# 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 = 2 sizeStates = 5 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 = "t in component environment (second)" legend_constants[0] = "D_Ca in component parameters (second)" legend_constants[1] = "k_1 in component parameters (per_second)" legend_constants[2] = "k_2 in component parameters (per_second)" legend_constants[3] = "f in component parameters (per_second)" legend_constants[4] = "g in component parameters (per_second)" legend_constants[5] = "Ca_max in component parameters (dimensionless)" legend_constants[6] = "Total_Tn in component parameters (dimensionless)" legend_constants[7] = "Total_CB in component parameters (dimensionless)" legend_algebraic[0] = "Ca_t in component Ca_t (dimensionless)" legend_states[0] = "TnCa in component TnCa (dimensionless)" legend_states[1] = "CB_on in component CB_on (dimensionless)" legend_states[2] = "CumCB_on in component CumCB (dimensionless)" legend_states[3] = "CumCB_off in component CumCB (dimensionless)" legend_algebraic[1] = "F in component force_development (force)" legend_states[4] = "FTI in component force_development (force_second)" legend_constants[15] = "FLA in component force_development (energy)" legend_constants[8] = "phi in component force_development (force)" legend_constants[9] = "s in component force_development (dimensionless)" legend_constants[10] = "L in component force_development (meter)" legend_constants[11] = "L_0 in component force_development (meter)" legend_constants[12] = "F_max in component force_development (force)" legend_constants[17] = "ATP in component ATP (dimensionless)" legend_constants[18] = "ATP_energy in component ATP (energy)" legend_constants[13] = "epsilon in component ATP (energy)" legend_constants[14] = "CumCB_on_end in component ATP (dimensionless)" legend_constants[19] = "Efficiency in component equations_main (dimensionless)" legend_constants[16] = "Economy in component equations_main (second_per_meter)" legend_rates[0] = "d/dt TnCa in component TnCa (dimensionless)" legend_rates[1] = "d/dt CB_on in component CB_on (dimensionless)" legend_rates[2] = "d/dt CumCB_on in component CumCB (dimensionless)" legend_rates[3] = "d/dt CumCB_off in component CumCB (dimensionless)" legend_rates[4] = "d/dt FTI in component force_development (force_second)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 0.1 constants[1] = 40 constants[2] = 20 constants[3] = 10 constants[4] = 10 constants[5] = 1 constants[6] = 1 constants[7] = 1 states[0] = 0 states[1] = 0 states[2] = 0 states[3] = 0 states[4] = 0 constants[8] = 1 constants[9] = 1 constants[10] = 1 constants[11] = 0 constants[12] = 0.228 constants[13] = 1 constants[14] = 1 constants[15] = constants[12]*constants[9]*(constants[10]-constants[11]) constants[16] = (constants[8]/constants[13])*(1.00000/constants[4]) constants[17] = constants[14] constants[18] = constants[17]*constants[13] constants[19] = constants[15]/constants[18] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[1] = constants[3]*states[0]*(constants[7]-states[1])-constants[4]*states[1] rates[2] = constants[3]*states[0]*(constants[7]-states[1]) rates[3] = constants[4]*states[1] algebraic[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 0.300000*constants[0]), (constants[5]*(1.00000+sin(( pi*(voi/constants[0]-0.150000))/0.300000)))/2.00000 , greater_equal(voi , 0.300000*constants[0]) & less(voi , constants[0]), (constants[5]*(1.00000-sin(( pi*(voi/constants[0]-0.650000))/0.700000)))/2.00000 , True, 0.00000]) rates[0] = constants[1]*algebraic[0]*(constants[6]-states[0])-constants[2]*states[0] algebraic[1] = states[1]*constants[8] rates[4] = algebraic[1] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 0.300000*constants[0]), (constants[5]*(1.00000+sin(( pi*(voi/constants[0]-0.150000))/0.300000)))/2.00000 , greater_equal(voi , 0.300000*constants[0]) & less(voi , constants[0]), (constants[5]*(1.00000-sin(( pi*(voi/constants[0]-0.650000))/0.700000)))/2.00000 , True, 0.00000]) algebraic[1] = states[1]*constants[8] 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)