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 = 9
sizeStates = 8
sizeConstants = 20
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 (day)"
legend_constants[0] = "mu_T in component uninfected_CD4 (per_day)"
legend_constants[1] = "r in component uninfected_CD4 (per_day)"
legend_states[0] = "T_1 in component latently_infected_CD4 (per_micro_L)"
legend_constants[2] = "T_max in component uninfected_CD4 (per_micro_L)"
legend_constants[3] = "k_1 in component HIV1 (micro_L_per_day)"
legend_states[1] = "V in component HIV1 (per_micro_L)"
legend_constants[4] = "k_1_ in component hybrid_HIV1 (micro_L_per_day)"
legend_states[2] = "V_ in component hybrid_HIV1 (per_micro_L)"
legend_constants[5] = "s_0 in component uninfected_CD4 (per_micro_L_day)"
legend_constants[6] = "theta in component uninfected_CD4 (per_micro_L)"
legend_algebraic[0] = "s_V in component uninfected_CD4 (per_micro_L_day)"
legend_states[3] = "T in component uninfected_CD4 (per_micro_L)"
legend_constants[7] = "k_2 in component latently_infected_CD4 (per_day)"
legend_constants[8] = "k_1D in component actively_infected_CD4 (micro_L_per_day)"
legend_algebraic[1] = "D in component DIV (per_micro_L)"
legend_constants[9] = "mu_b in component actively_infected_CD4 (per_day)"
legend_states[4] = "T_2 in component actively_infected_CD4 (per_micro_L)"
legend_constants[10] = "k_s in component actively_coinfected_CD4 (per_day)"
legend_constants[11] = "mu_bD in component actively_coinfected_CD4 (per_day)"
legend_states[5] = "T_D2 in component actively_coinfected_CD4 (per_micro_L)"
legend_constants[12] = "mu_TD in component stably_coinfected_CD4 (per_day)"
legend_states[6] = "T_D1 in component stably_coinfected_CD4 (per_micro_L)"
legend_algebraic[4] = "N_D_t in component DIV (dimensionless)"
legend_algebraic[7] = "pi_D_t in component DIV (per_day)"
legend_constants[13] = "mu_D in component DIV (per_day)"
legend_algebraic[2] = "N_t in component production_function (dimensionless)"
legend_constants[14] = "t_DIV in component DIV (day)"
legend_states[7] = "D_ode in component DIV (per_micro_L)"
legend_constants[15] = "D_0 in component DIV (per_micro_L)"
legend_algebraic[5] = "N_2_t in component HIV1 (dimensionless)"
legend_constants[16] = "mu_V in component HIV1 (per_day)"
legend_algebraic[6] = "N_t_ in component hybrid_HIV1 (dimensionless)"
legend_algebraic[8] = "pi_t_ in component hybrid_HIV1 (per_day)"
legend_constants[17] = "N_0 in component production_function (dimensionless)"
legend_constants[18] = "gamma in component production_function (dimensionless)"
legend_constants[19] = "t_c in component production_function (day)"
legend_algebraic[3] = "T_tot in component cell_population (per_micro_L)"
legend_rates[3] = "d/dt T in component uninfected_CD4 (per_micro_L)"
legend_rates[0] = "d/dt T_1 in component latently_infected_CD4 (per_micro_L)"
legend_rates[4] = "d/dt T_2 in component actively_infected_CD4 (per_micro_L)"
legend_rates[5] = "d/dt T_D2 in component actively_coinfected_CD4 (per_micro_L)"
legend_rates[6] = "d/dt T_D1 in component stably_coinfected_CD4 (per_micro_L)"
legend_rates[7] = "d/dt D_ode in component DIV (per_micro_L)"
legend_rates[1] = "d/dt V in component HIV1 (per_micro_L)"
legend_rates[2] = "d/dt V_ in component hybrid_HIV1 (per_micro_L)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 0.02
constants[1] = 0.03
states[0] = 0
constants[2] = 1500
constants[3] = 2.4E-5
states[1] = 1E-3
constants[4] = 2.4E-7
states[2] = 0
constants[5] = 10
constants[6] = 1
states[3] = 1000
constants[7] = 0.017
constants[8] = 2.4E-5
constants[9] = 0.24
states[4] = 0
constants[10] = 0.48
constants[11] = 0.12
states[5] = 0
constants[12] = 0.02
states[6] = 0
constants[13] = 0.76
constants[14] = 2557
states[7] = 0
constants[15] = 0.1
constants[16] = 2.4
constants[17] = 300
constants[18] = 25
constants[19] = 7305
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[0] = ((constants[3]*states[1]*states[3]+constants[4]*states[2]*states[3])-constants[0]*states[0])-constants[7]*states[0]
rates[6] = constants[10]*states[5]-constants[12]*states[6]
algebraic[0] = (constants[5]*constants[6])/(constants[6]+states[1])
rates[3] = (((algebraic[0]-constants[0]*states[3])+constants[1]*states[3]*(1.00000-(states[3]+states[0])/constants[2]))-constants[3]*states[1]*states[3])-constants[4]*states[2]*states[3]
algebraic[1] = custom_piecewise([less(voi , constants[14]), 0.00000 , True, states[7]])
rates[4] = (constants[7]*states[0]-constants[8]*algebraic[1]*states[4])-constants[9]*states[4]
rates[5] = (constants[8]*algebraic[1]*states[4]-constants[10]*states[5])-constants[11]*states[5]
algebraic[2] = constants[17]*(1.00000+constants[18]*((power(voi, 2.00000))/(power(voi, 2.00000)+power(constants[19], 2.00000))))
algebraic[5] = 0.100000*algebraic[2]
rates[1] = ((algebraic[2]*constants[9]*states[4]+algebraic[5]*constants[11]*states[5])-constants[3]*states[1]*states[3])-constants[16]*states[1]
algebraic[4] = 0.200000*algebraic[2]
algebraic[7] = 0.500000*constants[9]*algebraic[2]
rates[7] = custom_piecewise([less(voi , constants[14]), constants[15]/constants[14] , True, (algebraic[4]*constants[11]*states[5]+algebraic[7]*states[6])-constants[13]*states[7]])
algebraic[6] = 0.100000*algebraic[2]
algebraic[8] = 0.0100000*constants[9]*algebraic[2]
rates[2] = ((algebraic[6]*constants[11]*states[5]+algebraic[8]*states[6])-constants[16]*states[2])-constants[4]*states[3]*states[2]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = (constants[5]*constants[6])/(constants[6]+states[1])
algebraic[1] = custom_piecewise([less(voi , constants[14]), 0.00000 , True, states[7]])
algebraic[2] = constants[17]*(1.00000+constants[18]*((power(voi, 2.00000))/(power(voi, 2.00000)+power(constants[19], 2.00000))))
algebraic[5] = 0.100000*algebraic[2]
algebraic[4] = 0.200000*algebraic[2]
algebraic[7] = 0.500000*constants[9]*algebraic[2]
algebraic[6] = 0.100000*algebraic[2]
algebraic[8] = 0.0100000*constants[9]*algebraic[2]
algebraic[3] = states[3]+states[0]+states[4]+states[5]+states[6]
return algebraic
def custom_piecewise(cases):
"""Compute result of a piecewise function"""
return select(cases[0::2],cases[1::2])
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)