Merge pull request #310 from DimitriPlotnikov/master

Renamings of language constructs and predefined functions.

docker/DockerfileRelease

@@ -28,7 +28,7 @@ RUN python setup.py install
 # Define working directory.doc
 RUN mkdir -p /data/nestml/target/
 WORKDIR /data/nestml/target/
-RUN wget https://github.com/nest/nestml/releases/download/1.3.1/nestml.jar
+RUN wget https://github.com/nest/nestml/releases/download/1.4.0/nestml.jar
 
 # Define default command.
 # Entry point is constructed in the invoking script

models/aeif_cond_alpha.nestml

@@ -44,15 +44,15 @@ neuron aeif_cond_alpha_neuron:
     # Add aliases to simplify the equation definition of V_m
     exp_arg real = (V_m-V_th)/delta_T
     I_spike pA = delta_T*exp(exp_arg)
-    I_syn_exc pA =   Cond_sum(g_ex, spikesExc) * ( V_m - E_ex )
-    I_syn_inh pA =   Cond_sum(g_in, spikesInh) * ( V_m - E_in )
+    I_syn_exc pA =   cond_sum(g_ex, spikesExc) * ( V_m - E_ex )
+    I_syn_inh pA =   cond_sum(g_in, spikesInh) * ( V_m - E_in )
 
     V_m' = ( -g_L * ( ( V_m - E_L ) - I_spike ) - I_syn_exc - I_syn_inh - w + I_e + I_stim ) / C_m
     w' = (a*(V_m - E_L) - w)/tau_w
 
   end
 
-  parameter:
+  parameters:
     # membrane parameters
     C_m   pF = 281.0pF       # Membrane Capacitance in pF
     t_ref ms = 0.0ms         # Refractory period in ms
@@ -81,7 +81,7 @@ neuron aeif_cond_alpha_neuron:
     I_stim pA = 0pA
   end
 
-  internal:
+  internals:
 
     # Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
     # conductance excursion.

models/aeif_cond_alpha_implicit.nestml

@@ -53,14 +53,14 @@ neuron aeif_cond_alpha_implicit:
     # Add aliases to simplify the equation definition of V_m
     exp_arg real = (V_m-V_th)/delta_T
     I_spike pA = delta_T*exp(exp_arg)
-    I_syn_exc pA =   Cond_sum(g_ex, spikesExc) * ( V_m - E_ex )
-    I_syn_inh pA =   Cond_sum(g_in, spikesInh) * ( V_m - E_in )
+    I_syn_exc pA =   cond_sum(g_ex, spikesExc) * ( V_m - E_ex )
+    I_syn_inh pA =   cond_sum(g_in, spikesInh) * ( V_m - E_in )
 
     V_m' = ( -g_L * ( ( V_m - E_L ) - I_spike ) - I_syn_exc - I_syn_inh - w + I_e + I_stim ) / C_m
 
   end
 
-  parameter:
+  parameters:
     # membrane parameters
     C_m   pF = 281.0pF       # Membrane Capacitance in pF
     t_ref ms = 0.0ms         # Refractory period in ms
@@ -89,7 +89,7 @@ neuron aeif_cond_alpha_implicit:
     I_stim pA = 0pA
   end
 
-  internal:
+  internals:
 
     # Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
     # conductance excursion.

models/aeif_cond_exp.nestml

@@ -47,14 +47,14 @@ neuron aeif_cond_exp_neuron:
     # Add aliases to simplify the equation definition of V_m
     exp_arg real = (V_m-V_th)/delta_T
     I_spike pA = delta_T*exp(exp_arg)
-    I_syn_exc pA = Cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
-    I_syn_inh pA = Cond_sum(g_in, spikeInh) * ( V_m - E_in )
+    I_syn_exc pA = cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
+    I_syn_inh pA = cond_sum(g_in, spikeInh) * ( V_m - E_in )
 
     V_m' = ( -g_L * ( ( V_m - E_L ) - I_spike ) - I_syn_exc - I_syn_inh - w + I_e + I_stim ) / C_m
     w' = (a*(V_m - E_L) - w)/tau_w
   end
 
-  parameter:
+  parameters:
     # membrane parameters
     C_m   pF = 281.0pF     # Membrane Capacitance in pF
     t_ref ms = 0.0ms       # Refractory period in ms
@@ -83,7 +83,7 @@ neuron aeif_cond_exp_neuron:
     I_stim pA = 0pA
   end
 
-  internal:
+  internals:
     # refractory time in steps
     RefractoryCounts integer = steps(t_ref)
     # counts number of tick during the refractory period

models/aeif_cond_exp_implicit.nestml

@@ -52,13 +52,13 @@ neuron aeif_cond_exp_implicit:
     # Add aliases to simplify the equation definition of V_m
     exp_arg real = (V_m-V_th)/delta_T
     I_spike pA = delta_T*exp(exp_arg)
-    I_syn_exc pA = Cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
-    I_syn_inh pA = Cond_sum(g_in, spikeInh) * ( V_m - E_in )
+    I_syn_exc pA = cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
+    I_syn_inh pA = cond_sum(g_in, spikeInh) * ( V_m - E_in )
 
     V_m' = ( -g_L * ( ( V_m - E_L ) - I_spike ) - I_syn_exc - I_syn_inh - w + I_e + I_stim ) / C_m
   end
 
-  parameter:
+  parameters:
     # membrane parameters
     C_m   pF = 281.0pF     # Membrane Capacitance in pF
     t_ref ms = 0.0ms       # Refractory period in ms
@@ -87,7 +87,7 @@ neuron aeif_cond_exp_implicit:
     I_stim pA = 0pA
   end
 
-  internal:
+  internals:
     # refractory time in steps
     RefractoryCounts integer = steps(t_ref)
     # counts number of tick during the refractory period

models/hh_cond_exp_traub.nestml

@@ -54,8 +54,8 @@ neuron hh_cond_exp_traub_neuron:
     I_Na  pA = g_Na * Act_m * Act_m * Act_m * Act_h * ( V_m - E_Na )
     I_K   pA  = g_K * Inact_n * Inact_n * Inact_n * Inact_n * ( V_m - E_K )
     I_L   pA = g_L * ( V_m - E_L )
-    I_syn_exc pA = Cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
-    I_syn_inh pA = Cond_sum(g_in, spikeInh) * ( V_m - E_in )
+    I_syn_exc pA = cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
+    I_syn_inh pA = cond_sum(g_in, spikeInh) * ( V_m - E_in )
 
     shape g_in = exp(-1/tau_syn_in*t)
     shape g_ex = exp(-1/tau_syn_ex*t)
@@ -77,7 +77,7 @@ neuron hh_cond_exp_traub_neuron:
 
   end
 
-  parameter:
+  parameters:
     g_Na nS = 20000.0nS       # Threshold Potential in mV
     g_K nS = 6000.0nS         # K Conductance
     g_L nS = 10nS             # Leak Conductance
@@ -95,7 +95,7 @@ neuron hh_cond_exp_traub_neuron:
     I_stim pA = 0pA           # External input current
   end
 
-  internal:
+  internals:
     RefractoryCounts integer = 20
     r integer # counts number of tick during the refractory period
   end

models/hh_cond_exp_traub_implicit.nestml

@@ -57,8 +57,8 @@ neuron hh_cond_exp_traub_implicit:
     I_Na  pA = g_Na * Act_m * Act_m * Act_m * Act_h * ( V_m - E_Na )
     I_K   pA  = g_K * Inact_n * Inact_n * Inact_n * Inact_n * ( V_m - E_K )
     I_L   pA = g_L * ( V_m - E_L )
-    I_syn_exc pA = Cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
-    I_syn_inh pA = Cond_sum(g_in, spikeInh) * ( V_m - E_in )
+    I_syn_exc pA = cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
+    I_syn_inh pA = cond_sum(g_in, spikeInh) * ( V_m - E_in )
 
     V_m' =( -I_Na - I_K - I_L - I_syn_exc - I_syn_inh + I_stim + I_e ) / C_m
 
@@ -80,7 +80,7 @@ neuron hh_cond_exp_traub_implicit:
     g_in' = -g_in / tau_syn_in
   end
 
-  parameter:
+  parameters:
     g_Na nS = 20000.0nS       # Threshold Potential in mV
     g_K nS = 6000.0nS         # K Conductance
     g_L nS = 10nS             # Leak Conductance
@@ -98,7 +98,7 @@ neuron hh_cond_exp_traub_implicit:
     I_stim pA = 0pA           # External input current
   end
 
-  internal:
+  internals:
     RefractoryCounts integer = 20
     r integer # counts number of tick during the refractory period
   end

models/hh_psc_alpha.nestml

@@ -66,8 +66,8 @@ neuron hh_psc_alpha_neuron:
     shape g_in = (e/tau_syn_in) * t * exp(-1/tau_syn_in*t)
     shape g_ex = (e/tau_syn_ex) * t * exp(-1/tau_syn_ex*t)
 
-    I_syn_exc pA = I_sum(g_ex, spikeExc)
-    I_syn_inh pA = I_sum(g_in, spikeExc)
+    I_syn_exc pA = curr_sum(g_ex, spikeExc)
+    I_syn_inh pA = curr_sum(g_in, spikeExc)
     I_Na  pA = g_Na * Act_m * Act_m * Act_m * Act_h * ( V_m - E_Na )
     I_K   pA  = g_K * Inact_n * Inact_n * Inact_n * Inact_n * ( V_m - E_K )
     I_L   pA = g_L * ( V_m - E_L )
@@ -89,7 +89,7 @@ neuron hh_psc_alpha_neuron:
     Act_h' = alpha_h * ( 1 - Act_h ) - beta_h * Act_h # h-variable
   end
 
-  parameter:
+  parameters:
     t_ref ms = 2.0 ms      # Refractory period
     g_Na nS = 12000.0nS    # Sodium peak conductance
     g_K nS = 3600.0nS      # Potassium peak conductance
@@ -103,7 +103,7 @@ neuron hh_psc_alpha_neuron:
     I_e pA = 0pA           # Constant Current in pA
   end
 
-  internal:
+  internals:
     # Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
     # conductance excursion.
     PSConInit_E real = 1.0 * e / tau_syn_ex

models/hh_psc_alpha_implicit.nestml

@@ -71,8 +71,8 @@ neuron hh_psc_alpha_implicit:
     g_in'' = -g_in' / tau_syn_in
     g_in' = g_in' - ( g_in / tau_syn_in )
 
-    I_syn_exc pA = I_sum(g_ex, spikeExc)
-    I_syn_inh pA = I_sum(g_in, spikeExc)
+    I_syn_exc pA = curr_sum(g_ex, spikeExc)
+    I_syn_inh pA = curr_sum(g_in, spikeExc)
     I_Na  pA = g_Na * Act_m * Act_m * Act_m * Act_h * ( V_m - E_Na )
     I_K   pA  = g_K * Inact_n * Inact_n * Inact_n * Inact_n * ( V_m - E_K )
     I_L   pA = g_L * ( V_m - E_L )
@@ -94,7 +94,7 @@ neuron hh_psc_alpha_implicit:
     Act_h' = alpha_h * ( 1 - Act_h ) - beta_h * Act_h # h-variable
   end
 
-  parameter:
+  parameters:
     t_ref ms = 2.0 ms      # Refractory period
     g_Na nS = 12000.0nS    # Sodium peak conductance
     g_K nS = 3600.0nS      # Potassium peak conductance
@@ -108,7 +108,7 @@ neuron hh_psc_alpha_implicit:
     I_e pA = 0pA           # Constant Current in pA
   end
 
-  internal:
+  internals:
     # Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
     # conductance excursion.
     PSConInit_E real = 1.0 * e / tau_syn_ex

models/ht_neuron.nestml

@@ -86,17 +86,17 @@ neuron ht_neuron_nestml:
     INaP_slope mV = 7.7pA
     m_inf_NaP real = 1.0 / ( 1.0 + exp( -( V_m - INaP_thresh ) / INaP_slope ) )
     # Persistent Na current; member only to allow recording
-    record I_NaP pA = -NaP_g_peak * pow( m_inf_NaP, 3.0 )* ( V_m - NaP_E_rev )
+    recordable I_NaP pA = -NaP_g_peak * pow( m_inf_NaP, 3.0 )* ( V_m - NaP_E_rev )
 
     d_half real = 0.25
     m_inf_KNa real = 1.0 / ( 1.0 + pow( d_half / IKNa_D, 3.5 ) )
     # Depol act. K current; member only to allow recording
-    record I_KNa pA = -KNa_g_peak * m_inf_KNa * ( V_m - KNa_E_rev )
+    recordable I_KNa pA = -KNa_g_peak * m_inf_KNa * ( V_m - KNa_E_rev )
 
     # Low-thresh Ca current; member only to allow recording
-    record I_T pA = -T_g_peak * IT_m * IT_m * IT_h * ( V_m - T_E_rev )
+    recordable I_T pA = -T_g_peak * IT_m * IT_m * IT_h * ( V_m - T_E_rev )
 
-    record I_h pA = -h_g_peak * Ih_m  * ( V_m - h_E_rev )
+    recordable I_h pA = -h_g_peak * Ih_m  * ( V_m - h_E_rev )
     # The spike current is only activate immediately after a spike.
     I_spike mV = (g_spike) ? -( V_m - E_K ) / Tau_spike : 0
     V_m'  = ( I_Na + I_K + I_syn + I_NaP + I_KNa + I_T + I_h + I_stim ) / Tau_m + I_spike
@@ -148,7 +148,7 @@ neuron ht_neuron_nestml:
     g_GABAB' = g_GABAB' - g_GABAB /GABA_B_Tau_2
   end
 
-  parameter:
+  parameters:
     E_Na mV = 30.0mV
     E_K mV = -90.0mV
     g_NaL nS =  0.2nS
@@ -191,7 +191,7 @@ neuron ht_neuron_nestml:
     KNa_D_EQ pA = 0.001pA
   end
 
-  internal:
+  internals:
     AMPAInitialValue real = compute_synapse_constant( AMPA_Tau_1, AMPA_Tau_2, AMPA_g_peak )
     NMDAInitialValue real = compute_synapse_constant( NMDA_Tau_1, NMDA_Tau_2, NMDA_g_peak )
 

models/iaf_chxk_2008_implicit.nestml

@@ -42,15 +42,15 @@ neuron iaf_chxk_2008_implicit:
     G_ahp'' = -G_ahp' / tau_ahp
     G_ahp' = G_ahp' -  G_ahp / tau_ahp
 
-    I_syn_exc pA = Cond_sum(g_ex, spikesInh) * ( V_m - E_ex )
-    I_syn_inh pA = Cond_sum(g_in, spikesExc) * ( V_m - E_in )
+    I_syn_exc pA = cond_sum(g_ex, spikesInh) * ( V_m - E_ex )
+    I_syn_inh pA = cond_sum(g_in, spikesExc) * ( V_m - E_in )
     I_ahp pA = G_ahp * ( V_m - E_ahp )
     I_leak pA = g_L * ( V_m - E_L )
 
     V_m' = ( -I_leak - I_syn_exc - I_syn_inh - I_ahp + I_stim + I_e ) / C_m
   end
 
-  parameter:
+  parameters:
     V_th mV = -45.0mV        # Threshold Potential
     E_ex mV = 20mV           # Excitatory reversal potential
     E_in mV = -90mV          # Inhibitory reversal potential
@@ -70,7 +70,7 @@ neuron iaf_chxk_2008_implicit:
     I_stim pA = 0pA
   end
 
-  internal:
+  internals:
     # Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
     # conductance excursion.
     PSConInit_E real = 1.0 * e / tau_syn_ex

models/iaf_cond_alpha.nestml

@@ -41,14 +41,14 @@ neuron iaf_cond_alpha_neuron:
     shape g_in = (e/tau_syn_in) * t * exp(-1/tau_syn_in*t)
     shape g_ex = (e/tau_syn_ex) * t * exp(-1/tau_syn_ex*t)
 
-    I_syn_exc pA = Cond_sum(g_ex, spikeExc)  * ( V_m - E_ex )
-    I_syn_inh pA =  Cond_sum(g_in, spikeInh)  * ( V_m - E_in )
+    I_syn_exc pA = cond_sum(g_ex, spikeExc)  * ( V_m - E_ex )
+    I_syn_inh pA =  cond_sum(g_in, spikeInh)  * ( V_m - E_in )
     I_leak pA = g_L * ( V_m - E_L )
 
     V_m' = ( -I_leak - I_syn_exc - I_syn_inh + I_stim + I_e ) / C_m
   end
 
-  parameter:
+  parameters:
     V_th mV = -55.0mV    # Threshold Potential in mV
     V_reset mV = -60.0mV # Reset Potential in mV
     t_ref ms = 2.ms     # Refractory period in ms
@@ -66,7 +66,7 @@ neuron iaf_cond_alpha_neuron:
     I_stim pA = 0pA
   end
 
-  internal:
+  internals:
     RefractoryCounts integer = steps(t_ref) # refractory time in steps
     r integer                               # counts number of tick during the refractory period
   end

models/iaf_cond_alpha_implicit.nestml

@@ -48,14 +48,14 @@ neuron iaf_cond_alpha_implicit:
     g_ex'' = -g_ex'/tau_syn_ex
     g_ex' = g_ex'  -g_ex/tau_syn_ex
 
-    I_syn_exc pA = Cond_sum(g_ex, spikeExc)  * ( V_m - E_ex )
-    I_syn_inh pA = Cond_sum(g_in, spikeInh)  * ( V_m - E_in )
+    I_syn_exc pA = cond_sum(g_ex, spikeExc)  * ( V_m - E_ex )
+    I_syn_inh pA = cond_sum(g_in, spikeInh)  * ( V_m - E_in )
     I_leak pA = g_L * ( V_m - E_L )
 
     V_m' = ( -I_leak - I_syn_exc - I_syn_inh + I_stim + I_e ) / C_m
   end
 
-  parameter:
+  parameters:
     V_th mV = -55.0mV     # Threshold Potential in mV
     V_reset mV = -60.0mV  # Reset Potential in mV
     t_ref ms = 2.0ms      # Refractory period in ms
@@ -72,7 +72,7 @@ neuron iaf_cond_alpha_implicit:
                     # _dynamics function computing the derivative of the state vector.
   end
 
-  internal:
+  internals:
     # Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
     # conductance excursion.
     PSConInit_E real = 1.0 * e / tau_syn_ex

models/iaf_cond_beta.nestml

@@ -35,13 +35,13 @@ neuron iaf_cond_beta_neuron:
       GE'' = -GE'/tau_syn_rise_E
       GE' = GE' -GE/tau_syn_decay_E
 
-      I_syn_exc pA = (F_E + Cond_sum(GE, spikeExc)) * ( V_m - E_ex )
-      I_syn_inh pA = (F_I + Cond_sum(GI, spikeInh)) * ( V_m - E_in )
+      I_syn_exc pA = (F_E + cond_sum(GE, spikeExc)) * ( V_m - E_ex )
+      I_syn_inh pA = (F_I + cond_sum(GI, spikeInh)) * ( V_m - E_in )
       I_leak pA = g_L * ( V_m - E_L ) # pa = nS * mV
       V_m' =  (-I_leak - I_syn_exc - I_syn_inh + I_stim + I_e ) / C_m
   end
 
-  parameter:
+  parameters:
     E_L mV = -85.0mV # Leak reversal Potential (aka resting potential) in mV
     C_m pF = 250.0pF # Capacity of the membrane
     t_ref ms = 2.0ms # Refractory period in ms
@@ -62,7 +62,7 @@ neuron iaf_cond_beta_neuron:
                     # _dynamics function computing the derivative of the state vector.
   end
 
-  internal:
+  internals:
     # Impulse to add to GE' on spike arrival to evoke unit-amplitude
     # conductance excursion.
     PSConInit_E real = 1.0 * e / tau_syn_rise_E #