Remove units from spiking input ports (#882)

nest · Sep 4, 2023 · ddaa78b · ddaa78b
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diff --git a/doc/models_library/aeif_cond_alpha.rst b/doc/models_library/aeif_cond_alpha.rst
@@ -109,4 +109,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.943078
+   Generated at 2023-08-22 14:29:44.564178
diff --git a/doc/models_library/aeif_cond_exp.rst b/doc/models_library/aeif_cond_exp.rst
@@ -110,4 +110,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.899673
+   Generated at 2023-08-22 14:29:44.513192
diff --git a/doc/models_library/hh_cond_exp_destexhe.rst b/doc/models_library/hh_cond_exp_destexhe.rst
@@ -125,4 +125,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:49.081867
+   Generated at 2023-08-22 14:29:44.766222
diff --git a/doc/models_library/hh_cond_exp_traub.rst b/doc/models_library/hh_cond_exp_traub.rst
@@ -130,4 +130,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.607331
+   Generated at 2023-08-22 14:29:44.206568
diff --git a/doc/models_library/hh_moto_5ht.rst b/doc/models_library/hh_moto_5ht.rst
@@ -0,0 +1,137 @@
+hh_moto_5ht
+###########
+
+
+hh_moto_5ht_nestml - a motor neuron model in HH formalism with 5HT modulation
+
+Description
++++++++++++
+
+hh_moto_5ht is an implementation of a spiking motor neuron using the Hodgkin-Huxley formalism according to [2]_. Basically this model is an implementation of the existing NEURON model [1]_.
+
+The parameter that represents 5HT modulation is ``g_K_Ca_5ht``. When it equals 1, no modulation happens. An application of 5HT corresponds to its decrease. The default value for it is 0.6. This value was used in the Neuron simulator model. The range of this parameter is (0, 1] but you are free to play with any value.
+
+Post-synaptic currents and spike detection are the same as in hh_psc_alpha.
+
+
+References
+++++++++++
+
+.. [1] Muscle spindle feedback circuit by Moraud EM and Capogrosso M.
+       https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=189786
+
+.. [2] Compartmental model of vertebrate motoneurons for Ca2+-dependent spiking and plateau potentials under pharmacological treatment.
+       Booth V, Rinzel J, Kiehn O.
+       http://refhub.elsevier.com/S0896-6273(16)00010-6/sref4
+
+.. [3] Repository: https://github.com/research-team/hh-moto-5ht
+
+
+See also
+++++++++
+
+hh_psc_alpha
+
+
+
+Parameters
+++++++++++
+.. csv-table::
+    :header: "Name", "Physical unit", "Default value", "Description"
+    :widths: auto
+
+
+    "t_ref", "ms", "2.0ms", "Refractory period"    
+    "g_Na", "nS", "5000.0nS", "Sodium peak conductance"    
+    "g_L", "nS", "200.0nS", "Leak conductance"    
+    "g_K_rect", "nS", "30000.0nS", "Delayed Rectifier Potassium peak conductance"    
+    "g_Ca_N", "nS", "5000.0nS", ""    
+    "g_Ca_L", "nS", "10.0nS", ""    
+    "g_K_Ca", "nS", "30000.0nS", ""    
+    "g_K_Ca_5ht", "real", "0.6", "modulation of K-Ca channels by 5HT. Its value 1.0 == no modulation."    
+    "Ca_in_init", "mmol", "0.0001mmol", "Initial inside Calcium concentration"    
+    "Ca_out", "mmol", "2.0mmol", "Outside Calcium concentration. Remains constant during simulation."    
+    "C_m", "pF", "200.0pF", "Membrane capacitance"    
+    "E_Na", "mV", "50.0mV", ""    
+    "E_K", "mV", "-80.0mV", ""    
+    "E_L", "mV", "-70.0mV", ""    
+    "R_const", "real", "8.314472", "Nernst equation constants"    
+    "F_const", "real", "96485.34", ""    
+    "T_current", "real", "309.15", "36 Celcius"    
+    "tau_syn_ex", "ms", "0.2ms", "Rise time of the excitatory synaptic alpha function"    
+    "tau_syn_in", "ms", "2.0ms", "Rise time of the inhibitory synaptic alpha function"    
+    "I_e", "pA", "0pA", "Constant current"    
+    "V_m_init", "mV", "-65.0mV", ""    
+    "hc_tau", "ms", "50.0ms", ""    
+    "mc_tau", "ms", "15.0ms", ""    
+    "p_tau", "ms", "400.0ms", ""    
+    "alpha", "mmol / pA", "1e-05mmol / pA", ""
+
+
+
+State variables
++++++++++++++++
+
+.. csv-table::
+    :header: "Name", "Physical unit", "Default value", "Description"
+    :widths: auto
+
+
+    "r", "integer", "0", "number of steps in the current refractory phase"    
+    "V_m", "mV", "V_m_init", "Membrane potential"    
+    "Ca_in", "mmol", "Ca_in_init", "Inside Calcium concentration"    
+    "Act_m", "real", "alpha_m(V_m_init) / (alpha_m(V_m_init) + beta_m(V_m_init))", ""    
+    "Act_h", "real", "h_inf(V_m_init)", ""    
+    "Inact_n", "real", "n_inf(V_m_init)", ""    
+    "Act_p", "real", "p_inf(V_m_init)", ""    
+    "Act_mc", "real", "mc_inf(V_m_init)", ""    
+    "Act_hc", "real", "hc_inf(V_m_init)", ""
+
+
+
+
+Equations
++++++++++
+
+
+
+.. math::
+   \frac{ dV_{m} } { dt }= \frac 1 { C_{m} } \left( { (-(I_{Na} + I_{K} + I_{L} + I_{Ca,N} + I_{Ca,L} + I_{K,Ca}) + I_{stim} + I_{e} + I_{syn,inh} + I_{syn,exc}) } \right) 
+
+.. math::
+   \frac{ dInact_{n} } { dt }= \frac{ (\text{n_inf}(V_{m}) - Inact_{n}) } { \text{n_tau}(V_{m}) }
+
+.. math::
+   \frac{ dAct_{m} } { dt }= \text{alpha_m}(V_{m}) \cdot (1.0 - Act_{m}) - \text{beta_m}(V_{m}) \cdot Act_{m}
+
+.. math::
+   \frac{ dAct_{h} } { dt }= \frac{ (\text{h_inf}(V_{m}) - Act_{h}) } { \text{h_tau}(V_{m}) }
+
+.. math::
+   \frac{ dAct_{p} } { dt }= \frac 1 { p_{\tau} } \left( { (\text{p_inf}(V_{m}) - Act_{p}) } \right) 
+
+.. math::
+   \frac{ dAct_{mc} } { dt }= \frac 1 { mc_{\tau} } \left( { (\text{mc_inf}(V_{m}) - Act_{mc}) } \right) 
+
+.. math::
+   \frac{ dAct_{hc} } { dt }= \frac 1 { hc_{\tau} } \left( { (\text{hc_inf}(V_{m}) - Act_{hc}) } \right) 
+
+.. math::
+   \frac{ dCa_{in} } { dt }= (\frac{ 0.01 } { \mathrm{s} }) \cdot (-\alpha \cdot (I_{Ca,N} + I_{Ca,L}) - 4.0 \cdot Ca_{in})
+
+
+
+Source code
++++++++++++
+
+The model source code can be found in the NESTML models repository here: `hh_moto_5ht <https://github.com/nest/nestml/tree/master/models/neurons/hh_moto_5ht.nestml>`_.
+
+Characterisation
+++++++++++++++++
+
+.. include:: hh_moto_5ht_characterisation.rst
+
+
+.. footer::
+
+   Generated at 2023-08-22 14:29:44.636925
diff --git a/doc/models_library/hh_psc_alpha.rst b/doc/models_library/hh_psc_alpha.rst
@@ -124,4 +124,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:49.051544
+   Generated at 2023-08-22 14:29:44.732465
diff --git a/doc/models_library/hill_tononi.rst b/doc/models_library/hill_tononi.rst
@@ -151,4 +151,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.773169
+   Generated at 2023-08-22 14:29:44.380314
diff --git a/doc/models_library/iaf_chxk_2008.rst b/doc/models_library/iaf_chxk_2008.rst
@@ -101,4 +101,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.822099
+   Generated at 2023-08-22 14:29:44.431863
diff --git a/doc/models_library/iaf_cond_alpha.rst b/doc/models_library/iaf_cond_alpha.rst
@@ -97,4 +97,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.934362
+   Generated at 2023-08-22 14:29:44.552880
diff --git a/doc/models_library/iaf_cond_beta.rst b/doc/models_library/iaf_cond_beta.rst
@@ -113,4 +113,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.761456
+   Generated at 2023-08-22 14:29:44.369517
diff --git a/doc/models_library/iaf_cond_exp.rst b/doc/models_library/iaf_cond_exp.rst
@@ -87,4 +87,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.999982
+   Generated at 2023-08-22 14:29:44.627038
diff --git a/doc/models_library/iaf_cond_exp_sfa_rr.rst b/doc/models_library/iaf_cond_exp_sfa_rr.rst
@@ -109,4 +109,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.917439
+   Generated at 2023-08-22 14:29:44.534151
diff --git a/doc/models_library/iaf_psc_alpha.rst b/doc/models_library/iaf_psc_alpha.rst
@@ -116,4 +116,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.837818
+   Generated at 2023-08-22 14:29:44.449697
diff --git a/doc/models_library/iaf_psc_delta.rst b/doc/models_library/iaf_psc_delta.rst
@@ -94,7 +94,7 @@ Equations
 
 
 .. math::
-   \frac{ dV_{m} } { dt }= \frac{ -(V_{m} - E_{L}) } { \tau_{m} } + (\frac 1 { \mathrm{ms} } \left( { \frac{ \mathrm{mV} } { \mathrm{pA} } } \right) ) \cdot \text{convolve}(G, spikes) + \frac 1 { C_{m} } \left( { (I_{e} + I_{stim}) } \right) 
+   \frac{ dV_{m} } { dt }= \frac{ -(V_{m} - E_{L}) } { \tau_{m} } + \text{convolve}(G, spikes) \cdot (\frac{ \mathrm{mV} } { \mathrm{ms} }) + \frac 1 { C_{m} } \left( { (I_{e} + I_{stim}) } \right) 
 
 
 
@@ -111,4 +111,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.845377
+   Generated at 2023-08-22 14:29:44.459765
diff --git a/doc/models_library/iaf_psc_exp.rst b/doc/models_library/iaf_psc_exp.rst
@@ -95,4 +95,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.990089
+   Generated at 2023-08-22 14:29:44.614878
diff --git a/doc/models_library/iaf_psc_exp_dend.rst b/doc/models_library/iaf_psc_exp_dend.rst
@@ -96,4 +96,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.889657
+   Generated at 2023-08-22 14:29:44.501436
diff --git a/doc/models_library/iaf_psc_exp_htum.rst b/doc/models_library/iaf_psc_exp_htum.rst
@@ -108,4 +108,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.961309
+   Generated at 2023-08-22 14:29:44.584571
diff --git a/doc/models_library/ignore_and_fire.rst b/doc/models_library/ignore_and_fire.rst
@@ -65,4 +65,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-08-08 15:01:40.284515
+   Generated at 2023-08-22 14:29:44.764699
diff --git a/doc/models_library/izhikevich.rst b/doc/models_library/izhikevich.rst
@@ -97,4 +97,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.970819
+   Generated at 2023-08-22 14:29:44.595366
diff --git a/doc/models_library/izhikevich_psc_alpha.rst b/doc/models_library/izhikevich_psc_alpha.rst
@@ -48,7 +48,7 @@ Parameters
 
 
     "C_m", "pF", "200pF", "Membrane capacitance"    
-    "k", "pF / (ms mV)", "8pF / mV / ms", "Spiking slope"    
+    "k", "pF / (mV ms)", "8pF / mV / ms", "Spiking slope"    
     "V_r", "mV", "-65mV", "Resting potential"    
     "V_t", "mV", "-45mV", "Threshold potential"    
     "a", "1 / ms", "0.01 / ms", "Time scale of recovery variable"    
@@ -104,4 +104,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:48.680240
+   Generated at 2023-08-22 14:29:44.285400
diff --git a/doc/models_library/mat2_psc_exp.rst b/doc/models_library/mat2_psc_exp.rst
@@ -107,4 +107,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-22 17:48:49.118418
+   Generated at 2023-08-22 14:29:44.812580
diff --git a/doc/models_library/neuromodulated_stdp.rst b/doc/models_library/neuromodulated_stdp.rst
@@ -75,4 +75,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-23 09:41:54.875739
+   Generated at 2023-08-22 14:29:44.891623
diff --git a/doc/models_library/noisy_synapse.rst b/doc/models_library/noisy_synapse.rst
@@ -37,4 +37,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-23 09:41:54.864688
+   Generated at 2023-08-22 14:29:44.871968
diff --git a/doc/models_library/static_synapse.rst b/doc/models_library/static_synapse.rst
@@ -0,0 +1,38 @@
+static_synapse
+##############
+
+
+Static synapse
+
+Description
++++++++++++
+A synapse where the synaptic strength (weight) does not evolve with simulated time, but is defined as a (constant) parameter.
+
+
+
+Parameters
+++++++++++
+
+
+.. csv-table::
+    :header: "Name", "Physical unit", "Default value", "Description"
+    :widths: auto
+
+
+    "w", "real", "1", "Synaptic weight"    
+    "d", "ms", "1ms", "Synaptic transmission delay"
+Source code
++++++++++++
+
+The model source code can be found in the NESTML models repository here: `static_synapse <https://github.com/nest/nestml/tree/master/models/synapses/static_synapse.nestml>`_.
+
+
+Characterisation
+++++++++++++++++
+
+.. include:: static_synapse_characterisation.rst
+
+
+.. footer::
+
+   Generated at 2023-08-22 14:29:44.873822
diff --git a/doc/models_library/stdp.rst b/doc/models_library/stdp.rst
@@ -82,4 +82,4 @@ Characterisation
 
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-   Generated at 2023-03-23 09:41:54.884461
+   Generated at 2023-08-22 14:29:44.906792
diff --git a/doc/models_library/stdp_nn_pre_centered.rst b/doc/models_library/stdp_nn_pre_centered.rst
@@ -99,4 +99,4 @@ Characterisation
 
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-   Generated at 2023-03-23 09:41:54.882045
+   Generated at 2023-08-22 14:29:44.899570
diff --git a/doc/models_library/stdp_nn_restr_symm.rst b/doc/models_library/stdp_nn_restr_symm.rst
@@ -92,4 +92,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2023-03-23 09:41:54.872436
+   Generated at 2023-08-22 14:29:44.886314