# define explicit system of ODEs
def rule_odes(m, t):
exprs = dict()
exprs['A'] = -m.P['k1'] * m.Z[t, 'A']
exprs['B'] = m.P['k1'] * m.Z[t, 'A'] - m.P['k2'] * m.Z[t, 'B']
exprs['C'] = m.P['k2'] * m.Z[t, 'B']
return exprs
builder.set_odes_rule(rule_odes)
sim_model = builder.create_pyomo_model(0.0, 50.0)
#################################################################################
#: non absorbing species.
non_abs = ['C']
builder.set_non_absorbing_species(sim_model, non_abs)
#################################################################################
#=========================================================================
#USER INPUT SECTION - SIMULATOR - See user guide for how this section functions
#=========================================================================
# create instance of simulator
simulator = PyomoSimulator(sim_model)
simulator.apply_discretization('dae.collocation',
nfe=20,
ncp=3,
scheme='LAGRANGE-RADAU')
# simulate with fixed variances
sigmas = {'device': 1e-8, 'A': 1e-6, 'B': 1e-7}
results_sim = simulator.run_sim('ipopt',
exprs[c] = gammas[c][0] * m.Y[t, '0'] + gammas[c][1] * m.Y[t, '1']+gammas[c][2] * m.Y[t, '2']+gammas[c][3] * m.Y[t, '3']+ gammas[c][4] * m.Y[t, '4'] - exprs['V'] / V * m.Z[t, c]
if c == 'C':
exprs[c] += 0.02247311828 / (m.X[t, 'V'] * 210) * step
return exprs
builder.set_odes_rule(rule_odes)
#Add time points where feed as discrete jump should take place:
feed_times=[101.035, 303.126]#, 400.
builder.add_feed_times(feed_times)
model = builder.create_pyomo_model(0, 600)
non_abs = ['F']
builder.set_non_absorbing_species(model, non_abs)
#Load data:
dataDirectory = os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))), 'data_sets'))
filenameD = os.path.join(dataDirectory,'FeCaseexamplewithoutTemp_D_data_input_noiselesspoints2.csv')
D_frame = read_spectral_data_from_csv(filenameD)
builder.add_spectral_data(D_frame)
model = builder.create_pyomo_model(0., 600.)
#Absorbing Simulation for Initialization:
#=========================================================================
#USER INPUT SECTION - FE Factory
#=========================================================================
#call FESimulator
