def instantiate():
''' returns four objects:
p: the parameter dictionary
r: reaction rates
m: model object
s: simulator
'''
p = parameters.Parameters()
r = reactionrates.Reactions()
m = model.PETC2014(p, r)
s = modelbase.Simulator(m)
print('Created a virtual organism. Experiment ready to run')
return p, r, m, s
m.add_algebraicModule(feq, 'rapidEq', ['A'], ['X', 'Y'])
# constant influx to the pool A
m.set_rate('v0', lambda p: p.v0)
m.set_stoichiometry('v0', {'A': 1})
# mass-action outflux from the pool A
# note that rate expression depends on variable Y!
def v2(p, y):
return p.k2 * y
m.set_rate('v2', v2, 'Y')
m.set_stoichiometry('v2', {'A': -1})
# use the AlgmSimulate class to get access to the variables X and Y
s = modelbase.Simulator(m)
s.timeCourse(np.linspace(0, 100, 1000), np.zeros(1))
#a = s.getVar([0])
#xy = np.array([eqm.getConcentrations(np.array([z])) for z in a])
#plt.figure()
#plt.plot(s.getT(),a)
#plt.plot(s.getT(),xy)
#plt.draw()
#plt.show()
plt.figure()
plt.plot(s.getT(), s.getY())
plt.legend(m.allCpdNames())
plt.draw_if_interactive()
y0 = Test.set_initconc_cpd_labelpos(y0d)
y0[Test.cpdIdDict['Glc6P100000']] = 30e-3
Test.par.update(PPP_model.par2) # Berthon1993 parameters, see PPPmodel
# time simulation
begin = 0
end = 300 * 60
steps = 10000
T = np.linspace(begin, end, steps)
s = modelbase.Simulator(Test)
s.integrator.linear_solver = 'SPGMR'
s.integrator.atol = 1e-15
s.integrator.rtol = 1e-15
import time
start_time = time.time()
s.timeCourse(T, y0)
print("--- %s seconds ---" % (time.time() - start_time))
# plot
plt.plot(s.getT() / 60, s.getVarByName('Glc6P100000') * 1000, label='Glc6P-C1')
plt.plot(s.getT() / 60,
s.getVarByName('Glc6P001000') * 5 * 1000,