//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
//
// NOTICE OF COPYRIGHT AND OWNERSHIP OF SOFTWARE
//
// Copyright 2007, The University Of Pennsylvania
// 	School of Engineering & Applied Science.
//   All rights reserved.
//   For research use only; commercial use prohibited.
//   Distribution without permission of Maciej T. Lazarewicz not permitted.
//   mlazarew@seas.upenn.edu
//
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

//
// This mod file is based on the paper:
// Tort, A. B., Rotstein, H. G., Dugladze, T., et al. (2007). On the formation of gamma-coherent cell assemblies by oriens lacunosum-moleculare interneurons in the hippocampus. Proc Natl Acad Sci U S A,.
//

/*{load_file("syn.tem")}
{load_file("gap.tem")}
{load_file("iapp.tem")}*/

begintemplate Ok

external cvode

// PUBLIC VARIABLES
public x, y, z

// PUBLIC OBJECTS
public soma, spiketimes, idvec, synS, gapS, iappS, synlist

// PUBLIC METHODS
public position, getlocoS, connect2target, recordVoltage, is_art, addSynS, getTotalArea
public setScatteredVoltages, writeVoltage

create soma    

objref iappS, synS, gapS, locS, voltageRecS, recordT
objref spiketimes, idvec, nc, nil, synlist, inj

strdef cmd

// =================================================================================================
//
// init()
//
// =================================================================================================
proc init() {
    
    createCell()
        
    access soma
    
    synlist = new List()
    locS    = new SectionRef()
    iappS   = new IApp()
    synS    = new SynObj()
    gapS    = new GapObj()
    
    spiketimes  = new Vector()
    idvec       = new Vector()
    voltageRecS = new Vector()
    recordT     = new Vector()
  
    iappS.set_random_play($2, $3, $4, $1)
    
   	inj = new IClamp(0.5)
	inj.del = 0
	inj.dur = 1e9
	inj.amp = -16 * area(0.5) * 1e-5  // uA/cm2 -> nA
	
}




// =================================================================================================
//
// recordVoltage()
//
// =================================================================================================
proc recordVoltage() {
		
		//print "Started RECORDING VOLTAGE at OLM"	
		soma  cvode.record(&v(0.5), voltageRecS, recordT )
}





// =================================================================================================
//
// writeVoltage(gid)
//
// =================================================================================================
proc writeVoltage() { local i localobj fo, m

	//print "SIZE:", t, " ", recordT.size()

	m = new Matrix(recordT.size(), 6)

	m.setcol(0, recordT)
	m.setcol(1, voltageRecS)

	fo = new File()
	
	sprint(cmd,"data/%d.dat",$1)
	{fo.wopen(cmd)}
	
	{m.fprint(0, fo, "%6.3lf ")}
	
	{fo.close()}
}



// =================================================================================================
//
// connect2target()
//
// =================================================================================================
proc connect2target() { //$o1 target point process, $o2 returned NetCon
  
  soma $o2 = new NetCon(&v(0.5), $o1, 0 ,0, 0)
  
  if (numarg()==2) synS.addNetCon($o2)
}




// ========================================================================
//
// addSynS( tau1 (ms), tau2 (ms), Erev (mV), synapseName, synLoc )
//
// ========================================================================
func addSynS() {
    
    synlist.append(synS.synList.object( synS.addSyn( $1, $2, $3, $s4, $5)  ) )
	return synlist.count()-1
}




// =================================================================================================
//
// createCell()
//
// =================================================================================================
proc createCell() {

    totalArea = 100 // um2

    soma {
        nseg  = 1
        
        cm    = 1.3  // uF/cm2
        
        diam  = sqrt(totalArea) // um
        L     =  diam/PI  // um
    
    	insert pas
    		e_pas = -70     // mV
    		g_pas = 0.05e-3  // S/cm2 
  
	    insert NafOlmKop
    	insert KdrOlmKop
    	insert IhOlmKop
    	gamx_IhOlmKop = 12 // 8 or 12 I do not know
    	insert KaOlmKop	
	//insert extracellular
	//insert xtra	
    }
}




// ========================================================================
//
// getTotalArea()
//
// ========================================================================
func getTotalArea() {
	
	return totalArea
}


// =================================================================================================
//
// getlocoS()
//
// =================================================================================================
obfunc getlocoS() { return locS }



// =================================================================================================
//
// position()
//
// =================================================================================================
proc position() { x=$1 y=$2 z=$3 }




// =================================================================================================
//
// setScatteredVoltages(low, high)
//
// =================================================================================================
proc setScatteredVoltages() { localobj rand
  rand = new Random(startsw())
  rand.uniform($1,$2)

  forall v = rand.repick()
}




// =================================================================================================
//
// setIappR(mean [uA/cm2], std [uA/cm2], seed)
//
// =================================================================================================
proc setIappR() {

	locS mean_IappRrange = $1
	locS sd_IappRrange   = $2
	locS seed_IappRrange = $3
}




// =================================================================================================
//
// is_art()
//
// =================================================================================================
func is_art() { return 0}




endtemplate Ok