Generated Code
The following is python code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 16
sizeStates = 9
sizeConstants = 16
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_voi = "time in component environment (hour)"
legend_states[0] = "A in component A (molecules)"
legend_algebraic[0] = "RXN1 in component RXN1 (flux)"
legend_algebraic[1] = "RXN2 in component RXN2 (flux)"
legend_algebraic[4] = "RXN5 in component RXN5 (flux)"
legend_algebraic[10] = "RXN11 in component RXN11 (flux)"
legend_algebraic[5] = "RXN6 in component RXN6 (flux)"
legend_algebraic[9] = "RXN10 in component RXN10 (flux)"
legend_algebraic[11] = "RXN12 in component RXN12 (flux)"
legend_states[1] = "C in component C (molecules)"
legend_algebraic[2] = "RXN3 in component RXN3 (flux)"
legend_states[2] = "DA in component DA (molecules)"
legend_algebraic[6] = "RXN7 in component RXN7 (flux)"
legend_states[3] = "DAp in component DAp (molecules)"
legend_algebraic[7] = "RXN8 in component RXN8 (flux)"
legend_states[4] = "DR in component DR (molecules)"
legend_algebraic[12] = "RXN13 in component RXN13 (flux)"
legend_states[5] = "DRP in component DRP (molecules)"
legend_algebraic[13] = "RXN14 in component RXN14 (flux)"
legend_states[6] = "MA in component MA (molecules)"
legend_algebraic[8] = "RXN9 in component RXN9 (flux)"
legend_states[7] = "MR in component MR (molecules)"
legend_algebraic[14] = "RXN15 in component RXN15 (flux)"
legend_algebraic[15] = "RXN16 in component RXN16 (flux)"
legend_states[8] = "R in component R (molecules)"
legend_algebraic[3] = "RXN4 in component RXN4 (flux)"
legend_constants[0] = "Gamma_1 in component RXN1 (second_order_rate)"
legend_constants[1] = "Delta_1 in component RXN2 (first_order_rate)"
legend_constants[2] = "Delta_2 in component RXN3 (first_order_rate)"
legend_constants[3] = "Delta_3 in component RXN4 (first_order_rate)"
legend_constants[4] = "Gamma_2 in component RXN5 (second_order_rate)"
legend_constants[5] = "Thetha_1 in component RXN6 (first_order_rate)"
legend_constants[6] = "Alpha_1 in component RXN7 (first_order_rate)"
legend_constants[7] = "Alpha_2 in component RXN8 (first_order_rate)"
legend_constants[8] = "Delta_4 in component RXN9 (first_order_rate)"
legend_constants[9] = "BetaA_1 in component RXN10 (first_order_rate)"
legend_constants[10] = "Gamma_3 in component RXN11 (second_order_rate)"
legend_constants[11] = "Theta_2 in component RXN12 (first_order_rate)"
legend_constants[12] = "Alpha_3 in component RXN13 (first_order_rate)"
legend_constants[13] = "Alpha_4 in component RXN14 (first_order_rate)"
legend_constants[14] = "Delta_5 in component RXN15 (first_order_rate)"
legend_constants[15] = "BetaR_1 in component RXN16 (first_order_rate)"
legend_rates[0] = "d/dt A in component A (molecules)"
legend_rates[1] = "d/dt C in component C (molecules)"
legend_rates[2] = "d/dt DA in component DA (molecules)"
legend_rates[3] = "d/dt DAp in component DAp (molecules)"
legend_rates[4] = "d/dt DR in component DR (molecules)"
legend_rates[5] = "d/dt DRP in component DRP (molecules)"
legend_rates[6] = "d/dt MA in component MA (molecules)"
legend_rates[7] = "d/dt MR in component MR (molecules)"
legend_rates[8] = "d/dt R in component R (molecules)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.0
states[1] = 0.0
states[2] = 1
states[3] = 0.0
states[4] = 1
states[5] = 1
states[6] = 0.0
states[7] = 0.0
states[8] = 0.0
constants[0] = 2
constants[1] = 1
constants[2] = 1
constants[3] = 0.2
constants[4] = 1
constants[5] = 50
constants[6] = 50
constants[7] = 500
constants[8] = 10
constants[9] = 50
constants[10] = 1
constants[11] = 100
constants[12] = 0.01
constants[13] = 50
constants[14] = 0.5
constants[15] = 5
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[0] = states[0]*states[8]*constants[0]
algebraic[2] = states[1]*constants[2]
rates[1] = (1.00000/1.00000)*(-1.00000*algebraic[2]+algebraic[0])
algebraic[4] = states[0]*states[2]*constants[4]
algebraic[5] = states[3]*constants[5]
algebraic[6] = states[2]*constants[6]
rates[2] = (1.00000/1.00000)*(-1.00000*algebraic[4]+-1.00000*algebraic[6]+algebraic[5]+algebraic[6])
algebraic[7] = states[3]*constants[7]
rates[3] = (1.00000/1.00000)*(-1.00000*algebraic[5]+-1.00000*algebraic[7]+algebraic[4]+algebraic[7])
algebraic[9] = states[6]*constants[9]
algebraic[8] = states[6]*constants[8]
rates[6] = (1.00000/1.00000)*(-1.00000*algebraic[8]+-1.00000*algebraic[9]+algebraic[6]+algebraic[7]+algebraic[9])
algebraic[1] = states[0]*constants[1]
algebraic[10] = states[0]*states[4]*constants[10]
algebraic[11] = states[5]*constants[11]
rates[0] = (1.00000/1.00000)*(-1.00000*algebraic[0]+-1.00000*algebraic[1]+-1.00000*algebraic[4]+-1.00000*algebraic[10]+algebraic[5]+algebraic[9]+algebraic[11])
algebraic[12] = states[4]*constants[12]
rates[4] = (1.00000/1.00000)*(-1.00000*algebraic[10]+-1.00000*algebraic[12]+algebraic[11]+algebraic[12])
algebraic[13] = states[5]*constants[13]
rates[5] = (1.00000/1.00000)*(-1.00000*algebraic[11]+-1.00000*algebraic[13]+algebraic[10]+algebraic[13])
algebraic[14] = states[7]*constants[14]
algebraic[15] = states[7]*constants[15]
rates[7] = (1.00000/1.00000)*(-1.00000*algebraic[14]+-1.00000*algebraic[15]+algebraic[12]+algebraic[13]+algebraic[15])
algebraic[3] = states[8]*constants[3]
rates[8] = (1.00000/1.00000)*(-1.00000*algebraic[0]+-1.00000*algebraic[3]+algebraic[2]+algebraic[15])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = states[0]*states[8]*constants[0]
algebraic[2] = states[1]*constants[2]
algebraic[4] = states[0]*states[2]*constants[4]
algebraic[5] = states[3]*constants[5]
algebraic[6] = states[2]*constants[6]
algebraic[7] = states[3]*constants[7]
algebraic[9] = states[6]*constants[9]
algebraic[8] = states[6]*constants[8]
algebraic[1] = states[0]*constants[1]
algebraic[10] = states[0]*states[4]*constants[10]
algebraic[11] = states[5]*constants[11]
algebraic[12] = states[4]*constants[12]
algebraic[13] = states[5]*constants[13]
algebraic[14] = states[7]*constants[14]
algebraic[15] = states[7]*constants[15]
algebraic[3] = states[8]*constants[3]
return algebraic
def solve_model():
"""Solve model with ODE solver"""
from scipy.integrate import ode
# Initialise constants and state variables
(init_states, constants) = initConsts()
# Set timespan to solve over
voi = linspace(0, 10, 500)
# Construct ODE object to solve
r = ode(computeRates)
r.set_integrator('vode', method='bdf', atol=1e-06, rtol=1e-06, max_step=1)
r.set_initial_value(init_states, voi[0])
r.set_f_params(constants)
# Solve model
states = array([[0.0] * len(voi)] * sizeStates)
states[:,0] = init_states
for (i,t) in enumerate(voi[1:]):
if r.successful():
r.integrate(t)
states[:,i+1] = r.y
else:
break
# Compute algebraic variables
algebraic = computeAlgebraic(constants, states, voi)
return (voi, states, algebraic)
def plot_model(voi, states, algebraic):
"""Plot variables against variable of integration"""
import pylab
(legend_states, legend_algebraic, legend_voi, legend_constants) = createLegends()
pylab.figure(1)
pylab.plot(voi,vstack((states,algebraic)).T)
pylab.xlabel(legend_voi)
pylab.legend(legend_states + legend_algebraic, loc='best')
pylab.show()
if __name__ == "__main__":
(voi, states, algebraic) = solve_model()
plot_model(voi, states, algebraic)