NEURON Differential Algebraic Equations. More...

#include <nrndae.h>

Inheritance diagram for NrnDAE:

Public Member Functions
int	extra_eqn_count ()
	Find the number of state variables introduced by this object. More...

void	alloc (int start_index)
	Allocate space for these dynamics in the overall system. More...

void	lhs ()
	Compute the left side portion of. More...

void	rhs ()
	Compute the right side portion of. More...

void	dkres (double y, double yprime, double *delta)
	Compute the residual: More...

void	init ()
	Initialize the dynamics. More...

void	update ()
	Update states to reflect the changes over a time-step. More...

void	dkmap (std::vector< double * > &pv, std::vector< double * > &pvdot)
	Setup the map between voltages and states in y_. More...

virtual	~NrnDAE ()
	Destructor. More...

Protected Member Functions
	NrnDAE (Matrix cmat, Vect const yvec, Vect const y0, int nnode, Node const nodes, Vect const elayer, void(f_init)(void data)=NULL, void *const data=NULL)
	Constructor. More...

Private Member Functions
virtual void	f_ (Vect &y, Vect &yprime, int size)=0
	The right-hand-side function. More...

virtual MatrixMap *	jacobian_ (Vect &y)=0
	Compute the Jacobian. More...

virtual double	jacobian_multiplier_ ()

virtual void	alloc_ (int size, int start, int nnode, Node *nodes, int elayer)
	Additional allocation for subclasses. More...

void	v2y ()
	Transfer any voltage states to y_. More...

Private Attributes
void(*	f_init_ )(void *data)
	Function used for initializing the state variables. More...

void *	data_
	Data to pass to f_init_. More...

MatrixMap *	c_
	the matrix More...

Matrix *	assumed_identity_
	identity matrix if constructed with More...

Vect *	y0_
	vector of initial conditions More...

Vect &	y_
	vector to store the state variables in More...

int	size_
	total number of states declared or modified in this object More...

int *	bmap_
	mapping between the states in y and the states in the whole system More...

int	nnode_
	Number of voltage nodes used by the dynamics. More...

Node **	nodes_
	Pointers to voltage nodes used by the dynamics. More...

int	start_
	the position of the first added equation (if any) in the global system More...

Vect	cyp_
	temporary vector used for residual calculation. More...

Vect	yptmp_
	temporary vector used for residual calculation. More...

int *	elayer_
	Which voltage layers to read from. More...

Detailed Description

NEURON Differential Algebraic Equations.

Remarks: This is an abstract class; subclass this (or use a subclass) to add dynamics. LinearModelAddition is an example. See linmod.h.

Definition at line 27 of file nrndae.h.

Constructor & Destructor Documentation

◆ ~NrnDAE()

NrnDAE::~NrnDAE ( )

virtual

Destructor.

Definition at line 192 of file nrndae.cpp.

◆ NrnDAE()

NrnDAE::NrnDAE	(	Matrix *	cmat,
		Vect *const	yvec,
		Vect *const	y0,
		int	nnode,
		Node **const	nodes,
		Vect *const	elayer,
		void()(void data)	f_init = `NULL`,
		void *const	data = `NULL`
	)

protected

Constructor.

Parameters

cmat	the matrix \[$C$\] in \[$Cy'=f(y)$\] .
yvec	vector to store the state variables in
y0	initial conditions
nnode	number of voltage equations to modify
nodes	pointers to voltage nodes
elayer	which potential layer to use for each voltage node
f_init	function to call during an finitialize
data	data to pass to f_init

Remarks: If cmat is NULL, then assumes
\[$C$\]
is the identity matrix.; If f_init is non-NULL, that takes priority. Otherwise, if y0 is non-NULL, then initializes to those values. Otherwise initializes by setting all states to 0.

Definition at line 141 of file nrndae.cpp.

Member Function Documentation

◆ alloc()

void NrnDAE::alloc ( int start_index )

Allocate space for these dynamics in the overall system.

Parameters

start_index starting index for new states

Definition at line 108 of file nrndae.cpp.

◆ alloc_()

void NrnDAE::alloc_	(	int	size,
		int	start,
		int	nnode,
		Node **	nodes,
		int *	elayer
	)

inlineprivatevirtual

Additional allocation for subclasses.

Remarks: Called during alloc(). Unless overriden, this function is empty.

Reimplemented in LinearModelAddition.

Definition at line 106 of file nrndae.cpp.

◆ dkmap()

void NrnDAE::dkmap	(	std::vector< double * > &	pv,
		std::vector< double * > &	pvdot
	)

Setup the map between voltages and states in y_.

Parameters

pv	pointers to voltage nodes (set by this function)
pvdot	pointers to voltage derivatives (set by this function)

Definition at line 214 of file nrndae.cpp.

◆ dkres()

void NrnDAE::dkres	(	double *	y,
		double *	yprime,
		double *	delta
	)

Compute the residual:

\[$f(y) - C \frac{dy}{dt}$\]

Parameters

y	array of state variables
yprime	array of derivatives of state variables
delta	array to store the difference $f(y)-Cy'$

Definition at line 277 of file nrndae.cpp.

◆ extra_eqn_count()

int NrnDAE::extra_eqn_count ( )

Find the number of state variables introduced by this object.

Returns: The number of states added (not modified) by this instance.

Definition at line 207 of file nrndae.cpp.

◆ f_()

virtual void NrnDAE::f_	(	Vect &	y,
		Vect &	yprime,
		int	size
	)

privatepure virtual

The right-hand-side function.

Parameters

y	the state variables
yprime	a vector to store the derivatives
size	the number of state variables

Implemented in LinearModelAddition.

◆ init()

void NrnDAE::init ( )

Initialize the dynamics.

Remarks: Does this by calling f_init_. If f_init_ is NULL, initializes to values in y0_. If y0_ is NULL, initializes all states to 0.

Definition at line 236 of file nrndae.cpp.

◆ jacobian_()

virtual MatrixMap* NrnDAE::jacobian_ ( Vect & y )

privatepure virtual

Compute the Jacobian.

Parameters

y	the state variables

Returns: Pointer to a MatrixMap containing the jacobian.

Remarks: The calling function will not delete this pointer.; It is occasionally easier to return the Jacobian divided by a constant factor. If so, have jacobian_multiplier_ return a number that should be multiplied by the matrix returned by this function to get the true Jacobian.

Implemented in LinearModelAddition.

◆ jacobian_multiplier_()

virtual double NrnDAE::jacobian_multiplier_ ( )

inlineprivatevirtual

Reimplemented in LinearModelAddition.

Definition at line 150 of file nrndae.h.

◆ lhs()

void NrnDAE::lhs ( )

Compute the left side portion of.

\[$(C - J) \frac{dy}{dt} = f(y)$\]

.

Definition at line 314 of file nrndae.cpp.

◆ rhs()

void NrnDAE::rhs ( )

Compute the right side portion of.

\[$(C - J) \frac{dy}{dt} = f(y)$\]

.

Definition at line 305 of file nrndae.cpp.

◆ update()

void NrnDAE::update ( )

Update states to reflect the changes over a time-step.

Remarks: When this function is called, the changes have already been computed by the solver. This just updates the local variables.

Definition at line 224 of file nrndae.cpp.

◆ v2y()

void NrnDAE::v2y ( )

private

Transfer any voltage states to y_.

Definition at line 258 of file nrndae.cpp.

Member Data Documentation

◆ assumed_identity_

Matrix* NrnDAE::assumed_identity_

private

identity matrix if constructed with

\[$C$\]

NULL; else NULL.

Definition at line 165 of file nrndae.h.

◆ bmap_

int* NrnDAE::bmap_

private

mapping between the states in y and the states in the whole system

Definition at line 177 of file nrndae.h.

◆ c_

MatrixMap* NrnDAE::c_

private

the matrix

\[$C$ in $C y' = f(y)$\]

Definition at line 162 of file nrndae.h.

◆ cyp_

Vect NrnDAE::cyp_

private

temporary vector used for residual calculation.

Definition at line 189 of file nrndae.h.

◆ data_

void* NrnDAE::data_

private

Data to pass to f_init_.

Definition at line 147 of file nrndae.h.

◆ elayer_

int* NrnDAE::elayer_

private

Which voltage layers to read from.

Remarks: Normally elements are 0 and refer to internal potential. Otherwise range from 1 to nlayer and refer to vext[elayer-1]. vm+vext and vext must be placed in y for calculation of rhs

Definition at line 201 of file nrndae.h.

◆ f_init_

void(* NrnDAE::f_init_) (void *data)

private

Function used for initializing the state variables.

Definition at line 144 of file nrndae.h.

◆ nnode_

int NrnDAE::nnode_

private

Number of voltage nodes used by the dynamics.

Definition at line 180 of file nrndae.h.

◆ nodes_

Node** NrnDAE::nodes_

private

Pointers to voltage nodes used by the dynamics.

Definition at line 183 of file nrndae.h.

◆ size_

int NrnDAE::size_

private

total number of states declared or modified in this object

Definition at line 174 of file nrndae.h.

◆ start_

int NrnDAE::start_

private

the position of the first added equation (if any) in the global system

Definition at line 186 of file nrndae.h.

◆ y0_

Vect* NrnDAE::y0_

private

vector of initial conditions

Definition at line 168 of file nrndae.h.

◆ y_

Vect& NrnDAE::y_

private

vector to store the state variables in

Definition at line 171 of file nrndae.h.

◆ yptmp_

Vect NrnDAE::yptmp_

private

temporary vector used for residual calculation.

Definition at line 192 of file nrndae.h.

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

/home/docs/checkouts/readthedocs.org/user_builds/nrn/checkouts/3466/src/nrniv/nrndae.h
/home/docs/checkouts/readthedocs.org/user_builds/nrn/checkouts/3466/src/nrniv/nrndae.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ~NrnDAE()

◆ NrnDAE()

Member Function Documentation

◆ alloc()

◆ alloc_()

◆ dkmap()

◆ dkres()

◆ extra_eqn_count()

◆ f_()

◆ init()

◆ jacobian_()

◆ jacobian_multiplier_()

◆ lhs()

◆ rhs()

◆ update()

◆ v2y()

Member Data Documentation

◆ assumed_identity_

◆ bmap_

◆ c_

◆ cyp_

◆ data_

◆ elayer_

◆ f_init_

◆ nnode_

◆ nodes_

◆ size_

◆ start_

◆ y0_

◆ y_

◆ yptmp_