Add support for axonal delays

libnestutil/nest_types.h

@@ -91,9 +91,15 @@ constexpr uint8_t NUM_BITS_LCID = 27U;
 constexpr uint8_t NUM_BITS_PROCESSED_FLAG = 1U;
 constexpr uint8_t NUM_BITS_MARKER_SPIKE_DATA = 2U;
 constexpr uint8_t NUM_BITS_LAG = 14U;
-constexpr uint8_t NUM_BITS_DELAY = 21U;
 constexpr uint8_t NUM_BITS_NODE_ID = 62U;
 
+// These types are used in delay_types.h and denote the space available for the dendritic and axonal portions of the
+// total transmission delay. The delay is only split into two parts for selected synapse types.
+// Given that axonal delays can be much larger than dendritic/backpropagation delays, they require more bits.
+constexpr uint8_t NUM_BITS_DENDRITIC_DELAY = 14U;
+constexpr uint8_t NUM_BITS_AXONAL_DELAY = sizeof( unsigned int ) * 8 - NUM_BITS_DENDRITIC_DELAY;
+
+
 // Maximally allowed values for bitfields
 
 constexpr uint64_t MAX_LCID = generate_max_value( NUM_BITS_LCID );

models/ac_generator.cpp

@@ -56,30 +56,29 @@ RecordablesMap< ac_generator >::create()
 {
   insert_( Name( names::I ), &ac_generator::get_I_ );
 }
-}
 
 /* ----------------------------------------------------------------
  * Default constructors defining default parameters and state
  * ---------------------------------------------------------------- */
 
-nest::ac_generator::Parameters_::Parameters_()
+ac_generator::Parameters_::Parameters_()
   : amp_( 0.0 )     // pA
   , offset_( 0.0 )  // pA
   , freq_( 0.0 )    // Hz
   , phi_deg_( 0.0 ) // degree
 {
 }
 
-nest::ac_generator::Parameters_::Parameters_( const Parameters_& p )
+ac_generator::Parameters_::Parameters_( const Parameters_& p )
   : amp_( p.amp_ )
   , offset_( p.offset_ )
   , freq_( p.freq_ )
   , phi_deg_( p.phi_deg_ )
 {
 }
 
-nest::ac_generator::Parameters_&
-nest::ac_generator::Parameters_::operator=( const Parameters_& p )
+ac_generator::Parameters_&
+ac_generator::Parameters_::operator=( const Parameters_& p )
 {
   if ( this == &p )
   {
@@ -94,19 +93,19 @@ nest::ac_generator::Parameters_::operator=( const Parameters_& p )
   return *this;
 }
 
-nest::ac_generator::State_::State_()
+ac_generator::State_::State_()
   : y_0_( 0.0 )
   , y_1_( 0.0 ) // pA
   , I_( 0.0 )   // pA
 {
 }
 
-nest::ac_generator::Buffers_::Buffers_( ac_generator& n )
+ac_generator::Buffers_::Buffers_( ac_generator& n )
   : logger_( n )
 {
 }
 
-nest::ac_generator::Buffers_::Buffers_( const Buffers_&, ac_generator& n )
+ac_generator::Buffers_::Buffers_( const Buffers_&, ac_generator& n )
   : logger_( n )
 {
 }
@@ -116,7 +115,7 @@ nest::ac_generator::Buffers_::Buffers_( const Buffers_&, ac_generator& n )
  * ---------------------------------------------------------------- */
 
 void
-nest::ac_generator::Parameters_::get( DictionaryDatum& d ) const
+ac_generator::Parameters_::get( DictionaryDatum& d ) const
 {
   ( *d )[ names::amplitude ] = amp_;
   ( *d )[ names::offset ] = offset_;
@@ -125,14 +124,14 @@ nest::ac_generator::Parameters_::get( DictionaryDatum& d ) const
 }
 
 void
-nest::ac_generator::State_::get( DictionaryDatum& d ) const
+ac_generator::State_::get( DictionaryDatum& d ) const
 {
   ( *d )[ names::y_0 ] = y_0_;
   ( *d )[ names::y_1 ] = y_1_;
 }
 
 void
-nest::ac_generator::Parameters_::set( const DictionaryDatum& d, Node* node )
+ac_generator::Parameters_::set( const DictionaryDatum& d, Node* node )
 {
   updateValueParam< double >( d, names::amplitude, amp_, node );
   updateValueParam< double >( d, names::offset, offset_, node );
@@ -145,7 +144,7 @@ nest::ac_generator::Parameters_::set( const DictionaryDatum& d, Node* node )
  * Default and copy constructor for node
  * ---------------------------------------------------------------- */
 
-nest::ac_generator::ac_generator()
+ac_generator::ac_generator()
   : StimulationDevice()
   , P_()
   , S_()
@@ -154,7 +153,7 @@ nest::ac_generator::ac_generator()
   recordablesMap_.create();
 }
 
-nest::ac_generator::ac_generator( const ac_generator& n )
+ac_generator::ac_generator( const ac_generator& n )
   : StimulationDevice( n )
   , P_( n.P_ )
   , S_( n.S_ )
@@ -168,20 +167,20 @@ nest::ac_generator::ac_generator( const ac_generator& n )
  * ---------------------------------------------------------------- */
 
 void
-nest::ac_generator::init_state_()
+ac_generator::init_state_()
 {
   StimulationDevice::init_state();
 }
 
 void
-nest::ac_generator::init_buffers_()
+ac_generator::init_buffers_()
 {
   StimulationDevice::init_buffers();
   B_.logger_.reset();
 }
 
 void
-nest::ac_generator::pre_run_hook()
+ac_generator::pre_run_hook()
 {
   B_.logger_.init();
 
@@ -206,7 +205,7 @@ nest::ac_generator::pre_run_hook()
 }
 
 void
-nest::ac_generator::update( Time const& origin, const long from, const long to )
+ac_generator::update( Time const& origin, const long from, const long to )
 {
   long start = origin.get_steps();
 
@@ -231,7 +230,7 @@ nest::ac_generator::update( Time const& origin, const long from, const long to )
 }
 
 void
-nest::ac_generator::handle( DataLoggingRequest& e )
+ac_generator::handle( DataLoggingRequest& e )
 {
   B_.logger_.handle( e );
 }
@@ -241,7 +240,7 @@ nest::ac_generator::handle( DataLoggingRequest& e )
  * ---------------------------------------------------------------- */
 
 void
-nest::ac_generator::set_data_from_stimulation_backend( std::vector< double >& input_param )
+ac_generator::set_data_from_stimulation_backend( std::vector< double >& input_param )
 {
   Parameters_ ptmp = P_; // temporary copy in case of errors
 
@@ -264,3 +263,5 @@ nest::ac_generator::set_data_from_stimulation_backend( std::vector< double >& in
   // if we get here, temporary contains consistent set of properties
   P_ = ptmp;
 }
+
+} // namespace nest

models/aeif_cond_alpha.cpp

@@ -426,6 +426,8 @@ nest::aeif_cond_alpha::init_buffers_()
 void
 nest::aeif_cond_alpha::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/aeif_cond_alpha_astro.cpp

@@ -429,6 +429,8 @@ nest::aeif_cond_alpha_astro::init_buffers_()
 void
 nest::aeif_cond_alpha_astro::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/aeif_cond_alpha_multisynapse.cpp

@@ -441,6 +441,8 @@ aeif_cond_alpha_multisynapse::init_buffers_()
 void
 aeif_cond_alpha_multisynapse::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/aeif_cond_beta_multisynapse.cpp

@@ -449,6 +449,8 @@ aeif_cond_beta_multisynapse::init_buffers_()
 void
 aeif_cond_beta_multisynapse::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/aeif_cond_exp.cpp

@@ -421,6 +421,8 @@ nest::aeif_cond_exp::init_buffers_()
 void
 nest::aeif_cond_exp::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/aeif_psc_alpha.cpp

@@ -416,6 +416,8 @@ nest::aeif_psc_alpha::init_buffers_()
 void
 nest::aeif_psc_alpha::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/aeif_psc_delta.cpp

@@ -392,6 +392,8 @@ nest::aeif_psc_delta::init_buffers_()
 void
 nest::aeif_psc_delta::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/aeif_psc_delta_clopath.cpp

@@ -460,6 +460,8 @@ nest::aeif_psc_delta_clopath::init_buffers_()
 void
 nest::aeif_psc_delta_clopath::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/aeif_psc_exp.cpp

@@ -411,6 +411,8 @@ nest::aeif_psc_exp::init_buffers_()
 void
 nest::aeif_psc_exp::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/amat2_psc_exp.cpp

@@ -264,6 +264,8 @@ nest::amat2_psc_exp::init_buffers_()
 void
 nest::amat2_psc_exp::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
 

models/bernoulli_synapse.h

@@ -148,10 +148,10 @@ class bernoulli_synapse : public Connection< targetidentifierT >
   };
 
   void
-  check_connection( Node& s, Node& t, size_t receptor_type, const CommonPropertiesType& )
+  check_connection( Node& s, Node& t, const size_t receptor_type, const synindex syn_id, const CommonPropertiesType& )
   {
     ConnTestDummyNode dummy_target;
-    ConnectionBase::check_connection_( dummy_target, s, t, receptor_type );
+    ConnectionBase::check_connection_( dummy_target, s, t, syn_id, receptor_type );
   }
 
   bool

models/binary_neuron.h

@@ -434,6 +434,8 @@ template < class TGainfunction >
 void
 binary_neuron< TGainfunction >::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   // ensures initialization in case mm connected after Simulate
   B_.logger_.init();
   V_.rng_ = get_vp_specific_rng( get_thread() );

models/clopath_synapse.h

@@ -147,7 +147,7 @@ class clopath_synapse : public Connection< targetidentifierT >
   // ConnectionBase. This avoids explicit name prefixes in all places these
   // functions are used. Since ConnectionBase depends on the template parameter,
   // they are not automatically found in the base class.
-  using ConnectionBase::get_delay;
+  using ConnectionBase::get_delay_ms;
   using ConnectionBase::get_delay_steps;
   using ConnectionBase::get_rport;
   using ConnectionBase::get_target;
@@ -184,13 +184,13 @@ class clopath_synapse : public Connection< targetidentifierT >
   };
 
   void
-  check_connection( Node& s, Node& t, size_t receptor_type, const CommonPropertiesType& )
+  check_connection( Node& s, Node& t, const size_t receptor_type, const synindex syn_id, const CommonPropertiesType& )
   {
     ConnTestDummyNode dummy_target;
 
-    ConnectionBase::check_connection_( dummy_target, s, t, receptor_type );
+    ConnectionBase::check_connection_( dummy_target, s, t, syn_id, receptor_type );
 
-    t.register_stdp_connection( t_lastspike_ - get_delay(), get_delay() );
+    t.register_stdp_connection( t_lastspike_ - get_delay_ms(), get_delay_ms(), 0 );
   }
 
   void
@@ -241,7 +241,7 @@ clopath_synapse< targetidentifierT >::send( Event& e, size_t t, const CommonSyna
   // use accessor functions (inherited from Connection< >) to obtain delay and
   // target
   Node* target = get_target( t );
-  double dendritic_delay = get_delay();
+  double dendritic_delay = get_delay_ms();
 
   // get spike history in relevant range (t1, t2] from postsynaptic neuron
   std::deque< histentry_extended >::iterator start;

models/cm_default.cpp

@@ -303,6 +303,8 @@ nest::cm_default::init_recordables_pointers_()
 void
 nest::cm_default::pre_run_hook()
 {
+  ArchivingNode::pre_run_hook_();
+
   logger_.init();
 
   // initialize the pointers within the compartment tree