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 = 6
sizeStates = 4
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 (ms)"
legend_algebraic[3] = "Ca_i in component intracellular_ion_concentrations (uM)"
legend_algebraic[0] = "mtime in component intracellular_ion_concentrations (dimensionless)"
legend_states[0] = "xb in component crossbridges (dimensionless)"
legend_states[1] = "TRPN in component troponin (dimensionless)"
legend_constants[0] = "k_xb in component crossbridges (per_ms)"
legend_constants[1] = "nperm in component crossbridges (dimensionless)"
legend_constants[2] = "perm50 in component crossbridges (dimensionless)"
legend_algebraic[1] = "permtot in component crossbridges (dimensionless)"
legend_constants[3] = "Ca_50ref in component troponin (uM)"
legend_constants[4] = "beta_1 in component troponin (dimensionless)"
legend_constants[5] = "k_off in component troponin (per_ms)"
legend_constants[6] = "n_TRPN in component troponin (dimensionless)"
legend_constants[16] = "lambda_m in component filament_overlap (dimensionless)"
legend_constants[17] = "Ca_50 in component troponin (uM)"
legend_constants[14] = "lambda in component Myofilaments (dimensionless)"
legend_constants[15] = "dlambdadt in component Myofilaments (per_ms)"
legend_constants[19] = "overlap in component filament_overlap (dimensionless)"
legend_constants[7] = "beta_0 in component filament_overlap (dimensionless)"
legend_constants[18] = "lambda_s in component filament_overlap (dimensionless)"
legend_constants[8] = "T_ref in component isometric_tension (kPa)"
legend_algebraic[2] = "T_0 in component isometric_tension (kPa)"
legend_algebraic[4] = "Q in component dynamic_stiffness (dimensionless)"
legend_constants[9] = "a in component dynamic_stiffness (dimensionless)"
legend_states[2] = "Q_1 in component dynamic_stiffness (dimensionless)"
legend_states[3] = "Q_2 in component dynamic_stiffness (dimensionless)"
legend_constants[10] = "A_1 in component dynamic_stiffness (dimensionless)"
legend_constants[11] = "A_2 in component dynamic_stiffness (dimensionless)"
legend_constants[12] = "alpha_1 in component dynamic_stiffness (per_ms)"
legend_constants[13] = "alpha_2 in component dynamic_stiffness (per_ms)"
legend_algebraic[5] = "Tension in component dynamic_stiffness (kPa)"
legend_rates[0] = "d/dt xb in component crossbridges (dimensionless)"
legend_rates[1] = "d/dt TRPN in component troponin (dimensionless)"
legend_rates[2] = "d/dt Q_1 in component dynamic_stiffness (dimensionless)"
legend_rates[3] = "d/dt Q_2 in component dynamic_stiffness (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.00046
states[1] = 0.0752
constants[0] = 0.1
constants[1] = 5
constants[2] = 0.35
constants[3] = 0.8
constants[4] = -1.5
constants[5] = 0.1
constants[6] = 2
constants[7] = 1.65
constants[8] = 120
constants[9] = 0.35
states[2] = 0
states[3] = 0
constants[10] = -29
constants[11] = 116
constants[12] = 0.1
constants[13] = 0.5
constants[14] = 1.00000
constants[15] = 0.00000
constants[16] = custom_piecewise([greater(constants[14] , 1.20000), 1.20000 , True, constants[14]])
constants[17] = constants[3]*(1.00000+constants[4]*(constants[16]-1.00000))
constants[18] = custom_piecewise([greater_equal(constants[16] , 0.870000), 0.870000 , True, constants[16]])
constants[19] = 1.00000+constants[7]*((constants[16]+constants[18])-1.87000)
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[2] = constants[10]*constants[15]-constants[12]*states[2]
rates[3] = constants[11]*constants[15]-constants[13]*states[3]
algebraic[1] = power(power(states[1]/constants[2], constants[1]), 1.0/2)
rates[0] = constants[0]*(algebraic[1]*(1.00000-states[0])-(1.00000/algebraic[1])*states[0])
algebraic[0] = (voi-167.000*floor(voi/167.000))/1.00000
algebraic[3] = custom_piecewise([greater_equal(algebraic[0] , 1.17000) & less(algebraic[0] , 30.8400), 1.00000*1.85358e-05*(power(algebraic[0], 3.00000))+-0.00159034*(power(algebraic[0], 2.00000))+0.0436459*(power(algebraic[0], 1.00000))+0.167079 , greater_equal(algebraic[0] , 30.8400), ((1.00000*-5.74585e-08*(power(algebraic[0], 3.00000))+3.11222e-05*(power(algebraic[0], 2.00000)))-0.00661849*(power(algebraic[0], 1.00000)))+0.720442 , True, 0.216000])
rates[1] = constants[5]*((power(algebraic[3]/constants[17], constants[6]))*(1.00000-states[1])-states[1])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[1] = power(power(states[1]/constants[2], constants[1]), 1.0/2)
algebraic[0] = (voi-167.000*floor(voi/167.000))/1.00000
algebraic[3] = custom_piecewise([greater_equal(algebraic[0] , 1.17000) & less(algebraic[0] , 30.8400), 1.00000*1.85358e-05*(power(algebraic[0], 3.00000))+-0.00159034*(power(algebraic[0], 2.00000))+0.0436459*(power(algebraic[0], 1.00000))+0.167079 , greater_equal(algebraic[0] , 30.8400), ((1.00000*-5.74585e-08*(power(algebraic[0], 3.00000))+3.11222e-05*(power(algebraic[0], 2.00000)))-0.00661849*(power(algebraic[0], 1.00000)))+0.720442 , True, 0.216000])
algebraic[2] = constants[8]*states[0]*constants[19]
algebraic[4] = states[2]+states[3]
algebraic[5] = custom_piecewise([less(algebraic[4] , 0.00000), (algebraic[2]*(constants[9]*algebraic[4]+1.00000))/(1.00000-algebraic[4]) , True, (algebraic[2]*(1.00000+(constants[9]+2.00000)*algebraic[4]))/(1.00000+algebraic[4])])
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)