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Introduction

LEMS Elements

Example 1

Example 2

Example 3

Example 4

Example 5

Example 6

Example 7

Regimes example

Example n

Canonical form

Discussion

Regimes in Dynamics definitions

This example introduces the Regime, Transition and OnEntry elements within a Dynamics block. Rather than having a single state instance, the entity can be on one of the defined regimes at any given time. The Transition element occurring inside a condition block serves to move it from one regime to another. The OnEntry block inside a regime can contain initialization directives that apply each time the entity enters that regime.

<ComponentType name="refractiaf">
   <Parameter name="threshold" dimension="voltage" />
   <Parameter name="refractoryPeriod" dimension="time" />
   <Parameter name="capacitance" dimension="capacitance" />
   <Parameter name="vleak" dimension="voltage" />
   <Parameter name="gleak" dimension="conductance" />
   <Parameter name="current" dimension="current" />
   <Parameter name="vreset" dimension="voltage" />
   <Parameter name="deltaV" dimension="voltage" />
   <Parameter name="v0" dimension="voltage" />
   <EventPort name="out" direction="out" />
   <EventPort name="in" direction="in" />
   <Dynamics>
      <StateVariable name="v" dimension="voltage" />
      <OnStart>
         <StateAssignment variable="v" value="v0" />
      </OnStart>
      <Regime name="refr">
         <StateVariable name="tin" dimension="time" />
         <OnEntry>
            <StateAssignment variable="tin" value="t" />
            <StateAssignment variable="v" value="vreset" />
         </OnEntry>
         <OnCondition test="t .gt. tin + refractoryPeriod">
            <Transition regime="int" />
         </OnCondition>
      </Regime>
      <Regime name="int" initial="true">
         <TimeDerivative variable="v" value="(current + gleak * (vleak - v)) / capacitance" />
         <OnCondition test="v .gt. threshold">
            <EventOut port="out" />
            <Transition regime="refr" />
         </OnCondition>
         <OnEvent port="in">
            <StateAssignment variable="v" value="v + deltaV" />
         </OnEvent>
      </Regime>
   </Dynamics>
</ComponentType>

Full listing:

example8.xml (xml)

<Lems>
   <Target component="sim1" />
   <Include file="ex2dims.xml" />
   <Include file="spikegenerators.xml" />
   <Include file="misciaf.xml" />
   <ComponentType name="refractiaf">
      <Parameter name="threshold" dimension="voltage" />
      <Parameter name="refractoryPeriod" dimension="time" />
      <Parameter name="capacitance" dimension="capacitance" />
      <Parameter name="vleak" dimension="voltage" />
      <Parameter name="gleak" dimension="conductance" />
      <Parameter name="current" dimension="current" />
      <Parameter name="vreset" dimension="voltage" />
      <Parameter name="deltaV" dimension="voltage" />
      <Parameter name="v0" dimension="voltage" />
      <EventPort name="out" direction="out" />
      <EventPort name="in" direction="in" />
      <Exposure name="v" dimension="voltage" />
      <Dynamics>
         <StateVariable name="v" exposure="v" dimension="voltage" />
         <StateVariable name="tin" dimension="time" />
         <OnStart>
            <StateAssignment variable="v" value="v0" />
         </OnStart>
         <Regime name="refr">
            <OnEntry>
               <StateAssignment variable="tin" value="t" />
               <StateAssignment variable="v" value="vreset" />
            </OnEntry>
            <OnCondition test="t .gt. tin + refractoryPeriod">
               <Transition regime="int" />
            </OnCondition>
         </Regime>
         <Regime name="int" initial="true">
            <TimeDerivative variable="v" value="(current + gleak * (vleak - v)) / capacitance" />
            <OnCondition test="v .gt. threshold">
               <EventOut port="out" />
               <Transition regime="refr" />
            </OnCondition>
            <OnEvent port="in">
               <StateAssignment variable="v" value="v + deltaV" />
            </OnEvent>
         </Regime>
      </Dynamics>
   </ComponentType>

   <Component id="gen1" type="spikeGenerator" period="7ms" />

   <Component id="multiregime" type="refractiaf" threshold="-50mV" v0="-80mV" refractoryPeriod="20ms" capacitance="1pF" vreset="-80mV" vleak="-90mV" gleak="5pS" current="0.00001nA" deltaV="5mV" />
   <ComponentType name="Network">
      <Children name="populations" type="Population" />
      <Children name="connectivities" type="EventConnectivity" />
   </ComponentType>
   <ComponentType name="Population">
      <ComponentReference name="component" type="Component" />
      <Parameter name="size" dimension="none" />
      <Structure>
         <MultiInstantiate number="size" component="component" />
      </Structure>
   </ComponentType>
   <ComponentType name="EventConnectivity">
      <Link name="source" type="Population" />
      <Link name="target" type="Population" />
      <Child name="Connections" type="ConnectionPattern" />
   </ComponentType>
   <ComponentType name="ConnectionPattern" />
   <ComponentType name="AllAll" extends="ConnectionPattern">
      <Structure>
         <ForEach instances="../source" as="a">
            <ForEach instances="../target" as="b">
               <EventConnection from="a" to="b" />
            </ForEach>
         </ForEach>
      </Structure>
   </ComponentType>

   <Network id="net1">
      <Population id="p1" component="gen1" size="1" />
      <Population id="p3" component="multiregime" size="2" />
      <EventConnectivity id="p1-p3" source="p1" target="p3">
         <Connections type="AllAll" />
      </EventConnectivity>
   </Network>
   <Include file="SingleSimulation.xml" />

   <Simulation id="sim1" length="80ms" step="0.05ms" target="net1">
      <Display id="d0" title="Example 8: Regimes in dynamics definitions" timeScale="1ms" xmin="-10" xmax="90" ymin="-90" ymax="20">
         <Line id="gen_vmr" quantity="p3[0]/v" scale="1mV" timeScale="1ms" color="#00c000" />
         <Line id="gen_sv" quantity="p1[0]/tsince" scale="1ms" timeScale="1ms" color="#f00000" />
      </Display>
   </Simulation>
</Lems>