/*
* iaf_tum_2000.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/>.
*
*/
#include "exceptions.h"
#include "iaf_tum_2000.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>
/* ----------------------------------------------------------------
* Recordables map
* ---------------------------------------------------------------- */
nest::RecordablesMap<nest::iaf_tum_2000> nest::iaf_tum_2000::recordablesMap_;
namespace nest
{
// Override the create() method with one call to RecordablesMap::insert_()
// for each quantity to be recorded.
template <>
void RecordablesMap<iaf_tum_2000>::create()
{
// use standard names whereever you can for consistency!
insert_(names::V_m, &iaf_tum_2000::get_V_m_);
insert_(names::I_syn_ex, &iaf_tum_2000::get_I_syn_ex_);
insert_(names::I_syn_in, &iaf_tum_2000::get_I_syn_in_);
}
}
/* ----------------------------------------------------------------
* Default constructors defining default parameters and state
* ---------------------------------------------------------------- */
nest::iaf_tum_2000::Parameters_::Parameters_()
: Tau_ ( 10.0 ), // in ms
C_ (250.0 ), // in pF
tau_ref_tot_ ( 2.0 ), // in ms
tau_ref_abs_ ( 2.0 ), // in ms
U0_ (-70.0 ), // in mV
I_e_ ( 0.0 ), // in pA
Theta_ (-55.0 - U0_), // relative U0_
V_reset_ (-70.0 - U0_), // in mV
tau_ex_ ( 2.0 ), // in ms
tau_in_ ( 2.0 ) // in ms
{}
nest::iaf_tum_2000::State_::State_()
: i_0_ (0.0),
i_syn_ex_ (0.0),
i_syn_in_ (0.0),
V_m_ (0.0),
r_abs_ (0),
r_tot_ (0)
{}
/* ----------------------------------------------------------------
* Parameter and state extractions and manipulation functions
* ---------------------------------------------------------------- */
void nest::iaf_tum_2000::Parameters_::get(DictionaryDatum &d) const
{
def<double>(d, names::E_L, U0_); // Resting potential
def<double>(d, names::I_e, I_e_);
def<double>(d, names::V_th, Theta_+U0_); // threshold value
def<double>(d, names::V_reset, V_reset_+U0_);
def<double>(d, names::C_m, C_);
def<double>(d, names::tau_m, Tau_);
def<double>(d, names::tau_syn_ex, tau_ex_);
def<double>(d, names::tau_syn_in, tau_in_);
def<double>(d, names::t_ref_abs, tau_ref_abs_);
def<double>(d, names::t_ref_tot, tau_ref_tot_);
}
double nest::iaf_tum_2000::Parameters_::set(const DictionaryDatum& d)
{
// if U0_ is changed, we need to adjust all variables defined relative to U0_
const double ELold = U0_;
updateValue<double>(d, names::E_L, U0_);
const double delta_EL = U0_ - ELold;
if(updateValue<double>(d, names::V_reset, V_reset_))
V_reset_ -= U0_;
else
V_reset_ -= delta_EL;
if (updateValue<double>(d, names::V_th, Theta_))
Theta_ -= U0_;
else
Theta_ -= delta_EL;
updateValue<double>(d, names::I_e, I_e_);
updateValue<double>(d, names::C_m, C_);
updateValue<double>(d, names::tau_m, Tau_);
updateValue<double>(d, names::tau_syn_ex, tau_ex_);
updateValue<double>(d, names::tau_syn_in, tau_in_);
updateValue<double>(d, names::t_ref_abs, tau_ref_abs_);
updateValue<double>(d, names::t_ref_tot, tau_ref_tot_);
if ( V_reset_ >= Theta_ )
throw BadProperty("Reset potential must be smaller than threshold.");
if ( tau_ref_abs_ > tau_ref_tot_ )
throw BadProperty("Total refractory period must be larger or equal than absolute refractory time.");
if ( C_ <= 0 )
throw BadProperty("Capacitance must be strictly positive.");
if ( Tau_ <= 0 || tau_ex_ <= 0 || tau_in_ <= 0 ||
tau_ref_tot_ <= 0 || tau_ref_abs_ <=0)
throw BadProperty("All time constants must be strictly positive.");
if ( Tau_ == tau_ex_ || Tau_ == tau_in_ )
throw BadProperty("Membrane and synapse time constant(s) must differ."
"See note in documentation.");
return delta_EL;
}
void nest::iaf_tum_2000::State_::get(DictionaryDatum &d, const Parameters_& p) const
{
def<double>(d, names::V_m, V_m_ + p.U0_); // Membrane potential
}
void nest::iaf_tum_2000::State_::set(const DictionaryDatum& d, const Parameters_& p, double delta_EL)
{
if ( updateValue<double>(d, names::V_m, V_m_) )
V_m_ -= p.U0_;
else
V_m_ -= delta_EL;
}
nest::iaf_tum_2000::Buffers_::Buffers_(iaf_tum_2000 &n)
: logger_(n)
{}
nest::iaf_tum_2000::Buffers_::Buffers_(const Buffers_ &, iaf_tum_2000 &n)
: logger_(n)
{}
/* ----------------------------------------------------------------
* Default and copy constructor for node
* ---------------------------------------------------------------- */
nest::iaf_tum_2000::iaf_tum_2000()
: Archiving_Node(),
P_(),
S_(),
B_(*this)
{
recordablesMap_.create();
}
nest::iaf_tum_2000::iaf_tum_2000(const iaf_tum_2000& n)
: Archiving_Node(n),
P_(n.P_),
S_(n.S_),
B_(n.B_, *this)
{}
/* ----------------------------------------------------------------
* Node initialization functions
* ---------------------------------------------------------------- */
void nest::iaf_tum_2000::init_state_(const Node& proto)
{
const iaf_tum_2000& pr = downcast<iaf_tum_2000>(proto);
S_ = pr.S_;
}
void nest::iaf_tum_2000::init_buffers_()
{
B_.spikes_ex_.clear(); // includes resize
B_.spikes_in_.clear(); // includes resize
B_.currents_.clear(); // includes resize
B_.logger_.reset(); // includes resize
Archiving_Node::clear_history();
}
void nest::iaf_tum_2000::calibrate()
{
B_.logger_.init();
const double h = Time::get_resolution().get_ms();
// numbering of state vaiables: i_0 = 0, i_syn_ = 1, V_m_ = 2
// commented out propagators: forward Euler
// needed to exactly reproduce Tsodyks network
// these P are independent
V_.P11ex_ = std::exp(-h/P_.tau_ex_);
//P11ex_ = 1.0-h/tau_ex_;
V_.P11in_ = std::exp(-h/P_.tau_in_);
//P11in_ = 1.0-h/tau_in_;
V_.P22_ = std::exp(-h/P_.Tau_);
//P22_ = 1.0-h/Tau_;
// these depend on the above. Please do not change the order.
// TODO: use expm1 here to improve accuracy for small timesteps
V_.P21ex_ = P_.Tau_/(P_.C_*(1.0-P_.Tau_/P_.tau_ex_)) * V_.P11ex_
* (1.0 - std::exp(h*(1.0/P_.tau_ex_-1.0/P_.Tau_)));
//P21ex_ = h/C_;
V_.P21in_ = P_.Tau_/(P_.C_*(1.0-P_.Tau_/P_.tau_in_)) * V_.P11in_
* (1.0 - std::exp(h*(1.0/P_.tau_in_-1.0/P_.Tau_)));
//P21in_ = h/C_;
V_.P20_ = P_.Tau_/P_.C_*(1.0 - V_.P22_);
//P20_ = h/C_;
// TauR specifies the length of the absolute refractory period as
// a double_t in ms. The grid based iaf_tum_2000 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.
//
// 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_.RefractoryCountsAbs_ = Time(Time::ms(P_.tau_ref_abs_)).get_steps();
V_.RefractoryCountsTot_ = Time(Time::ms(P_.tau_ref_tot_)).get_steps();
if ( V_.RefractoryCountsAbs_ < 1 )
throw BadProperty("Absolute refractory time must be at least one time step.");
if ( V_.RefractoryCountsTot_ < 1 )
throw BadProperty("Total refractory time must be at least one time step.");
}
void nest::iaf_tum_2000::update(Time const & origin, const long_t from, const long_t to)
{
assert(to >= 0 && (delay) from < Scheduler::get_min_delay());
assert(from < to);
// evolve from timestep 'from' to timestep 'to' with steps of h each
for ( long_t lag = from ; lag < to ; ++lag )
{
if ( S_.r_abs_ == 0 ) // neuron not refractory, so evolve V
S_.V_m_ = S_.V_m_*V_.P22_ + S_.i_syn_ex_*V_.P21ex_ + S_.i_syn_in_*V_.P21in_ + (P_.I_e_+S_.i_0_)*V_.P20_;
else
--S_.r_abs_; // neuron is absolute refractory
// exponential decaying PSCs
S_.i_syn_ex_ *= V_.P11ex_;
S_.i_syn_in_ *= V_.P11in_;
S_.i_syn_ex_ += B_.spikes_ex_.get_value(lag); // the spikes arriving at T+1 have an
S_.i_syn_in_ += B_.spikes_in_.get_value(lag); // the spikes arriving at T+1 have an
// immediate effect on the state of the neuron
if (S_.r_tot_ == 0)
{
if (S_.V_m_ >= P_.Theta_) // threshold crossing
{
S_.r_abs_ = V_.RefractoryCountsAbs_;
S_.r_tot_ = V_.RefractoryCountsTot_;
S_.V_m_ = P_.V_reset_;
set_spiketime(Time::step(origin.get_steps()+lag+1));
SpikeEvent se;
network()->send(*this, se, lag);
}
}
else
--S_.r_tot_; // neuron is totally refractory (cannot generate spikes)
// set new input current
S_.i_0_ = B_.currents_.get_value(lag);
// logging
B_.logger_.record_data(origin.get_steps()+lag);
}
}
void nest::iaf_tum_2000::handle(SpikeEvent & e)
{
assert(e.get_delay() > 0);
if (e.get_weight() >= 0.0)
B_.spikes_ex_.add_value(e.get_rel_delivery_steps(network()->get_slice_origin()),
e.get_weight() * e.get_multiplicity() );
else
B_.spikes_in_.add_value(e.get_rel_delivery_steps(network()->get_slice_origin()),
e.get_weight() * e.get_multiplicity() );
}
void nest::iaf_tum_2000::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_tum_2000::handle(DataLoggingRequest& e)
{
B_.logger_.handle(e);
}