#include <cm_tree.h>

Collaboration diagram for nest::CompTree:

Public Member Functions
	CompTree ()

	~CompTree ()

void	add_compartment (const long parent_index)
	add a compartment to the tree structure

void	add_compartment (const long parent_index, const Dictionary &compartment_params)

void	add_compartment (Compartment *compartment, const long parent_index)

void	pre_run_hook ()
	initialize the tree for simulation

void	init_pointers ()
	fix all pointers in the tree, the tree structure should not be modified between calling this function and starting the simulation

void	set_syn_buffers (std::vector< RingBuffer > &syn_buffers)
	associate each receptor with a spike buffer

std::map< std::string, double * >	get_recordables ()
	make all state variables accessible for recording

Compartment *	get_compartment (const long compartment_index) const
	get a compartment pointer from the tree

Compartment *	get_compartment (const long compartment_index, Compartment *compartment, const long raise_flag) const

Compartment *	get_compartment_opt (const long compartment_indx) const
	Get the compartment corresponding to the provided index in the tree.

Compartment *	get_root () const

long	get_size () const
	get tree size (number of compartments)

std::vector< double >	get_voltage () const
	get voltage values

double	get_compartment_voltage (const long compartment_index)
	Return voltage of single compartment voltage, indicated by the compartment_index.

void	construct_matrix (const long lag)
	construct the numerical integration matrix and vector

void	solve_matrix ()
	solve the matrix equation for next timestep voltage

void	print_tree () const
	print function

Private Member Functions
void	solve_matrix_downsweep (Compartment compartment_ptr, std::vector< Compartment >::iterator leaf_it)
	recursion functions for matrix inversion

void	solve_matrix_upsweep (Compartment *compartment, double vv)

void	set_parents ()
	functions for pointer initialization

void	set_compartments ()
	Creates a vector of compartment pointers, organized in the order in which they were added by `add_compartment()`

void	set_leafs ()
	Creates a vector of compartment pointers of compartments that are also leafs of the tree.

Private Attributes
Compartment	root_
	structural data containers for the compartment model

std::vector< long >	compartment_indices_

std::vector< Compartment * >	compartments_

std::vector< Compartment * >	leafs_

long	size_ = 0

Constructor & Destructor Documentation

◆ CompTree()

nest::CompTree::CompTree ( )

References compartments_, and leafs_.

◆ ~CompTree()

nest::CompTree::~CompTree ( )

inline

Member Function Documentation

◆ add_compartment() [1/3]

void nest::CompTree::add_compartment	(	Compartment *	compartment,
		const long	parent_index
	)

we do not raise an UnknownCompartment exception from within get_compartment(), because we want to print a more informative exception message

References nest::Compartment::children, nest::Compartment::comp_index, compartment_indices_, get_compartment(), get_root(), root_, set_compartments(), and size_.

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◆ add_compartment() [2/3]

void nest::CompTree::add_compartment ( const long parent_index )

add a compartment to the tree structure

Add a compartment to the tree structure via the python interface root should have -1 as parent index.

Add root compartment first. Assumes parent of compartment is already added

References add_compartment(), and size_.

Referenced by add_compartment(), add_compartment(), and nest::cm_default::add_compartment_().

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◆ add_compartment() [3/3]

void nest::CompTree::add_compartment	(	const long	parent_index,
		const Dictionary &	compartment_params
	)

References add_compartment(), and size_.

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◆ construct_matrix()

void nest::CompTree::construct_matrix ( const long lag )

construct the numerical integration matrix and vector

Construct the matrix equation to be solved to advance the model one timestep.

References compartments_.

Referenced by nest::cm_default::update().

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◆ get_compartment() [1/2]

Compartment * nest::CompTree::get_compartment ( const long compartment_index ) const

get a compartment pointer from the tree

Get the compartment corresponding to the provided index in the tree.

This function gets the compartments by a recursive search through the tree.

The overloaded functions looks only in the subtree of the provided compartment, and also has the option to throw an error if no compartment corresponding to compartment_index is found in the tree

References get_compartment(), and get_root().

Referenced by add_compartment(), nest::cm_default::add_receptor_(), get_compartment(), get_compartment(), nest::cm_default::get_status(), nest::cm_default::handles_test_event(), set_compartments(), and set_parents().

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◆ get_compartment() [2/2]

Compartment * nest::CompTree::get_compartment	(	const long	compartment_index,
		Compartment *	compartment,
		const long	raise_flag
	)		const

References nest::Compartment::children, nest::Compartment::comp_index, and get_compartment().

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◆ get_compartment_opt()

Compartment * nest::CompTree::get_compartment_opt ( const long compartment_idx ) const

Get the compartment corresponding to the provided index in the tree.

Optimized trough the use of a pointer vector containing all compartments. Calling this function before CompTree::init_pointers() is called will result in a segmentation fault

References compartments_.

Referenced by nest::cm_default::handle().

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◆ get_compartment_voltage()

double nest::CompTree::get_compartment_voltage ( const long compartment_index )

Return voltage of single compartment voltage, indicated by the compartment_index.

References compartments_.

◆ get_recordables()

std::map< std::string, double * > nest::CompTree::get_recordables ( )

make all state variables accessible for recording

Returns a map of variable names and pointers to the recordables.

add recordables for all compartments, suffixed by compartment_idx, to "recordables"

References compartments_.

Referenced by nest::cm_default::init_recordables_pointers_().

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◆ get_root()

Compartment * nest::CompTree::get_root ( ) const

inline

References root_.

Referenced by add_compartment(), get_compartment(), nest::cm_default::handles_test_event(), and nest::cm_default::update().

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◆ get_size()

long nest::CompTree::get_size ( ) const

inline

get tree size (number of compartments)

References size_.

Referenced by nest::cm_default::get_status(), nest::cm_default::handles_test_event(), and nest::cm_default::set_status().

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◆ get_voltage()

std::vector< double > nest::CompTree::get_voltage ( ) const

get voltage values

Returns vector of voltage values, indices correspond to compartments in compartments_

References compartments_.

◆ init_pointers()

void nest::CompTree::init_pointers ( )

fix all pointers in the tree, the tree structure should not be modified between calling this function and starting the simulation

Initialize all tree structure pointers.

References set_compartments(), set_leafs(), and set_parents().

Referenced by nest::cm_default::pre_run_hook().

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◆ pre_run_hook()

void nest::CompTree::pre_run_hook ( )

initialize the tree for simulation

Initialize state variables.

References nest::Compartment::comp_index, compartments_, and root_.

Referenced by nest::cm_default::pre_run_hook().

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◆ print_tree()

void nest::CompTree::print_tree ( ) const

print function

Print the tree graph.

References nest::Compartment::ca, nest::Compartment::comp_index, compartments_, nest::Compartment::el, nest::Compartment::gc, nest::Compartment::gl, and nest::Compartment::parent.

◆ set_compartments()

void nest::CompTree::set_compartments ( )

private

Creates a vector of compartment pointers, organized in the order in which they were added by add_compartment()

References compartment_indices_, compartments_, and get_compartment().

Referenced by add_compartment(), and init_pointers().

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◆ set_leafs()

void nest::CompTree::set_leafs ( )

private

Creates a vector of compartment pointers of compartments that are also leafs of the tree.

References compartments_, and leafs_.

Referenced by init_pointers().

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◆ set_parents()

void nest::CompTree::set_parents ( )

private

functions for pointer initialization

For each compartments, sets its pointer towards its parent compartment.

References compartment_indices_, get_compartment(), nest::Compartment::p_index, nest::Compartment::parent, and root_.

Referenced by init_pointers().

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◆ set_syn_buffers()

void nest::CompTree::set_syn_buffers ( std::vector< RingBuffer > & syn_buffers )

associate each receptor with a spike buffer

Initializes pointers for the spike buffers for all synapse receptors.

References nest::Compartment::compartment_currents, compartments_, and nest::CompartmentCurrents::set_syn_buffers().

Referenced by nest::cm_default::pre_run_hook().

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◆ solve_matrix()

void nest::CompTree::solve_matrix ( )

solve the matrix equation for next timestep voltage

Solve matrix with O(n) algorithm.

References leafs_, root_, solve_matrix_downsweep(), and solve_matrix_upsweep().

Referenced by nest::cm_default::update().

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◆ solve_matrix_downsweep()

void nest::CompTree::solve_matrix_downsweep	(	Compartment *	compartment_ptr,
		std::vector< Compartment * >::iterator	leaf_it
	)

private

recursion functions for matrix inversion

References nest::Compartment::children, nest::Compartment::gather_input(), nest::Compartment::io(), leafs_, nest::Compartment::n_passed, nest::Compartment::parent, and solve_matrix_downsweep().

Referenced by solve_matrix(), and solve_matrix_downsweep().

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◆ solve_matrix_upsweep()

void nest::CompTree::solve_matrix_upsweep	(	Compartment *	compartment,
		double	vv
	)

private

References nest::Compartment::calc_v(), nest::Compartment::children, and solve_matrix_upsweep().

Referenced by solve_matrix(), and solve_matrix_upsweep().

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Member Data Documentation

◆ compartment_indices_

std::vector< long > nest::CompTree::compartment_indices_

private

Referenced by add_compartment(), set_compartments(), and set_parents().

◆ compartments_

std::vector< Compartment* > nest::CompTree::compartments_

private

Referenced by CompTree(), construct_matrix(), get_compartment_opt(), get_compartment_voltage(), get_recordables(), get_voltage(), pre_run_hook(), print_tree(), set_compartments(), set_leafs(), and set_syn_buffers().

◆ leafs_

std::vector< Compartment* > nest::CompTree::leafs_

private

Referenced by CompTree(), set_leafs(), solve_matrix(), and solve_matrix_downsweep().

◆ root_

Compartment nest::CompTree::root_

mutableprivate

structural data containers for the compartment model

Referenced by add_compartment(), get_root(), pre_run_hook(), set_parents(), and solve_matrix().

◆ size_

long nest::CompTree::size_ = 0

private

Referenced by add_compartment(), add_compartment(), add_compartment(), and get_size().

The documentation for this class was generated from the following files:

	NEST main@caf0ae8

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ CompTree()

◆ ~CompTree()

Member Function Documentation

◆ add_compartment() [1/3]

◆ add_compartment() [2/3]

◆ add_compartment() [3/3]

◆ construct_matrix()

◆ get_compartment() [1/2]

◆ get_compartment() [2/2]

◆ get_compartment_opt()

◆ get_compartment_voltage()

◆ get_recordables()

◆ get_root()

◆ get_size()

◆ get_voltage()

◆ init_pointers()

◆ pre_run_hook()

◆ print_tree()

◆ set_compartments()

◆ set_leafs()

◆ set_parents()

◆ set_syn_buffers()

◆ solve_matrix()

◆ solve_matrix_downsweep()

◆ solve_matrix_upsweep()

Member Data Documentation

◆ compartment_indices_

◆ compartments_

◆ leafs_

◆ root_

◆ size_