<PSICSRun timeStep="0.01ms" runTime="500ms" startPotential="-65mV" 
	environment="environment"
	properties="membrane"
	access="recording"
	activity="activity"
	morphology="cell"
	stochThreshold="0">
	 

	<StructureDiscretization baseElementSize="12um"/>


	<RunSet vary="timeStep" values="[0.01, 0.02, 0.05]ms"
		filepattern="out-$"/>

	<info>Simple cell with distributions of synapses and event generators to activate them</info>


	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="potential / mV"/>

		<LineSet file="out-0.01.txt" color="red"/>
	    <LineSet file="out-0.02.txt" color="green"/>
        <LineSet file="out-0.05.txt" color="blue"/>
 
		 <View id="whole" xmin="-10." xmax="500." ymin="-100." ymax="80."/>
		  <View id="enlarged" xmin="-10." xmax="50." ymin="-70." ymax="0."/>
		</LineGraph>
	</ViewConfig>


</PSICSRun>

<CellMorphology id="cell">
	<Point id="p0" x="0" y="0" z="0" r="0.5"/>
	<Point parent="p0" id="p1" x="10" y="0" z = "0" r="0.5"/>
	<Point parent="p1" id="p2" x="20" y="0" z = "0" r="0.5"/>
	<Point parent="p2" id="p3" x="1000" y="5" z = "0" r="0.5"/> 

<!-- 
 	<Point parent="p0" id="p3" x="200" y="200" z = "0" r="0.5"/>
 -->
	
</CellMorphology>

<CellProperties id="membrane"
      cytoplasmResistivity="1000ohm_cm"
      membraneCapacitance="1uF_per_cm2">

     <ChannelPopulation id="population_1"
       channel="leak"
       density="20per_um2"/>

	<SynapsePopulation id="sypop1" synapse="syn1" density="0.1per_um2" seed="1010"> 
		<LogUniformWeights min="0.1" max="3"/>
	</SynapsePopulation>
	
	
	<SynapsePopulation id="sypop2" synapse="syn1" density="0.01per_um2"> 
		<!-- 
		<NormalWeights min="0.1" max="3" sd="0.5"/>
		<UniformWeights min="0.1" max="3"/>
		<LogUniformWeights min="0.1" max="3"/>
		 -->
		<LogNormalWeights min="0.1" max="3" sd="0.5"/>
	</SynapsePopulation>
	
	
	
	<SingleSynapse id="sy3" synapse="syn2" at="p0"/>
    <SingleSynapse id="sy4" synapse="syn2" at="p1"/>
    <SingleSynapse id="sy5" synapse="syn1" at="p2"/>

</CellProperties>

<CellEnvironment id="environment">
	<Ion id="Na" name="Sodium" reversalPotential="40mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-80mV"/>
</CellEnvironment>

<Access id="recording" recordClamps="true">

	<CellLocation id="pA" path="10" rankBy="radius" sequenceFraction="1."/> 
	<CellLocation id="pB" path="50" rankBy="radius" sequenceFraction="1."/>
	<CellLocation id="pC" path="120" rankBy="radius" sequenceIndex="1."/>

 
    <VoltageRecorder location="pA" lineColor="blue"/>
    <VoltageRecorder location="pB" lineColor="blue"/>
    <VoltageRecorder location="pC" lineColor="blue"/>
    <VoltageRecorder at="p3" lineColor="blue"/>

</Access>

<Activity id="activity">


	<AfferentEvents population="sypop1">	
        <UniformGenerator frequency="0.001Hz"/>
        <!-- 
		<EventSequence file="stim1"/>
         -->		
	</AfferentEvents>
	
	
	
	
	<AfferentEvents population="sypop2">
		<PoissonGenerator frequency="2Hz" seed="101"/>
		<!-- 
		<UniformGenerator frequency="20Hz"/>
		<GammaGenerator theta="5ms" k="4"/>
   		-->
	</AfferentEvents>


    <AfferentEvents population="sypop1">    
        <ThresholdSensor threshold="-50mV"/>
        <!-- 
            This delivers an event to every synapse in population "sypop1" when the potential
            in the first compartment (fixed for now - could allow sensors to be moved in future)
            passes -50 mV from below.
         -->        
    </AfferentEvents>
    

</Activity>

<KSChannel id="leak" gSingle="0.01pS" permeantIon="K">
	<OpenState id="o1"/>
</KSChannel>

<Synapse id="syn1" permeantIon="Na" baseConductance="400pS">
	
	<ExponentialTimecourse tau="4ms"/>
	<!--  
	<BiExponentialTimecourse rise="2ms" tau="12ms"/>
	<AlphaTimecourse tau="4ms"/>
	<ProfileTimecourse file="stim1.txt" timeUnit="1ms"/>
	 -->
	
</Synapse>

<Synapse id="syn2" permeantIon="K" baseConductance="100pS">
	
	<BiExponentialTimecourse rise="1ms" tau="5ms"/>
	<!--  
	<BiExponentialTimecourse rise="2ms" tau="12ms"/>
	<AlphaTimecourse tau="4ms"/>
	<ProfileTimecourse file="stim1.txt" timeUnit="1ms"/>
	 -->
	
</Synapse>