///////////////////////// /* model specification */ /////////////////////////
/////// topology ////////
create soma, apical, basilar, axon
connect apical(0), soma(1)
connect basilar(0), soma(0) 
connect axon(0), soma(0)

access soma

/////// geometry ////////
//To calculate number of segments use formula: (pg. 29, Chapter 5 of the NEURON book):
//forall {nseg = int((L/(0.1*lambda_f(100))+0.9)/2)*2 + 1} 
//forall {print nseg}

//This makes use of the function included in standard NEURON library (stdlib.hoc)
//func lambda_f() { // currently accessed section, $1 == frequency
//return 1e5*sqrt(diam/(4*PI*$1*Ra*cm))
//}


soma { L = 30
diam = 30 
nseg = 1
}
apical { L = 600
diam = 1
nseg = 23
}

basilar { L = 200
diam = 2 
nseg = 5
}

axon { L = 1000
diam = 1 
nseg = 3
}

/////// biophysics //////
forall { 
Ra = 100
cm = 1
}

soma {
insert hh
}

apical { 
insert pas 
g_pas = 0.0002 
e_pas = -65
} 

basilar {
insert pas 
g_pas = 0.0002
e_pas = -65
}

axon { 
insert hh
}


func conductance() {
	return 0.12 - 0.12*$1
	}


forsec "axon" {
	for (x) gnabar_hh(x) = conductance(x) 
	for (x)  print "pos = ", x, "condunctance = ", gnabar_hh(x)   
	
}

// alternative listing:
//access axon 
//for (x) gnabar_hh(x) = conductance(x) 
//for (x)  print "pos = ", x, "condunctance = ", axon.gnabar_hh(x)