// A simulation on the longest basal dendrite of a Meynert2 cell - long inhibition at 0
// Written by Oz kahana 26.4.1999

// This meynert cell was fixed (muliply by 10) using treemul
// Converting from ranka to neuron:
// 1. Multiply the ranka format file by 10 - use the treemul program
// 2. Converting to Neuron - use 'perl Oz_neuron <sourcefile> > <destination file>

objref LDistancesVec

print "Meynert simulation on the a5_1121 pathway + inhibition"

objref file

NoOfLSyn = 500
objref Lsynapse[500]

NoOfInhibitorySynapses = 1

InhibitionDelay = 2


objref In_synapse


print "load the Meynert cell"
xopen("../Cells/meynert2/meynert2.hoc")

load_proc("nrnmainmenu")
  objref vec, file
  strdef fileN

  proc Set_nsegs() {
     forsec "a9" {diam_hold = diam   cm_hold = cm nseg=nseg*2 diam = diam_hold   cm = cm_hold }
     forall { area(0) }
     }

  proc BasicInit() {
	stdinit()
	setdt()
  }

  proc RunTill() {
	continuerun($1)
  }

proc SetSynapseProperties() {
//     $o1.gmax = 0.0016
     $o1.gmax = 0.0004
     $o1.e=0
     // taus as the default
     tau1 = 40
     tau2 = 0.33

     // $2-> onset time
     $o1.onset = $2
  }

  proc SetInSynapseProperties() {
     $o1.gmax = 0.03217
     if ($2==50000) {
       $o1.gmax = 0.00453
     }

     $o1.risetime = 0.5
     $o1.tfast = 7.5
     $o1.tslow = 33
     $o1.e=-70
     $o1.onset = $3
  }

proc runForTotalTime(){
     Total__Time = $1

     base_time = -Total__Time
     if (base_time<0) {
       base_time=0
     }
     deltaT = Total__Time/(LTotalDistance)

     print "Total Time=",Total__Time
     for index=0,NoOfLSyn-1 {
       SetSynapseProperties(Lsynapse[index],base_time+deltaT*(LTotalDistance-LDistancesVec.x[index]))
     }

     SetInSynapseProperties(In_synapse,Rm,base_time+deltaT*LTotalDistance+InhibitionDelay)
     if (Total__Time<0) {
       SetInSynapseProperties(In_synapse,Rm,InhibitionDelay)
     }
}

proc runAndSave(){

// Run  the simulation for T time
     BasicInit()
     RunTill(400)

// Save the voltage vector
     sprint(fileN, "vecT%d.dat",$1)
     file = new File()
     file.wopen(fileN)
     vec.printf(file)
     file.close()
}

  StartTime = 0
  tstop = 400
  steps_per_ms=10
  dt=0.1


  // Loop of different Rm

    Rm = 5000
    //if (rm_index==1) {
    //  Rm = 50000
    //}

    // Mainen cell
    forall { insert pas }
    forall { e_pas = -65 }
    forall { g_pas = 1/Rm }
    forall { Ra = 150 }
    forall { cm = 1 }


    print "Set the nsegs"
    forall nseg=1

    forall { area(0.5) }
    xopen("../Files/eparam3.hoc")
    Set_nsegs()

    print "Loading Synapses"
      xopen("../Files/muki_nmdaMeyLongSynfile3.hoc")
//      xopen("../Files/meyShortSynfile1.hoc")
      objref In_synapse
      soma In_synapse = new two_exp_syn1(0)

    print "End of Synapses"

    nsegments = 0
    forall {
      nsegments = nsegments + nseg
    }
    print nsegments," segments."

  NoOfTraces=287

  objref TotalTimes
  TotalTimes = new Vector(288,0)

  i=0
  for ii=0,111 {
    TotalTimes.x[i] = -300 + 600 * ii / 240
    i=i+1
  }

TotalTimes.x[i] = -22
i=i+1
TotalTimes.x[i] = -21.5
i=i+1
TotalTimes.x[i] = -21
i=i+1
TotalTimes.x[i] = -20.5
i=i+1
TotalTimes.x[i] = -20
i=i+1
TotalTimes.x[i] = -19.5
i=i+1
TotalTimes.x[i] = -19
i=i+1
TotalTimes.x[i] = -18.5
i=i+1
TotalTimes.x[i] = -18
i=i+1
TotalTimes.x[i] = -17.5
i=i+1
TotalTimes.x[i] = -15
i=i+1
TotalTimes.x[i] = -12.5
i=i+1
TotalTimes.x[i] = -10
i=i+1
TotalTimes.x[i] = -9.5
i=i+1
TotalTimes.x[i] = -9
i=i+1
TotalTimes.x[i] = -8.5
i=i+1
TotalTimes.x[i] = -8
i=i+1
TotalTimes.x[i] = -7.5
i=i+1
TotalTimes.x[i] = -7
i=i+1
TotalTimes.x[i] = -6.5
i=i+1
TotalTimes.x[i] = -6
i=i+1
TotalTimes.x[i] = -5.5
i=i+1
TotalTimes.x[i] = -5
i=i+1
TotalTimes.x[i] = -2.5
i=i+1
TotalTimes.x[i] = -2
i=i+1
TotalTimes.x[i] = -1.5
i=i+1
TotalTimes.x[i] = -1.3
i=i+1
TotalTimes.x[i] = -1.1
i=i+1
TotalTimes.x[i] = -0.8
i=i+1
TotalTimes.x[i] = -0.7
i=i+1
TotalTimes.x[i] = -0.6
i=i+1
TotalTimes.x[i] = -0.0001
i=i+1
TotalTimes.x[i] = 0.6
i=i+1
TotalTimes.x[i] = 0.7
i=i+1
TotalTimes.x[i] = 0.8
i=i+1
TotalTimes.x[i] = 1.1
i=i+1
TotalTimes.x[i] = 1.3
i=i+1
TotalTimes.x[i] = 1.5
i=i+1
TotalTimes.x[i] = 2
i=i+1
TotalTimes.x[i] = 2.5
i=i+1
TotalTimes.x[i] = 5
i=i+1
TotalTimes.x[i] = 5.5
i=i+1
TotalTimes.x[i] = 6
i=i+1
TotalTimes.x[i] = 6.5
i=i+1
TotalTimes.x[i] = 7
i=i+1
TotalTimes.x[i] = 7.5
i=i+1
TotalTimes.x[i] = 8
i=i+1
TotalTimes.x[i] = 8.5
i=i+1
TotalTimes.x[i] = 9
i=i+1
TotalTimes.x[i] = 9.5
i=i+1
TotalTimes.x[i] = 10
i=i+1
TotalTimes.x[i] = 12.5
i=i+1
TotalTimes.x[i] = 15
i=i+1
TotalTimes.x[i] = 17.5
i=i+1
TotalTimes.x[i] = 18
i=i+1
TotalTimes.x[i] = 18.5
i=i+1
TotalTimes.x[i] = 19
i=i+1
TotalTimes.x[i] = 19.5
i=i+1
TotalTimes.x[i] = 20
i=i+1
TotalTimes.x[i] = 20.5
i=i+1
TotalTimes.x[i] = 21
i=i+1
TotalTimes.x[i] = 21.5
i=i+1
TotalTimes.x[i] = 22
i=i+1

for ii=129,241 {
  TotalTimes.x[i] = -300 + 600 * ii / 240
  i=i+1
 }


    for iii=0,NoOfTraces {

     // create the voltage vector
     vec = new Vector(200000,0)
     vec.record(&soma.v(0.5))

     //TotalTime = -300 + 600 * iii / 240
     TotalTime = TotalTimes.x[iii]
     runForTotalTime(TotalTime)

     runAndSave(iii)
    }