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from neuron import h, rxd
from neuron.units import μM, mV, ms
from matplotlib import pyplot
h.load_file('stdrun.hoc')

# define a very simple rxd model
dend = h.Section('dend')
dend.nseg = 101
cyt = rxd.Region(h.allsec(), name='cyt', nrn_region='i')
ca = rxd.Species(cyt, name="ca", d=1.0, charge=2, initial=60 * μM)

h.CVode().active(True)

# record
tvec = h.Vector().record(h._ref_t)
cavec = h.Vector().record(dend(0.5)._ref_cai)


def abrupt_change():
        # change the concentration via the nodes
        # to change all the concentration use 
        # ca.nodes.concentration = 100
        
        # to change the concentration for a region use
        # ca.nodes(cyt).concentration = 100e-3
        
        # to change them for a specific section use
        # ca.nodes(dend).concentration = 100e-3
        # to change for a specific segment use
        ca.nodes(dend(0.5)).concentration = 100 * μM
 
        # calling  h.CVode().re_init() is a general NEURON requirement
        # anytime a state is changed during variable step
        h.CVode().re_init() 

# declare events
def setup_events():
    h.CVode().event(5 * ms, abrupt_change)

fih = h.FInitializeHandler(setup_events)

# initialize and run
h.finitialize(-70 * mV)
h.continuerun(10 * ms)

# plot the result
pyplot.plot(tvec, cavec)
pyplot.xlabel('time (ms)')
pyplot.ylabel('concentration (μM)')
pyplot.show()