def test_verbose(self):
solver = CupSodaSimulator(model, tspan=self.tspan, verbose=True,
vol=1e-5,
integrator_options={'atol': 1e-12,
'rtol': 1e-12,
'max_steps': 20000})
solver.run()
def test_multi_chunks(self):
sim = CupSodaSimulator(model,
tspan=self.tspan,
verbose=False,
initials=self.y0,
integrator_options={
'atol': 1e-12,
'rtol': 1e-12,
'chunksize': 25,
'max_steps': 20000
})
res = sim.run()
assert res.nsims == self.n_sims
def setUp(self):
self.n_sims = 50
self.tspan = np.linspace(0, 500, 101)
self.solver = CupSodaSimulator(model, tspan=self.tspan, verbose=False,
integrator_options={'atol': 1e-12,
'rtol': 1e-12,
'max_steps': 20000})
len_model_species = len(model.species)
y0 = np.zeros((self.n_sims, len_model_species))
for ic in model.initial_conditions:
for j in range(len_model_species):
if str(ic[0]) == str(model.species[j]):
y0[:, j] = ic[1].value
break
self.y0 = y0
def run():
n_sims = 100
vol = model.parameters['vol'].value
tspan = np.linspace(0, 500, 501)
sim = CupSodaSimulator(model,
tspan,
vol=vol,
verbose=True,
integrator_options={
'atol': 1e-12,
'rtol': 1e-6,
'max_steps': 20000
})
# Rate constants
param_values = np.ones((n_sims, len(model.parameters)))
for i in range(len(param_values)):
for j in range(len(param_values[i])):
param_values[i][j] *= model.parameters[j].value
# Initial concentrations
initials = np.zeros((n_sims, len(model.species)))
for i in range(len(initials)):
for ic in model.initial_conditions:
for j in range(len(initials[i])):
if str(ic[0]) == str(model.species[j]):
initials[i][j] = ic[1].value
break
x = sim.run(initials=initials, param_values=param_values)
# Plot results of the first simulation
t = x.tout[0]
plt.plot(t, x.all[0]['CT'], lw=2, label='CT') # should be constant
plt.plot(t, x.all[0]['YT'], lw=2, label='YT')
plt.plot(t, x.all[0]['M'], lw=2, label='M')
plt.xlabel('time')
plt.ylabel('population')
plt.legend(loc=0)
plt.show()
def test_invalid_integrator_option(self):
CupSodaSimulator(model,
tspan=self.tspan,
integrator_options={'spam': 'eggs'})
def test_invalid_init_kwarg(self):
CupSodaSimulator(model, tspan=self.tspan, spam='eggs')
# repeated_parameter_values[:, idx] = sample_lognormal(par, size=samples)
# np.save('earm_diff_IC_par0.npy', repeated_parameter_values)
repeated_parameter_values = np.load('earm_diff_IC_par0.npy')
rate_params = model.parameters_rules()
rate_idxs = [idx for idx, p in enumerate(model.parameters) if p in rate_params]
for par_idx in rate_idxs:
repeated_parameter_values[:, par_idx] = par_clus4[par_idx]
t = np.linspace(0, 20000, 100)
vol = 1e-19
integrator_opt = {'rtol': 1e-6, 'atol': 1e-6, 'mxsteps': 20000}
sims = CupSodaSimulator(model,
tspan=t,
obs_species_only=False,
gpu=0,
memory_usage='shared_constant',
vol=vol,
integrator_options=integrator_opt).run(
param_values=repeated_parameter_values)
sims.save('earm_cupsoda_sims_ic_par1.h5')
signatures = run_tropical_multi(model=model,
simulations=sims,
cpu_cores=30,
verbose=True)
with open('earm_signatures_ic_par1.pickle', 'wb') as handle:
pickle.dump(signatures, handle, protocol=pickle.HIGHEST_PROTOCOL)