From 5ec5e251bd8aff07bde7bd97e6dfc16bce28a3c7 Mon Sep 17 00:00:00 2001
From: DimitriPlotnikov <d.plotnikov@fz-juelich.de>
Date: Thu, 15 Sep 2016 16:06:26 +0200
Subject: [PATCH] Update models which are used in the NESTML tutorial

---
 ...1_integrate.nestml => 11.rc_neuron.nestml} |  6 +--
 .../tutorial/12.rc_neuron_rel.nestml          | 32 +++++++++++++
 src/test/resources/tutorial/21_rc_fire.nestml | 37 +++++++++++++++
 ...d_reset.nestml => 22_rc_refractory.nestml} | 13 ++---
 .../resources/tutorial/23_rc_alpha.nestml     | 47 +++++++++++++++++++
 5 files changed, 125 insertions(+), 10 deletions(-)
 rename src/test/resources/tutorial/{1_integrate.nestml => 11.rc_neuron.nestml} (79%)
 create mode 100644 src/test/resources/tutorial/12.rc_neuron_rel.nestml
 create mode 100644 src/test/resources/tutorial/21_rc_fire.nestml
 rename src/test/resources/tutorial/{2_integrate_and_reset.nestml => 22_rc_refractory.nestml} (75%)
 create mode 100644 src/test/resources/tutorial/23_rc_alpha.nestml

diff --git a/src/test/resources/tutorial/1_integrate.nestml b/src/test/resources/tutorial/11.rc_neuron.nestml
similarity index 79%
rename from src/test/resources/tutorial/1_integrate.nestml
rename to src/test/resources/tutorial/11.rc_neuron.nestml
index cba72718e..4778f6c0c 100644
--- a/src/test/resources/tutorial/1_integrate.nestml
+++ b/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
\ No newline at end of file
diff --git a/src/test/resources/tutorial/12.rc_neuron_rel.nestml b/src/test/resources/tutorial/12.rc_neuron_rel.nestml
new file mode 100644
index 000000000..1adb8920a
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/src/test/resources/tutorial/21_rc_fire.nestml b/src/test/resources/tutorial/21_rc_fire.nestml
new file mode 100644
index 000000000..c908bf090
--- /dev/null
+++ b/src/test/resources/tutorial/21_rc_fire.nestml
@@ -0,0 +1,37 @@
+/*
+  A straight forward implementation of the RC circuit approach.
+  Extends the integrate method with a threshold and fire behaviour.
+*/
+neuron rc_fire:
+
+  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 = 0pA
+    alias V_th mV =  -55mV - E_L
+    alias V_reset mV =  -65mV - E_L
+  end
+
+  input:
+    spikes   <- spike
+  end
+
+  output: spike
+
+  update:
+    integrate(V_abs)
+
+  end
+
+end
\ No newline at end of file
diff --git a/src/test/resources/tutorial/2_integrate_and_reset.nestml b/src/test/resources/tutorial/22_rc_refractory.nestml
similarity index 75%
rename from src/test/resources/tutorial/2_integrate_and_reset.nestml
rename to src/test/resources/tutorial/22_rc_refractory.nestml
index deb5ada05..6ae79b566 100644
--- a/src/test/resources/tutorial/2_integrate_and_reset.nestml
+++ b/src/test/resources/tutorial/22_rc_refractory.nestml
@@ -2,12 +2,11 @@
   A straight forward implementation of the RC circuit approach.
   Extends the integrate method with a threshold and fire behaviour.
 */
-neuron iaf_reset:
+neuron rc_refractory:
 
   state:
     V_abs mV = 0mV
     alias V_m mV = V_abs + E_L
-    I_syn pA = 0pA
   end
 
   equations:
@@ -15,11 +14,12 @@ neuron iaf_reset:
   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
\ No newline at end of file
diff --git a/src/test/resources/tutorial/23_rc_alpha.nestml b/src/test/resources/tutorial/23_rc_alpha.nestml
new file mode 100644
index 000000000..9a24b6d77
--- /dev/null
+++ b/src/test/resources/tutorial/23_rc_alpha.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
\ No newline at end of file