added nml experiments

Author: adampdp

.gitignore

@@ -42,3 +42,4 @@
 /RoyalSociety2018/main
 /Worm2D/main
 /network2021/main
+/experiments/izq_runs_nets/*/*.gv

exampleRun21W2D/behavior.pdf

@@ -0,0 +1,97 @@
+<Lems>
+
+
+    <ComponentType name="outputSynapse"
+                   extends="baseGradedSynapse"
+                   description="For Worm2D...">
+
+        <Property name="weight" dimension="none" defaultValue="1"/>
+
+        <Constant name="PAMP_SCALE" dimension="current" value="1pA"/>
+
+        <Exposure name="i" dimension="current"/>
+
+        <Requirement name="output" dimension="none"/>
+
+        <InstanceRequirement name="peer" type="outputSynapse"/>
+
+        <Dynamics>
+            <DerivedVariable name="outputpeer" dimension="none" select="peer/output"/>
+            <DerivedVariable name="i" exposure="i"  value="weight * outputpeer * PAMP_SCALE"/>
+        </Dynamics>
+    </ComponentType>
+
+<ComponentType name="cellX"
+    extends="baseCellMembPot"
+    description="...">
+    
+    <Parameter name="bias" dimension="none" description="..."/>
+    <Parameter name="gain" dimension="none" description="..."/>
+    <Parameter name="tau" dimension="time"/>
+
+    <Constant name="COND_SCALE" dimension="conductance" value="1nS"/>
+    <DerivedParameter name="C" dimension="capacitance" value="tau*COND_SCALE"/>
+
+    <!--
+    Defined in baseCellMembPotCap:
+    <Parameter name="C" dimension="capacitance"/>
+    -->
+
+    <!-- Initial Conditions -->
+    <Parameter name="state0" dimension="none"/>
+
+    <Attachments name="synapses" type="basePointCurrent"/>
+
+    <Constant name="MVOLT" dimension="voltage" value="1mV"/>
+    <Constant name="PAMP" dimension="current" value="1pA"/>
+
+    <!-- <Exposure name="v" dimension="none"/> --> <!-- Already exposed from baseCellMembPotDL -->
+    <Exposure name="spiking" dimension="none"/>
+    <Exposure name="state" dimension="none"/>
+    <Exposure name="output" dimension="none"/>
+
+    <Exposure name="iSyn" dimension="current" description="Total current due to synaptic inputs"/>
+    <Exposure name="iMemb" dimension="current" description="Total current crossing the cell membrane"/>
+    
+    <Dynamics>
+        
+        <StateVariable name="v" dimension="voltage" exposure="v" description="Membrane potential state variable"/>
+        <StateVariable name="spiking" dimension="none" exposure="spiking"/>
+        <!--<StateVariable name="state" dimension="none" exposure="state"/>-->
+        
+        <DerivedVariable name="iSyn" dimension="current" exposure="iSyn" select="synapses[*]/i" reduce="add" />
+        <DerivedVariable name="state" dimension="none" exposure="state" value="v/MVOLT" />
+        <DerivedVariable name="output" dimension="none" exposure="output" value="1/(1 + exp(-1 * gain * (state+bias)))" />
+
+
+        <DerivedVariable name="iMemb" dimension="current" exposure="iMemb" value="((0-state)*PAMP + iSyn)"/>
+
+        <TimeDerivative variable="v" value="iMemb / C"/>
+        
+        <OnStart>
+            <StateAssignment variable="v" value="state0*MVOLT"/>
+        </OnStart>
+
+        <OnCondition test="v .gt. 0 .and. spiking .lt. 0.5">
+            <StateAssignment variable="spiking" value="1"/>
+            <EventOut port="spike"/>
+        </OnCondition>
+
+        <OnCondition test="v .lt. 0">
+            <StateAssignment variable="spiking" value="0"/>
+        </OnCondition>
+    
+
+    </Dynamics>
+    
+</ComponentType>
+
+
+<silentSynapse id="silentSyn"/>
+<outputSynapse id="neuron_to_neuron_syn_x"/>
+
+<gapJunction id="gapJunction0" conductance="1nS"/>
+
+
+</Lems>
+    

exampleRun21W2D_nml/behavior.pdf

@@ -0,0 +1,9 @@
+<Lems>
+<cellX id="AS" bias="1.4367671641254902" gain="1.0" state0="-1.4367671641254902" tau="0.4849361289529017s"/>
+<cellX id="DA" bias="1.8631749604810641" gain="1.0" state0="-1.8631749604810641" tau="0.9542940551618031s"/>
+<cellX id="DB" bias="-10.69537964582045" gain="1.0" state0="10.69537964582045" tau="0.13286119285866627s"/>
+<cellX id="DD" bias="-11.364561460110986" gain="1.0" state0="11.364561460110986" tau="0.14744509838706876s"/>
+<cellX id="VA" bias="-8.17163385157873" gain="1.0" state0="8.17163385157873" tau="1.4225591094228598s"/>
+<cellX id="VB" bias="-7.507828002321248" gain="1.0" state0="7.507828002321248" tau="1.3758595721391322s"/>
+<cellX id="VD" bias="-1.4519250087816058" gain="1.0" state0="1.4519250087816058" tau="1.2824646902801182s"/>
+</Lems>

exampleRunCEW2D/behavior.pdf

@@ -1,6 +1,6 @@
 {
     "Duration": 40,
     "PopulationSize": 100,
-    "randomseed": 77765,
+    "randomseed": 597293,
     "MaxGenerations": 2000
 }