/*
* hh_psc_alpha.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 "hh_psc_alpha.h"
#ifdef HAVE_GSL
#include "exceptions.h"
#include "network.h"
#include "dict.h"
#include "integerdatum.h"
#include "doubledatum.h"
#include "dictutils.h"
#include "numerics.h"
#include <limits>
#include "universal_data_logger_impl.h"
#include <iomanip>
#include <iostream>
#include <cstdio>
nest::RecordablesMap<nest::hh_psc_alpha> nest::hh_psc_alpha::recordablesMap_;
namespace nest
{
// Override the create() method with one call to RecordablesMap::insert_()
// for each quantity to be recorded.
template <>
void RecordablesMap<hh_psc_alpha>::create()
{
// use standard names whereever you can for consistency!
insert_(names::V_m,
&hh_psc_alpha::get_y_elem_<hh_psc_alpha::State_::V_M>);
insert_(names::I_ex,
&hh_psc_alpha::get_y_elem_<hh_psc_alpha::State_::I_EXC>);
insert_(names::I_in,
&hh_psc_alpha::get_y_elem_<hh_psc_alpha::State_::I_INH>);
insert_(names::Act_m,
&hh_psc_alpha::get_y_elem_<hh_psc_alpha::State_::HH_M>);
insert_(names::Act_h,
&hh_psc_alpha::get_y_elem_<hh_psc_alpha::State_::HH_H>);
insert_(names::Inact_n,
&hh_psc_alpha::get_y_elem_<hh_psc_alpha::State_::HH_N>);
}
extern "C"
int hh_psc_alpha_dynamics (double, const double y[], double f[], void* pnode)
{
// a shorthand
typedef nest::hh_psc_alpha::State_ S;
// get access to node so we can almost work as in a member function
assert(pnode);
const nest::hh_psc_alpha& node = *(reinterpret_cast<nest::hh_psc_alpha*>(pnode));
// y[] here is---and must be---the state vector supplied by the integrator,
// not the state vector in the node, node.S_.y[].
// The following code is verbose for the sake of clarity. We assume that a
// good compiler will optimize the verbosity away ...
// shorthand for state variables
const double_t& V = y[S::V_M ];
const double_t& m = y[S::HH_M ];
const double_t& h = y[S::HH_H ];
const double_t& n = y[S::HH_N ];
const double_t& dI_ex = y[S::DI_EXC];
const double_t& I_ex = y[S::I_EXC ];
const double_t& dI_in = y[S::DI_INH];
const double_t& I_in = y[S::I_INH ];
const double_t alpha_n = (0.01 * (V+55.)) / (1. -std::exp( -(V+55.)/10.));
const double_t beta_n = 0.125 * std::exp( -(V+65.)/80.);
const double_t alpha_m = (0.1 * (V+40.)) / (1. - std::exp( -(V+40.)/10.) );
const double_t beta_m = 4. * std::exp( -(V+65.)/18.);
const double_t alpha_h = 0.07 * std::exp( -(V+65.) / 20.);
const double_t beta_h = 1. / (1. + std::exp(-(V+35.) / 10. ));
const double_t I_Na = node.P_.g_Na * m * m * m * h * (V - node.P_.E_Na);
const double_t I_K = node.P_.g_K * n * n * n * n * (V - node.P_.E_K );
const double_t I_L = node.P_.g_L * (V - node.P_.E_L );
// V dot -- synaptic input are currents, inhib current is negative
f[S::V_M] = ( -(I_Na + I_K + I_L) + node.B_.I_stim_ + node.P_.I_e + I_ex + I_in) / node.P_.C_m;
//channel dynamics
f[S::HH_M] = alpha_m * (1-y[S::HH_M]) - beta_m * y[S::HH_M]; // m-variable
f[S::HH_H] = alpha_h * (1-y[S::HH_H]) - beta_h * y[S::HH_H]; // h-variable
f[S::HH_N] = alpha_n * (1-y[S::HH_N]) - beta_n * y[S::HH_N]; // n-variable
// synapses: alpha functions
f[S::DI_EXC] = -dI_ex / node.P_.tau_synE;
f[S::I_EXC ] = dI_ex - (I_ex / node.P_.tau_synE);
f[S::DI_INH] = -dI_in / node.P_.tau_synI;
f[S::I_INH ] = dI_in - (I_in / node.P_.tau_synI);
return GSL_SUCCESS;
}
}
/* ----------------------------------------------------------------
* Default constructors defining default parameters and state
* ---------------------------------------------------------------- */
nest::hh_psc_alpha::Parameters_::Parameters_()
: t_ref_ ( 2.0 ), // ms
g_Na (12000.0 ), // nS
g_K ( 3600.0 ), // nS
g_L ( 30.0 ), // nS
C_m ( 100.0 ), // pF
E_Na ( 50.0 ), // mV
E_K ( -77.0 ), // mV
E_L ( -54.402), // mV
tau_synE( 0.2 ), // ms
tau_synI( 2.0 ), // ms
I_e ( 0.0 ) // pA
{
}
nest::hh_psc_alpha::State_::State_(const Parameters_&)
: r_(0)
{
y_[0] = -65;//p.E_L;
for ( size_t i = 1 ; i < STATE_VEC_SIZE ; ++i )
y_[i] = 0;
// equilibrium values for (in)activation variables
const double_t alpha_n = (0.01 * (y_[0]+55.)) / (1. -std::exp( -(y_[0]+55.)/10.));
const double_t beta_n = 0.125 * std::exp( -(y_[0]+65.)/80.);
const double_t alpha_m = (0.1 * (y_[0]+40.)) / (1. - std::exp( -(y_[0]+40.)/10.) );
const double_t beta_m = 4. * std::exp( -(y_[0]+65.)/18.);
const double_t alpha_h = 0.07 * std::exp( -(y_[0]+65.) / 20.);
const double_t beta_h = 1. / (1. + std::exp(-(y_[0]+35.) / 10. ));
y_[HH_H] = alpha_h/(alpha_h+beta_h);
y_[HH_N] = alpha_n/(alpha_n+beta_n);
y_[HH_M] = alpha_m/(alpha_m+beta_m);
}
nest::hh_psc_alpha::State_::State_(const State_& s)
: r_(s.r_)
{
for ( size_t i = 0 ; i < STATE_VEC_SIZE ; ++i )
y_[i] = s.y_[i];
}
nest::hh_psc_alpha::State_& nest::hh_psc_alpha::State_::operator=(const State_& s)
{
assert(this != &s); // would be bad logical error in program
for ( size_t i = 0 ; i < STATE_VEC_SIZE ; ++i )
y_[i] = s.y_[i];
r_ = s.r_;
return *this;
}
/* ----------------------------------------------------------------
* Parameter and state extractions and manipulation functions
* ---------------------------------------------------------------- */
void nest::hh_psc_alpha::Parameters_::get(DictionaryDatum &d) const
{
def<double>(d,names::t_ref, t_ref_);
def<double>(d,names::g_Na, g_Na);
def<double>(d,names::g_K, g_K);
def<double>(d,names::g_L, g_L);
def<double>(d,names::E_Na, E_Na);
def<double>(d,names::E_K, E_K);
def<double>(d,names::E_L, E_L);
def<double>(d,names::C_m, C_m);
def<double>(d,names::tau_syn_ex, tau_synE);
def<double>(d,names::tau_syn_in, tau_synI);
def<double>(d,names::I_e, I_e);
}
void nest::hh_psc_alpha::Parameters_::set(const DictionaryDatum& d)
{
updateValue<double>(d,names::t_ref, t_ref_);
updateValue<double>(d,names::C_m, C_m);
updateValue<double>(d,names::g_Na,g_Na);
updateValue<double>(d,names::E_Na,E_Na);
updateValue<double>(d,names::g_K, g_K);
updateValue<double>(d,names::E_K, E_K);
updateValue<double>(d,names::g_L, g_L);
updateValue<double>(d,names::E_L, E_L);
updateValue<double>(d,names::tau_syn_ex,tau_synE);
updateValue<double>(d,names::tau_syn_in,tau_synI);
updateValue<double>(d,names::I_e, I_e);
if ( C_m <= 0 )
throw BadProperty("Capacitance must be strictly positive.");
if ( t_ref_ < 0 )
throw BadProperty("Refractory time cannot be negative.");
if ( tau_synE <= 0 || tau_synI <= 0 )
throw BadProperty("All time constants must be strictly positive.");
if ( g_K < 0 || g_Na < 0 || g_L < 0 )
throw BadProperty("All conductances must be non-negative.");
}
void nest::hh_psc_alpha::State_::get(DictionaryDatum &d) const
{
def<double>(d,names::V_m , y_[V_M]);
def<double>(d,names::Act_m , y_[HH_M]);
def<double>(d,names::Act_h , y_[HH_H]);
def<double>(d,names::Inact_n, y_[HH_N]);
}
void nest::hh_psc_alpha::State_::set(const DictionaryDatum& d)
{
updateValue<double>(d,names::V_m , y_[V_M]);
updateValue<double>(d,names::Act_m , y_[HH_M]);
updateValue<double>(d,names::Act_h , y_[HH_H]);
updateValue<double>(d,names::Inact_n, y_[HH_N]);
if ( y_[HH_M] < 0 || y_[HH_H] < 0 || y_[HH_N] < 0 )
throw BadProperty("All (in)activation variables must be non-negative.");
}
nest::hh_psc_alpha::Buffers_::Buffers_(hh_psc_alpha& n)
: logger_(n),
s_(0),
c_(0),
e_(0)
{
// Initialization of the remaining members is deferred to
// init_buffers_().
}
nest::hh_psc_alpha::Buffers_::Buffers_(const Buffers_&, hh_psc_alpha& n)
: logger_(n),
s_(0),
c_(0),
e_(0)
{
// Initialization of the remaining members is deferred to
// init_buffers_().
}
/* ----------------------------------------------------------------
* Default and copy constructor for node, and destructor
* ---------------------------------------------------------------- */
nest::hh_psc_alpha::hh_psc_alpha()
: Archiving_Node(),
P_(),
S_(P_),
B_(*this)
{
recordablesMap_.create();
}
nest::hh_psc_alpha::hh_psc_alpha(const hh_psc_alpha& n)
: Archiving_Node(n),
P_(n.P_),
S_(n.S_),
B_(n.B_, *this)
{
}
nest::hh_psc_alpha::~hh_psc_alpha()
{
// GSL structs may not have been allocated, so we need to protect destruction
if ( B_.s_ ) gsl_odeiv_step_free(B_.s_);
if ( B_.c_ ) gsl_odeiv_control_free(B_.c_);
if ( B_.e_ ) gsl_odeiv_evolve_free(B_.e_);
}
/* ----------------------------------------------------------------
* Node initialization functions
* ---------------------------------------------------------------- */
void nest::hh_psc_alpha::init_state_(const Node& proto)
{
const hh_psc_alpha& pr = downcast<hh_psc_alpha>(proto);
S_ = pr.S_;
}
void nest::hh_psc_alpha::init_buffers_()
{
B_.spike_exc_.clear(); // includes resize
B_.spike_inh_.clear(); // includes resize
B_.currents_.clear(); // includes resize
Archiving_Node::clear_history();
B_.logger_.reset();
B_.step_ = Time::get_resolution().get_ms();
B_.IntegrationStep_ = B_.step_;
static const gsl_odeiv_step_type* T1 = gsl_odeiv_step_rkf45;
if ( B_.s_ == 0 )
B_.s_ = gsl_odeiv_step_alloc (T1, State_::STATE_VEC_SIZE);
else
gsl_odeiv_step_reset(B_.s_);
if ( B_.c_ == 0 )
B_.c_ = gsl_odeiv_control_y_new (1e-3, 0.0);
else
gsl_odeiv_control_init(B_.c_, 1e-3, 0.0, 1.0, 0.0);
if ( B_.e_ == 0 )
B_.e_ = gsl_odeiv_evolve_alloc(State_::STATE_VEC_SIZE);
else
gsl_odeiv_evolve_reset(B_.e_);
B_.sys_.function = hh_psc_alpha_dynamics;
B_.sys_.jacobian = NULL;
B_.sys_.dimension = State_::STATE_VEC_SIZE;
B_.sys_.params = reinterpret_cast<void*>(this);
B_.I_stim_ = 0.0;
}
void nest::hh_psc_alpha::calibrate()
{
B_.logger_.init(); // ensures initialization in case mm connected after Simulate
V_.PSCurrInit_E_ = 1.0 * numerics::e / P_.tau_synE;
V_.PSCurrInit_I_ = 1.0 * numerics::e / P_.tau_synI;
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::hh_psc_alpha::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 )
{
double_t t = 0.0 ;
const double_t U_old = S_.y_[State_::V_M];
// numerical integration with adaptive step size control:
// ------------------------------------------------------
// gsl_odeiv_evolve_apply performs only a single numerical
// integration step, starting from t and bounded by step;
// the while-loop ensures integration over the whole simulation
// step (0, step] if more than one integration step is needed due
// to a small integration step size;
// note that (t+IntegrationStep > step) leads to integration over
// (t, step] and afterwards setting t to step, but it does not
// enforce setting IntegrationStep to step-t; this is of advantage
// for a consistent and efficient integration across subsequent
// simulation intervals
while ( t < B_.step_ )
{
const int status = gsl_odeiv_evolve_apply(B_.e_, B_.c_, B_.s_,
&B_.sys_, // system of ODE
&t, // from t
B_.step_, // to t <= step
&B_.IntegrationStep_, // integration step size
S_.y_); // neuronal state
if ( status != GSL_SUCCESS )
throw GSLSolverFailure(get_name(), status);
}
S_.y_[State_::DI_EXC] += B_.spike_exc_.get_value(lag) * V_.PSCurrInit_E_;
S_.y_[State_::DI_INH] += B_.spike_inh_.get_value(lag) * V_.PSCurrInit_I_;
// sending spikes: crossing 0 mV, pseudo-refractoriness and local maximum...
// refractory?
if ( S_.r_ > 0 )
--S_.r_;
else
// ( threshold && maximum )
if ( S_.y_[State_::V_M] >= 0 && U_old > S_.y_[State_::V_M])
{
S_.r_ = V_.RefractoryCounts_;
set_spiketime(Time::step(origin.get_steps()+lag+1));
SpikeEvent se;
network()->send(*this, se, lag);
}
// log state data
B_.logger_.record_data(origin.get_steps() + lag);
// set new input current
B_.I_stim_ = B_.currents_.get_value(lag);
}
}
void nest::hh_psc_alpha::handle(SpikeEvent & e)
{
assert(e.get_delay() > 0);
if(e.get_weight() > 0.0)
B_.spike_exc_.add_value(e.get_rel_delivery_steps(network()->get_slice_origin()),
e.get_weight() * e.get_multiplicity() );
else
B_.spike_inh_.add_value(e.get_rel_delivery_steps(network()->get_slice_origin()),
e.get_weight() * e.get_multiplicity() ); // current input, keep negative weight
}
void nest::hh_psc_alpha::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::hh_psc_alpha::handle(DataLoggingRequest& e)
{
B_.logger_.handle(e);
}
#endif //HAVE_GSL