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patch_ModelDB_synaptic_paper.patch
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patch_ModelDB_synaptic_paper.patch
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diff --git a/models/CMakeLists.txt b/models/CMakeLists.txt
index 01012b56a..2a145ce54 100644
--- a/models/CMakeLists.txt
+++ b/models/CMakeLists.txt
@@ -78,6 +78,8 @@ set( models_sources
iaf_psc_exp_ps.cpp iaf_psc_exp_ps.h
iaf_psc_exp_ps_lossless.cpp iaf_psc_exp_ps_lossless.h
izhikevich.h izhikevich.cpp
+ migliore.h migliore.cpp
+ migliore_ode.h migliore_ode.cpp
jonke_synapse.h
lin_rate.h lin_rate.cpp
mat2_psc_exp.h mat2_psc_exp.cpp
diff --git a/models/migliore.cpp b/models/migliore.cpp
new file mode 100755
index 000000000..1cdcd9b2f
--- /dev/null
+++ b/models/migliore.cpp
@@ -0,0 +1,1038 @@
+/*
+ * migliore.cpp
+ *
+ * This file is part of NEST.
+ *
+ * Copyright (C) 2004 The NEST Initiative
+ *
+ * NEST is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * NEST is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with NEST. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include "migliore.h"
+
+// C++ includes:
+#include <limits>
+
+// Includes from libnestutil:
+#include "dict_util.h"
+#include "numerics.h"
+#include "propagator_stability.h"
+
+// Includes from nestkernel:
+//#include "event_delivery_manager_impl.h"
+#include "exceptions.h"
+#include "kernel_manager.h"
+#include "universal_data_logger_impl.h"
+
+// Includes from sli:
+#include "dict.h"
+#include "dictutils.h"
+#include "doubledatum.h"
+#include "integerdatum.h"
+
+/* ----------------------------------------------------------------
+ * Recordables map
+ * ---------------------------------------------------------------- */
+
+//nest::RecordablesMap< nest::migliore > nest::migliore::recordablesMap_;
+
+namespace nest
+{
+ // Override the create() method with one call to RecordablesMap::insert_()
+ // for each quantity to be recorded.
+ template <>
+ void
+ DynamicRecordablesMap< migliore >::create( migliore& host )
+ {
+ // use standard names wherever you can for consistency!
+ insert( names::V_m, host.get_data_access_functor( migliore::State_::V_M ) );
+ // insert( names::I, host.get_data_access_functor( migliore::State_::I ) );
+ insert( names::I_syn, host.get_data_access_functor( migliore::State_::I_ve ) );
+
+ insert( names::Iadap_ini, host.get_data_access_functor( migliore::State_::Iadap ) );
+ insert( names::Idep_ini, host.get_data_access_functor( migliore::State_::Idep ) );
+
+ host.insert_current_recordables();
+ }
+ // void
+ // RecordablesMap< migliore >::create()
+ // {
+ // // use standard names whereever you can for consistency!
+ // insert_( names::V_m, &migliore::get_V_m_ );
+ // insert_( names::I, &migliore::get_I_inj_ );
+ // insert_( names::init_sign, &migliore::get_init_sign_ );
+ // insert_( names::Iadap_ini, &migliore::get_Iadap_ini_ );
+ // insert_( names::Idep_ini, &migliore::get_Idep_ini_ );
+ // insert_( names::sis, &migliore::get_sis_ );
+ // insert_( names::I_syn, &migliore::get_I_syn_ );
+ // }
+
+
+ Name
+ nest::migliore::get_i_syn_name( size_t elem )
+ {
+ std::stringstream i_syn_name;
+ i_syn_name << "I_syn_" << elem + 1;
+ return Name( i_syn_name.str() );
+ }
+
+ void
+ migliore::insert_current_recordables( size_t first )
+ {
+ // std::cout << "migliore taus syn size " << P_.tau_syn_.size() << "\n";
+ for ( size_t receptor = first; receptor < P_.tau_syn_.size(); ++receptor )
+ {
+ size_t elem = migliore::State_::I_SYN
+ + receptor * migliore::State_::NUM_STATE_ELEMENTS_PER_RECEPTOR;
+ Name a = get_i_syn_name( receptor );
+ recordablesMap_.insert( a , this->get_data_access_functor( elem ) );
+ }
+ }
+
+ DataAccessFunctor< migliore >
+ migliore::get_data_access_functor( size_t elem )
+ {
+ return DataAccessFunctor< migliore >( *this, elem );
+ }
+
+ /* ----------------------------------------------------------------
+ * Default constructors defining default parameters and state
+ * ---------------------------------------------------------------- */
+
+ nest::migliore::Parameters_::Parameters_()
+ : E_L_( -72.5 )
+ , vres_( -65.0 )
+ , vtm_( -52.0 )
+ , Cm_( 2047.4164432004916 )
+ , ith_( 300.9987901902274 )
+ , tao_m_( 3310.462136574088 )
+ , sc_( 4526.328798037026 )
+ , bet_( 0.24522251335200956 )
+ , delta1_( 0.009906254244852036 )
+ , cost_idep_ini_( 0.017625482908326662 )
+ , Idep_ini_vr_( 1.0122905259090516 )
+ , psi1_( 0.1975362978159442 )
+ , a_( 14.2787 )
+ , b_( -2.10966 )
+ , c_( 0.0608809 )
+ , alp_( 225.491 )
+ , istim_min_spikinig_exp_( 400 )
+ , istim_max_spikinig_exp_( 1000 )
+ , corrcostatratti_( 1 )
+ , corrcost_( 0 )
+ , Delta_T( 2.0 ) // mV
+ , I_e_( 0.0 ) // pA
+ , V_th_( -52.0 ) // mV
+ , V_min_( -90.0 ) //-std::numeric_limits< double >::max() ) // mV
+ , t_ref_( 2.0 ) // in ms
+ , tau_syn_( 3, 2.0 ) // in ms
+ , firstSpikeFlag_( false)
+ , has_connections_( false )
+ {
+ }
+
+ nest::migliore::State_::State_()
+ : V_m_( -72.5 ) // membrane potential (E_L_+(1-exp(-S_.current_/1000))*(vtm-E_L_))/V_.Vconvfact TOBEFIXED
+ , init_sign_( 0.0 ) // membrane adaptation variable
+ , Iadap_ini_( 0.0 ) // membrane adaptation variable
+ , Idep_ini_( 0.0 ) // membrane dependent variable
+ , sis_( 0.0 ) // counter variable
+ , counter_( 0.0 ) // counter variable
+ , I_inj_( 0.0 ) // input current
+ , r_ref_( 0 )
+ {
+ i_syn_.clear();
+ }
+
+ /* ----------------------------------------------------------------
+ * Parameter and state extractions and manipulation functions
+ * ---------------------------------------------------------------- */
+
+ void
+ nest::migliore::Parameters_::get( DictionaryDatum& d ) const
+ {
+ def< double >( d, names::I_e, I_e_ );
+ def< double >( d, names::V_th, V_th_ ); // threshold value
+ def< double >( d, names::V_min, V_min_ );
+ def< double >( d, names::E_L, E_L_ );
+ def< double >( d, names::vres, vres_ );
+ def< double >( d, names::vtm, vtm_);
+ def< double >( d, names::Cm, Cm_);
+ def< double >( d, names::ith, ith_);
+ def< double >( d, names::tao_m, tao_m_);
+ def< double >( d, names::sc, sc_);
+ def< double >( d, names::bet, bet_);
+ def< double >( d, names::delta1, delta1_);
+ def< double >( d, names::cost_idep_ini, cost_idep_ini_);
+ def< double >( d, names::Idep_ini_vr, Idep_ini_vr_);
+ def< double >( d, names::psi1, psi1_);
+ def< double >( d, names::a, a_);
+ def< double >( d, names::b, b_);
+ def< double >( d, names::c, c_);
+ def< double >( d, names::alp, alp_);
+ def< double >( d, names::istim_min_spikinig_exp, istim_min_spikinig_exp_);
+ def< double >( d, names::istim_max_spikinig_exp, istim_max_spikinig_exp_);
+ def< double >( d, names::corrcostatratti, corrcostatratti_);
+ def< double >( d, names::corrcost, corrcost_);
+ def< double >( d, names::Delta_T, Delta_T );
+ def< double >( d, names::t_ref, t_ref_ );
+ def< int >( d, names::n_synapses, n_receptors_() );
+ def< bool >( d, names::has_connections, has_connections_ );
+
+ ArrayDatum tau_syn_ad( tau_syn_ );
+ def< ArrayDatum >( d, names::tau_syn, tau_syn_ad );
+ }
+
+ void
+ nest::migliore::Parameters_::set( const DictionaryDatum& d, Node* node )
+ {
+ updateValueParam< double >( d, names::V_th, V_th_, node );
+ updateValueParam< double >( d, names::V_min, V_min_, node );
+ updateValueParam< double >( d, names::I_e, I_e_, node );
+ updateValueParam< double >( d, names::E_L, E_L_, node );
+ updateValueParam< double >( d, names::vres, vres_, node );
+ updateValueParam< double >( d, names::vtm, vtm_, node );
+ updateValueParam< double >( d, names::Cm, Cm_, node );
+ updateValueParam< double >( d, names::ith, ith_, node );
+ updateValueParam< double >( d, names::tao_m, tao_m_, node );
+ updateValueParam< double >( d, names::sc, sc_, node );
+ updateValueParam< double >( d, names::bet, bet_, node );
+ updateValueParam< double >( d, names::delta1, delta1_, node );
+ updateValueParam< double >( d, names::cost_idep_ini, cost_idep_ini_, node );
+ updateValueParam< double >( d, names::Idep_ini_vr, Idep_ini_vr_, node );
+ updateValueParam< double >( d, names::psi1, psi1_, node );
+ updateValueParam< double >( d, names::a, a_, node );
+ updateValueParam< double >( d, names::b, b_, node );
+ updateValueParam< double >( d, names::c, c_, node );
+ updateValueParam< double >( d, names::alp, alp_, node );
+ updateValueParam< double >( d, names::istim_min_spikinig_exp, istim_min_spikinig_exp_, node );
+ updateValueParam< double >( d, names::istim_max_spikinig_exp, istim_max_spikinig_exp_, node );
+ updateValueParam< double >( d, names::corrcostatratti, corrcostatratti_, node );
+ updateValueParam< double >( d, names::corrcost, corrcost_, node );
+ updateValueParam< double >( d, names::Delta_T, Delta_T, node );
+ updateValueParam< double >( d, names::t_ref, t_ref_, node );
+ // updateValueParam< double >( d, names::miglp1, miglp1_, node );
+ // updateValueParam< double >( d, names::miglp2, miglp2_, node );
+ // updateValueParam< double >( d, names::miglp3, miglp3_, node );
+ // updateValueParam< double >( d, names::miglp4, miglp4_, node );
+ if ( t_ref_ < 0 )
+ {
+ throw BadProperty( "Refractory time must not be negative." );
+ }
+
+ const size_t old_n_receptors = this->n_receptors_();
+ if ( updateValue< std::vector< double > >( d, "tau_syn", tau_syn_ ) )
+ {
+ if ( this->n_receptors_() != old_n_receptors && has_connections_ == true )
+ {
+ throw BadProperty( "The neuron has connections, therefore the number of ports cannot be reduced." );
+ }
+ for ( size_t i = 0; i < tau_syn_.size(); ++i )
+ {
+ if ( tau_syn_[ i ] <= 0 )
+ {
+ throw BadProperty( "All synaptic time constants must be strictly positive." );
+ }
+ if ( tau_syn_[ i ] == tao_m_ )
+ {
+ throw BadProperty( "Membrane and synapse time constant(s) must differ. See note in documentation." );
+ }
+ }
+ }
+ // std::cout << "migliore set taus syn size " << tau_syn_.size() << "\n";
+ // std::cout << "migliore n_receptors " << this->n_receptors_() << "\n";
+ }
+
+ void
+ nest::migliore::State_::get( DictionaryDatum& d, const Parameters_& ) const
+ {
+ def< double >( d, names::init_sign, init_sign_ ); // Membrane potential adaptationariable
+ def< double >( d, names::Iadap_ini, Iadap_ini_ ); // Membrane potential adaptationariable
+ def< double >( d, names::Idep_ini , Idep_ini_ ); // Membrane potential adaptationariable
+ def< double >( d, names::sis , sis_ ); // Membrane potential adaptationariable
+ def< double >( d, names::I, I_inj_ ); // Membrane potential
+ def< double >( d, names::V_m, V_m_ ); // Membrane potential
+ }
+
+ void
+ nest::migliore::State_::set( const DictionaryDatum& d, const Parameters_&, Node* node )
+ {
+ updateValueParam< double >( d, names::init_sign, init_sign_, node );
+ updateValueParam< double >( d, names::Iadap_ini, Iadap_ini_, node );
+ updateValueParam< double >( d, names::Idep_ini, Idep_ini_, node );
+ updateValueParam< double >( d, names::sis, sis_, node );
+ updateValueParam< double >( d, names::V_m, V_m_, node );
+ updateValueParam< double >( d, names::I, I_inj_, node );
+ }
+
+ nest::migliore::Buffers_::Buffers_( migliore& n )
+ : logger_( n )
+ {
+ }
+
+ nest::migliore::Buffers_::Buffers_( const Buffers_&, migliore& n )
+ : logger_( n )
+ {
+ }
+
+ /* ----------------------------------------------------------------
+ * Default and copy constructor for node
+ * ---------------------------------------------------------------- */
+
+ nest::migliore::migliore()
+ : ArchivingNode()
+ , P_()
+ , S_()
+ , B_( *this )
+ {
+ recordablesMap_.create( *this );
+ }
+
+ nest::migliore::migliore( const migliore& n )
+ : ArchivingNode( n )
+ , P_( n.P_ )
+ , S_( n.S_ )
+ , B_( n.B_, *this )
+ {
+ recordablesMap_.create( *this );
+ }
+
+ /* ----------------------------------------------------------------
+ * Node initialization functions
+ * ---------------------------------------------------------------- */
+
+ void
+ nest::migliore::init_buffers_()
+ {
+ B_.spikes_.clear(); // includes resize
+ B_.currents_.clear(); // includes resize
+ B_.logger_.reset(); // includes resize
+ ArchivingNode::clear_history();
+ }
+
+ void
+ nest::migliore::calibrate()
+ {
+ B_.logger_.init();
+
+ // t_ref_ specifies the length of the absolute refractory period as
+ // a double in ms. The grid based iaf_psc_exp can only handle refractory
+ // periods that are integer multiples of the computation step size (h).
+ // To ensure consistency with the overall simulation scheme such conversion
+ // should be carried out via objects of class nest::Time. The conversion
+ // requires 2 steps:
+ // 1. A time object r is constructed, defining representation of
+ // t_ref_ in tics. This representation is then converted to computation
+ // time steps again by a strategy defined by class nest::Time.
+ // 2. The refractory time in units of steps is read out get_steps(), a
+ // member function of class nest::Time.
+ //
+ // Choosing a t_ref_ that is not an integer multiple of the computation time
+ // step h will lead to accurate (up to the resolution h) and self-consistent
+ // results. However, a neuron model capable of operating with real valued
+ // spike time may exhibit a different effective refractory time.
+
+ const double h = Time::get_resolution().get_ms();
+
+ V_.P11_syn_.resize( P_.n_receptors_() );
+ V_.P21_syn_.resize( P_.n_receptors_() );
+
+ S_.i_syn_.resize( P_.n_receptors_() );
+
+ B_.spikes_.resize( P_.n_receptors_() );
+
+ V_.P22_ = std::exp( -h / P_.tao_m_ );
+ V_.P20_ = P_.tao_m_ / P_.Cm_ * ( 1.0 - V_.P22_ );
+
+ for ( size_t i = 0; i < P_.n_receptors_(); i++ )
+ {
+ V_.P11_syn_[ i ] = std::exp( -h / P_.tau_syn_[ i ] );
+ // std::cout << "tau syn " << P_.tau_syn_[ i] << "\n";
+ // these are determined according to a numeric stability criterion
+ V_.P21_syn_[ i ] = propagator_32( P_.tau_syn_[ i ], P_.tao_m_, P_.Cm_, h );
+
+ B_.spikes_[ i ].resize();
+ }
+
+ V_.RefractoryCounts_ = Time( Time::ms( P_.t_ref_ ) ).get_steps();
+ // since t_ref_ >= 0, this can only fail in error
+ assert( V_.RefractoryCounts_ >= 0 );
+
+ V_.time_scale_ = 1 / (-P_.sc_ / (P_.Cm_ * P_.E_L_));
+ V_.d_dt = h;
+ V_.dt = V_.d_dt/V_.time_scale_;
+
+ V_.beta2 = pow(P_.bet_,2);
+ V_.t_step = V_.dt;
+ V_.t_spk = -0.3;
+
+ V_.H = (90+P_.E_L_)*P_.sc_*(P_.bet_-P_.delta1_)/(P_.E_L_*(-200));
+ V_.Vconvfact = -P_.E_L_;
+ V_.vrm = P_.vres_/V_.Vconvfact;
+ V_.psi1 = pow((-4)*P_.bet_+pow(1+P_.delta1_,2.0),0.5);
+ // t_step = t - t0
+ V_.VV_1 = 0.5 / ((P_.bet_ -P_.delta1_) * (pow(P_.bet_,2.0) + (P_.bet_-1.0) * P_.delta1_) * (4.0 * P_.bet_ - pow((1.0 + P_.delta1_), 2.0))) * P_.psi1_;
+ V_.VV_2 = 2.0 * exp(-V_.t_step * P_.bet_) * (P_.bet_-1.0) * P_.bet_ * (P_.bet_ - P_.delta1_) * P_.psi1_;
+ V_.VV_3 = (pow(P_.bet_,2) + ((- 1.0) + P_.bet_) * P_.delta1_) * P_.psi1_;
+ V_.VV_4 = exp((1.0 / 2.0) * V_.t_step * (-1.0 + P_.delta1_ -P_.psi1_));
+ V_.VV_5 = P_.bet_ * (P_.bet_ -P_.delta1_) * (-1.0 -P_.delta1_ + P_.bet_ * (3.0 + P_.delta1_ -P_.psi1_) + P_.psi1_);
+ V_.VV_6 = (pow(P_.bet_,2) -P_.delta1_ + P_.bet_ * P_.delta1_);
+ V_.VV_7 = (1.0 + (-2.0) * P_.bet_ + P_.delta1_ -P_.psi1_);
+ V_.VV_8 = exp((1.0 / 2.0) * V_.t_step * (-1.0 + P_.delta1_ + P_.psi1_));
+ V_.VV_9 = P_.bet_ * (P_.bet_-P_.delta1_) * (-1.0 -P_.delta1_ -P_.psi1_ + P_.bet_ * (3.0 + P_.delta1_ + P_.psi1_));
+ V_.VV_10 = (pow(P_.bet_,2) - P_.delta1_ + P_.bet_ * P_.delta1_);
+ V_.VV_11 = (1.0 + (-2.0) * P_.bet_ + P_.delta1_ + P_.psi1_);
+ // V_.GG = P_.bet_ * (P_.bet_ - P_.delta1_) * (-1 - P_.delta1_ - P_.psi1_ + P_.bet_ * (3 + P_.delta1_ + P_.psi1_));
+ V_.C = P_.bet_ - P_.delta1_;
+ // V_.JJ = 2 * exp(-V_.t_step * P_.bet_) * (P_.bet_ - 1) * P_.bet_ * V_.C * P_.psi1_;
+ // V_.JJ_1 = exp(0.5 * V_.t_step * (-1 + P_.delta1_ - P_.psi1_));
+ // V_.JJ_2 = (-1 - P_.delta1_ + P_.bet_ * (3 + P_.delta1_ - P_.psi1_) + P_.psi1_);
+ // V_.JJ_3 = (V_.beta2 + (P_.bet_ - 1) * P_.delta1_) * P_.psi1_;
+ // V_.JJ_4 = (V_.beta2 - P_.delta1_ + P_.bet_ * P_.delta1_);
+ // V_.JJ_5 = (1 + (-2) * P_.bet_ + P_.delta1_ - P_.psi1_);
+ // V_.JJ_6 = exp(0.5 * V_.t_step * (-1 + P_.delta1_ + P_.psi1_));
+ // V_.JJ_7 = 0.5 / V_.C / (V_.beta2 + (P_.bet_ - 1) * P_.delta1_) / (4 * P_.bet_ - pow((1 + P_.delta1_), 2)) * P_.psi1_;
+
+ V_.pdelta = pow((1 + P_.delta1_), 2);
+
+ // V_.AA_4 = P_.bet_ * V_.C * (-V_.pdelta + (-1.0 + P_.delta1_) * P_.psi1_ + 2.0 * P_.bet_ * (2.0 + P_.psi1_));
+ // V_.AA_5 = V_.beta2 + (-1.0 + P_.bet_) * P_.delta1_;
+ // V_.AA_6 = 1.0 -4.0 * P_.bet_ + P_.delta1_ * (2.0 + P_.delta1_ - P_.psi1_) + P_.psi1_;
+ // V_.AA_7 = (1.0 + P_.delta1_) * (-1.0 - P_.delta1_ + P_.psi1_);
+
+ // V_.AA_9 = P_.bet_ * V_.C * (V_.pdelta + 2.0 * P_.bet_ * (-2.0 + P_.psi1_) + (-1.0 + P_.delta1_) * P_.psi1_);
+ // V_.AA_10 = V_.beta2 + (-1.0 + P_.bet_) * P_.delta1_;
+ // V_.AA_11 = -4.0 * P_.bet_ + V_.pdelta + (-1.0 + P_.delta1_) * P_.psi1_;
+ // V_.AA_12 = (1.0 + P_.delta1_) * (1.0 + P_.delta1_ + P_.psi1_);
+
+ V_.AA_1 = -4.0 * pow(P_.bet_,3.0) + pow(P_.bet_,2.0) * pow((-1.0+P_.delta1_),2.0) - P_.delta1_ * pow((1.0 + P_.delta1_),2.0) + P_.bet_ * P_.delta1_ * (5 + 2.0 * P_.delta1_ + pow(P_.delta1_,2.0));
+ V_.AA_2 = 2.0 * exp(-V_.t_step * P_.bet_) * P_.bet_ * (4.0 * pow(P_.bet_,2.0) + P_.delta1_ * pow((1.0+P_.delta1_),2.0) - P_.bet_ * (1.0 + 6 * P_.delta1_ + pow(P_.delta1_,2.0)));
+ V_.AA_3 = exp((1.0 / 2.0)*V_.t_step*(-1.0+P_.delta1_+P_.psi1_));
+ V_.AA_4 = -1.0-2.0*P_.delta1_ - pow(P_.delta1_,2.0) - P_.psi1_ + P_.delta1_ * P_.psi1_+2.0*P_.bet_*(2.0+P_.psi1_);
+ V_.AA_5 = (pow(P_.bet_,2.0)-P_.delta1_+P_.bet_*P_.delta1_);
+ V_.AA_6 = (1.0-4.0*P_.bet_+2.0*P_.delta1_+pow(P_.delta1_,2.0)+P_.psi1_-P_.delta1_*P_.psi1_);
+ V_.AA_7 = (1.0+P_.delta1_)*(-1.0-P_.delta1_+P_.psi1_);
+ V_.AA_8 = exp((-1.0)*(1.0 / 2.0) * V_.t_step * (1.0-P_.delta1_+P_.psi1_));
+ V_.AA_9 = P_.bet_ * (P_.bet_-P_.delta1_)*(1.0+2.0*P_.delta1_+ pow(P_.delta1_,2.0)-P_.psi1_+P_.delta1_*P_.psi1_+2.0*P_.bet_*(-2.0+P_.psi1_));
+ V_.AA_10 = (pow(P_.bet_,2.0)-P_.delta1_+P_.bet_*P_.delta1_);
+ V_.AA_11 = (1.0-4.0*P_.bet_+2.0*P_.delta1_ + pow(P_.delta1_,2.0) - P_.psi1_+P_.delta1_*P_.psi1_);
+ V_.AA_12 = (2.0*(P_.bet_-P_.delta1_)*(pow(P_.bet_,2.0)+(-1.0+P_.bet_)*P_.delta1_)*(4.0*P_.bet_-pow((1.0+P_.delta1_),2.0)));
+
+ V_.DD_1 = exp(-V_.t_step * P_.bet_);
+ }
+
+ /* ----------------------------------------------------------------
+ * Update and spike handling functions
+ */
+
+ double
+ nest::migliore::tagliorette(double corr)
+ {
+ double dur_sign = std::numeric_limits<double>::infinity();
+ //# I = sym.Symbol('I')
+ double vinc_inf = 700;
+ double lin_func_sup;
+ // # lin_func_inf=0.68*I - 190.0
+ // # if corr<vinc_inf and corr>0:
+ // # dur_sign=lin_func_inf.subs(I,corr)
+ if (corr < vinc_inf && corr > 0)
+ {
+ dur_sign = 0.68*corr - 190.0;
+ // lin_func_inf = 0.68*corr - 190.0;
+ }
+ double vinc_sup = 1300;
+ if (corr > vinc_sup)
+ {
+ lin_func_sup = 76.86-0.028*corr;
+ dur_sign = lin_func_sup;
+ // dur_sign = corr + std::numeric_limits<double>::infinity();
+ //double lin_func_sup = corr + std::numeric_limits<double>::infinity();
+ }
+ return dur_sign;
+ }
+
+ double
+ nest::migliore::migliV(double t, double delta, double Psi,
+ double alpha, double beta, double IaA0,
+ double IdA0, double t0, double V0,
+ int r_ref_, double vrm)
+ {
+ double to_return = V_.VV_1 * (V_.VV_2 * IdA0 + -2.0 * (alpha -beta + delta) * V_.VV_3 + V_.VV_4 * (IdA0 * V_.VV_5 - V_.VV_6 * (alpha * V_.VV_7 + (beta -delta) * (-1.0 + 2.0 * IaA0 * beta -delta + Psi + V0 * (-1.0 -delta + Psi)))) + V_.VV_8 * (-IdA0 * V_.VV_9 + V_.VV_10 * (alpha * V_.VV_11 + (beta -delta) * (-1.0 + 2.0 * IaA0 * beta-delta -Psi -V0 * (1.0 + delta + Psi)))));
+ // double G = (V_.beta2 - delta + beta * delta) * (alpha * (1 + (-2) * beta + delta + Psi) + V_.C * (-1 + 2 * IaA0 * beta - delta - Psi - V0 * (1 + delta + Psi)));
+ // double F = -IdA0 * V_.GG + G;
+ // double D = V_.JJ * IdA0 - 2 * (alpha - beta + delta) * V_.JJ_3 + V_.JJ_1 * (IdA0 * beta * V_.C * V_.JJ_2 - V_.JJ_4 * (alpha * V_.JJ_5 + V_.C * (-1 + 2 * IaA0 * beta - delta + Psi + V0 * (-1 - delta + Psi)))) + V_.JJ_6 * F;
+ // double D = (2 * exp(((-1) * t + t0) * beta) * IdA0 * (beta - 1) * beta * C * Psi -2 * (alpha - beta + delta) * (beta2 + (beta - 1) * delta) * Psi + exp(0.5 * (t - t0) * ((-1) + delta - Psi)) * (IdA0 * beta * C * ((-1) - delta + beta * (3 + delta - Psi) + Psi) - (beta2 - delta + beta * delta) * (alpha * (1 + (-2) * beta + delta - Psi) + C * ((-1) + 2 * IaA0 * beta - delta + Psi + V0 * ((-1) - delta + Psi)))) + exp(0.5 * (t - t0) * ((-1) + delta + Psi)) * ((-1) * IdA0 * beta * (beta+(-1) * delta) * ((-1) - delta - Psi + beta * (3 + delta + Psi)) + (beta2 - delta+beta * delta) * (alpha * (1 + (-2) * beta + delta + Psi) + C * ((-1) + 2 * IaA0 * beta+(-1) * delta - Psi - V0 * (1 + delta + Psi)))));
+ if (r_ref_ == 0)
+ {
+ //return 0.5 / C / (beta2 + (beta - 1) * delta) / (4 * beta + (- 1) * pow((1 + delta),2)) * Psi * D;
+ // return V_.JJ_7 * D;
+ return to_return;
+ }
+ else
+ {
+ return vrm;
+ }
+ }
+
+ double
+ nest::migliore::set_v_ini(double to_v_ini,
+ int r_ref_, double vrm)
+ {
+ if (r_ref_ == 0)
+ {
+ return to_v_ini;
+ }
+ else
+ {
+ return vrm;
+ }
+ }
+
+
+
+ double
+ nest::migliore::Iadap(double t, double delta, double Psi, double alpha,
+ double beta, double IaA0, double IdA0, double t0,
+ double V0, int r_ref_)
+ {
+ double to_return = (-2.0 * alpha * V_.AA_1 + IdA0 * V_.AA_2 + V_.AA_3 * (-IdA0 * beta * (beta - delta) * V_.AA_4 + V_.AA_5 * (alpha * V_.AA_6 + (beta - delta) * (4.0 * IaA0 * beta -2.0 * (1.0 + V0) * Psi + IaA0 * V_.AA_7))) + V_.AA_8 * (IdA0 * V_.AA_9 + V_.AA_10 * (alpha * V_.AA_11 - (beta-delta) * (-4.0 * IaA0 * beta - 2.0*(1.0+V0)*Psi+IaA0*(1.0+delta)*(1.0+delta+Psi)))))/ V_.AA_12;
+ if (r_ref_ == 0)
+ {
+ return to_return;
+ }
+ else
+ {
+ // std::cout << "465 Refractrory\n";
+ return IaA0;
+ }
+ }
+
+ double
+ nest::migliore::Idep(double t, double beta, double IdA0, double t0, int r_ref_)
+ {
+ if (r_ref_ == 0)
+ {
+ return V_.DD_1 * IdA0;
+ }
+ else
+ {
+ return IdA0;
+ }
+ }
+
+ double
+ nest::migliore::exp_cum(double x, double a, double b)
+ {
+ return a * (1 - exp(-b * x));
+ }
+
+ double
+ nest::migliore::monod(double x, double a, double b, double c, double alp)
+ {
+ double to_return = c + (a * exp(b) * x) / (alp + x);
+ return to_return;
+ }
+
+ void
+ nest::migliore::update( Time const& origin, const long from, const long to )
+ {
+ assert( to >= 0 && ( delay ) from < kernel().connection_manager.get_min_delay() );
+ assert( from < to );
+
+ // const double h = Time::get_resolution().get_ms();
+ // double v_old;
+ // double Iadap_ini_old, Idep_ini_old;
+ double t0_val = origin.get_ms() / V_.time_scale_;
+ double local_time_step = V_.dt;
+ double t_final = t0_val + local_time_step;
+
+ // For breakpoint conditions
+ double timess;
+ double current;
+ double vmss;
+
+ // double afirst = 0;
+ double meancorlastis = 0;
+ double stdcorlastis = 0;
+ double meancorlastprec = 0;
+ double stdcorlastprec = 0;
+ double v_ini = S_.V_m_ / V_.Vconvfact;
+ double vini_prec = v_ini;
+ double teta;
+ double c_aux;
+ double paramL_;
+
+
+
+ for ( long lag = from; lag < to; ++lag )
+ {
+ // neuron is never refractory
+ // use standard forward Euler numerics
+ // double I_syn = B_.spikes_.get_value( lag );
+ double corpre = S_.I_inj_; // + S_.I;
+ // set new input current
+ S_.I_inj_ = B_.currents_.get_value( lag );
+ S_.current_ = S_.I_inj_; // + S_.I;
+ // std::cout << "\n";
+ // std::cout << "552 Begin " << " cor " << S_.current_ << " Inj " << S_.I_inj_ << " syn " << S_.i_syn_[1] << "\n";
+
+ if ( S_.r_ref_ == 0 ) // neuron not refractory, so evolve add synaptic currents
+ for ( size_t i = 0; i < P_.n_receptors_(); i++ )
+ {
+ // S_.V_m_ += V_.P21_syn_[ i ] * S_.i_syn_[ i ];
+ // std::cout << "syn " << S_.i_syn_[ i ] << "\n";
+ S_.current_ += S_.i_syn_[ i ]; // not sure about this
+ }
+ for ( size_t i = 0; i < P_.n_receptors_(); i++ )
+ {
+ // exponential decaying PSCs
+ S_.i_syn_[ i ] *= V_.P11_syn_[ i ];
+
+ // collect spikes
+ S_.i_syn_[ i ] += B_.spikes_[ i ].get_value( lag ); // not sure about this
+ }
+
+
+ // For Breakpoint conditions
+ current = S_.current_;
+ vmss = S_.V_m_;
+ timess = t_final * V_.time_scale_;
+
+ // Update integration time window
+ t0_val = t_final;
+ t_final = t0_val + local_time_step;
+
+ // t0_val = origin.get_ms() / V_.time_scale_;
+ // t_final = t0_val + (lag + 1) * V_.dt ;//Time::step( origin.get_steps() + lag + 1 );
+ // timess = t_final * V_.time_scale_;
+ // std::cout << "t_final =" << t_final*V_.time_scale_ << " ms. " << "Vm " << S_.V_m_ << " V_ini " << v_ini << "\n";
+ // std::cout << "\n439 Time from (" << from << ") =" << t0_val*V_.time_scale_ << " ms to (" << to<< ") =" << t_final*V_.time_scale_ << " ms.\n";
+ // v_old = v_ini;
+ // Iadap_ini_old = S_.Iadap_ini_;
+ // Idep_ini_old = S_.Idep_ini_;
+ // std::cout << "Vm " << v_ini * V_.Vconvfact << "\n";
+ // v_ini +=
+ // h * ( 0.04 * v_old * v_old + 5.0 * v_old + 140.0 - miglv1_old + S_.I_inj_ + P_.I_e_ ) + I_syn;
+ // S_.miglv1_ += h * P_.miglp1_ * ( P_.miglp2_ * v_old - miglv1_old );
+
+ // if (S_.current_ > 0)
+ // {
+ // // std::cout << "591 corr > 0 \n";
+ // S_.sis_ = S_.sis_+1;
+ // if (S_.sis_ >= 2)
+ // {
+ // meancorlastprec = meancorlastis;
+ // stdcorlastprec = stdcorlastis;
+ // stdcorlastis = ((S_.sis_-2)*stdcorlastis+(S_.sis_-1)*pow(meancorlastis,2) + pow(S_.current_,2)-S_.sis_*pow(((S_.sis_-1)*meancorlastis+S_.current_)/S_.sis_,2))/(S_.sis_-1);
+ // meancorlastis = ((S_.sis_-1)*meancorlastis+S_.current_)/S_.sis_;
+ // }
+ // else
+ // {
+ // stdcorlastis = 0;
+ // meancorlastis = S_.current_;
+ // }
+ // }
+ if ((t_final-S_.init_sign_)*V_.time_scale_ >= nest::migliore::tagliorette(S_.current_))
+ {
+ // std::cout << "604 tagliorette " << nest::migliore::tagliorette(S_.current_) << " cor " << S_.current_ << "\n";
+ if (P_.corrcostatratti_)
+ {
+ // std::cout << "611 corrcostatratti " << " cor " << S_.current_ << "\n";
+ if (S_.current_ > P_.ith_)
+ {
+ // std::cout << "614 cor > ith " << S_.current_ << "\n";
+ if (corpre < P_.ith_ ) //|| i == 0)
+ {
+ S_.init_sign_ = t_final;
+ S_.Idep_ini_ = P_.cost_idep_ini_*(S_.current_-P_.ith_);
+ S_.Iadap_ini_ = 0;
+ }
+ if (corpre > P_.ith_ && corpre < S_.current_)
+ {
+ S_.init_sign_ = S_.init_sign_*(1+(corpre-P_.ith_)/corpre);
+ S_.Idep_ini_ = P_.cost_idep_ini_*(S_.current_-P_.ith_);
+ }
+ }
+ }
+ if (P_.corrcost_)
+ {
+ if (S_.current_ > P_.ith_)
+ {
+ if (corpre < P_.ith_ )
+ {
+ S_.init_sign_ = t_final;
+ S_.Idep_ini_ = P_.cost_idep_ini_*(S_.current_-P_.ith_);
+ S_.Iadap_ini_ = 0;
+ }
+ }
+ }
+ if (corpre == 0)
+ {
+ v_ini = vini_prec;
+ }
+ else
+ {
+ // Set the v_ini depending on the refractory period
+ v_ini = set_v_ini((P_.E_L_+(1-exp(-S_.current_/1000))*(P_.vtm_-P_.E_L_))/V_.Vconvfact, S_.r_ref_, V_.vrm);
+ }
+ vini_prec = v_ini;
+ V_.out.push_back(v_ini);
+ // t_out.append(t_final);
+ // Iada.append(S_.Iadap_ini_);
+ // Ide.append(S_.Idep_ini_);
+ }
+ else
+ {
+ // std::cout << "688 NO tagliorette " << S_.current_ << "\n";
+ vini_prec = v_ini;
+ if ((S_.current_ < P_.ith_ && S_.current_ >= 0) ) //|| i == 0)
+ {
+ // std::cout << "691 cor < ith " << S_.current_ << "\n";
+ if (corpre < 0)
+ {
+ S_.Iadap_ini_ = 90/P_.E_L_ + 1;
+ S_.Idep_ini_ = 0;
+ v_ini = set_v_ini(vini_prec, S_.r_ref_, V_.vrm);
+ }
+ if (((S_.current_ / P_.sc_) / (P_.bet_ - P_.delta1_) - 1) <= v_ini)
+ {
+ S_.Idep_ini_ = 0;
+ S_.Iadap_ini_ = (S_.current_ / P_.sc_) / (P_.bet_ - P_.delta1_);
+ v_ini = set_v_ini(((S_.current_ / P_.sc_) / (P_.bet_ - P_.delta1_) - 1), S_.r_ref_, V_.vrm);
+ }
+ else
+ {
+ v_ini = migliV(t_final, P_.delta1_, V_.psi1, S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_, V_.vrm);
+ S_.Iadap_ini_ = Iadap(t_final, P_.delta1_, V_.psi1, S_.current_ / P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_);
+ S_.Idep_ini_ = Idep(t_final, P_.bet_, S_.Idep_ini_, t0_val, S_.r_ref_);
+ }
+ if (v_ini * V_.Vconvfact < -90)
+ {
+ v_ini = set_v_ini(-90 / V_.Vconvfact, S_.r_ref_, V_.vrm);
+ S_.Iadap_ini_ = 0;
+ }
+ V_.out.push_back(v_ini);
+ }
+ else
+ {
+ if (S_.current_ < corpre && S_.current_ > 0 && (V_.t_spk+2*V_.d_dt) < t_final*V_.time_scale_ && V_.out.size() > 2)
+ {
+ // std::cout << "726 v_ini " << v_ini << "\n";
+ teta = (V_.out[V_.out.size()-1]/(corpre / P_.sc_))*(1/V_.dt-P_.delta1_) - (V_.out[V_.out.size()-2]/((corpre / P_.sc_)*V_.dt))-P_.delta1_/(corpre / P_.sc_)-1;
+ if (teta < 0)
+ {
+ teta = 0;
+ }
+ S_.Idep_ini_ = S_.Iadap_ini_ + teta * (S_.current_ / P_.sc_) / P_.bet_;
+ // tetalist.append(teta);
+ v_ini = migliV(t_final, P_.delta1_, V_.psi1,
+ S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_, V_.vrm);
+ S_.Iadap_ini_ = Iadap(t_final, P_.delta1_, V_.psi1,
+ S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_);
+ S_.Idep_ini_ = Idep(t_final, P_.bet_,
+ S_.Idep_ini_, t0_val, S_.r_ref_);
+ }
+ else
+ {
+ if (S_.current_ > 0)
+ {
+ v_ini = migliV(t_final, P_.delta1_, V_.psi1,
+ S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_, V_.vrm);
+ S_.Iadap_ini_ = Iadap(t_final, P_.delta1_, V_.psi1,
+ S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_);
+ S_.Idep_ini_ = Idep(t_final, P_.bet_, S_.Idep_ini_, t0_val, S_.r_ref_);
+ }
+ }
+ if (corpre != S_.current_ and (S_.current_ < 0 and S_.current_ > -200))
+ {
+ S_.Iadap_ini_ = (90+P_.E_L_)*S_.current_/(P_.E_L_*(-200));
+ S_.Idep_ini_ = 0;
+ v_ini = set_v_ini(vini_prec, S_.r_ref_, V_.vrm);
+ }
+ if (S_.current_ < 0 and S_.current_ > -200)
+ {
+ // std::cout << "785 v_ini " << v_ini << "\n";
+ v_ini = migliV(t_final, P_.delta1_, V_.psi1, V_.H * S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_, V_.vrm);
+ S_.Iadap_ini_ = Iadap(t_final, P_.delta1_, V_.psi1, V_.H * S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_);
+ S_.Idep_ini_ = Idep(t_final, P_.bet_,
+ S_.Idep_ini_, t0_val, S_.r_ref_);
+ }
+ if (corpre != S_.current_ and S_.current_ <= -200)
+ {
+ // std::cout << "793 v_ini " << v_ini << "\n";
+ S_.Iadap_ini_ = 90/P_.E_L_ + 1;
+ S_.Idep_ini_ = 0;
+ v_ini = set_v_ini(vini_prec, S_.r_ref_, V_.vrm);
+ }
+ if (S_.current_ <= -200)
+ {
+ v_ini = migliV(t_final, P_.delta1_, V_.psi1, V_.H * S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_, V_.vrm);
+ S_.Iadap_ini_ = Iadap(t_final, P_.delta1_, V_.psi1, V_.H * S_.current_/P_.sc_, P_.bet_, S_.Iadap_ini_, S_.Idep_ini_, t0_val, v_ini, S_.r_ref_);
+ S_.Idep_ini_ = Idep(t_final, P_.bet_, S_.Idep_ini_, t0_val, S_.r_ref_);
+ }
+ if (v_ini*V_.Vconvfact < -90)
+ {
+ v_ini = set_v_ini(-90/V_.Vconvfact, S_.r_ref_, V_.vrm);
+ S_.Iadap_ini_ = 0;
+ }
+ V_.out.push_back(v_ini);
+ }
+ // t_out.append(t_final);
+ // Iada.append(S_.Iadap_ini_);
+ // Ide.append(S_.Idep_ini_);
+ if (P_.corrcostatratti_)
+ {
+ // std::cout << "817 corrcostatratti_\n";
+ if (S_.current_ > P_.ith_)
+ {
+ if (corpre < P_.ith_) // || i == 0)
+ {
+ // std::cout << "822 cor > P_.ith_ " << S_.current_ << "," << P_.ith_ << "\n";
+ S_.init_sign_ = t_final;
+ S_.Idep_ini_ = P_.cost_idep_ini_*(S_.current_-P_.ith_);
+ S_.Iadap_ini_ = 0;
+ }
+
+ if (corpre > P_.ith_ && corpre < S_.current_)
+ {
+ S_.init_sign_ = S_.init_sign_*(1+(corpre-P_.ith_)/corpre);
+ S_.Idep_ini_ = P_.cost_idep_ini_*(S_.current_-P_.ith_);
+ S_.Iadap_ini_ = 0;
+ }
+ }
+ }
+ if (P_.corrcost_)
+ {
+ if (S_.current_ > P_.ith_)
+ {
+ if (corpre < P_.ith_) // || i == 0)
+ {
+ S_.init_sign_ = t_final;
+ S_.Idep_ini_ = P_.cost_idep_ini_*(S_.current_-P_.ith_);
+ S_.Iadap_ini_ = 0;
+ }
+ }
+ }
+ // vini_prec = v_ini;
+ }
+ // i = i + 1;
+ // t0_val = t_final;
+ // t_final = t0_val+V_.dt;
+
+ S_.V_m_ = v_ini * V_.Vconvfact;
+ if (S_.V_m_ < -85.0) {
+ std::cout << "Low VM " << origin.get_ms() << "\n";
+ }
+ std::cout << "Low VM " << origin.get_ms() << "\n";
+
+ // std::cout << "655 S_.v_ v_ini final " << S_.v_ << " Iadap_ini_ " << S_.Iadap_ini_ << "\n";
+
+ while (V_.out.size() > 3)
+ {
+ V_.out.erase(V_.out.begin());
+ }
+ // lower bound of membrane potential
+ S_.V_m_ = ( S_.V_m_ < P_.V_min_ ? P_.V_min_ : S_.V_m_ );
+ // std::cout << "665 S_.v_ v_ini lower bound " << S_.V_m_ << "\n";
+
+ // Count down for refractory period
+ if (S_.r_ref_ > 0) {--S_.r_ref_;}
+
+ // threshold crossing
+ if ( S_.V_m_ > P_.V_th_ ) // V_th_ = -52
+ {
+ S_.r_ref_ = V_.RefractoryCounts_; // Inizialize refractory
+ V_.t_spk = t_final*V_.time_scale_;
+ // f.write(str(round(V_.t_spk, 3)) + ' \n')
+ S_.V_m_ = V_.vrm * V_.Vconvfact; // -65
+
+ // print('^*spike^*')
+ // print('t ', t_final, 'val_ist V', V_m_ * V_.Vconvfact, 'adap',
+ // S_.Iadap_ini_, 'adap', S_.Iadap_ini_, 't_ini', S_.init_sign_)
+ // print('^^^^^^')
+ c_aux = P_.c_;
+ if (S_.current_ < P_.istim_min_spikinig_exp_ || S_.current_ > P_.istim_max_spikinig_exp_)
+ {
+ if (P_.corrcost_ or P_.corrcostatratti_)
+ {
+ // check solo al primo spike
+ if (P_.firstSpikeFlag_ == false or corpre != S_.current_)
+ {
+ P_.firstSpikeFlag_ = true;
+ paramL_ = monod((t_final-S_.init_sign_)*V_.time_scale_,P_.a_,P_.b_*S_.current_/1000,P_.c_,P_.alp_);
+ if (paramL_ < 0)
+ {
+ // print('monod negativa, paramL: '+str(paramL));
+ if (P_.a_ > 0)
+ {
+ //c*
+ c_aux = P_.c_ - paramL_;
+ // print(c_aux)
+ }
+ else
+ {
+ // a<0
+ // c**
+ c_aux = -P_.a_* exp(P_.b_ * S_.current_/1000);
+ // print(c_aux)
+ }
+ }
+ else
+ {
+ c_aux = P_.c_;
+ }
+ }
+ S_.Iadap_ini_ = monod((t_final-S_.init_sign_) * V_.time_scale_, P_.a_, P_.b_ * S_.current_/1000, c_aux, P_.alp_);
+ }
+ else
+ {
+ // sinapt
+ c_aux = P_.c_;
+ S_.Iadap_ini_ = monod((t_final-S_.init_sign_) *
+ V_.time_scale_, P_.a_, P_.b_ * S_.current_/1000, c_aux, P_.alp_);
+ }
+ }
+ else
+ {
+ // std::cout << "899 Monod\n";
+ S_.Iadap_ini_ = monod((t_final-S_.init_sign_) * V_.time_scale_, P_.a_, P_.b_*S_.current_/1000, P_.c_, P_.alp_);
+ if (S_.Iadap_ini_<0)
+ {
+ // print('monod negativa');
+ if (P_.firstSpikeFlag_ == false or corpre!=S_.current_)
+ {
+ P_.firstSpikeFlag_ = true;
+ paramL_ = monod((t_final-S_.init_sign_)*V_.time_scale_, P_.a_,P_.b_*S_.current_/1000,P_.c_,P_.alp_);
+ //print('paramL: ',paramL)
+ }
+ if (S_.counter_<2)
+ {
+ //print('monod a zero - ',S_.counter_)
+ S_.Iadap_ini_ = 0;
+ S_.counter_ = S_.counter_ + 1;
+ }
+ else if (S_.counter_ == 2)
+ {
+ c_aux = P_.c_;
+ if (P_.a_ > 0)
+ {
+ c_aux = P_.c_ - paramL_;
+ // print(c_aux)
+ }
+ else
+ {
+ c_aux = -P_.a_* exp(P_.b_ * S_.current_/1000);
+ // print(c_aux)
+ }
+ S_.Iadap_ini_ = monod((t_final-S_.init_sign_) * V_.time_scale_, P_.a_, P_.b_ * S_.current_/1000, c_aux, P_.alp_);
+ S_.counter_ = S_.counter_ + 1;
+ }
+ else
+ {
+ // print('S_.counter_ > 3 - c_aux: ',c_aux)
+ S_.Iadap_ini_ = monod((t_final-S_.init_sign_) * V_.time_scale_, P_.a_, P_.b_ * S_.current_/1000, c_aux, P_.alp_);
+ // print('monod traslata: ',Iadap_ini)
+ }
+ }
+ }
+ if (S_.current_ < P_.ith_)
+ {
+ S_.Idep_ini_ = 0;
+ S_.Iadap_ini_ = 0;
+ }
+ else
+ {
+ S_.Idep_ini_ = P_.Idep_ini_vr_;
+ }
+ // // Refractory time management
+ // for (k in range(int(ref_t / V_.d_dt)))
+ // {
+ // // out.append(V_m_);
+ // t_final = t_final + V_.dt;
+ // // t_out.append(t_final);
+ // // Iada.append(S_.Iadap_ini_);
+ // // Ide.append(S_.Idep_ini_);
+ // i = i + 1;
+ // S_.sis_ = S_.sis_+1;
+ // if (S_.sis_ >= 2)
+ // {
+ // stdcorlastis = ((S_.sis_-2)*stdcorlastis+(S_.sis_-1)*meancorlastis^2 +
+ // S_.current_^2-S_.sis_*(((S_.sis_-1)*meancorlastis+S_.current_)/S_.sis_)^2)/(S_.sis_-1);
+ // meancorlastis = ((S_.sis_-1)*meancorlastis+S_.current_)/S_.sis_;
+ // }
+ // else
+ // {
+ // stdcorlastis = 0;
+ // meancorlastis = S_.current_;
+ // }
+ // }
+