# 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 = 0 sizeStates = 4 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 (millisecond)" legend_states[0] = "R in component R (dimensionless)" legend_constants[0] = "ki in component reaction_constants (second_order_rate_constant)" legend_constants[1] = "ko in component reaction_constants (third_order_rate_constant)" legend_constants[2] = "kim in component reaction_constants (first_order_rate_constant)" legend_constants[3] = "kom in component reaction_constants (first_order_rate_constant)" legend_states[1] = "RI in component RI (dimensionless)" legend_states[2] = "O in component O (dimensionless)" legend_constants[4] = "Ca in component reaction_constants (millimolar)" legend_states[3] = "I in component I (dimensionless)" legend_rates[0] = "d/dt R in component R (dimensionless)" legend_rates[2] = "d/dt O in component O (dimensionless)" legend_rates[3] = "d/dt I in component I (dimensionless)" legend_rates[1] = "d/dt RI in component RI (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 1 constants[0] = 0.5 constants[1] = 35 constants[2] = 0.005 constants[3] = 0.06 states[1] = 1 states[2] = 1 constants[4] = 0.0001 states[3] = 1 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = (constants[3]*states[2]+constants[2]*states[1])-(constants[1]*(power(constants[4], 2.00000))*states[0]+constants[0]*constants[4]*states[0]) rates[2] = (constants[2]*states[3]+constants[1]*(power(constants[4], 2.00000))*states[0])-(constants[3]*states[2]+constants[0]*constants[4]*states[2]) rates[3] = (constants[0]*constants[4]*states[2]+constants[1]*(power(constants[4], 2.00000))*states[1])-(constants[2]*states[3]+constants[3]*states[3]) rates[1] = (constants[0]*constants[4]*states[0]+constants[3]*states[3])-(constants[2]*states[1]+constants[1]*(power(constants[4], 2.00000))*states[1]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) return algebraic 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)