is not a number.")
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_batch_measles.xml")
simulation.runConfig.setParameter("output_prefix", "BatchThreadTesting")
## Create Forks
# measles_16
for i in range(0, amount_of_runs):
fork = simulation.fork("measles_16_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
fork.runConfig.setParameter("r0", 16)
# measles_60
for i in range(0, amount_of_runs):
fork = simulation.fork("measles_60_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
fork.runConfig.setParameter("r0", 60)
#############################################################################
# Script for simulations with no-vaccination clustering #
# using Imitation belief policy. #
#############################################################################
import itertools
import pystride
from pystride.Simulation import Simulation
# TODO callback to vaccinate + seed after x days
sim = Simulation()
sim.loadRunConfig("config/common.xml")
# Set parameters that are the same for all simulations
sim.runConfig.setParameter("output_prefix", "Imitation")
sim.runConfig.setParameter("seeding_rate", 0)
# TODO natural immunity?
sim.runConfig.setParameter("immunity_rate", 0)
sim.runConfig.setParameter("vaccine_rate", 0)
sim.runConfig.setParameter("local_information_policy", "LocalDiscussion")
sim.runConfig.setParameter("global_information_policy", "NoLocalInformation")
sim.runConfig.setParameter("belief_policy/name", "Imitation")
sim.runConfig.setParameter("belief_policy/accept_threshold", 0.95)
sim.runConfig.setParameter("belief_policy/no_accept_threshold", -0.95)
sim.runConfig.setParameter("behaviour_policy", "Vaccination")
seeds = list(range(10))
import pystride
from pystride.Simulation import Simulation
simulation = Simulation()
# Load disease from configuration file
simulation.loadDiseaseConfig("../data/disease_influenza.xml")
simulation.diseaseConfig.setParameter("transmission/b0", 0.35)
# Configure simulation
simulation.runConfig.setParameter("rng_seed", 1)
simulation.runConfig.setParameter("r0", 5)
simulation.runConfig.setParameter("seeding_rate", 0.002)
simulation.runConfig.setParameter("seeding_age_min", 1)
simulation.runConfig.setParameter("seeding_age_max", 99)
simulation.runConfig.setParameter("immunity_rate", 0.8)
simulation.runConfig.setParameter("immunity_profile", "None")
simulation.runConfig.setParameter("vaccine_profile", "Random")
simulation.runConfig.setParameter("vaccine_rate", 0.8)
simulation.runConfig.setParameter("vaccine_link_probability", 0)
simulation.runConfig.setParameter("population_file", "pop_antwerp.csv")
simulation.runConfig.setParameter("num_days", 10)
simulation.runConfig.setParameter("output_prefix", "simulation1")
simulation.runConfig.setParameter("output_persons", "true")
simulation.runConfig.setParameter("num_participants_survey", 10)
simulation.runConfig.setParameter("start_date", "2017-01-01")
simulation.runConfig.setParameter("holidays_file",
"holidays_flanders_2017.json")
simulation.runConfig.setParameter("age_contact_matrix_file",
"contact_matrix_flanders_subpop.xml")
simulation.runConfig.setParameter("log_level", "Transmissions")
from pystride.Simulation import Simulation
def vaccinate(sim, timestep):
if timestep == 20:
print("Vaccinating everyone who is not yet infected")
pop = sim.GetSimulator().GetPopulation()
for pIndex in range(pop.size()):
if pop[pIndex].GetHealth().IsSusceptible():
pop[pIndex].GetHealth().SetImmune()
# Build simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
# Register the "vaccinate" callback
simulation.registerCallback(vaccinate)
simulation.run()
from pystride.Simulation import Simulation
# The callback function
def printInfected(sim, timestep):
if (timestep % 2) == 0:
print("Amount infected at timestep {}: {}".format(
timestep, sim.GetSimulator().GetPopulation().GetInfectedCount()))
# Build simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
# Register callback
simulation.registerCallback(printInfected)
simulation.run()
##########################################################
# Script to obtain number of cases for various RNG values #
##########################################################
import csv
import os
import time
import pystride
from pystride.Simulation import Simulation
t_start = time.perf_counter()
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
simulation.runConfig.setParameter("output_prefix", "RNGRuns")
# Create forks with different values for RNG
RNG_values = [
7432523, 4755593, 4830240, 5399722, 9682632, 988142, 3270739, 6738734,
9510033
]
for rng in RNG_values:
# Create fork
fork = simulation.fork("rng_" + str(rng))
fork.runConfig.setParameter("rng_seed", rng)
# Run all forks
simulation.runForks()
import pystride
from pystride.Simulation import Simulation
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_default.xml")
simulation.runConfig.setParameter("num_days", 10)
# Create 5 identical forks except for the seed
for index in range(5):
fork = simulation.fork("instance" + str(index))
fork.runConfig.setParameter("rng_seed", index)
# Run all forks
simulation.runForks()
if not len(sys.argv) == 2:
sys.exit(
"Please add the amount of runs as an argument: \npython3 runThreads_influenza.py 100"
)
try:
amount_of_runs = int(sys.argv[1])
except ValueError:
sys.exit("amount of runs is not a number.")
# Set the workspace (default = .)
pystride.workspace = "simulations"
# Configure simulation
simulation = Simulation()
simulation.loadRunConfig("../config/run_batch_default.xml")
simulation.runConfig.setParameter("output_prefix", "BatchThreadTesting")
## Create Forks
# Influenza_a
for i in range(0, amount_of_runs):
fork = simulation.fork("influenza_a_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
# influenza_b
for i in range(0, amount_of_runs):
fork = simulation.fork("influenza_b_" + str(i))
fork.runConfig.setParameter("rng_seed", random.randint(0, 4294967294))
fork.runConfig.setParameter("seeding_rate", 0)
# influenza_c
for i in range(0, amount_of_runs):
