Skip to content

Commit

Permalink
Merge pull request #382 from DimitriPlotnikov/initial_values_block
Browse files Browse the repository at this point in the history 
Introduces Initial values block (cf. #368 for the discussion)
  • Loading branch information
Plotnikov committed Oct 4, 2017
2 parents e03bf13 + 6dd0a96 commit e452b92
Show file tree
Hide file tree
Showing 130 changed files with 2,330 additions and 2,616 deletions.
134 changes: 61 additions & 73 deletions models/aeif_cond_alpha.nestml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,17 +32,17 @@ SeeAlso: iaf_cond_alpha, aeif_cond_exp
*/
neuron aeif_cond_alpha_neuron:

state:
V_m mV = E_L ## Membrane potential
w pA = 0pA ## Spike-adaptation current
initial_values:
V_m mV = E_L # Membrane potential
w pA = 0pA # Spike-adaptation current
end

equations:
function V_bounded mV = bounded_min(V_m, V_peak) # prevent exponential divergence
shape g_in = (e/tau_syn_in) * t * exp(-t/tau_syn_in)
shape g_ex = (e/tau_syn_ex) * t * exp(-t/tau_syn_ex)

## Add functions to simplify the equation definition of V_m
# Add functions to simplify the equation definition of V_m
function exp_arg real = (V_bounded-V_th)/Delta_T
function I_spike pA = g_L*Delta_T*exp(exp_arg)
function I_syn_exc pA = cond_sum(g_ex, spikesExc) * ( V_bounded - E_ex )
Expand All @@ -55,46 +55,45 @@ neuron aeif_cond_alpha_neuron:

parameters:
# membrane parameters
C_m pF = 281.0pF ## Membrane Capacitance in pF
t_ref ms = 0.0ms ## Refractory period in ms
V_reset mV = -60.0mV ## Reset Potential in mV
g_L nS = 30.0nS ## Leak Conductance in nS
E_L mV = -70.6mV ## Leak reversal Potential (aka resting potential) in mV
I_e pA = 0pA ## Constant Current in pA
C_m pF = 281.0pF # Membrane Capacitance in pF
t_ref ms = 0.0ms # Refractory period in ms
V_reset mV = -60.0mV # Reset Potential in mV
g_L nS = 30.0nS # Leak Conductance in nS
E_L mV = -70.6mV # Leak reversal Potential (aka resting potential) in mV
I_e pA = 0pA # Constant Current in pA

# spike adaptation parameters
a nS = 4nS ## Subthreshold adaptation
b pA = 80.5pA ## pike-triggered adaptation
Delta_T mV = 2.0mV ## Slope factor
tau_w ms = 144.0ms ## Adaptation time constant
V_th mV = -50.4mV ## Threshold Potential in mV
V_peak mV = 0mV ## Spike detection threshold
a nS = 4nS # Subthreshold adaptation
b pA = 80.5pA # pike-triggered adaptation
Delta_T mV = 2.0mV # Slope factor
tau_w ms = 144.0ms # Adaptation time constant
V_th mV = -50.4mV # Threshold Potential in mV
V_peak mV = 0mV # Spike detection threshold

# synaptic parameters
E_ex mV = 0mV ## Excitatory reversal Potential in mV
tau_syn_ex ms = 0.2ms ## Synaptic Time Constant Excitatory Synapse in ms
E_in mV = -85.0mV ## Inhibitory reversal Potential in mV
tau_syn_in ms = 2.0ms ## Synaptic Time Constant for Inhibitory Synapse in ms

## Input current injected by CurrentEvent.
## This variable is used to transport the current applied into the
## _dynamics function computing the derivative of the state vector.
E_ex mV = 0mV # Excitatory reversal Potential in mV
tau_syn_ex ms = 0.2ms # Synaptic Time Constant Excitatory Synapse in ms
E_in mV = -85.0mV # Inhibitory reversal Potential in mV
tau_syn_in ms = 2.0ms # Synaptic Time Constant for Inhibitory Synapse in ms

# Input current injected by CurrentEvent.
# This variable is used to transport the current applied into the
# _dynamics function computing the derivative of the state vector.
I_stim pA = 0pA
end

internals:

## Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
## conductance excursion.
# Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
# conductance excursion.
PSConInit_E nS/ms = nS * e / tau_syn_ex

## Impulse to add to DG_INH on spike arrival to evoke unit-amplitude
## conductance excursion.
# Impulse to add to DG_INH on spike arrival to evoke unit-amplitude
# conductance excursion.
PSConInit_I nS/ms = nS * e / tau_syn_in

## refractory time in steps
# refractory time in steps
RefractoryCounts integer = steps(t_ref)
## counts number of tick during the refractory period
# counts number of tick during the refractory period
r integer
end

Expand All @@ -119,7 +118,6 @@ neuron aeif_cond_alpha_neuron:
emit_spike()
end


end

end
Expand Down Expand Up @@ -159,24 +157,25 @@ SeeAlso: iaf_cond_alpha, aeif_cond_exp
neuron aeif_cond_alpha_implicit:

state:
V_m mV = E_L ## Membrane potential
w pA = 0 pA ## Spike-adaptation current
g_in nS = 0 nS ## Excitatory synaptic conductance
g_in' nS/mS = 0 nS/ms ## Excitatory synaptic conductance
g_ex nS = 0 nS ## Inhibitory synaptic conductance in nS
g_ex' nS/mS = 0 nS/ms ## Inhibitory synaptic conductance in nS
r integer ## counts number of tick during the refractory period
r integer # counts number of tick during the refractory period
end

initial_values:
V_m mV = E_L # Membrane potential
w pA = 0 pA # Spike-adaptation current
g_in nS = 0 nS # Excitatory synaptic conductance
g_in' nS/mS = nS * e / tau_syn_in # Excitatory synaptic conductance
g_ex nS = 0 nS # Inhibitory synaptic conductance in nS
g_ex' nS/mS = nS * e / tau_syn_ex # Inhibitory synaptic conductance in nS
end

equations:
function V_bounded mV = min(V_m, V_peak) # prevent exponential divergence
## alpha function for the g_in
g_in'' = (-2/tau_syn_in) * g_in'-(1/tau_syn_in**2) * g_in
g_in' = g_in'
# alpha function for the g_in
shape g_in'' = (-2/tau_syn_in) * g_in'-(1/tau_syn_in**2) * g_in

## alpha function for the g_ex
g_ex'' = (-2/tau_syn_ex) * g_ex'-(1/tau_syn_ex**2) * g_ex
g_ex' = g_ex'
# alpha function for the g_ex
shape g_ex'' = (-2/tau_syn_ex) * g_ex'-(1/tau_syn_ex**2) * g_ex

# Add aliases to simplify the equation definition of V_m
function exp_arg real = (V_bounded-V_th)/Delta_T
Expand All @@ -190,39 +189,30 @@ neuron aeif_cond_alpha_implicit:

parameters:
# membrane parameters
C_m pF = 281.0 pF ## Membrane Capacitance in pF
t_ref ms = 0.0 ms ## Refractory period in ms
V_reset mV = -60.0 mV ## Reset Potential in mV
g_L nS = 30.0 nS ## Leak Conductance in nS
E_L mV = -70.6 mV ## Leak reversal Potential (aka resting potential) in mV
I_e pA = 0 pA ## Constant Current in pA
C_m pF = 281.0 pF # Membrane Capacitance in pF
t_ref ms = 0.0 ms # Refractory period in ms
V_reset mV = -60.0 mV # Reset Potential in mV
g_L nS = 30.0 nS # Leak Conductance in nS
E_L mV = -70.6 mV # Leak reversal Potential (aka resting potential) in mV
I_e pA = 0 pA # Constant Current in pA

# spike adaptation parameters
a nS = 4 nS ## Subthreshold adaptation
b pA = 80.5 pA ## pike-triggered adaptation
Delta_T mV = 2.0 mV ## Slope factor
tau_w ms = 144.0 ms ## Adaptation time constant
V_th mV = -50.4 mV ## Threshold Potential in mV
V_peak mV = 0 mV ## Spike detection threshold
a nS = 4 nS # Subthreshold adaptation
b pA = 80.5 pA # pike-triggered adaptation
Delta_T mV = 2.0 mV # Slope factor
tau_w ms = 144.0 ms # Adaptation time constant
V_th mV = -50.4 mV # Threshold Potential in mV
V_peak mV = 0 mV # Spike detection threshold

# synaptic parameters
E_ex mV = 0 mV ## Excitatory reversal Potential in mV
tau_syn_ex ms = 0.2 ms ## Synaptic Time Constant Excitatory Synapse in ms
E_in mV = -85.0 mV ## Inhibitory reversal Potential in mV
tau_syn_in ms = 2.0 ms ## Synaptic Time Constant for Inhibitory Synapse in ms
E_ex mV = 0 mV # Excitatory reversal Potential in mV
tau_syn_ex ms = 0.2 ms # Synaptic Time Constant Excitatory Synapse in ms
E_in mV = -85.0 mV # Inhibitory reversal Potential in mV
tau_syn_in ms = 2.0 ms # Synaptic Time Constant for Inhibitory Synapse in ms
end

internals:

## Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
## conductance excursion.
PSConInit_E nS/ms = nS * e / tau_syn_ex

## Impulse to add to DG_INH on spike arrival to evoke unit-amplitude
## conductance excursion.
PSConInit_I nS/ms = nS * e / tau_syn_in

## refractory time in steps
# refractory time in steps
RefractoryCounts integer = steps(t_ref)
end

Expand All @@ -247,8 +237,6 @@ neuron aeif_cond_alpha_implicit:
emit_spike()
end

g_ex' += spikesExc * PSConInit_E
g_in' += spikesInh * PSConInit_I
end

end
17 changes: 9 additions & 8 deletions models/aeif_cond_exp.nestml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ SeeAlso: iaf_cond_alpha, aeif_cond_exp
*/
neuron aeif_cond_exp_neuron:

state:
initial_values:
V_m mV = E_L # Membrane potential
w pA = 0 pA # Spike-adaptation current
end
Expand Down Expand Up @@ -153,18 +153,21 @@ SeeAlso: iaf_cond_alpha, aeif_cond_exp
neuron aeif_cond_exp_implicit:

state:
r integer # counts number of tick during the refractory period
end

initial_values:
V_m mV = E_L # Membrane potential
w pA = 0pA # Spike-adaptation current
g_in nS = 0nS # Inhibitory synaptic conductance
g_ex nS = 0nS # Excitatory synaptic conductance
r integer # counts number of tick during the refractory period
g_in nS = 1nS # Inhibitory synaptic conductance
g_ex nS = 1nS # Excitatory synaptic conductance
end

equations:
function V_bounded mV = min(V_m, V_peak) # prevent exponential divergence
# exp function for the g_in, g_ex
g_in' = -g_in/tau_syn_in
g_ex' = -g_ex/tau_syn_ex
shape g_in' = -g_in/tau_syn_in
shape g_ex' = -g_ex/tau_syn_ex

# Add aliases to simplify the equation definition of V_m
function exp_arg real = (V_bounded-V_th)/Delta_T
Expand Down Expand Up @@ -226,8 +229,6 @@ neuron aeif_cond_exp_implicit:
emit_spike()
end

g_ex += spikeExc * nS
g_in += spikeInh * nS
end

end
46 changes: 19 additions & 27 deletions models/hh_cond_exp_traub.nestml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,11 @@ SeeAlso: hh_psc_alpha
neuron hh_cond_exp_traub_neuron:

state:
V_m mV = E_L # Membrane potential
r integer # counts number of tick during the refractory period
end

g_in nS = 0nS # Inhibitory synaptic conductance
g_ex nS = 0nS # Excitatory synaptic conductance
initial_values:
V_m mV = E_L # Membrane potential

function alpha_n_init 1/ms = 0.032/(ms* mV ) * ( 15. mV - V_m) / ( exp( ( 15. mV - V_m) / 5. mV ) - 1. )
function beta_n_init 1/ms = 0.5 /ms * exp( ( 10. mV - V_m ) / 40. mV )
Expand All @@ -49,16 +50,18 @@ neuron hh_cond_exp_traub_neuron:
Act_m real = alpha_m_init / ( alpha_m_init + beta_m_init )
Act_h real = alpha_h_init / ( alpha_h_init + beta_h_init )
Inact_n real = alpha_n_init / ( alpha_n_init + beta_n_init )

r integer # counts number of tick during the refractory period

end

equations:
# synapses: exponential conductance
shape g_in = exp(-1/tau_syn_in*t)
shape g_ex = exp(-1/tau_syn_ex*t)

# Add aliases to simplify the equation definition of V_m
function I_Na pA = g_Na * Act_m * Act_m * Act_m * Act_h * ( V_m - E_Na )
function I_K pA = g_K * Inact_n * Inact_n * Inact_n * Inact_n * ( V_m - E_K )
function I_L pA = g_L * ( V_m - E_L )

function I_syn_exc pA = cond_sum(g_ex, spikeExc) * ( V_m - E_ex )
function I_syn_inh pA = cond_sum(g_in, spikeInh) * ( V_m - E_in )

Expand All @@ -77,9 +80,6 @@ neuron hh_cond_exp_traub_neuron:
Act_h' = ( alpha_h - ( alpha_h + beta_h ) * Act_h )
Inact_n' = ( alpha_n - ( alpha_n + beta_n ) * Inact_n )

# synapses: exponential conductance
g_ex' = -g_ex / tau_syn_ex
g_in' = -g_in / tau_syn_in
end

parameters:
Expand Down Expand Up @@ -123,10 +123,6 @@ neuron hh_cond_exp_traub_neuron:
emit_spike()
end



g_ex += spikeExc * nS
g_in += spikeInh * nS
end

end
Expand Down Expand Up @@ -167,10 +163,14 @@ SeeAlso: hh_psc_alpha
neuron hh_cond_exp_traub_implicit:

state:
r integer # counts number of tick during the refractory period
end

initial_values:
V_m mV = E_L # Membrane potential

g_in nS = 0nS # Inhibitory synaptic conductance
g_ex nS = 0nS # Excitatory synaptic conductance
g_in nS = 1nS # Inhibitory synaptic conductance
g_ex nS = 1nS # Excitatory synaptic conductance

function alpha_n_init 1/ms = 0.032/(ms* mV ) * ( 15. mV - V_m) / ( exp( ( 15. mV - V_m) / 5. mV ) - 1. )
function beta_n_init 1/ms = 0.5 /ms * exp( ( 10. mV - V_m ) / 40. mV )
Expand All @@ -182,12 +182,13 @@ neuron hh_cond_exp_traub_implicit:
Act_m real = alpha_m_init / ( alpha_m_init + beta_m_init )
Act_h real = alpha_h_init / ( alpha_h_init + beta_h_init )
Inact_n real = alpha_n_init / ( alpha_n_init + beta_n_init )

r integer # counts number of tick during the refractory period

end

equations:
# synapses: exponential conductance
shape g_ex' = -g_ex / tau_syn_ex
shape g_in' = -g_in / tau_syn_in

# Add aliases to simplify the equation definition of V_m
function I_Na pA = g_Na * Act_m * Act_m * Act_m * Act_h * ( V_m - E_Na )
function I_K pA = g_K * Inact_n * Inact_n * Inact_n * Inact_n * ( V_m - E_K )
Expand All @@ -209,10 +210,6 @@ neuron hh_cond_exp_traub_implicit:
Act_m' = ( alpha_m - ( alpha_m + beta_m ) * Act_m )
Act_h' = ( alpha_h - ( alpha_h + beta_h ) * Act_h )
Inact_n' = ( alpha_n - ( alpha_n + beta_n ) * Inact_n )

# synapses: exponential conductance
g_ex' = -g_ex / tau_syn_ex
g_in' = -g_in / tau_syn_in
end

parameters:
Expand Down Expand Up @@ -255,11 +252,6 @@ neuron hh_cond_exp_traub_implicit:
r = RefractoryCounts
emit_spike()
end



g_ex += spikeExc * nS
g_in += spikeInh * nS
end

end
Loading

0 comments on commit e452b92

Please sign in to comment.