# 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 = 4 sizeStates = 1 sizeConstants = 5 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 (second)" legend_constants[0] = "a in component contraction (mNpermmsq)" legend_constants[1] = "b in component contraction (pms)" legend_constants[2] = "Po in component contraction (mNpermmsq)" legend_constants[3] = "alpha in component contraction (mNpermmsq)" legend_constants[4] = "L_se_o in component contraction (dimensionless)" legend_algebraic[0] = "L in component contraction (dimensionless)" legend_algebraic[3] = "v in component contraction (pms)" legend_algebraic[1] = "L_se in component contraction (dimensionless)" legend_states[0] = "L_ce in component contraction (dimensionless)" legend_algebraic[2] = "P in component contraction (mNpermmsq)" legend_rates[0] = "d/dt L_ce in component contraction (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 37.24 constants[1] = 0.325 constants[2] = 144.9 constants[3] = 1449.027 constants[4] = 0.3 states[0] = 0.7 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = custom_piecewise([less_equal(voi , 1.00000), 1.00000 , greater(voi , 1.00000) & less(voi , 5.00000), 0.920000 , True, 0.900000]) algebraic[1] = algebraic[0]-states[0] algebraic[2] = constants[3]*(algebraic[1]-constants[4]) algebraic[3] = (-constants[1]*(constants[2]-algebraic[2]))/(algebraic[2]+constants[0]) rates[0] = algebraic[3] 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 , 1.00000), 1.00000 , greater(voi , 1.00000) & less(voi , 5.00000), 0.920000 , True, 0.900000]) algebraic[1] = algebraic[0]-states[0] algebraic[2] = constants[3]*(algebraic[1]-constants[4]) algebraic[3] = (-constants[1]*(constants[2]-algebraic[2]))/(algebraic[2]+constants[0]) 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)