def simulate_stoch(base,
vol,
t=None,
ntraj=1,
increment=0.01,
job_id='',
y0_pop=None,
nrep=1):
stoch_fn = SSAModel(base, vol, nrep=nrep, y0_pop=y0_pop)
trajectories = stk.stochkit(stoch_fn,
job_id='Oregonator' + str(job_id),
t=t,
number_of_trajectories=ntraj,
increment=increment)
ts = trajectories[0][:, 0]
traj = np.array(trajectories)[:, :, 1:]
# Restructure trajectory array to recreate (replicate, time, state)
# indexing scheme
traj = traj.reshape((ntraj, len(ts), nrep, base.NEQ)) # Expand
traj = traj.swapaxes(2, 1) # Bring reps and traj to front
traj = traj.reshape(
(nrep * ntraj, len(ts), base.NEQ)) # Collapse to single axis
traj = traj / vol # return concentrations
return ts, traj
def simulate_stoch(base, vol, t=None, traj=100, increment=0.01, job_id=''):
stoch_fn = SSAModel(base, vol)
trajectories = stk.stochkit(stoch_fn,
job_id='brusselator' + str(job_id),
t=t,
number_of_trajectories=traj,
increment=increment)
ts = trajectories[0][:, 0]
traj = np.array(trajectories)[:, :, 1:] / vol
return ts, traj