Generated Code
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The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 13
sizeStates = 2
sizeConstants = 30
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 (millisecond)"
legend_algebraic[10] = "P_CE in component equations (dimensionless)"
legend_algebraic[5] = "P_PE in component equations (dimensionless)"
legend_algebraic[6] = "P_SE in component equations (dimensionless)"
legend_algebraic[0] = "Ca in component equations (dimensionless)"
legend_algebraic[12] = "C_2 in component equations (per_millisec)"
legend_algebraic[1] = "phi_A_1 in component equations (dimensionless)"
legend_algebraic[11] = "pi_n in component equations (dimensionless)"
legend_algebraic[8] = "A in component equations (dimensionless)"
legend_states[0] = "A_1 in component equations (dimensionless)"
legend_algebraic[3] = "S in component equations (um)"
legend_algebraic[9] = "n in component equations (dimensionless)"
legend_algebraic[7] = "n_1 in component equations (dimensionless)"
legend_states[1] = "n_2 in component equations (dimensionless)"
legend_constants[27] = "G_V in component equations (dimensionless)"
legend_constants[26] = "q_V in component equations (per_millisec)"
legend_constants[25] = "V in component equations (um_per_millisec)"
legend_constants[28] = "F_V in component equations (dimensionless)"
legend_constants[29] = "p_V in component equations (dimensionless)"
legend_constants[0] = "alpha_1 in component equations (per_um)"
legend_constants[1] = "alpha_2 in component equations (per_um)"
legend_constants[2] = "beta_1 in component equations (dimensionless)"
legend_constants[3] = "beta_2 in component equations (dimensionless)"
legend_constants[4] = "lambda in component equations (per_um)"
legend_constants[5] = "V_max in component equations (um_per_millisec)"
legend_constants[6] = "Ca_m in component equations (dimensionless)"
legend_constants[7] = "t_d in component equations (millisecond)"
legend_constants[8] = "a_c in component equations (per_millisec2)"
legend_constants[9] = "b_c in component equations (per_millisec2)"
legend_constants[10] = "C_1 in component equations (per_millisec)"
legend_constants[11] = "C_20 in component equations (per_millisec)"
legend_constants[12] = "q_k in component equations (dimensionless)"
legend_constants[24] = "V_1 in component equations (um_per_millisec)"
legend_constants[13] = "a in component equations (dimensionless)"
legend_constants[14] = "m_0 in component equations (dimensionless)"
legend_constants[15] = "g_1 in component equations (per_um)"
legend_constants[16] = "g_2 in component equations (dimensionless)"
legend_constants[17] = "pi_min in component equations (dimensionless)"
legend_constants[18] = "S_0 in component equations (um)"
legend_constants[19] = "q_1 in component equations (per_millisec)"
legend_constants[20] = "q_2 in component equations (per_millisec)"
legend_constants[21] = "q_3 in component equations (per_millisec)"
legend_constants[22] = "TnC in component equations (dimensionless)"
legend_algebraic[2] = "l_1 in component user_defined (um)"
legend_algebraic[4] = "l_2 in component user_defined (um)"
legend_constants[23] = "dl_1_dt in component user_defined (um_per_millisec)"
legend_rates[0] = "d/dt A_1 in component equations (dimensionless)"
legend_rates[1] = "d/dt n_2 in component equations (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0
states[1] = 0
constants[0] = 14.6
constants[1] = 14.6
constants[2] = 1
constants[3] = 0.0012
constants[4] = 30
constants[5] = 0.0043
constants[6] = 45e-3
constants[7] = 170
constants[8] = 2.4e-4
constants[9] = 5e-4
constants[10] = 2.9e-2
constants[11] = 0.2
constants[12] = 4
constants[13] = 0.25
constants[14] = 0.87
constants[15] = 0.4
constants[16] = 0.6
constants[17] = 5e-2
constants[18] = 0.77
constants[19] = 0.017
constants[20] = 0.26
constants[21] = 0.03
constants[22] = 1
constants[23] = 0.00000
constants[24] = 0.100000*constants[5]
constants[25] = -constants[23]
constants[26] = custom_piecewise([less_equal(constants[25] , 0.00000), constants[19]-(constants[20]*constants[25])/constants[5] , True, constants[21]])
constants[27] = 1.00000+(0.600000*constants[25])/constants[5]
constants[28] = (constants[13]*(1.00000+constants[25]/constants[5]))/(constants[13]-constants[25]/constants[5])
constants[29] = constants[28]/constants[27]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[1] = constants[26]*(constants[14]*constants[27]-states[1])
algebraic[0] = custom_piecewise([less_equal(voi , constants[7]), constants[6]*(power(1.00000-exp(-constants[8]*(power(voi, 2.00000))), 2.00000)) , True, constants[6]*(power((1.00000-exp(-constants[8]*(power(voi, 2.00000))))*exp(-constants[9]*(power(voi-constants[7], 2.00000))), 2.00000))])
algebraic[1] = exp(-constants[12]*states[0])
algebraic[2] = custom_piecewise([less_equal(200.000 , voi) & less_equal(voi , 201.000), 0.00000 , True, 0.00000])
algebraic[7] = custom_piecewise([less(constants[15]*algebraic[2]+constants[16] , 0.00000), 0.00000 , less_equal(0.00000 , constants[15]*algebraic[2]+constants[16]) & less_equal(constants[15]*algebraic[2]+constants[16] , 1.00000), constants[15]*algebraic[2]+constants[16] , True, 1.00000])
algebraic[9] = algebraic[7]*states[1]
algebraic[11] = custom_piecewise([less_equal(0.750000 , algebraic[9]) & less_equal(algebraic[9] , 1.00000), constants[17] , less_equal(0.250000 , algebraic[9]) & less(algebraic[9] , 0.750000), power(constants[17], 2.00000*algebraic[9]-0.500000) , True, 1.00000])
rates[0] = constants[10]*algebraic[0]*(constants[22]-states[0])-constants[11]*algebraic[11]*algebraic[1]*states[0]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = custom_piecewise([less_equal(voi , constants[7]), constants[6]*(power(1.00000-exp(-constants[8]*(power(voi, 2.00000))), 2.00000)) , True, constants[6]*(power((1.00000-exp(-constants[8]*(power(voi, 2.00000))))*exp(-constants[9]*(power(voi-constants[7], 2.00000))), 2.00000))])
algebraic[1] = exp(-constants[12]*states[0])
algebraic[2] = custom_piecewise([less_equal(200.000 , voi) & less_equal(voi , 201.000), 0.00000 , True, 0.00000])
algebraic[7] = custom_piecewise([less(constants[15]*algebraic[2]+constants[16] , 0.00000), 0.00000 , less_equal(0.00000 , constants[15]*algebraic[2]+constants[16]) & less_equal(constants[15]*algebraic[2]+constants[16] , 1.00000), constants[15]*algebraic[2]+constants[16] , True, 1.00000])
algebraic[9] = algebraic[7]*states[1]
algebraic[11] = custom_piecewise([less_equal(0.750000 , algebraic[9]) & less_equal(algebraic[9] , 1.00000), constants[17] , less_equal(0.250000 , algebraic[9]) & less(algebraic[9] , 0.750000), power(constants[17], 2.00000*algebraic[9]-0.500000) , True, 1.00000])
algebraic[3] = 0.500000*algebraic[2]+constants[18]
algebraic[4] = algebraic[2]+1.87000
algebraic[5] = constants[3]*(exp(constants[1]*algebraic[4])-1.00000)
algebraic[6] = constants[2]*(exp(constants[0]*(algebraic[4]-algebraic[2]))-1.00000)
algebraic[8] = (states[0]*algebraic[3])/1.00000
algebraic[10] = constants[4]*algebraic[3]*states[0]*algebraic[9]*constants[29]
algebraic[12] = constants[11]*algebraic[11]*algebraic[1]
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)