iaf_cond_alpha.h

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/*
 *  iaf_cond_alpha.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_ALPHA_H
#define IAF_COND_ALPHA_H
 
// Generated includes:
#include "config.h"
 
#ifdef HAVE_GSL
 
// C 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_alpha_dynamics( double, const double*, double*, void* );
 
/* BeginUserDocs: neuron, integrate-and-fire, conductance-based, hard threshold
 
Short description
+++++++++++++++++
 
Simple conductance based leaky integrate-and-fire neuron model
 
Description
+++++++++++
 
``iaf_cond_alpha`` is an implementation of a spiking neuron using IAF dynamics with
conductance-based synapses. Incoming spike events induce a postsynaptic change
of conductance modelled by an alpha function. The alpha function
is normalized such that an event of weight 1.0 results in a peak conductance of 1 nS
at :math:`t = \tau_{syn}`.
 
See also :footcite:p:`Meffin2004`, :footcite:p:`Bernander1991`, :footcite:p:`Kuhn2004`.
 
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      Rise time of the excitatory synaptic alpha function
 tau_syn_in ms      Rise time of the inhibitory synaptic alpha function
 I_e        pA      Constant input current
=========== ======= ===========================================================
 
Sends
+++++
 
SpikeEvent
 
Receives
++++++++
 
SpikeEvent, CurrentEvent, DataLoggingRequest
 
References
++++++++++
 
.. footbibliography::
 
See also
++++++++
 
iaf_cond_exp, iaf_cond_alpha_mc
 
Examples using this model
+++++++++++++++++++++++++
 
.. listexamples:: iaf_cond_alpha
 
EndUserDocs */
 
void register_iaf_cond_alpha( const std::string& name );
 
class iaf_cond_alpha : public ArchivingNode
{
 
  // Boilerplate function declarations --------------------------------
 
public:
  iaf_cond_alpha();
  iaf_cond_alpha( const iaf_cond_alpha& );
  ~iaf_cond_alpha() override;
 
  /*
   * Import all overloaded virtual functions that we
   * override in this class.  For background information,
   * see http://www.gotw.ca/gotw/005.htm.
   */
 
  using Node::handle;
  using Node::handles_test_event;
 
  size_t send_test_event( Node& tagret, size_t receptor_type, synindex, bool ) 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 handle( SpikeEvent& ) override;
  void handle( CurrentEvent& ) override;
  void handle( DataLoggingRequest& ) 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_alpha_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_alpha >;
  friend class UniversalDataLogger< iaf_cond_alpha >;
 
private:
  // Parameters class -------------------------------------------------
 
  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;       
 
    Parameters_();  
 
    void get( Dictionary& ) const;              
    void set( const Dictionary&, Node* node );  
  };
 
  // State variables class --------------------------------------------
 
public:
  struct State_
  {
    enum StateVecElems
    {
      V_M = 0,
      DG_EXC,
      G_EXC,
      DG_INH,
      G_INH,
      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:
  // Buffers class --------------------------------------------------------
 
  struct Buffers_
  {
    Buffers_( iaf_cond_alpha& );                   
    Buffers_( const Buffers_&, iaf_cond_alpha& );  
 
    UniversalDataLogger< iaf_cond_alpha > logger_;
 
    RingBuffer spike_exc_;
    RingBuffer spike_inh_;
    RingBuffer currents_;
 
    /* GSL ODE stuff */
    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_;
  };
 
  // Variables class -------------------------------------------------------
 
  struct Variables_
  {
    double PSConInit_E;
 
    double PSConInit_I;
 
    int RefractoryCounts;
  };
 
  // Access functions for UniversalDataLogger -------------------------------
 
  template < State_::StateVecElems elem >
  double
  get_y_elem_() const
  {
    return S_.y[ elem ];
  }
 
  double
  get_r_() const
  {
    return Time::get_resolution().get_ms() * S_.r;
  }
 
  // Data members -----------------------------------------------------------
 
  // keep the order of these lines, seems to give best performance
  Parameters_ P_;
  State_ S_;
  Variables_ V_;
  Buffers_ B_;
 
  static RecordablesMap< iaf_cond_alpha > recordablesMap_;
};
 
 
// Boilerplate inline function definitions ----------------------------------
 
inline size_t
iaf_cond_alpha::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_alpha::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_alpha::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_alpha::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_alpha::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_alpha::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  // IAF_COND_ALPHA_H
 
#endif  // HAVE_GSL