// 
// Simulation of a pair of FS neurons connected through gap junctions.
// Input is read from the INDATA directory.
//
// Johannes Hjorth, Feburary 2007
// hjorth@nada.kth.se
//
//

echo "### Start of script ###################"
echo "Johannes Hjorth (hjorth@nada.kth.se)"
echo "Last updated: December 2007"
echo " "

// Read maxTime from parameter file!


str outputName = "TWOFS-FIG4A-NC"
float maxTime = 0.5
int numCells = 2

echo "Simulating "{numCells}" FS neurons for "{maxTime}" seconds"
echo "Writing output to "{outputName}

//simulation time and time steps
float spikeoutdt=1e-3
float vmOutDt=1e-4
float simDt=1e-5 //1e-6 needed for voltage clamp

// Number of synapse sites

int nAMPA = 127 // per cell
int nGABA = 93

//read in functions for creating and running simulations
include protodefs 
include ../genesisScripts/fsInputFromFile
include ../genesisScripts/fsSomaOutput
include ../genesisScripts/fsInputInject
include fsCurrentRecorder

//setclocks
setclock 1 {vmOutDt}
setclock 0 {simDt}

// Use the SPRNG random number generator
setrand -sprng
randseed 21483789

// Read input location from parameter file

str spikeInputFile = "INDATA/FIG4AinputSpikes.txt"

// Create neuron
echo "Creating "{numCells}" FS neurons"
copyFsNeuron "/fs" {numCells}

loadSpikeTrain {spikeInputFile} spikeTrain

//connectNamedSpikeTrain spikeTrain /fs[0]/soma AMPA
connectNamedSpikeTrain spikeTrain /fs[0]/primdend1 AMPA
connectNamedSpikeTrain spikeTrain /fs[0]/secdend1 AMPA
connectNamedSpikeTrain spikeTrain /fs[0]/primdend2 AMPA
connectNamedSpikeTrain spikeTrain /fs[0]/tertdend2 AMPA


// Create gap junction

//connectGap /fs[0]/primdend1 /fs[1]/primdend1 2e9


makeOutput "/fs" {outputName} {vmOutDt}
// makeCurrentOutput {outputName}

// addCurrentOutput {outputName} /fs[0]/primdend1/AMPA_channel


check

  



reset       
reset

step {maxTime} -t

clearOutput {outputName}

// close files
quit