// written by Gabriela Cirtala
// Heterogenous ion channel conductance density model
// This code corresponds to Branch 13 of the PC
// This code will automatically run for PF in [2:2:150] for 2.2CaP
// Generates many .dat files corresponding to each PF and each point at which the voltage is recorded (check Results folder)
// Shows the dendritic spike propagation (check at PF activation time)

// this code is based on the homogenous model proposed by Zang et al. (Zang 2021).

load_file("nrngui.hoc")

Default_Eleak = -65
membranecap = 0.64      	/* specific membrane capacitance in uF cm^-2 */
membraneresist = 120236 	/* specific membrane resistance in ohm cm^2 */
axialresist = 120	     	/* axial resistivity in ohm cm */

xopen("PurkinjeMorphology_allbr.nrn")	// Load the morphology file.
forsec "axon" delete_section()	// Delete original axon and add a fake AIS

objref g2, b2,c2, distrx, distry, cdistry, p

	forall {
		insert pas e_pas=Default_Eleak	/* Insert Leak everywhere */
	    insert hpkj	// Ih inserted everywhere
		insert ds
		insert pk
	}

    AIS {  g_pas=1/membraneresist Ra=axialresist cm=membranecap}
	forsec spinydend {g_pas=5.3/membraneresist Ra=axialresist cm=5.3*membranecap}
    forsec maindend {g_pas=1.2/membraneresist Ra=axialresist cm=1.2*membranecap}
	forsec "soma" { g_pas=1/membraneresist Ra=axialresist cm=membranecap}

	forsec maindend {insert cdp4N}
	forsec alldend {
			insert Kv3
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 4
			insert newCaP
			pcabar_newCaP = 1.90e-4
			vshift_newCaP =-5
			insert CaT3_1
			pcabar_CaT3_1 = 2.7e-5
			insert mslo
			gbar_mslo = 0.21504
			insert SK2
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			ghbar_hpkj = 0.00036
			insert Kv1
			gbar_Kv1 = 0.002//*2
			insert Kv4
			gbar_Kv4 = 0.0252
			insert Kv4s
			gbar_Kv4s = 0.015

	}
	forsec spinydend {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}


	forsec branch1 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch2 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP  = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch3 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch4 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch5 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*1.9
			gbar_Kv4s = 0.015*1.9
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch6 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*2.2
			gbar_Kv4s = 0.015*2.2
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 =  0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch7 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*2.6
			gbar_Kv4s = 0.015*2.6
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 =  0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch8 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*2.2
			gbar_Kv4s = 0.015*2.2
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP  = 7.6000e-04*0.9
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch9 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch10 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch11 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*1.2
			gbar_Kv4s = 0.015*1.2
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 =  0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch12 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*1.3
			gbar_Kv4s = 0.015*1.3
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04*0.8
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch13 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*1.9
			gbar_Kv4s = 0.015*1.9
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04*2.2
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch14 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 =  0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch15 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 =  0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch16 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch17 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch18 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*1.0
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch19 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*1.0
			gbar_Kv4s  = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch20 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264*1.0
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 =  0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch21 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 =  0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP  =7.6000e-04*0.8
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

	forsec branch22 {
			insert cdp4Nsp
			gkbar_SK2 = 3.6000e-04
			scal_SK2 = 1.0
			gbar_Kv4 = 0.0264
			gbar_Kv4s = 0.015
			ghbar_hpkj = 3.2400e-04
			vshift_Kv4 = 0
			gbar_Kv1 = 0.001
			gbar_Kv3 = 0.1512
			vshift_Kv3 = 0
			pcabar_CaT3_1 = 1.0800e-04
			pcabar_newCaP = 7.6000e-04*0.8
			vshift_newCaP = -5
			scale_cdp4Nsp = 3.5
			gbar_mslo = 0.0896
			insert abBK
			gabkbar_abBK = 0.15
	}

access somaA
somaA distance(0,0.5)

forsec "soma" {
	 // INa & IK's at soma only
	//for soma, I make it fire under dissociated condition. The firing properties is comparable with Bean's data
			insert naRsg		// INa + resurgent
			gbar_naRsg = 0.03168
			vshifta_naRsg = 0
			vshiftk_naRsg = 0
			vshifti_naRsg = -5

			insert nap
			gbar_nap =  1.4000e-04
			insert pk
			ena = 63
			ghbar_hpkj = 1.0800e-04 // Default = 1

			insert cdp20N_FD2
			insert Kv3
			gbar_Kv3 = 1.8
			vshift_Kv3 = 4

			insert Kv1
			gbar_Kv1 = 0
			insert newCaP
			pcabar_newCaP = 1.9000e-04
			kt_newCaP = 1
			vshift_newCaP = -5
			insert mslo
			gbar_mslo = 0.8736
			insert abBK
			gabkbar_abBK = 0.3
			insert SK2
			gkbar_SK2 = 0.0075
	}

	AIS {
				insert naRsg		// INa + resurgent
				gbar_naRsg = 0.56
				vshifta_naRsg = 15
				vshiftk_naRsg = 5
				vshifti_naRsg = -5

				insert nap
				gbar_nap = 0.0023

				insert CaT3_1
				pcabar_CaT3_1 =  1.2800e-04
				ena = 63
				ghbar_hpkj =  1.0800e-04


				insert cdpAIS
				insert Kv3
				gbar_Kv3 = 115.2
				vshift_Kv3 = 4
				insert Kv1
				gbar_Kv1 = 0

				insert newCaP
				pcabar_newCaP = 0.00228
				kt_newCaP = 1
				vshift_newCaP = -5

				insert mslo
				gbar_mslo = 6
				insert abBK
				gabkbar_abBK = 1.05
				insert SK2
				gkbar_SK2 = 0.0278
		}


objref patch_site
patch_site = new List()

ip = 0
forsec patch_list {
patch_site.append(new SectionRef())
}

celsius = 34
dt = 0.02
steps_per_ms = 1/dt
dtsim = 0.02

objref g2, b2,c2, distrm, distrd

xopen ("electrode.hoc")
xopen("distri.hoc")	//voltage spatial distribution

proc clamp_cc() {

	somaA {
		stim1.del = 0
		stim1.dur = 1000000
		stim1.amp = $1
	}
}

v_init = -70

tstop = 600

objref scalefile
scalefile=new File()

xopen("distri_synapse.hoc")

objref pc
pc = new ParallelContext()

//function farmed out to slave nodes
func distscale() {local key, errval, cu_id, fr_id, dend_id localobj parvec, returnlist
	key = $1
	cu_id = int($1/100000000)
	fr_id = int(($1 - cu_id*100000000)/1000000)
	site_id = int(($1 - cu_id*100000000-fr_id*1000000)/10000)
	dend_id = int(($1 - cu_id*100000000-fr_id*1000000-site_id*10000)/100)
	trial_id = $1 - cu_id*100000000-fr_id*1000000-site_id*10000-dend_id*100
	returnlist = new List()
	returnlist = calc_EPSP_single(cu_id,fr_id,site_id,dend_id,trial_id)

	pc.pack(returnlist.o(0))
	pc.pack(returnlist.o(1))
	pc.pack(returnlist.o(2))
	pc.pack(returnlist.o(3))
	pc.pack(returnlist.o(4))
	pc.pack(returnlist.o(5))
	pc.pack(returnlist.o(6))
	pc.pack(returnlist.o(7))
	pc.pack(returnlist.o(8))
	pc.pack(returnlist.o(9))
	pc.pack(returnlist.o(10))
	pc.pack(returnlist.o(11))
	pc.pack(returnlist.o(12))
	pc.pack(returnlist.o(13))
	pc.pack(returnlist.o(14))
	pc.pack(returnlist.o(15))
	pc.post(key)
	return key
}

objref aSynapseList[11]
obfunc calc_EPSP_single() {localobj outlist, currecord, integ_soma, br1,br9_dist,br9_prox,br9_mid,br10_dist,br10_prox,br10_mid,br11_dist,br11_prox,br11_mid,br12_dist,br12_prox,br12_mid,br13_dist,br13_prox,br13_mid
	//function to calculate the max deflection due to a single synapse
	cu_id = $1
	fr_id = $2
	siteval = $3
	synval= $4
	tr_id = $5
	curr = -0.4+(cu_id-1)*0.2

	nlist = fr_id	// in fact nlist can be multiple, make synapses firing at bursting

	Npf = 2+(synval-1)*2
for i = 1,nlist {aSynapseList[i-1] = new List() }	// every time this will be initialized.
randomseed = cu_id*100000000+fr_id*1000000+siteval*10000 +synval*100 + tr_id

br1 = new SectionList()

patch_site.o(siteval-1).sec br1.subtree()
br1.remove(cf)
br1.unique()

if (siteval==12) {
	br1 = new SectionList()
	forsec "dendA1_001101100*" br1.append()
}
if (i==13) {
	br1 = new SectionList()
	forsec "dendA1_0011011100*" br1.append()
	forsec "dendA1_0011011101*" br1.append()
}

for i = 1,nlist {aSynapseList[i-1] = distSyns(Npf,br1,randomseed)}

for i = 1,nlist {
	for ii=1,aSynapseList[i-1].count() {
  	  aSynapseList[i-1].object(ii-1).onset = 405
  	  aSynapseList[i-1].object(ii-1).tau0 = 0.3
  	  aSynapseList[i-1].object(ii-1).tau1 = 3
   	 aSynapseList[i-1].object(ii-1).e = 0
   	 aSynapseList[i-1].object(ii-1).gmax = 0.5e-3//
	}
}

outlist=new List()
integ_soma = new Vector()
integ_soma.record(&somaA.v(0.5))

br9_dist = new Vector()
br9_dist.record(&dendA1_001100110001110.v(0.05))
br9_prox = new Vector()
br9_prox.record(&dendA1_001100.v(0.05))
br9_mid = new Vector()
br9_mid.record(&dendA1_00110011000.v(0.05))


br10_dist = new Vector()
br10_dist.record(&dendA1_00111000010.v(0.05))
br10_prox = new Vector()
br10_prox.record(&dendA1_00111.v(0.05)) // branch10 - proximal
br10_mid = new Vector()
br10_mid.record(&dendA1_00111000000.v(0.05))


br11_dist = new Vector()
br11_dist.record(&dendA1_00110101101101.v(0.05))
br11_prox = new Vector()
br11_prox.record(&dendA1_00110100.v(0.05)) //proximal
br11_mid = new Vector()
br11_mid.record(&dendA1_00110101.v(0.05)) //middle


br12_dist = new Vector()
br12_dist.record(&dendA1_0011011000001011100.v(0.05))
br12_prox = new Vector()
br12_prox.record(&dendA1_001101100.v(0.05)) // branch12 - proximal point
br12_mid = new Vector()
br12_mid.record(&dendA1_0011011000001.v(0.05)) // branch12 - middle point


br13_dist = new Vector()
br13_dist.record(&dendA1_0011011101010010 .v(0.05))//branch 13 - distal
br13_prox = new Vector()
br13_prox.record(&dendA1_00110111.v(0.05))//branch 13 - proximal
br13_mid = new Vector()
br13_mid.record(&dendA1_00110111010101.v(0.05))//branch 13 - middle

clamp_cc(curr)
finitialize(v_init)
continuerun(tstop)

outlist.append(integ_soma)
outlist.append(br9_dist)
outlist.append(br9_prox)
outlist.append(br9_mid)
outlist.append(br10_dist)
outlist.append(br10_prox)
outlist.append(br10_mid)
outlist.append(br11_dist)
outlist.append(br11_prox)
outlist.append(br11_mid)
outlist.append(br12_dist)
outlist.append(br12_prox)
outlist.append(br12_mid)
outlist.append(br13_dist)
outlist.append(br13_prox)
outlist.append(br13_mid)
return outlist
}

pc.runworker()

objref somavec,br9_distvec, br9_proxvec, br9_midvec,br10_distvec, br10_proxvec, br10_midvec,br11_distvec, br11_proxvec, br11_midvec,br12_distvec, br12_proxvec, br12_midvec,br13_distvec, br13_proxvec, br13_midvec

somavec = new Vector()
br9_distvec = new Vector()
br9_proxvec = new Vector()
br9_midvec = new Vector()
br10_distvec = new Vector()
br10_proxvec = new Vector()
br10_midvec = new Vector()
br11_distvec = new Vector()
br11_proxvec = new Vector()
br11_midvec = new Vector()
br12_distvec = new Vector()
br12_proxvec = new Vector()
br12_midvec = new Vector()
br13_distvec = new Vector()
br13_proxvec = new Vector()
br13_midvec = new Vector()

strdef tmpstr
strdef outDir
strdef cmd
objref outfile
outfile = new File()

proc calcEPSPs() {
	sprint(outDir,"Results")
	sprint(cmd, "system(\"mkdir -p %s\")",outDir)
	execute(cmd)
	somaA distance(0,0.5)
	for cu = 3, $1 {
		for freq = 1, $2 {
			for site = $3, $3 {
				for m = 1, $4 {
					for nt =$5 ,$5 {
						mmtag=cu*100000000 + freq*1000000 + site*10000+m*100 + nt
						pc.submit("distscale",mmtag)	//send out the error calculations
					}
				}
			}
		}
	}
	//collect error values
	while (pc.working()) {
		key = pc.retval()	//retrieve the tag
		pc.look_take(key)	//remove the tag/job from the bulletin
		somavec = pc.upkvec()	//unpack the error value associated with the tag
		br9_distvec = pc.upkvec()
		br9_proxvec = pc.upkvec()
		br9_midvec = pc.upkvec()
		br10_distvec = pc.upkvec()
		br10_proxvec = pc.upkvec()
		br10_midvec = pc.upkvec()
		br11_distvec = pc.upkvec()
		br11_proxvec = pc.upkvec()
		br11_midvec = pc.upkvec()
		br12_distvec = pc.upkvec()
		br12_proxvec = pc.upkvec()
		br12_midvec = pc.upkvec()
		br13_distvec = pc.upkvec()
		br13_proxvec = pc.upkvec()
		br13_midvec = pc.upkvec()

		print "received key ",key
		cuno = int(key/100000000)
		frno = int((key- cuno*100000000)/1000000)
		siteno = int((key - cuno*100000000 - frno*1000000)/10000)
		synno= int((key - cuno*100000000 - frno*1000000 - siteno*10000)/100)
		trno  = key - cuno*100000000-frno*1000000-siteno*10000-synno*100

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vsoma.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		somavec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr9_dist.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br9_distvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr9_prox.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br9_proxvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr9_mid.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br9_midvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr10_dist.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br10_distvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr10_prox.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br10_proxvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr10_mid.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br10_midvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr11_dist.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br11_distvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr11_prox.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br11_proxvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr11_mid.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br11_midvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr12_dist.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br12_distvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr12_prox.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br12_proxvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr12_mid.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br12_midvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr13_dist.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br13_distvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr13_prox.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br13_proxvec.printf(outfile)
		outfile.close()

		sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr13_mid.dat",outDir,cuno,frno,siteno,synno,trno)
		outfile.wopen(tmpstr)
		br13_midvec.printf(outfile)
		outfile.close()
	}
}

calcEPSPs(3,1,13,75,1)// Here, 75 corresponds to Npf = 75x2 (the PF step) = 150PF.
//If you wish to change the total number of PF, just change this number to whatever you prefer.
// If you prefer to run for only one PF choice please change the following line inside of the proc calcESP:
// for m = 1, $4  ---> for m = $4, $4