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# Size of variable arrays: sizeAlgebraic = 0 sizeStates = 0 sizeConstants = 11 from math import * from numpy import * def createLegends(): legend_states = [""] * sizeStates legend_rates = [""] * sizeStates legend_algebraic = [""] * sizeAlgebraic legend_voi = "" legend_constants = [""] * sizeConstants legend_constants[0] = "d_0 in component parameter_Ica (nS_per_pF)" legend_constants[1] = "d_1 in component parameter_Ica (dimensionless)" legend_constants[2] = "d_2 in component parameter_Ica (dimensionless)" legend_constants[3] = "d_5 in component parameter_Ica (dimensionless)" legend_constants[4] = "d_6 in component parameter_Ica (dimensionless)" legend_constants[5] = "f_1 in component parameter_Ica (dimensionless)" legend_constants[6] = "f_2 in component parameter_Ica (dimensionless)" legend_constants[7] = "f_5 in component parameter_Ica (dimensionless)" legend_constants[8] = "f_6 in component parameter_Ica (dimensionless)" legend_constants[9] = "tau_d_const in component parameter_Ica (dimensionless)" legend_constants[10] = "tau_f_const in component parameter_Ica (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 0.30802769 constants[1] = 12.966294189 constants[2] = 7.0791459 constants[3] = 0.044909415 constants[4] = -6.909880369 constants[5] = 5.12589826e-4 constants[6] = -49.505712 constants[7] = 1931.21122 constants[8] = 5.73002749 constants[9] = 1.6582469 constants[10] = 100.462559 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic 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)