# Sabaody
# Copyright 2018 J Kyle Medley
from __future__ import print_function, division, absolute_import
from roadrunner import RoadRunner, Logger
Logger.disableConsoleLogging()
Logger.setLevel(Logger.LOG_FATAL)
from params import getDefaultParamValues, getUpperBound, getLowerBound
from b2problem import B2_UDP
from pygmo import island as pg_island, problem, rosenbrock, simulated_annealing, de, mp_island
from math import sqrt
def benchmark_loading_time():
import arrow
time_start = arrow.utcnow()
r = RoadRunner('../../../../../sbml/b2.xml')
delta_t = arrow.utcnow() - time_start
print('Loading time:', delta_t)
def benchmark_simulated_annealing():
island = pg_island(
algo=simulated_annealing(Ts=1.,Tf=.01),
prob=problem(B2_UDP(getLowerBound(),getUpperBound(),'../../../../../sbml/b2.xml')),
size=10)
N = 10
import arrow
time_start = arrow.utcnow()
from roadrunner import RoadRunner, Logger
#Logger.setLevel(Logger.LOG_DEBUG) # too verbose
Logger.setLevel(Logger.LOG_WARNING)
# Load model
rr = RoadRunner('/tmp/tx.sbml')
#rr = RoadRunner('/tmp/tx-reduced.sbml')
#rr = RoadRunner('/tmp/antsbml.xml')
# Simulate model
results = rr.simulate(0, 10, 30, integrator='gillespie')
print(results)
# Write results to temp file
with open('/tmp/sim_res.csv', 'w') as f:
f.write(str(results))
# Plot
rr.plot()
