/*
* iaf_psc_delta.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_PSC_DELTA_H
#define IAF_PSC_DELTA_H
// Includes from nestkernel:
#include "archiving_node.h"
#include "connection.h"
#include "event.h"
#include "nest_types.h"
#include "ring_buffer.h"
#include "universal_data_logger.h"
namespace nest
{
/* BeginDocumentation
Name: iaf_psc_delta - Leaky integrate-and-fire neuron model.
Description:
iaf_psc_delta is an implementation of a leaky integrate-and-fire model
where the potential jumps on each spike arrival.
The threshold crossing is followed by an absolute refractory period
during which the membrane potential is clamped to the resting potential.
Spikes arriving while the neuron is refractory, are discarded by
default. If the property "refractory_input" is set to true, such
spikes are added to the membrane potential at the end of the
refractory period, dampened according to the interval between
arrival and end of refractoriness.
The linear subthresold dynamics is integrated by the Exact
Integration scheme [1]. 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
[1]. A flow chart can be found in [2].
Critical tests for the formulation of the neuron model are the
comparisons of simulation results for different computation step
sizes. sli/testsuite/nest contains a number of such tests.
The iaf_psc_delta is the standard model used to check the consistency
of the nest simulation kernel because it is at the same time complex
enough to exhibit non-trivial dynamics and simple enough compute
relevant measures analytically.
Remarks:
The present implementation uses individual variables for the
components of the state vector and the non-zero matrix elements of
the propagator. Because the propagator is a lower triangular matrix
no full matrix multiplication needs to be carried out and the
computation can be done "in place" i.e. no temporary state vector
object is required.
The template support of recent C++ compilers enables a more succinct
formulation without loss of runtime performance already at minimal
optimization levels. A future version of iaf_psc_delta will probably
address the problem of efficient usage of appropriate vector and
matrix objects.
Parameters:
The following parameters can be set in the status dictionary.
V_m double - Membrane potential in mV
E_L double - Resting membrane potential in mV.
C_m double - Capacitance of the membrane in pF
tau_m double - Membrane time constant in ms.
t_ref double - Duration of refractory period in ms.
V_th double - Spike threshold in mV.
V_reset double - Reset potential of the membrane in mV.
I_e double - Constant input current in pA.
V_min double - Absolute lower value for the membrane potential in mV
refractory_input bool - If true, do not discard input during
refractory period. Default: false.
References:
[1] Rotter S & Diesmann M (1999) Exact digital simulation of time-invariant
linear systems with applications to neuronal modeling. Biologial Cybernetics
81:381-402.
[2] Diesmann M, Gewaltig M-O, Rotter S, & Aertsen A (2001) State space
analysis of synchronous spiking in cortical neural networks.
Neurocomputing 38-40:565-571.
Sends: SpikeEvent
Receives: SpikeEvent, CurrentEvent, DataLoggingRequest
Author: September 1999, Diesmann, Gewaltig
SeeAlso: iaf_psc_alpha, iaf_psc_exp, iaf_neuron, iaf_psc_delta_canon
*/
/**
* Leaky integrate-and-fire neuron with delta-shaped PSCs.
*/
class iaf_psc_delta : public Archiving_Node
{
public:
iaf_psc_delta();
iaf_psc_delta( const iaf_psc_delta& );
/**
* Import sets of overloaded virtual functions.
* @see Technical Issues / Virtual Functions: Overriding, Overloading, and
* Hiding
*/
using Node::handle;
using Node::handles_test_event;
port send_test_event( Node&, rport, synindex, bool );
void handle( SpikeEvent& );
void handle( CurrentEvent& );
void handle( DataLoggingRequest& );
port handles_test_event( SpikeEvent&, rport );
port handles_test_event( CurrentEvent&, rport );
port handles_test_event( DataLoggingRequest&, rport );
void get_status( DictionaryDatum& ) const;
void set_status( const DictionaryDatum& );
private:
void init_state_( const Node& proto );
void init_buffers_();
void calibrate();
void update( Time const&, const long_t, const long_t );
// The next two classes need to be friends to access the State_ class/member
friend class RecordablesMap< iaf_psc_delta >;
friend class UniversalDataLogger< iaf_psc_delta >;
// ----------------------------------------------------------------
/**
* Independent parameters of the model.
*/
struct Parameters_
{
/** Membrane time constant in ms. */
double_t tau_m_;
/** Membrane capacitance in pF. */
double_t c_m_;
/** Refractory period in ms. */
double_t t_ref_;
/** Resting potential in mV. */
double_t E_L_;
/** External DC current */
double_t I_e_;
/** Threshold, RELATIVE TO RESTING POTENTAIL(!).
I.e. the real threshold is (E_L_+V_th_). */
double_t V_th_;
/** Lower bound, RELATIVE TO RESTING POTENTAIL(!).
I.e. the real lower bound is (V_min_+V_th_). */
double_t V_min_;
/** reset value of the membrane potential */
double_t V_reset_;
bool with_refr_input_; //!< spikes arriving during refractory period are
//!< counted
Parameters_(); //!< Sets default parameter values
void get( DictionaryDatum& ) const; //!< Store current values in dictionary
/** Set values from dictionary.
* @returns Change in reversal potential E_L, to be passed to State_::set()
*/
double set( const DictionaryDatum& );
};
// ----------------------------------------------------------------
/**
* State variables of the model.
*/
struct State_
{
double_t y0_;
//! This is the membrane potential RELATIVE TO RESTING POTENTIAL.
double_t y3_;
int_t r_; //!< Number of refractory steps remaining
/** Accumulate spikes arriving during refractory period, discounted for
decay until end of refractory period.
*/
double_t refr_spikes_buffer_;
State_(); //!< Default initialization
void get( DictionaryDatum&, const Parameters_& ) const;
/** Set values from dictionary.
* @param dictionary to take data from
* @param current parameters
* @param Change in reversal potential E_L specified by this dict
*/
void set( const DictionaryDatum&, const Parameters_&, double );
};
// ----------------------------------------------------------------
/**
* Buffers of the model.
*/
struct Buffers_
{
Buffers_( iaf_psc_delta& );
Buffers_( const Buffers_&, iaf_psc_delta& );
/** buffers and summs up incoming spikes/currents */
RingBuffer spikes_;
RingBuffer currents_;
//! Logger for all analog data
UniversalDataLogger< iaf_psc_delta > logger_;
};
// ----------------------------------------------------------------
/**
* Internal variables of the model.
*/
struct Variables_
{
double_t P30_;
double_t P33_;
int_t RefractoryCounts_;
};
// Access functions for UniversalDataLogger -------------------------------
//! Read out the real membrane potential
double_t
get_V_m_() const
{
return S_.y3_ + P_.E_L_;
}
// ----------------------------------------------------------------
/**
* @defgroup iaf_psc_alpha_data
* Instances of private data structures for the different types
* of data pertaining to the model.
* @note The order of definitions is important for speed.
* @{
*/
Parameters_ P_;
State_ S_;
Variables_ V_;
Buffers_ B_;
/** @} */
//! Mapping of recordables names to access functions
static RecordablesMap< iaf_psc_delta > recordablesMap_;
};
inline port
nest::iaf_psc_delta::send_test_event( Node& target,
rport receptor_type,
synindex,
bool )
{
SpikeEvent e;
e.set_sender( *this );
return target.handles_test_event( e, receptor_type );
}
inline port
iaf_psc_delta::handles_test_event( SpikeEvent&, rport receptor_type )
{
if ( receptor_type != 0 )
throw UnknownReceptorType( receptor_type, get_name() );
return 0;
}
inline port
iaf_psc_delta::handles_test_event( CurrentEvent&, rport receptor_type )
{
if ( receptor_type != 0 )
throw UnknownReceptorType( receptor_type, get_name() );
return 0;
}
inline port
iaf_psc_delta::handles_test_event( DataLoggingRequest& dlr,
rport receptor_type )
{
if ( receptor_type != 0 )
throw UnknownReceptorType( receptor_type, get_name() );
return B_.logger_.connect_logging_device( dlr, recordablesMap_ );
}
inline void
iaf_psc_delta::get_status( DictionaryDatum& d ) const
{
P_.get( d );
S_.get( d, P_ );
Archiving_Node::get_status( d );
( *d )[ names::recordables ] = recordablesMap_.get_list();
}
inline void
iaf_psc_delta::set_status( const DictionaryDatum& d )
{
Parameters_ ptmp = P_; // temporary copy in case of errors
const double delta_EL = ptmp.set( d ); // throws if BadProperty
State_ stmp = S_; // temporary copy in case of errors
stmp.set( d, ptmp, delta_EL ); // 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.
Archiving_Node::set_status( d );
// if we get here, temporaries contain consistent set of properties
P_ = ptmp;
S_ = stmp;
}
} // namespace
#endif /* #ifndef IAF_PSC_DELTA_H */