/* Use run.hoc to start simulation. Creates a raster plot similar to Figure 2C in "Variability in respiratory rhythm generation: in vitro and in silico models", C Fietkiewicz, GO Shafer, EA Platt, CG Wilson, Communications in Nonlinear Science and Numerical Simulation, Volume 32, March 2016, Pages 158–168 (doi: 10.1016/j.cnsns.2015.08.018).
NOTE: To get more bursts, increase the simulation time.
Author contact: chris.fietkiewicz@case.edu
Author website: http://filer.case.edu/cxf47
*/

//******************************Pacemaker Template***************************
begintemplate PM
public is_art
public init, topol, basic_shape, subsets, geom, biophys, geom_nseg, biophys_inhomo
public synlist, x, y, z, position, connect2target

public soma
public all

objref synlist

proc init() {
  topol()
  subsets()
  geom()
  biophys()
  geom_nseg()
  synlist = new List()
  synapses()
  x = y = z = 0 // only change via position
}

create soma

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

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

}
proc geom() {
  forsec all {  /*area = 3000 */ L = diam = 30.9019  }
  soma {  /*area = 3000 */ L = diam = 30.9019  }
}
//external lambda_f
proc geom_nseg() {
//  forsec all { nseg = int((L/(0.1*lambda_f(100))+.9)/2)*2 + 1  }
}
proc biophys() {
  soma {
    Ra = 100
	cm = 0.7
    insert na
      gmax_na = 0.0013333
    insert nap
      gmax_nap = 0.00002907
    insert k
      gmax_k = 0.000533333
    insert leak
      gmax_leak = 0.00003091
  }
}
proc biophys_inhomo(){}
proc position() { local i
  soma for i = 0, n3d()-1 {
    pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
  }
  x = $1  y = $2  z = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
  soma nc = new NetCon(&v(1), $o1)
  nc.threshold = 0
  if (numarg() == 2) { $o2 = nc } // for backward compatibility
  return nc
}
objref syn_
proc synapses() {
  /* Itonic0 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 5
  /* Isyn1 */   soma syn_ = new ExpSyn(0.5)  synlist.append(syn_)
    syn_.tau = 5
}
func is_art() { return 0 }

endtemplate PM

//***********************TONIC CELL TEMPLATE***************************

begintemplate NoisyTonicECells_NetStim
public pp, connect2target, x, y, z, position, is_art
objref pp

proc init() {
	pp = new NetStim()
    pp.number = 1e+09
    pp.start = $1
    pp.noise = $2
	pp.seed($3)
	pp.interval = $4
	
}
func is_art() { return 1 }
obfunc connect2target() { localobj nc
  nc = new NetCon(pp, $o1)
  if (numarg() == 2) { $o2 = nc }
  return nc
}
proc position(){x=$1  y=$2  z=$3}
endtemplate NoisyTonicECells_NetStim