# 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 = 1 sizeStates = 16 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 (hour)" legend_states[0] = "x in component x (dimensionless)" legend_constants[0] = "d in component model_parameters (first_order_rate_constant)" legend_constants[1] = "gamma in component model_parameters (first_order_rate_constant)" legend_constants[2] = "lambda in component model_parameters (first_order_rate_constant)" legend_constants[3] = "beta in component model_parameters (first_order_rate_constant)" legend_states[1] = "v in component v (dimensionless)" legend_states[2] = "y0 in component y0 (dimensionless)" legend_constants[4] = "a0 in component model_parameters (first_order_rate_constant)" legend_constants[5] = "eta in component model_parameters (first_order_rate_constant)" legend_constants[6] = "phi in component model_parameters (first_order_rate_constant)" legend_states[3] = "L in component L (dimensionless)" legend_constants[7] = "pa in component model_parameters (first_order_rate_constant)" legend_states[4] = "za in component za (dimensionless)" legend_constants[8] = "p_i in component model_parameters (first_order_rate_constant)" legend_states[5] = "zi in component zi (dimensionless)" legend_states[6] = "y1 in component y1 (dimensionless)" legend_constants[9] = "a1 in component model_parameters (first_order_rate_constant)" legend_constants[10] = "k in component model_parameters (first_order_rate_constant)" legend_constants[11] = "u in component model_parameters (first_order_rate_constant)" legend_states[7] = "m_8 in component m_8 (dimensionless)" legend_constants[12] = "r in component model_parameters (first_order_rate_constant)" legend_states[8] = "m_7 in component m_7 (dimensionless)" legend_states[9] = "m_6 in component m_6 (dimensionless)" legend_states[10] = "m_5 in component m_5 (dimensionless)" legend_states[11] = "m_4 in component m_4 (dimensionless)" legend_states[12] = "m_3 in component m_3 (dimensionless)" legend_states[13] = "m_2 in component m_2 (dimensionless)" legend_states[14] = "m_1 in component m_1 (dimensionless)" legend_states[15] = "m_0 in component m_0 (dimensionless)" legend_constants[13] = "alpha in component model_parameters (first_order_rate_constant)" legend_constants[14] = "ca in component model_parameters (first_order_rate_constant)" legend_constants[15] = "ba in component model_parameters (first_order_rate_constant)" legend_constants[16] = "xi in component model_parameters (first_order_rate_constant)" legend_constants[17] = "ci in component model_parameters (first_order_rate_constant)" legend_constants[18] = "bi in component model_parameters (first_order_rate_constant)" legend_algebraic[0] = "log_zi in component zi (dimensionless)" legend_constants[19] = "R0 in component R0 (dimensionless)" legend_rates[0] = "d/dt x in component x (dimensionless)" legend_rates[2] = "d/dt y0 in component y0 (dimensionless)" legend_rates[6] = "d/dt y1 in component y1 (dimensionless)" legend_rates[3] = "d/dt L in component L (dimensionless)" legend_rates[1] = "d/dt v in component v (dimensionless)" legend_rates[7] = "d/dt m_8 in component m_8 (dimensionless)" legend_rates[8] = "d/dt m_7 in component m_7 (dimensionless)" legend_rates[9] = "d/dt m_6 in component m_6 (dimensionless)" legend_rates[10] = "d/dt m_5 in component m_5 (dimensionless)" legend_rates[11] = "d/dt m_4 in component m_4 (dimensionless)" legend_rates[12] = "d/dt m_3 in component m_3 (dimensionless)" legend_rates[13] = "d/dt m_2 in component m_2 (dimensionless)" legend_rates[14] = "d/dt m_1 in component m_1 (dimensionless)" legend_rates[15] = "d/dt m_0 in component m_0 (dimensionless)" legend_rates[4] = "d/dt za in component za (dimensionless)" legend_rates[5] = "d/dt zi in component zi (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] = 0.1 constants[1] = 0.5 constants[2] = 10 constants[3] = 0.1 states[1] = 1 states[2] = 0 constants[4] = 0.1 constants[5] = 0.01 constants[6] = 0.1 states[3] = 0 constants[7] = 0.000001 states[4] = 1 constants[8] = 1 states[5] = 0.1 states[6] = 0 constants[9] = 0.2 constants[10] = 1 constants[11] = 1 states[7] = 0 constants[12] = 1 states[8] = 0 states[9] = 0 states[10] = 0 states[11] = 0 states[12] = 0 states[13] = 0 states[14] = 0 states[15] = 0 constants[13] = 0.2 constants[14] = 15.5 constants[15] = 0.1 constants[16] = 0.01 constants[17] = 12 constants[18] = 0.1 constants[19] = ((constants[2]*constants[5])/(constants[0]*constants[9]*(constants[4]+constants[5])))*(constants[3]+(constants[1]*constants[6])/(constants[6]+constants[0])) return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = constants[2]-(constants[0]*states[0]+constants[3]*states[0]*states[1]+constants[1]*states[0]*states[1]) rates[2] = (constants[3]*states[0]*states[1]-(constants[4]*states[2]+constants[5]*states[2]+constants[7]*states[2]*states[4]+constants[8]*states[2]*states[5]))+constants[6]*states[3] rates[6] = constants[5]*states[2]-(constants[9]*states[6]+constants[7]*states[6]*states[4]+constants[8]*states[6]*states[5]) rates[3] = constants[1]*states[0]*states[1]-(constants[6]*states[3]+constants[0]*states[3]) rates[1] = constants[10]*states[6]-constants[11]*states[1] rates[7] = 2.00000*constants[12]*states[8]-constants[12]*states[7] rates[8] = 2.00000*constants[12]*states[9]-constants[12]*states[8] rates[9] = 2.00000*constants[12]*states[10]-constants[12]*states[9] rates[10] = 2.00000*constants[12]*states[11]-constants[12]*states[10] rates[11] = 2.00000*constants[12]*states[12]-constants[12]*states[11] rates[12] = 2.00000*constants[12]*states[13]-constants[12]*states[12] rates[13] = 2.00000*constants[12]*states[14]-constants[12]*states[13] rates[14] = 2.00000*constants[12]*states[15]-constants[12]*states[14] rates[15] = -constants[12]*states[15] rates[4] = (constants[13]*states[7]+constants[14]*(states[2]+states[6])*states[4])-constants[15]*states[4] rates[5] = (constants[16]+constants[17]*(states[2]+states[6])*states[5])-constants[18]*states[5] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = log(states[5], 10) 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)