/*
* iaf_psc_delta.cpp
*
* 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/>.
*
*/
/* iaf_psc_delta is a neuron where the potential jumps on each spike arrival. */
#include "exceptions.h"
#include "iaf_psc_delta.h"
#include "network.h"
#include "dict.h"
#include "integerdatum.h"
#include "doubledatum.h"
#include "dictutils.h"
#include "numerics.h"
#include "universal_data_logger_impl.h"
#include <limits>
namespace nest
{
/* ----------------------------------------------------------------
* Recordables map
* ---------------------------------------------------------------- */
RecordablesMap<iaf_psc_delta> iaf_psc_delta::recordablesMap_;
// Override the create() method with one call to RecordablesMap::insert_()
// for each quantity to be recorded.
template <>
void RecordablesMap<iaf_psc_delta>::create()
{
// use standard names whereever you can for consistency!
insert_(names::V_m, &iaf_psc_delta::get_V_m_);
}
/* ----------------------------------------------------------------
* Default constructors defining default parameters and state
* ---------------------------------------------------------------- */
nest::iaf_psc_delta::Parameters_::Parameters_()
: tau_m_ ( 10.0 ), // ms
c_m_ (250.0 ), // pF
t_ref_ ( 2.0 ), // ms
E_L_ (-70.0 ), // mV
I_e_ ( 0.0 ), // pA
V_th_ (-55.0-E_L_), // mV, rel to U0_
V_min_ (-std::numeric_limits<double_t>::max()),
// relative U0_-55.0-U0_), // mV, rel to U0_
V_reset_ (-70.0-E_L_),
with_refr_input_(false)
{}
nest::iaf_psc_delta::State_::State_()
: y0_ (0.0),
y3_ (0.0),
r_ (0),
refr_spikes_buffer_(0.0)
{}
/* ----------------------------------------------------------------
* Parameter and state extractions and manipulation functions
* ---------------------------------------------------------------- */
void nest::iaf_psc_delta::Parameters_::get(DictionaryDatum &d) const
{
def<double>(d, names::E_L, E_L_); // Resting potential
def<double>(d, names::I_e, I_e_);
def<double>(d, names::V_th, V_th_+E_L_); // threshold value
def<double>(d, names::V_reset, V_reset_+E_L_);
def<double>(d, names::V_min, V_min_+E_L_);
def<double>(d, names::C_m, c_m_);
def<double>(d, names::tau_m, tau_m_);
def<double>(d, names::t_ref, t_ref_);
def<bool>(d, "refractory_input", with_refr_input_);
}
double nest::iaf_psc_delta::Parameters_::set(const DictionaryDatum& d)
{
// if U0_ is changed, we need to adjust all variables defined relative to U0_
const double ELold = E_L_;
updateValue<double>(d, names::E_L, E_L_);
const double delta_EL = E_L_ - ELold;
if(updateValue<double>(d, names::V_reset, V_reset_))
V_reset_ -= E_L_;
else
V_reset_ -= delta_EL;
if (updateValue<double>(d, names::V_th, V_th_))
V_th_ -= E_L_;
else
V_th_ -= delta_EL;
if (updateValue<double>(d, names::V_min, V_min_))
V_min_ -= E_L_;
else
V_min_ -= delta_EL;
updateValue<double>(d, names::I_e, I_e_);
updateValue<double>(d, names::C_m, c_m_);
updateValue<double>(d, names::tau_m, tau_m_);
updateValue<double>(d, names::t_ref, t_ref_);
if ( V_reset_ >= V_th_ )
throw BadProperty("Reset potential must be smaller than threshold.");
if ( c_m_ <= 0 )
throw BadProperty("Capacitance must be >0.");
if ( t_ref_ < 0 )
throw BadProperty("Refractory time must not be negative.");
if ( tau_m_ <= 0 )
throw BadProperty("Membrane time constant must be > 0.");
updateValue<bool>(d, "refractory_input", with_refr_input_);
return delta_EL;
}
void nest::iaf_psc_delta::State_::get(DictionaryDatum &d, const Parameters_& p) const
{
def<double>(d, names::V_m, y3_ + p.E_L_); // Membrane potential
}
void nest::iaf_psc_delta::State_::set(const DictionaryDatum& d, const Parameters_& p, double delta_EL)
{
if ( updateValue<double>(d, names::V_m, y3_) )
y3_ -= p.E_L_;
else
y3_ -= delta_EL;
}
nest::iaf_psc_delta::Buffers_::Buffers_(iaf_psc_delta &n)
: logger_(n)
{}
nest::iaf_psc_delta::Buffers_::Buffers_(const Buffers_ &, iaf_psc_delta &n)
: logger_(n)
{}
/* ----------------------------------------------------------------
* Default and copy constructor for node
* ---------------------------------------------------------------- */
nest::iaf_psc_delta::iaf_psc_delta()
: Archiving_Node(),
P_(),
S_(),
B_(*this)
{
recordablesMap_.create();
}
nest::iaf_psc_delta::iaf_psc_delta(const iaf_psc_delta& n)
: Archiving_Node(n),
P_(n.P_),
S_(n.S_),
B_(n.B_, *this)
{}
/* ----------------------------------------------------------------
* Node initialization functions
* ---------------------------------------------------------------- */
void nest::iaf_psc_delta::init_state_(const Node& proto)
{
const iaf_psc_delta& pr = downcast<iaf_psc_delta>(proto);
S_ = pr.S_;
}
void nest::iaf_psc_delta::init_buffers_()
{
B_.spikes_.clear(); // includes resize
B_.currents_.clear(); // includes resize
B_.logger_.reset(); // includes resize
Archiving_Node::clear_history();
}
void nest::iaf_psc_delta::calibrate()
{
B_.logger_.init();
const double h = Time::get_resolution().get_ms();
V_.P33_ = std::exp(-h/P_.tau_m_);
V_.P30_ = 1/P_.c_m_*(1-V_.P33_)*P_.tau_m_;
// TauR specifies the length of the absolute refractory period as
// a double_t in ms. The grid based iaf_psp_delta can only handle refractory
// periods that are integer multiples of the computation step size (h).
// To ensure consistency with the overall simulation scheme such conversion
// should be carried out via objects of class nest::Time. The conversion
// requires 2 steps:
// 1. A time object r is constructed defining representation of
// TauR in tics. This representation is then converted to computation time
// steps again by a strategy defined by class nest::Time.
// 2. The refractory time in units of steps is read out get_steps(), a member
// function of class nest::Time.
//
// The definition of the refractory period of the iaf_psc_delta is consistent
// the one of iaf_neuron_ps.
//
// Choosing a TauR that is not an integer multiple of the computation time
// step h will leed to accurate (up to the resolution h) and self-consistent
// results. However, a neuron model capable of operating with real valued spike
// time may exhibit a different effective refractory time.
//
V_.RefractoryCounts_ = Time(Time::ms(P_.t_ref_)).get_steps();
assert(V_.RefractoryCounts_ >= 0); // since t_ref_ >= 0, this can only fail in error
}
/* ----------------------------------------------------------------
* Update and spike handling functions
*/
void nest::iaf_psc_delta::update(Time const & origin,
const long_t from, const long_t to)
{
assert(to >= 0 && (delay) from < Scheduler::get_min_delay());
assert(from < to);
for ( long_t lag = from ; lag < to ; ++lag )
{
if ( S_.r_ == 0 )
{
// neuron not refractory
S_.y3_ = V_.P30_*(S_.y0_ + P_.I_e_) + V_.P33_*S_.y3_ + B_.spikes_.get_value(lag);
// if we have accumulated spikes from refractory period,
// add and reset accumulator
if ( P_.with_refr_input_ && S_.refr_spikes_buffer_ != 0.0 )
{
S_.y3_ += S_.refr_spikes_buffer_;
S_.refr_spikes_buffer_ = 0.0;
}
// lower bound of membrane potential
S_.y3_ = ( S_.y3_<P_.V_min_ ? P_.V_min_ : S_.y3_);
}
else // neuron is absolute refractory
{
// read spikes from buffer and accumulate them, discounting
// for decay until end of refractory period
if ( P_.with_refr_input_ )
S_.refr_spikes_buffer_ += B_.spikes_.get_value(lag)
* std::exp(-S_.r_ * Time::get_resolution().get_ms() / P_.tau_m_);
else
B_.spikes_.get_value(lag); // clear buffer entry, ignore spike
--S_.r_;
}
// threshold crossing
if (S_.y3_ >= P_.V_th_)
{
S_.r_ = V_.RefractoryCounts_;
S_.y3_ = P_.V_reset_;
// EX: must compute spike time
set_spiketime(Time::step(origin.get_steps()+lag+1));
SpikeEvent se;
network()->send(*this, se, lag);
}
// set new input current
S_.y0_ = B_.currents_.get_value(lag);
// voltage logging
B_.logger_.record_data(origin.get_steps()+lag);
}
}
void nest::iaf_psc_delta::handle(SpikeEvent & e)
{
assert(e.get_delay() > 0);
// EX: We must compute the arrival time of the incoming spike
// explicity, since it depends on delay and offset within
// the update cycle. The way it is done here works, but
// is clumsy and should be improved.
B_.spikes_.add_value(e.get_rel_delivery_steps(network()->get_slice_origin()),
e.get_weight() * e.get_multiplicity() );
}
void nest::iaf_psc_delta::handle(CurrentEvent& e)
{
assert(e.get_delay() > 0);
const double_t c=e.get_current();
const double_t w=e.get_weight();
// add weighted current; HEP 2002-10-04
B_.currents_.add_value(e.get_rel_delivery_steps(network()->get_slice_origin()),
w *c);
}
void nest::iaf_psc_delta::handle(DataLoggingRequest &e)
{
B_.logger_.handle(e);
}
} // namespace