objref G1,vVec,indVec,nc, nil,apVec,G2,fn,voltMat,voltVec,axonVec,axonMat,dendVec,dendMat,stateMatNa,stateMatMut,stateMatNax

getcwd()
proc runSCN2A(){
voltMat = new Matrix(100.01/dt,600)
axonMat = new Matrix(100.01/dt,600)
dendMat = new Matrix(100.01/dt,600)
inactAtVinitRation = 1
simnum=0
counter = 0
soma nc = new NetCon(&v(.5), nil)
nc.threshold = -5 // watch out! only one threshold per presyn location
apVec = new Vector(1100)
indVec = new Vector()
nc.record(indVec)
G1 = new Graph()

na_somaOrig = na_soma1	
na_aisOrig     = na_ais1
nax_aisOrig1		=	7000/2			
nax_nodeOrig1		=	7000/2
nax_collatOrig1	=	500/2
nax_myelinOrig1	=	40/2
	init()
	
	
for (aa=1;aa>=0;aa-=0.1){
	na_soma1 = na_somaOrig*aa
	na_ais1 = na_aisOrig*aa
	nax_ais1		=	nax_aisOrig1*aa		
	nax_node1		=	nax_nodeOrig1*aa
	nax_collat1	=	nax_collatOrig1*aa
	nax_myelin1	=	nax_myelinOrig1*aa
	IClamp[0].amp = 0.5
	init_channels()
counter = 0
	printf("runing %f %% of Na density\n",aa*100)	

	//na_soma		=	0.5*500		

	tstop = 600
	IClamp[0].del = 500
	IClamp[0].dur = 100

		voltVec = new Vector(10001)
		axonVec = new Vector(10001)
		dendVec = new Vector(10001)
	p = 0
	
			flg0 = 1
		flg1 = 1
	while(IClamp[0].amp<=3){
		init()
		timeSteps = (tstop-t)/dt
	
		counter=0
		printf("runing %f",IClamp[0].amp)

		while (t<tstop) {
			G1.line(t,v(0.5))
			voltVec.x(counter) = v(0.5)
			axonVec.x(counter) = axon[0].v(1)
			dendVec.x(counter) = apic[37].v(0.5)
			if(v(0.5)>-10 && flg0){
				print "soma ap"
				flg0 = 0
			}
			if(axon[0].v(1)>-10&& flg1){
				print "ap axon"
				flg1 = 0
			}
			if(apic[37].v(0.5)>-10 ){
				print "dend ap"
				flg0 = 0
			}
			fadvance()
			counter+=1
		}
		IClamp[0].amp +=0.05
		printf("printing %f %f\n",aa,simnum)
		voltMat = voltMat.setcol(simnum,voltVec) 
		axonMat = axonMat.setcol(simnum,axonVec) 
		dendMat = dendMat.setcol(simnum,dendVec) 
		simnum +=1
		
	}
	G1.flush()
	
	//apVec.x(simnum) = IClamp[0].amp
	//printf("somaCurrent1.amp is %f\n",apVec.x(simnum))
		//apVec.x(simnum) = somaCurrent1.amp
		
}
fn = new File()
fn.wopen("Volts.csv")
voltMat.fprint(fn,"%f,","\n")
fn.close()
fn.wopen("VoltsAxon.csv")
axonMat.fprint(fn,"%f,","\n")
fn.close()
fn.wopen("VoltsDend.csv")
dendMat.fprint(fn,"%f,","\n")
fn.close()
}
/*
proc printStates(){
voltMat = new Matrix(100.01/dt,200)
stateMatNa = new Matrix(100.01/dt,3)
stateMatNax = new Matrix(100.01/dt,3)
stateMatMut = new Matrix(100.01/dt,3)
inactAtVinitRation = 0.93
simnum=0
counter = 0
soma nc = new NetCon(&v(.5), nil)
nc.threshold = -5 // watch out! only one threshold per presyn location
apVec = new Vector(1100)
indVec = new Vector()
nc.record(indVec)
G1 = new Graph()
Kv_soma1 = Kv_soma
Kv1_soma1 = Kv1_soma
Kv7_soma1 = Kv7_soma
Kv1_ais1 = Kv1_ais
Kv7_ais1 = Kv7_ais
na_soma1 = na_soma	
na_ais1      = na_ais
	init()
	
	
for (aa=10;aa<=10;aa+=.5){
	IClamp[0].amp = 0
counter = 0
	printf("runing %f/10 of Na density\n",aa)	

	

	tstop = 600
	IClamp[0].del = 500
	IClamp[0].dur = 100
	IClamp[0].amp = 1.7

		voltVec = new Vector(10001)

	p = 0
	
			flg0 = 1
		flg1 = 1
	while(IClamp[0].amp<=1.7){
		init()
		timeSteps = (tstop-t)/dt
	
		counter=0
		printf("runing %f",IClamp[0].amp)

		while (t<tstop) {
			G1.line(t,v(0.5))
			voltVec.x(counter) = v(0.5)
			
			stateMatNa.x(counter,0) = axon[0].c1_na(0.2)+axon[0].c2_na(0.2)+axon[0].c3_na(0.2)
			stateMatNax.x(counter,0) = axon[0].c1_nax(0.4)+axon[0].c2_nax(0.4)+axon[0].c3_nax(0.4)
			stateMatMut.x(counter,0) = axon[0].c1_nad12n(0.2)+axon[0].c2_nad12n(0.2)+axon[0].c3_nad12n(0.2)
			stateMatNa.x(counter,1) = axon[0].i1_na(0.2)+axon[0].i2_na(0.2)+axon[0].i3_na(0.2)+axon[0].i4_na(0.2)
			stateMatNax.x(counter,1) = axon[0].i1_nax(0.4)+axon[0].i2_nax(0.4)+axon[0].i3_nax(0.4)+axon[0].i4_nax(0.4)
			stateMatMut.x(counter,1) = axon[0].i1_nad12n(0.2)+axon[0].i2_nad12n(0.2)+axon[0].i3_nad12n(0.2)+axon[0].i4_nad12n(0.2)					
			stateMatNa.x(counter,2) = axon[0].o_na(0.2)
			stateMatNax.x(counter,2) = axon[0].o_nax(0.4)
			stateMatMut.x(counter,2) = axon[0].o_nad12n(0.2)		
			if(v(0.5)>-10 && flg0){
				print "soma ap"
				flg0 = 0
			}
			if(axon[0].v(1)>-10&& flg1){
				print "ap axon"
				flg1 = 0
			}
			if(apic[37].v(0.5)>-10 ){
				print "dend ap"
				flg0 = 0
			}
			fadvance()
			counter+=1
		}
		IClamp[0].amp +=0.1
		printf("printing %f %f\n",aa,simnum)
		voltMat = voltMat.setcol(simnum,voltVec) 
		simnum +=1
		
	}
	G1.flush()
	
	//apVec.x(simnum) = IClamp[0].amp
	//printf("somaCurrent1.amp is %f\n",apVec.x(simnum))
		//apVec.x(simnum) = somaCurrent1.amp
		
}
fn = new File()
fn.wopen("VoltsStates.csv")
voltMat.fprint(fn,"%f,","\n")
fn.close()

fn = new File()
fn.wopen("StatesNa.csv")
stateMatNa.fprint(fn,"%f,","\n")
fn.close()

fn = new File()
fn.wopen("StatesNaMut.csv")
stateMatMut.fprint(fn,"%f,","\n")
fn.close()

fn = new File()
fn.wopen("StatesNax.csv")
stateMatNax.fprint(fn,"%f,","\n")
fn.close()


}


*/