Adding VClamp to new tut model

Author: pgleeson

Tutorial2/NeuroML2/HHTutorial.net.nml

@@ -2,13 +2,16 @@
 
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2  https://raw.githubusercontent.com/NeuroML/NeuroML2/master/Schemas/NeuroML2/NeuroML_v2beta3.xsd"   
+         xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2  https://raw.githubusercontent.com/NeuroML/NeuroML2/master/Schemas/NeuroML2/NeuroML_v2beta4.xsd"   
          id="HHTutorial">
 
     <include href="hhneuron.cell.nml"/> <!-- Include the cell definition -->
+    
+    <include href="vclamp.xml"/>
 
     <!-- Short small current pulse input & short larger current pulse input -->
     <pulseGenerator id="IClamp" delay="5ms" duration="25ms" amplitude="0.002nA"/>
+    
 
     <network id="HHTutorial">
 
@@ -23,7 +26,11 @@
             </instance>
         </population>
 
-        <inputList id="Input_0" component="IClamp" population="hhpop">
+        <inputList id="IClampInput" component="IClamp" population="hhpop">
+            <input id="0" target="../hhpop/0/hhneuron" destination="synapses"/>
+        </inputList>
+        
+        <inputList id="VClampInput" component="vClamp" population="hhpop">
             <input id="0" target="../hhpop/0/hhneuron" destination="synapses"/>
         </inputList>
 

Tutorial2/NeuroML2/LEMS_HHTutorial.xml

@@ -14,7 +14,6 @@
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
 
-
     <Include file="HHTutorial.net.nml"/>
 
     <Simulation id="sim1" length="50ms" step="0.001ms" target="HHTutorial">
@@ -43,6 +42,10 @@
         <Display id="d5" title="Hodgkin-Huxley Neuron: I_inj (nA)" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.0005" ymax="0.0025">
             <Line id="I_inj (nA)" quantity="hhpop/0/hhneuron/IClamp/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>
         </Display>
+
+        <Display id="d6" title="Hodgkin-Huxley Neuron: VClamp i (nA)" timeScale="1ms" xmin="-5" xmax="55" ymin="-0.0005" ymax="0.0025">
+            <Line id="VClamp i (nA)" quantity="hhpop/0/hhneuron/vClamp/i" scale="1nA"  color="#ffffff" timeScale="1ms"/>
+        </Display>
 
         <OutputFile id="of0" fileName="hh_tut_v.dat">
             <OutputColumn id="v" quantity="hhpop/0/hhneuron/v"/> 

Tutorial2/NeuroML2/vclamp.xml

@@ -0,0 +1,57 @@
+<Lems xmlns="http://www.neuroml.org/lems/0.7.4"
+      xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+      xsi:schemaLocation="http://www.neuroml.org/lems/0.7.4 ../../LEMS/Schemas/LEMS/LEMS_v0.7.4.xsd"
+      description="New voltage clamp">
+
+
+    <ComponentType name="voltageClampTriple" extends="baseVoltageDepPointCurrent"
+                   description="Voltage clamp. Applies a variable current _i to try to keep parent at _targetVoltage. ">
+
+        <Parameter name="active" dimension="none" description="Whether the voltage clamp is active (1) or inactive (0)."/>
+        
+        <Parameter name="delay" dimension="time" description="Delay before switching from conditioningVoltage to testingVoltage."/>
+        <Parameter name="duration" dimension="time" description="Duration to hold at testingVoltage."/>
+        <Parameter name="conditioningVoltage" dimension="voltage" description="Target voltage before time delay"/>
+        <Parameter name="testingVoltage" dimension="voltage" description="Target voltage between times delay and delay + duration"/>
+        <Parameter name="returnVoltage" dimension="voltage" description="Target voltage after time duration"/>
+        
+        <!-- seriesResistance renamed to simpleSeriesResistance & factor of 1e-5 removed from calculation of current. Still being tested... -->
+        <Parameter name="simpleSeriesResistance" dimension="resistance" description="Current will be calculated by the difference in voltage between the target and parent, divided by this value"/>
+
+        <!--TODO: remove! Only required as EventConnection is used in explicitInput to
+        connect inputs to cells. Events aren't passed! ... -->
+        <EventPort name="in" direction="in" description="Note this is not used here. Will be removed in future"/>
+
+        <Dynamics>
+
+            <StateVariable name="i" exposure="i" dimension="current"/>
+
+            <OnEvent port="in"><!--TODO: remove, see above...
+            <StateAssignment variable="i" value="0"/>-->
+            </OnEvent>
+
+            <OnCondition test="active .eq. 1 .and. t .lt. delay">
+                <StateAssignment variable="i" value="(conditioningVoltage - v) / simpleSeriesResistance"/>
+            </OnCondition>
+
+            <OnCondition test="active .eq. 1 .and. t .geq. delay">
+                <StateAssignment variable="i" value="(testingVoltage - v) / simpleSeriesResistance"/>
+            </OnCondition>
+
+            <OnCondition test="active .eq. 1 .and. t .gt. duration + delay">
+                <StateAssignment variable="i" value="(returnVoltage - v) / simpleSeriesResistance"/>
+            </OnCondition>
+
+        </Dynamics>
+
+    </ComponentType>
+    
+    <voltageClampTriple id="vClamp" 
+                        active = "0"
+                        delay="10ms" duration="30ms"
+                        conditioningVoltage="-63.77mV" 
+                        testingVoltage="10mV" 
+                        returnVoltage="-63.77mV" 
+                        simpleSeriesResistance="1e4ohm"/>
+    
+</Lems>