Conductance model dynamic with stimulation

This code highlith how to retrieve particle dynamics in results.

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import nrv
import matplotlib.pyplot as plt

if __name__ == '__main__':

    # nrvon def
    y = 0                                                                   # nrvon y position, in [um]
    z = 0                                                                   # nrvon z position, in [um]
    d = 1                                                                   # nrvon diameter, in [um]

    plot_node = 50

    dt = 0.005
    t_sim = 8

    # first test pulse
    L = 5000
    t_start = 1
    duration = 0.5
    amplitude = 0.35

    axon1 = nrv.unmyelinated(y,z,d,L,T = 21,model='HH',dt=0.001,Nrec=100)
    axon1.insert_I_Clamp(0.5, t_start, duration, amplitude)
    results = axon1.simulate(t_sim=t_sim,record_I_ions=True, record_particles=True)

    del axon1

    color_1 = "#1B148A"
    color_2 = "#C60A00"
    color_3 = "#009913"
    color_4 = "#E2AD00"

    V_rest= results['V_mem'][plot_node][0]

    fig, axs = plt.subplots(2)
    fig.set_size_inches(5, 7)
    axs[0].plot(results['t'],results['V_mem'][plot_node],color = color_1,alpha = 1)
    axs[0].axhline(y = V_rest, color = 'gray', linestyle = '--')
    #axs[0].set_xlabel('time (ms)')
    axs[0].set_ylabel('$V_m$ (mV)')
    axs[0].set_xlim(0,t_sim)
    axs[0].set_ylim(-100,40)
    axs[0].grid(True)
    axs[0].text(0.6,-38.0,'(1)')
    axs[0].text(1.9,-13.0,'(2)')
    axs[0].text(2.5,-85.0,'(3)')


    axs[1].plot(results['t'],results['m'][plot_node],label='m',color = color_2,alpha = 1)
    axs[1].plot(results['t'],results['n'][plot_node],label='n',color = color_3)
    axs[1].plot(results['t'],results['h'][plot_node],label='h',color = color_4)
    axs[1].set_xlabel('Time (ms)')
    axs[1].set_ylabel('Gating Variables')
    axs[1].set_xlim(0,t_sim)
    axs[1].set_ylim(0,1.1)
    axs[1].grid(True)
    axs[1].text(7,0.70,'h',color = color_4)
    axs[1].text(7,0.30,'n',color = color_3)
    axs[1].text(7,0.07,'m',color = color_2)
    axs[0].set_title('Dynamics for suprathreshold stimulation')


    amplitude = 0.195
    axon1 = nrv.unmyelinated(y,z,d,L,model='HH',dt=0.001,Nrec=100,T=21)
    axon1.insert_I_Clamp(0.5, t_start, duration, amplitude)
    results = axon1.simulate(t_sim=t_sim,record_I_ions=True, record_particles=True)

    del axon1

    V_rest= results['V_mem'][plot_node][0]
    fig, axs = plt.subplots(2)
    fig.set_size_inches(5, 7)
    axs[0].plot(results['t'],results['V_mem'][plot_node],color = color_1,alpha = 1)
    axs[0].axhline(y = V_rest, color = 'gray', linestyle = '--')
    #axs[0].set_xlabel('time (ms)')
    axs[0].set_ylabel(r'$V_m$ (mV)')
    axs[0].set_xlim(0,t_sim)
    axs[0].set_ylim(-100,40)
    axs[0].grid(True)


    axs[1].plot(results['t'],results['m'][plot_node],label='m',color = color_2,alpha = 1)
    axs[1].plot(results['t'],results['n'][plot_node],label='n',color = color_3)
    axs[1].plot(results['t'],results['h'][plot_node],label='h',color = color_4)
    axs[1].set_xlabel('Time (ms)')
    axs[1].set_ylabel('Gating Variables')
    axs[1].set_xlim(0,t_sim)
    axs[1].set_ylim(0,1.1)
    axs[1].grid(True)
    axs[1].text(7,0.70,'h',color = color_4)
    axs[1].text(7,0.30,'n',color = color_3)
    axs[1].text(7,0.07,'m',color = color_2)
    axs[0].set_title('Dynamics for subthreshold stimulation')
    plt.show()