proc celldef() {
  topol()
  subsets()
  geom()
  biophys()
  geom_nseg()
}

create soma, axon

proc topol() { local i
  connect axon(0), soma(1)
  basic_shape()
}
proc basic_shape() {
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
  axon {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(120, 0, 0, 1)}
}

objref all
proc subsets() { local i
  objref all
  all = new SectionList()
    soma all.append()
    axon all.append()

}
proc geom() {
  forsec all {  }
   soma.L = 150
   axon.L =	8000		//40000
   soma.diam = 6
   axon.diam = 12
  soma {  }
  axon {  }
}
proc geom_nseg() {
   soma { nseg = 15 }
   axon { nseg = 800 }		// 4000
}
proc biophys() {
  forsec all {
    Ra = 28
  }
  soma {
    insert hhsoma
      gnabar_hhsoma = 0.48
      gkbar_hhsoma = 1.088
      gl_hhsoma = 0.0016
      el_hhsoma = -60

  }
  axon {
    insert hhaxon
      gnabar_hhaxon = 0.48
      gkbar_hhaxon = 1.088
      gl_hhaxon = 0.0016
      el_hhaxon = -60
	  q10m_hhaxon = 1
	  q10h_hhaxon = 1
      q10n_hhaxon = 1
  }
}
access axon

celldef()
load_file("40ms.ses")

objectvar stim
soma stim = new IClamp(0.5)
stim.del = 10
stim.dur = 1
stim.amp = 17



objref rec, rec2, rec3, rec4, rec5, rec6, rec7, rec8, rec8, rec9, nil
objref APtim, APtim2, APtim3, APtim4, APtim5, APtim6, APtim7, APtim8, APtim9
objref spkid, spkid2, spkid3, spkid4, spkid5, spkid6, spkid7, spkid8, spkid9
objref savefreq, savefreq2, savefreq3, savefreq4, savefreq5, savefreq6, savefreq7, savefreq8, savefreq9
objref	ascifile, f1

ascifile = new Vector()


f1 = new File()
f1.ropen("q10s_non-spiker_at13nA.txt")
ascifile.scanf(f1)


savefreq = new File()				//creates an output file where things can be saved



	for l=0, 4096 {
		axon.q10n_hhaxon = ascifile.x[(7*l)]		//changes the Potassium gate tau value by 1/q10
		axon.q10m_hhaxon = ascifile.x[(7*l)+1]		//change the sodium ma dn h gates by 1/q10
		axon.q10h_hhaxon = ascifile.x[(7*l)+2]
		axon.gnabar_hhaxon = ascifile.x[(7*l)+3]*0.48	//changes the sodium conductance
		axon.gkbar_hhaxon = ascifile.x[(7*l)+4]*1.088		//changes the potassium conductance 
    	axon.gl_hhaxon = ascifile.x[(7*l)+5]*0.0016			//changes the leak channel conductance 


		axon rec = new NetCon(&v(0.125), nil, 0, 1, 0)		//watches axon at 0.1cm
		axon rec2 = new NetCon(&v(.625), nil, 0, 1, 0)	//watches axon at .5cm


		APtim = new Vector()				//vector to record netcon into
		APtim2 = new Vector()				//vector to record netcon into
	

		spkid = new Vector()				//vector to hold the spike number identification
		spkid2 = new Vector()				//vector to hold the spike number identification


		rec.record(APtim, spkid)			//puts the values of APtim and spkid into the network connection (netcon) SOOOO rec contains AP time and spike id at axon = 0.75
		rec2.record(APtim2, spkid2)			//puts the values of APtim and spkid into the second network connection SOOOO rec2 contains the AP time and spike id numbers at axon = 0.5

		savefreq = new File()				//creates new file to save data to
		savefreq2 = new File()				//creates new file to save data to
		savefreq3 = new File()				//creates new file to save data to
	
		savefreq.aopen("Arrival_time_and_counter_17nA.dat")//opens new file


		//run()

		APtim.resize(3)
		APtim2.resize(3)
			
		savefreq.printf("%g\t%g\t%g\t%g\t%g\n", APtim.x(0), APtim.x(1), APtim2.x(0), APtim2.x(1), ascifile.x[(7*l)+6])

		savefreq.close()


	}