hh_cond_exp_traub.h

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/*
 *  hh_cond_exp_traub.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 HH_COND_EXP_TRAUB_H
#define HH_COND_EXP_TRAUB_H
 
// Generated includes:
#include "config.h"
 
#ifdef HAVE_GSL
 
// C includes:
#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 hh_cond_exp_traub_dynamics( double, const double*, double*, void* );
 
/* BeginUserDocs: neuron, Hodgkin-Huxley, conductance-based, soft threshold
 
Short description
+++++++++++++++++
 
Hodgkin-Huxley model for Brette et al (2007) review
 
Description
+++++++++++
 
``hh_cond_exp_traub`` is an implementation of a modified Hodgkin-Huxley model.
 
This model was specifically developed for a major review of simulators :footcite:p:`Brette2007`,
based on a model of hippocampal pyramidal cells by Traub and Miles :footcite:p:`Traub1991`.
The key differences between the current model and the model in :footcite:p:`Traub1991` are:
 
- This model is a point neuron, not a compartmental model.
- This model includes only ``I_Na`` and ``I_K``, with simpler ``I_K`` dynamics than
  in :footcite:p:`Traub1991`, so it has only three instead of eight gating variables;
  in particular, all Ca dynamics have been removed.
- Incoming spikes induce an instantaneous conductance change followed by
  exponential decay instead of activation over time.
 
This model is primarily provided as reference implementation for hh_coba
example of the Brette et al (2007) review. Default parameter values are chosen
to match those used with NEST 1.9.10 when preparing data for :footcite:p:`Brette2007`. Code for all
simulators covered is available from ModelDB :footcite:p:`Traub1991b`.
 
.. note::
 
   In this model, a spike is emitted if :math:`V_m \geq V_T + 30` mV and :math:`V_m`
   has fallen during the current time step.
 
   To avoid multiple spikes from occurring during the falling flank of a
   spike, it is essential to choose a sufficiently long refractory period.
   Traub and Miles used  :math:`t_{ref} = 3` ms (:footcite:p:`Traub1991`, p 118), while we used
   :math:`t_{ref} = 2` ms in :footcite:p:`Traub1991`.
 
   For further details on asynchronicity in spike and firing events with Hodgkin Huxley models
   see :ref:`here <hh_details>`.
 
Parameters
++++++++++
 
The following parameters can be set in the status Dictionary.
 
=========== ======  =========================================================
V_m          mV     Membrane potential
V_T          mV     Voltage offset that controls dynamics. For default
                    parameters, V_T = -63mV results in a threshold around
                    -50mV.
E_L          mV     Leak reversal potential
C_m          pF     Capacity of the membrane
g_L          nS     Leak conductance
tau_syn_ex   ms     Time constant of the excitatory synaptic exponential
                    function
tau_syn_in   ms     Time constant of the inhibitory synaptic exponential
                    function
t_ref        ms     Duration of refractory period (see Note).
E_ex         mV     Excitatory synaptic reversal potential
E_in         mV     Inhibitory synaptic reversal potential
E_Na         mV     Sodium reversal potential
g_Na         nS     Sodium peak conductance
E_K          mV     Potassium reversal potential
g_K          nS     Potassium peak conductance
I_e          pA     External input current
=========== ======  =========================================================
 
References
++++++++++
 
.. footbibliography::
 
Sends
+++++
 
SpikeEvent
 
Receives
++++++++
 
SpikeEvent, CurrentEvent, DataLoggingRequest
 
See also
++++++++
 
hh_psc_alpha
 
Examples using this model
+++++++++++++++++++++++++
 
.. listexamples:: hh_cond_exp_traub
 
EndUserDocs */
 
void register_hh_cond_exp_traub( const std::string& name );
 
class hh_cond_exp_traub : public ArchivingNode
{
 
public:
  hh_cond_exp_traub();
  hh_cond_exp_traub( const hh_cond_exp_traub& );
  ~hh_cond_exp_traub() 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 hh_cond_exp_traub_dynamics( double, const double*, double*, void* );
 
  // The next two classes need to be friends to access the State_ class/member
  friend class RecordablesMap< hh_cond_exp_traub >;
  friend class UniversalDataLogger< hh_cond_exp_traub >;
 
private:
  // ----------------------------------------------------------------
 
  struct Parameters_
  {
    double g_Na;  
    double g_K;   
    double g_L;   
    double C_m;   
 
    double E_Na;  
    double E_K;   
    double E_L;   
 
    double V_T;
 
    double E_ex;      
    double E_in;      
    double tau_synE;  
    double tau_synI;  
    double t_ref_;    
    double I_e;       
 
    Parameters_();
 
    void get( Dictionary& ) const;              
    void set( const Dictionary&, Node* node );  
  };
 
public:
  // ----------------------------------------------------------------
 
  struct State_
  {
    enum StateVecElems
    {
      V_M = 0,
      HH_M,   // 1
      HH_H,   // 2
      HH_N,   // 3
      G_EXC,  // 4
      G_INH,  // 5
      STATE_VEC_SIZE
    };
 
    double y_[ STATE_VEC_SIZE ];
    int r_;  
 
    State_( const Parameters_& p );
    State_( const State_& s );
 
    State_& operator=( const State_& );
 
    void get( Dictionary& ) const;
    void set( const Dictionary&, const Parameters_&, Node* );
  };
 
  // ----------------------------------------------------------------
 
  struct Variables_
  {
    int refractory_counts_;
    double U_old_;  // for spike-detection
  };
 
  // ----------------------------------------------------------------
 
  struct Buffers_
  {
    Buffers_( hh_cond_exp_traub& );  
    Buffers_( const Buffers_&, hh_cond_exp_traub& );
 
    UniversalDataLogger< hh_cond_exp_traub > 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_;
  };
 
  // 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< hh_cond_exp_traub > recordablesMap_;
};
 
inline size_t
hh_cond_exp_traub::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
hh_cond_exp_traub::handles_test_event( SpikeEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
hh_cond_exp_traub::handles_test_event( CurrentEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
hh_cond_exp_traub::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
hh_cond_exp_traub::get_status( Dictionary& d ) const
{
  P_.get( d );
  S_.get( d );
  ArchivingNode::get_status( d );
 
  d[ names::recordables ] = recordablesMap_.get_list();
 
  d[ names::t_spike ] = get_spiketime_ms();
}
 
inline void
hh_cond_exp_traub::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;
 
  pre_run_hook();
}
 
}  // namespace
 
 
#endif  // HAVE_GSL
#endif  // HH_COND_EXP_TRAUB_H