Merge pull request #260 from DimitriPlotnikov/master

Update models which are used in the NESTML tutorial

src/main/java/org/nest/codegeneration/converters/NESTReferenceConverter.java

@@ -66,7 +66,7 @@ public String convertFunctionCall(final ASTFunctionCall astFunctionCall) {
     }
     // Time.steps -> nest::Time(nest::Time::ms( args )).get_steps());
     if ("steps".equals(functionName)) {
-      return "nest::Time(nest::Time::ms(%s)).get_steps()";
+      return "nest::Time(nest::Time::ms((double) %s)).get_steps()";
     }
 
     if (PredefinedFunctions.POW.equals(functionName)) {

src/main/resources/org/nest/nestml/function/MemberInitialization.ftl

@@ -1,8 +1,9 @@
 <#--
-  Generates C++ declaration
+  In general case creates an
 
-  @param variable VariableSymbol
-  @param tc templatecontroller
+  @param variable VariableSymbol Variable for which the initialization should be done
+  @param printer The particular pretty printer which prints expressions. Is used to handel differences where the
+                 variable is declared (inside a struct or in another method)
 -->
 ${signature("variable", "printer")}
 

src/test/resources/tutorial/1_integrate.nestml → src/test/resources/tutorial/11.rc_neuron.nestml

@@ -1,12 +1,10 @@
 /*
   A straight forward implementation of the RC circuit approach
 */
-neuron iaf:
+neuron rc_neuron:
 
   state:
     V_abs mV = 0mV
-    alias V_m mV = V_abs - E_L
-    I_syn pA = 0pA
   end
 
   equations:
@@ -17,6 +15,7 @@ neuron iaf:
     E_L   mV = -65mV
     C_m   pF = 250pF
     tau_m ms = 10ms
+    I_syn pA = 10pA
   end
 
   input:
@@ -27,7 +26,6 @@ neuron iaf:
 
   update:
     integrate(V_abs)
-    I_syn = spikes.get_sum()
   end
 
 end

src/test/resources/tutorial/12.rc_neuron_rel.nestml

@@ -0,0 +1,32 @@
+/*
+  A straight forward implementation of the RC circuit approach
+*/
+neuron rc_neuron_rel:
+
+  state:
+    V_abs mV = 0mV
+    alias V_m mV = V_abs + E_L
+  end
+
+  equations:
+      V_abs' = -1/tau_m * V_abs + 1/C_m*I_syn
+  end
+
+  parameter:
+    E_L   mV = -70mV
+    C_m   pF = 250pF
+    tau_m ms = 10ms
+    I_syn pA = 10pA
+  end
+
+  input:
+    spikes   <- spike
+  end
+
+  output: spike
+
+  update:
+    integrate(V_abs)
+  end
+
+end

src/test/resources/tutorial/2_integrate_and_reset.nestml → src/test/resources/tutorial/21_rc_fire.nestml

@@ -2,24 +2,24 @@
   A straight forward implementation of the RC circuit approach.
   Extends the integrate method with a threshold and fire behaviour.
 */
-neuron iaf_reset:
+neuron rc_fire:
 
   state:
     V_abs mV = 0mV
     alias V_m mV = V_abs + E_L
-    I_syn pA = 0pA
   end
 
   equations:
       V_abs' = -1/tau_m * V_abs + 1/C_m*I_syn
   end
 
   parameter:
-    E_L   mV = -65mV
+    E_L   mV = -70mV
     C_m   pF = 250pF
     tau_m ms = 10ms
-    alias V_th mV =  55mV + E_L
-    alias V_reset mV =  10mV + E_L
+    I_syn pA = 10pA
+    alias V_th mV =  -55mV - E_L
+    alias V_reset mV =  -65mV - E_L
   end
 
   input:
@@ -32,8 +32,9 @@ neuron iaf_reset:
     integrate(V_abs)
     if V_abs > V_th:
       V_abs = V_reset
+      emit_spike()
     end
-    I_syn = spikes.get_sum()
   end
 
+
 end

src/test/resources/tutorial/22_rc_refractory.nestml

@@ -0,0 +1,47 @@
+/*
+  A straight forward implementation of the RC circuit approach.
+  Extends firing model with an additional refractory state. It is entered directly after a spike is fired.
+*/
+neuron rc_refractory:
+
+  state:
+    V_abs mV = 0mV
+    alias V_m mV = V_abs + E_L
+  end
+
+  equations:
+    V_abs' = -1/tau_m * V_abs + 1/C_m*I_syn
+  end
+
+  parameter:
+    E_L   mV = -70mV
+    C_m   pF = 250pF
+    tau_m ms = 10ms
+    I_syn pA = 10pA
+    alias V_th mV = -55mV - E_L
+    alias V_reset mV = -65mV - E_L
+    refractory_timeout ms = 5ms
+    refractory_counts integer = 0
+  end
+
+  input:
+    spikes   <- spike
+  end
+
+  output: spike
+
+  update:
+    if refractory_counts == 0:
+      integrate(V_abs)
+      if V_abs > V_th:
+        V_abs = V_reset
+        emit_spike()
+        refractory_counts = steps(refractory_timeout)
+      end
+    else:
+      refractory_counts -= 1
+    end
+  end
+
+
+end

src/test/resources/tutorial/23_rc_alpha.nestml

@@ -0,0 +1,58 @@
+/*
+  A straight forward implementation of the RC circuit approach.
+  Extends firing model with an additional refractory state. It is entered directly after a spike is fired.
+*/
+neuron rc_alpha:
+
+  state:
+    V_abs mV = 0mV
+    alias V_m mV = V_abs + E_L
+    g_in pA = 0pA    # inputs from the inh conductance
+  end
+
+  equations:
+    # alpha function for the g_in
+    g_in'' = -g_in'/tau_syn_in
+    g_in' = g_in' - g_in/tau_syn_in
+    I_syn pA = g_in
+    V_abs' = -1/tau_m * V_abs + 1/C_m*I_syn
+  end
+
+  parameter:
+    E_L   mV = -70mV
+    C_m   pF = 250pF
+    tau_m ms = 10ms
+
+    alias V_th mV = -55mV - E_L
+    alias V_reset mV = -65mV - E_L
+    refractory_timeout ms = 5ms
+    refractory_counts integer = 0
+  end
+
+  input:
+    spikes   <- spike
+  end
+
+  internal:
+    tau_syn_in ms = 2ms
+    PSConInit_I real = 1.0 * e / tau_syn_in
+  end
+
+  output: spike
+
+  update:
+    if refractory_counts == 0:
+      integrate(V_abs)
+      if V_abs > V_th:
+        V_abs = V_reset
+        emit_spike()
+        refractory_counts = steps(refractory_timeout)
+      end
+    else:
+      refractory_counts -= 1
+    end
+    g_in' += PSConInit_I*spikes.get_sum()
+  end
+
+
+end