The SPManager class is in charge of managing the dynamic creation and deletion of synapses in the simulation when structural plasticity is enabled. More...

#include <sp_manager.h>

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Public Member Functions
	SPManager ()

	~SPManager () override

void	initialize (const bool) override
	Prepare manager for operation.

void	finalize (const bool) override
	Take down manager after operation.

void	get_status (Dictionary &) override
	Retrieve the status of the manager.

void	set_status (const Dictionary &) override
	Set status of synaptic plasticity variables: synaptic update interval, synapses and synaptic elements.

GrowthCurve *	new_growth_curve (std::string name)
	Create a new Growth Curve object using the GrowthCurve Factory.

template<typename GrowthCurve >
void	register_growth_curve (const std::string &name)
	Add a growth curve for MSP.

void	disconnect (NodeCollectionPTR sources, NodeCollectionPTR targets, const Dictionary &conn_spec, const std::vector< Dictionary > &syn_specs)
	Disconnect two collections of nodes.

void	disconnect (const size_t snode_id, Node *target, size_t target_thread, const size_t syn_id)
	Disconnect two nodes.

void	update_structural_plasticity ()

void	update_structural_plasticity (SPBuilder *)

void	enable_structural_plasticity ()
	Enable structural plasticity.

void	disable_structural_plasticity ()
	Disable structural plasticity.

bool	is_structural_plasticity_enabled () const

double	get_structural_plasticity_update_interval () const

long	builder_min_delay () const
	Returns the minimum delay of all SP builders.

long	builder_max_delay () const
	Returns the maximum delay of all SP builders.

bool	create_synapses (std::vector< size_t > &pre_vacant_id, std::vector< int > &pre_vacant_n, std::vector< size_t > &post_vacant_id, std::vector< int > &post_vacant_n, SPBuilder *sp_conn_builder)

void	delete_synapses_from_pre (const std::vector< size_t > &pre_deleted_id, std::vector< int > &pre_deleted_n, const size_t synapse_model, const std::string &se_pre_name, const std::string &se_post_name)

void	delete_synapses_from_post (std::vector< size_t > &post_deleted_id, std::vector< int > &post_deleted_n, size_t synapse_model, std::string se_pre_name, std::string se_post_name)

void	delete_synapse (size_t source, size_t target, long syn_id, std::string se_pre_name, std::string se_post_name)

void	get_synaptic_elements (std::string se_name, std::vector< size_t > &se_vacant_id, std::vector< int > &se_vacant_n, std::vector< size_t > &se_deleted_id, std::vector< int > &se_deleted_n)

void	serialize_id (std::vector< size_t > &id, std::vector< int > &n, std::vector< size_t > &res)

Public Member Functions inherited from nest::ManagerInterface
	ManagerInterface (ManagerInterface const &)=delete

void	operator= (ManagerInterface const &)=delete

	ManagerInterface ()

virtual	~ManagerInterface ()

virtual void	prepare ()

virtual void	cleanup ()

Private Attributes
double	structural_plasticity_update_interval_
	Time interval for structural plasticity update (creation/deletion of synapses).

bool	structural_plasticity_enabled_
	Indicates whether the Structrual Plasticity functionality is On (True) of Off (False).

std::vector< SPBuilder * >	sp_conn_builders_

std::vector< GenericGrowthCurveFactory * >	growthcurve_factories_
	GrowthCurve factories, indexed by growthcurvedict_ elements.

Dictionary	growthcurvedict_
	Dictionary for growth rules.

Detailed Description

The SPManager class is in charge of managing the dynamic creation and deletion of synapses in the simulation when structural plasticity is enabled.

Otherwise it behaves as the normal ConnectionManager.

Parameters

Constructor & Destructor Documentation

◆ SPManager()

nest::SPManager::SPManager ( )

◆ ~SPManager()

nest::SPManager::~SPManager ( )

override

Member Function Documentation

◆ builder_max_delay()

long nest::SPManager::builder_max_delay ( ) const

Returns the maximum delay of all SP builders.

This influences the max_delay of the kernel, as the connections are build during the simulation. Hence, the ConnectionManager::max_delay() methods have to respect this delay as well.

References nest::Time::get_steps(), nest::Time::neg_inf(), and sp_conn_builders_.

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◆ builder_min_delay()

long nest::SPManager::builder_min_delay ( ) const

Returns the minimum delay of all SP builders.

This influences the min_delay of the kernel, as the connections are build during the simulation. Hence, the ConnectionManager::min_delay() methods have to respect this delay as well.

References nest::Time::get_steps(), nest::Time::pos_inf(), and sp_conn_builders_.

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◆ create_synapses()

bool nest::SPManager::create_synapses	(	std::vector< size_t > &	pre_vacant_id,
		std::vector< int > &	pre_vacant_n,
		std::vector< size_t > &	post_vacant_id,
		std::vector< int > &	post_vacant_n,
		SPBuilder *	sp_conn_builder
	)

References nest::get_rank_synced_rng(), nest::BaseRandomGenerator::partial_shuffle(), serialize_id(), and nest::SPBuilder::sp_connect().

Referenced by update_structural_plasticity().

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◆ delete_synapse()

void nest::SPManager::delete_synapse	(	size_t	source,
		size_t	target,
		long	syn_id,
		std::string	se_pre_name,
		std::string	se_post_name
	)

References nest::KernelManager::connection_manager, nest::ConnectionManager::disconnect(), nest::NodeManager::get_node_or_proxy(), nest::VPManager::get_thread_id(), nest::kernel(), nest::KernelManager::node_manager, and nest::KernelManager::vp_manager.

Referenced by delete_synapses_from_post(), and delete_synapses_from_pre().

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◆ delete_synapses_from_post()

void nest::SPManager::delete_synapses_from_post	(	std::vector< size_t > &	post_deleted_id,
		std::vector< int > &	post_deleted_n,
		size_t	synapse_model,
		std::string	se_pre_name,
		std::string	se_post_name
	)

References nest::MPIManager::communicate(), nest::KernelManager::connection_manager, delete_synapse(), nest::get_rank_synced_rng(), nest::ConnectionManager::get_sources(), nest::kernel(), nest::KernelManager::mpi_manager, and nest::BaseRandomGenerator::partial_shuffle().

Referenced by update_structural_plasticity().

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◆ delete_synapses_from_pre()

void nest::SPManager::delete_synapses_from_pre	(	const std::vector< size_t > &	pre_deleted_id,
		std::vector< int > &	pre_deleted_n,
		const size_t	synapse_model,
		const std::string &	se_pre_name,
		const std::string &	se_post_name
	)

References nest::MPIManager::communicate(), nest::KernelManager::connection_manager, delete_synapse(), nest::get_rank_synced_rng(), nest::ConnectionManager::get_targets(), nest::kernel(), nest::KernelManager::mpi_manager, and nest::BaseRandomGenerator::partial_shuffle().

Referenced by update_structural_plasticity().

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◆ disable_structural_plasticity()

void nest::SPManager::disable_structural_plasticity ( )

Disable structural plasticity.

References structural_plasticity_enabled_.

Referenced by nest::disable_structural_plasticity().

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◆ disconnect() [1/2]

void nest::SPManager::disconnect	(	const size_t	snode_id,
		Node *	target,
		size_t	target_thread,
		const size_t	syn_id
	)

Disconnect two nodes.

The source node is defined by its global ID. The target node is defined by the node. The connection is established on the thread/process that owns the target node.

Parameters

snode_id	node ID of the sending Node.
target	Pointer to target Node.
target_thread	Thread that hosts the target node.
syn_id	The synapse model to use.

References nest::KernelManager::connection_manager, nest::ConnectionManager::disconnect(), nest::NodeManager::get_node_or_proxy(), nest::VPManager::get_num_threads(), nest::kernel(), nest::KernelManager::node_manager, and nest::KernelManager::vp_manager.

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◆ disconnect() [2/2]

void nest::SPManager::disconnect	(	NodeCollectionPTR	sources,
		NodeCollectionPTR	targets,
		const Dictionary &	conn_spec,
		const std::vector< Dictionary > &	syn_specs
	)

Disconnect two collections of nodes.

The connection is established on the thread/process that owns the target node.

Obtains the right connection builder and performs a synapse deletion according to the specified connection specs.

Parameters

sources	Node collection of the source Nodes.
targets	Node collection of the target Nodes.
connectivity	Params connectivity Dictionary
synapse	Params synapse parameters Dictionary conn_spec disconnection specs. For now only all to all and one to one rules are implemented.

References Dictionary::all_entries_accessed(), nest::KernelManager::connection_manager, nest::BipartiteConnBuilder::disconnect(), Dictionary::get(), nest::ConnectionManager::get_conn_builder(), nest::ModelManager::get_synapse_model_id(), nest::VPManager::get_thread_id(), Dictionary::init_access_flags(), nest::kernel(), Dictionary::known(), nest::KernelManager::model_manager, nest::KernelManager::node_manager, nest::names::rule(), nest::ConnectionManager::set_connections_have_changed(), nest::BipartiteConnBuilder::set_synaptic_element_names(), nest::KernelManager::simulation_manager, sp_conn_builders_, nest::names::synapse_model(), nest::SimulationManager::update_connection_infrastructure(), nest::NodeManager::update_thread_local_node_data(), nest::ConnectionManager::valid_connection_rule(), and nest::KernelManager::vp_manager.

Referenced by nest::disconnect(), nest::disconnect(), and nest::BipartiteConnBuilder::single_disconnect_().

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◆ enable_structural_plasticity()

void nest::SPManager::enable_structural_plasticity ( )

Enable structural plasticity.

References nest::kernel(), and structural_plasticity_enabled_.

Referenced by nest::enable_structural_plasticity().

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◆ finalize()

void nest::SPManager::finalize ( const bool adjust_number_of_threads_or_rng_only )

overridevirtual

Take down manager after operation.

After this method has completed, all dynamic data structures created by the manager shall be deallocated and containers emptied. Plain variables need not be reset.

Note: Finalization of any given manager may depend on other managers not having been finalized yet. KernelManager::finalize() is responsible for calling the initialization routines on the specific managers in correct order, i.e., the opposite order of initialize() calls.

Parameters

adjust_number_of_threads_or_rng_only Pass true if calling from kernel_manager::change_number_of_threads() to limit operations to those necessary for thread adjustment.

See also: initialize()

Implements nest::ManagerInterface.

References Dictionary::clear(), growthcurve_factories_, growthcurvedict_, and sp_conn_builders_.

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◆ get_status()

void nest::SPManager::get_status ( Dictionary & )

overridevirtual

Retrieve the status of the manager.

Note: This would ideally be a const function. However, some managers delay the update of internal variables up to the point where they are needed (e.g., before reporting their values to the user, or before simulate is called). An example for this pattern is the call to update_delay_extrema_() right at the beginning of ConnectionManager::get_status().

See also: set_status()

Implements nest::ManagerInterface.

References nest::names::allow_autapses(), nest::names::allow_multapses(), nest::ModelManager::get_connection_model(), nest::ConnectorModel::get_name(), nest::names::growth_curves(), growthcurvedict_, nest::kernel(), nest::KernelManager::model_manager, nest::names::post_synaptic_element(), nest::names::pre_synaptic_element(), sp_conn_builders_, nest::names::structural_plasticity_synapses(), nest::names::structural_plasticity_update_interval(), structural_plasticity_update_interval_, and nest::names::synapse_model().

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◆ get_structural_plasticity_update_interval()

double nest::SPManager::get_structural_plasticity_update_interval ( ) const

inline

References structural_plasticity_update_interval_.

◆ get_synaptic_elements()

void nest::SPManager::get_synaptic_elements	(	std::string	se_name,
		std::vector< size_t > &	se_vacant_id,
		std::vector< int > &	se_vacant_n,
		std::vector< size_t > &	se_deleted_id,
		std::vector< int > &	se_deleted_n
	)

References nest::SparseNodeArray::begin(), nest::SparseNodeArray::end(), nest::NodeManager::get_local_nodes(), nest::VPManager::get_num_threads(), nest::Node::get_synaptic_elements_vacant(), nest::kernel(), nest::KernelManager::node_manager, nest::NodeManager::size(), and nest::KernelManager::vp_manager.

Referenced by update_structural_plasticity().

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◆ initialize()

void nest::SPManager::initialize ( const bool adjust_number_of_threads_or_rng_only )

overridevirtual

Prepare manager for operation.

After this method has completed, the manager should be completely initialized and "ready for action".

Note: Initialization of any given manager may depend on other managers having been initialized before. KernelManager::initialize() is responsible for calling the initialization routines on the specific managers in correct order.

Parameters

adjust_number_of_threads_or_rng_only Pass true if calling from kernel_manager::change_number_of_threads() or RandomManager::get_status() to limit operations to those necessary for thread adjustment or switch or re-seeding of RNG.