// specifiy-BC6.hoc

ax=2079 // number of axonal sections
de=205  // number of dend sections (basal)
ap=432  // number of apic sections (apical)

objref all, somadend, axonal, apical, basal
proc secdef() {
	all = new SectionList()
		soma all.append()
		for i=0, ax-1 axon[i] all.append()
		for i=0, de-1 dend[i] all.append()
		for i=0, ap-1 apic[i] all.append()

	somadend = new SectionList()
		soma somadend.append()
		for i=0, de-1 dend[i] somadend.append()
		for i=0, ap-1 apic[i] somadend.append()

	axonal = new SectionList()
	for i=0, ax-1 axon[i] axonal.append()

	apical = new SectionList()
	for i=0, ap-1 apic[i] apical.append()

	basal = new SectionList()
	for i=0, de-1 dend[i] basal.append()
}

topol()
secdef()

// Segmentation ----------------------------------------------------------
// The number of segments per section (nseg) was set according to the "d-lambda rule" (see Carnevale and Hines 2006, The NEURON Book, Cambridge Univ Press ). The alternating current length constant at 1 kHz ,lambda(1kHz), was calculated for each section, and nseg was increased until the length of all individual segments was <10% of lambda(1kHz), assuming Rm = 10 kOhm cm2, Cm = 1 µF cm-2, and Ri = 100 Ohm cm. Nseg was constrained to odd numbers;
strdef NsegFile
NsegFile="NsegOut-BC6.txt"
objref AllNseg
AllNseg=new Vector(1+ax+de+ap)
ropen(NsegFile)

for(i=0;i<AllNseg.size;i=i+1) {
	AllNseg.x[i]=fscan()
}

proc geom_nseg() {
   soma.nseg = AllNseg.x[0]
   axon.nseg = AllNseg.x[1]
   for i=1,ax-1 axon[i].nseg = AllNseg.x[i+1]
   dend.nseg = AllNseg.x[ax+1]
   for i=1,de-1 dend[i].nseg = AllNseg.x[i+ax+1]
   apic.nseg = AllNseg.x[ax+de+1]
   for i=1,ap-1 apic[i].nseg = AllNseg.x[i+ax+de+1]
   print "Segmentation defined."
}

geom_nseg()

//biophysics --------------------------------------------------------
proc biophys() {
	forsec all {
		Ra = $2
		cm = $3
		g_pas = 1/$1
	}
}

forsec all {
	insert pas
	e_pas = v_init
}