amat2_psc_exp.h

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/*
 *  amat2_psc_exp.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 AMAT2_PSC_EXP_H
#define AMAT2_PSC_EXP_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
{
 
/* BeginUserDocs: neuron, integrate-and-fire, current-based, adaptation, hard threshold
 
Short description
+++++++++++++++++
 
Non-resetting leaky integrate-and-fire neuron model with exponential
PSCs and adaptive threshold
 
Description
+++++++++++
 
``amat2_psc_exp`` is an implementation of a leaky integrate-and-fire model
with exponential shaped postsynaptic currents (PSCs). Thus, postsynaptic
currents have an infinitely short rise time.
 
The threshold is lifted when the neuron is fired and then decreases in a
fixed time scale toward a fixed level :footcite:p:`Kobayashi2009`.
 
The threshold crossing is followed by a total refractory period
during which the neuron is not allowed to fire, even if the membrane
potential exceeds the threshold. The membrane potential is NOT reset,
but continuously integrated.
 
The linear subthreshold dynamics is integrated by the Exact
Integration scheme :footcite:p:`Rotter1999`. The neuron dynamics is solved on the time
grid given by the computation step size. Incoming as well as emitted
spikes are forced to that grid.
 
An additional state variable and the corresponding differential
equation represents a piecewise constant external current.
 
The general framework for the consistent formulation of systems with
neuron like dynamics interacting by point events is described in
:footcite:p:`Rotter1999`. A flow chart can be found in :footcite:p:`Diesmann2001`.
 
The default parameter values for this model are different from the
corresponding parameter values for ``mat2_psc_exp``. If identical
parameters are used, and beta is 0, then this model shall behave
exactly as mat2_psc_exp.
 
The following state variables can be read out using a multimeter:
 
=========== ==== ==================================
 V_m        mV   Non-resetting membrane potential
 V_th       mV   Two-timescale adaptive threshold
=========== ==== ==================================
 
See also :footcite:p:`Yamauchi2011`.
 
Parameters
++++++++++
 
The following parameters can be set in the status dictionary:
 
=========== ======= ===========================================================
 C_m        pF      Capacity of the membrane
 E_L        mV      Resting potential
 tau_m      ms      Membrane time constant
 tau_syn_ex ms      Time constant of postsynaptic excitatory currents
 tau_syn_in ms      Time constant of postsynaptic inhibitory currents
 t_ref      ms      Duration of absolute refractory period (no spiking)
 V_m        mV      Membrane potential
 I_e        pA      Constant input current
 t_spike    ms      Point in time of last spike
 tau_1      ms      Short time constant of adaptive threshold [3, eqs 2-3]
 tau_2      ms      Long time constant of adaptive threshold [3, eqs 2-3]
 alpha_1    mV      Amplitude of short time threshold adaption [3, eqs 2-3]
 alpha_2    mV      Amplitude of long time threshold adaption [3, eqs 2-3]
 tau_v      ms      Time constant of kernel for voltage-dependent threshold
                    component [3, eqs 16-17]
 beta       1/ms    Scaling coefficient for voltage-dependent threshold
                    component [3, eqs 16-17]
 omega      mV      Resting spike threshold (absolute value, not
                    relative to E_L as in :footcite:p:`Kobayashi2009`)
=========== ======= ===========================================================
 
.. note::
 
   - The time constants in the model must fulfill the following conditions:
     - :math:`\tau_m != {\tau_{syn_{ex}}, \tau_{syn_{in}}}`
     - :math:`\tau_v != {\tau_{syn_{ex}}, \tau_{syn_{in}}}`
     - :math:`\tau_m != \tau_v`
     This is required to avoid singularities in the numerics. This is a
     problem of implementation only, not a principal problem of the model.
 
   - Expect unstable numerics if time constants that are required to be
     different are very close.
 
   - :math:`\tau_m != \tau_{syn_{ex,in}}` is required by the current
     implementation to avoid a degenerate case of the ODE describing the
     model :footcite:p:`Rotter1999`.  For very similar values, numerics will be unstable.
 
   - Some parameter values given in Table 1 of :footcite:p:`Yamauchi2011` are incorrect. For
     correct values, see Table 4 of :footcite:p:`Heiberg2018`.
 
References
++++++++++
 
.. footbibliography::
 
Sends
+++++
 
SpikeEvent
 
Receives
++++++++
 
SpikeEvent, CurrentEvent, DataLoggingRequest
 
Examples using this model
+++++++++++++++++++++++++
 
.. listexamples:: amat2_psc_exp
 
EndUserDocs */
 
void register_amat2_psc_exp( const std::string& name );
 
class amat2_psc_exp : public ArchivingNode
{
 
public:
  amat2_psc_exp();
  amat2_psc_exp( const amat2_psc_exp& );
 
  using Node::handle;
  using Node::handles_test_event;
 
  size_t send_test_event( Node&, size_t, 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;
 
  // The next two classes need to be friends to access private members
  friend class RecordablesMap< amat2_psc_exp >;
  friend class UniversalDataLogger< amat2_psc_exp >;
 
  // ----------------------------------------------------------------
 
  struct Parameters_
  {
    double Tau_;
 
    double C_;
 
    double tau_ref_;
 
    double E_L_;
 
    double I_e_;
 
    double tau_ex_;
 
    double tau_in_;
 
    double tau_1_;
    double tau_2_;
 
    double alpha_1_;
    double alpha_2_;
 
    double beta_;
 
    double tau_v_;
 
    double omega_;
 
    Parameters_();  
 
    void get( Dictionary& ) const;  
 
    double set( const Dictionary&, Node* node );
  };
 
  // ----------------------------------------------------------------
 
  struct State_
  {
    // state variables
    double i_0_;       
    double I_syn_ex_;  
    double I_syn_in_;  
    double V_m_;       
    double V_th_1_;    
    double V_th_2_;    
    double V_th_dv_;   
    double V_th_v_;    
 
    int r_;  
 
    State_();  
 
    void get( Dictionary&, const Parameters_& ) const;
 
    void set( const Dictionary&, const Parameters_&, double, Node* );
  };
 
  // ----------------------------------------------------------------
 
  struct Buffers_
  {
    Buffers_( amat2_psc_exp& );                   
    Buffers_( const Buffers_&, amat2_psc_exp& );  
 
    RingBuffer spikes_ex_;
    RingBuffer spikes_in_;
    RingBuffer currents_;
 
    UniversalDataLogger< amat2_psc_exp > logger_;
  };
 
  // ----------------------------------------------------------------
 
  struct Variables_
  {
 
    //    double PSCInitialValue_;
 
    double P00_;  // constant currents
    double P11_;
    double P22_;
    double P30_;
    double P31_;
    double P32_;
    double P33_;
    double P44_;
    double P55_;
    double P60_;
    double P61_;
    double P62_;
    double P63_;
    double P66_;
    double P70_;
    double P71_;
    double P72_;
    double P73_;
    double P76_;
    double P77_;
 
    int RefractoryCountsTot_;
  };
  // ----------------------------------------------------------------
 
  inline double
  get_V_m_() const
  {
    return S_.V_m_ + P_.E_L_;
  }
 
  inline double
  get_V_th_() const
  {
    return P_.E_L_ + P_.omega_ + S_.V_th_1_ + S_.V_th_2_ + S_.V_th_v_;
  }
 
  inline double
  get_V_th_v_() const
  {
    return S_.V_th_v_;
  }
 
  inline double
  get_I_syn_ex_() const
  {
    return S_.I_syn_ex_;
  }
 
  inline double
  get_I_syn_in_() const
  {
    return S_.I_syn_in_;
  }
 
  // ----------------------------------------------------------------
 
  Parameters_ P_;
  State_ S_;
  Variables_ V_;
  Buffers_ B_;
  static RecordablesMap< amat2_psc_exp > recordablesMap_;
};
 
 
inline size_t
amat2_psc_exp::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
amat2_psc_exp::handles_test_event( SpikeEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
amat2_psc_exp::handles_test_event( CurrentEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
amat2_psc_exp::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
amat2_psc_exp::get_status( Dictionary& d ) const
{
  P_.get( d );
  S_.get( d, P_ );
  ArchivingNode::get_status( d );
 
  d[ names::recordables ] = recordablesMap_.get_list();
}
 
inline void
amat2_psc_exp::set_status( const Dictionary& d )
{
  Parameters_ ptmp = P_;                        // temporary copy in case of errors
  const double delta_EL = ptmp.set( d, this );  // throws if BadProperty
  State_ stmp = S_;                             // temporary copy in case of errors
  stmp.set( d, ptmp, delta_EL, 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  // AMAT2_PSC_EXP_H