iaf_cond_exp_sfa_rr.h

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/*
 *  iaf_cond_exp_sfa_rr.h
 *
 *  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/>.
 *
 */
 
#ifndef IAF_COND_EXP_SFA_RR_H
#define IAF_COND_EXP_SFA_RR_H
 
// Generated includes:
#include "config.h"
 
#ifdef HAVE_GSL
 
// External includes:
#include <gsl/gsl_errno.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_odeiv.h>
 
// Includes from nestkernel:
#include "archiving_node.h"
#include "connection.h"
#include "event.h"
#include "nest_types.h"
#include "recordables_map.h"
#include "ring_buffer.h"
#include "universal_data_logger.h"
 
namespace nest
{
extern "C" int iaf_cond_exp_sfa_rr_dynamics( double, const double*, double*, void* );
 
/* BeginUserDocs: neuron, integrate-and-fire, conductance-based, hard threshold
 
Short description
+++++++++++++++++
 
Conductance based leaky integrate-and-fire model with spike-frequency
adaptation and relative refractory mechanisms
 
Description
+++++++++++
 
``iaf_cond_exp_sfa_rr`` is an implementation of a spiking neuron using
integrate-and-fire dynamics with conductance-based synapses, with additional
spike-frequency adaptation and relative refractory mechanisms as described in
:footcite:p:`Dayan2001`, page 166.
 
Incoming spike events induce a postsynaptic change of conductance modelled by
an exponential function. The exponential function is normalized such that an
event of weight 1.0 results in a peak conductance of 1 nS.
 
Outgoing spike events induce a change of the adaptation and relative refractory
conductances by ``q_sfa`` and ``q_rr``, respectively. Otherwise these conductances
decay exponentially with time constants ``tau_sfa`` and ``tau_rr``, respectively.
 
See also :footcite:p:`Meffin2004`.
 
Parameters
++++++++++
 
The following parameters can be set in the status Dictionary.
 
=========== ======  ===========================================================
 V_m        mV      Membrane potential
 E_L        mV      Leak reversal potential
 C_m        pF      Capacity of the membrane
 t_ref      ms      Duration of refractory period
 V_th       mV      Spike threshold
 V_reset    mV      Reset potential of the membrane
 E_ex       mV      Excitatory reversal potential
 E_in       mV      Inhibitory reversal potential
 g_L        nS      Leak conductance
 tau_syn_ex ms      Exponential decay time constant of excitatory synaptic
                    conductance kernel
 tau_syn_in ms      Exponential decay time constant of inhibitory synaptic
                    conductance kernel
 q_sfa      nS      Outgoing spike activated quantal spike-frequency adaptation
                    conductance increase in nS
 q_rr       nS      Outgoing spike activated quantal relative refractory
                    conductance increase in nS
 tau_sfa    ms      Time constant of spike-frequency adaptation in ms
 tau_rr     ms      Time constant of the relative refractory mechanism in ms
 E_sfa      mV      Spike-frequency adaptation conductance reversal potential
                    in mV
 E_rr       mV      Relative refractory mechanism conductance reversal
                    potential in mV
 I_e        pA      Constant input current
=========== ======  ===========================================================
 
 
Sends
+++++
 
SpikeEvent
 
Receives
++++++++
 
SpikeEvent, CurrentEvent, DataLoggingRequest
 
References
++++++++++
 
.. footbibliography::
 
See also
++++++++
 
aeif_cond_alpha, aeif_cond_exp, iaf_chxk_2008
 
Examples using this model
+++++++++++++++++++++++++
 
.. listexamples:: iaf_cond_exp_sfa_rr
 
EndUserDocs */
 
void register_iaf_cond_exp_sfa_rr( const std::string& name );
 
class iaf_cond_exp_sfa_rr : public ArchivingNode
{
 
public:
  iaf_cond_exp_sfa_rr();
  iaf_cond_exp_sfa_rr( const iaf_cond_exp_sfa_rr& );
  ~iaf_cond_exp_sfa_rr() override;
 
  using Node::handle;
  using Node::handles_test_event;
 
  size_t send_test_event( Node&, size_t, synindex, bool ) override;
 
  void handle( SpikeEvent& ) override;
  void handle( CurrentEvent& ) override;
  void handle( DataLoggingRequest& ) override;
 
  size_t handles_test_event( SpikeEvent&, size_t ) override;
  size_t handles_test_event( CurrentEvent&, size_t ) override;
  size_t handles_test_event( DataLoggingRequest&, size_t ) override;
 
  void get_status( Dictionary& ) const override;
  void set_status( const Dictionary& ) override;
 
private:
  void init_buffers_() override;
  void pre_run_hook() override;
  void update( Time const&, const long, const long ) override;
 
  // END Boilerplate function declarations ----------------------------
 
  // Friends --------------------------------------------------------
 
  // make dynamics function quasi-member
  friend int iaf_cond_exp_sfa_rr_dynamics( double, const double*, double*, void* );
 
  // The next two classes need to be friends to access the State_ class/member
  friend class RecordablesMap< iaf_cond_exp_sfa_rr >;
  friend class UniversalDataLogger< iaf_cond_exp_sfa_rr >;
 
private:
  // ----------------------------------------------------------------
 
  struct Parameters_
  {
    double V_th_;     
    double V_reset_;  
    double t_ref_;    
    double g_L;       
    double C_m;       
    double E_ex;      
    double E_in;      
    double E_L;       
    double tau_synE;  
    double tau_synI;  
    double I_e;       
    double tau_sfa;   
    double tau_rr;    
    double E_sfa;     
    double E_rr;      
    double q_sfa;     
    double q_rr;      
 
    Parameters_();  
 
    void get( Dictionary& ) const;              
    void set( const Dictionary&, Node* node );  
  };
 
public:
  // ----------------------------------------------------------------
 
  struct State_
  {
    enum StateVecElems
    {
      V_M = 0,
      G_EXC,
      G_INH,
      G_SFA,
      G_RR,
      STATE_VEC_SIZE
    };
 
    double y_[ STATE_VEC_SIZE ];
    int r_;  
 
    State_( const Parameters_& );  
    State_( const State_& );
 
    State_& operator=( const State_& );
 
    void get( Dictionary& ) const;
    void set( const Dictionary&, const Parameters_&, Node* );
  };
 
private:
  // ----------------------------------------------------------------
 
  struct Buffers_
  {
    Buffers_( iaf_cond_exp_sfa_rr& );  
    Buffers_( const Buffers_&, iaf_cond_exp_sfa_rr& );
 
    UniversalDataLogger< iaf_cond_exp_sfa_rr > logger_;
 
    RingBuffer spike_exc_;
    RingBuffer spike_inh_;
    RingBuffer currents_;
 
    gsl_odeiv_step* s_;     
    gsl_odeiv_control* c_;  
    gsl_odeiv_evolve* e_;   
    gsl_odeiv_system sys_;  
 
    // Since IntegrationStep_ is initialized with step_, and the resolution
    // cannot change after nodes have been created, it is safe to place both
    // here.
    double step_;             
    double IntegrationStep_;  
 
    double I_stim_;
  };
 
  // ----------------------------------------------------------------
 
  struct Variables_
  {
    int RefractoryCounts_;
  };
 
  // Access functions for UniversalDataLogger -------------------------------
 
  template < State_::StateVecElems elem >
  double
  get_y_elem_() const
  {
    return S_.y_[ elem ];
  }
 
  // ----------------------------------------------------------------
 
  Parameters_ P_;
  State_ S_;
  Variables_ V_;
  Buffers_ B_;
 
  static RecordablesMap< iaf_cond_exp_sfa_rr > recordablesMap_;
};
 
 
inline size_t
iaf_cond_exp_sfa_rr::send_test_event( Node& target, size_t receptor_type, synindex, bool )
{
  SpikeEvent e;
  e.set_sender( *this );
  return target.handles_test_event( e, receptor_type );
}
 
inline size_t
iaf_cond_exp_sfa_rr::handles_test_event( SpikeEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
iaf_cond_exp_sfa_rr::handles_test_event( CurrentEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
iaf_cond_exp_sfa_rr::handles_test_event( DataLoggingRequest& dlr, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return B_.logger_.connect_logging_device( dlr, recordablesMap_ );
}
 
 
inline void
iaf_cond_exp_sfa_rr::get_status( Dictionary& d ) const
{
  P_.get( d );
  S_.get( d );
  ArchivingNode::get_status( d );
 
  d[ names::recordables ] = recordablesMap_.get_list();
}
 
inline void
iaf_cond_exp_sfa_rr::set_status( const Dictionary& d )
{
  Parameters_ ptmp = P_;      // temporary copy in case of errors
  ptmp.set( d, this );        // throws if BadProperty
  State_ stmp = S_;           // temporary copy in case of errors
  stmp.set( d, ptmp, this );  // throws if BadProperty
 
  // We now know that (ptmp, stmp) are consistent. We do not
  // write them back to (P_, S_) before we are also sure that
  // the properties to be set in the parent class are internally
  // consistent.
  ArchivingNode::set_status( d );
 
  // if we get here, temporaries contain consistent set of properties
  P_ = ptmp;
  S_ = stmp;
}
 
}  // namespace
 
#endif  // HAVE_GSL
#endif  // IAF_COND_EXP_SFA_RR_H