c_elegans Class Reference

This class represents the c_elegans system. More...

#include <c_elegans.h>

Inheritance diagram for c_elegans:

Collaboration diagram for c_elegans:

Public Member Functions
virtual void	update ()
std::string	type () const
void	postprocess (input &in)
std::vector< std::string >	dependencies () const
int	dxdt (ptr_passer x, ptr_passer dx, double dt)
int	dwdt (ptr_passer x, ptr_passer dx, double dt)
void	mod_w (ptr_passer w, double t)
void	initial_condition (ptr_passer in, size_t len)
Public Member Functions inherited from rhs_type< double, rhs_sde >
virtual const std::type_info &	vtype () const
	returns the type of the current variable

Private Types
typedef Eigen::SparseMatrix < double, RowMajor >	sparse_type

Private Attributes
int	cur_ind
double	dummy
sparse_type	laplacian
sparse_type	AEchem_trans
sparse_type	AEchem_trans_full
sparse_type	ag_full
Array< double, num_neur, 1 >	vmean
Array< double, num_neur, 1 >	sig
Array< double, num_neur, 1 >	Echem
Array< double, num_neur, 1 >	eqS
Array< double, num_neur, 1 >	eqV
double	beta
double	memV
double	memG
double	gchem
double	gelec
double	tau
double	EchemEx
double	EchemInh
double	ar
double	ad
std::vector< size_t >	inj_nodes
std::vector< size_t >	abl_neur
double	cur_inj
bool	has_gone
bool	first_round

Static Private Attributes
static constexpr size_t	num_neur = 279
static constexpr size_t	al_num = 4
static constexpr size_t	dim_v = num_neur
static constexpr size_t	dim_s = dim_v

Additional Inherited Members
Static Public Member Functions inherited from item
static std::shared_ptr< item >	create (std::string name, engineimp *rval)
Public Attributes inherited from item
engineimp *	holder
Protected Member Functions inherited from item_dim
void	print_upstream ()
virtual void	_do_mem_update (size_t dim_old)
void	add_as_parent (item_dim *p)
void	add_as_parent (std::shared_ptr< item_dim > p)
void	update_dim (size_t dim_new)
Protected Attributes inherited from item_dim
mempool	memp
std::set< item_dim * >	children
item_dim *	parent
size_t	dimension

Detailed Description

This class represents the c_elegans system.

This class calculates the voltages and currents in the neural network of a c_elegans worm. In addition, it also allows for the ablation of specific neurons within the system to see how the system responds to the removal of neurons.

Definition at line 30 of file c_elegans.h.

Member Typedef Documentation

typedef Eigen::SparseMatrix<double, RowMajor> c_elegans::sparse_type

private

Definition at line 35 of file c_elegans.h.

Member Function Documentation

std::vector< std::string > c_elegans::dependencies ( ) const

virtual

Implements item_dim.

Definition at line 325 of file c_elegans.cpp.

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int c_elegans::dwdt ( ptr_passer  x, ptr_passer  dx, double  dt  )

virtual

Implements rhs_sde.

Definition at line 112 of file c_elegans.cpp.

int c_elegans::dxdt ( ptr_passer  x, ptr_passer  dx, double  dt  )

virtual

Implements rhs.

Definition at line 72 of file c_elegans.cpp.

void c_elegans::initial_condition ( ptr_passer  in, size_t  len  )

virtual

Reimplemented from rhs_type< double, rhs_sde >.

Definition at line 332 of file c_elegans.cpp.

void c_elegans::mod_w ( ptr_passer  w, double  t  )

virtual

Reimplemented from rhs_sde.

Definition at line 118 of file c_elegans.cpp.

void c_elegans::postprocess ( input &  in )

virtual

This function does the processing for the c_elegans class.

It initializes the various matrices and reads values from the input files

Reimplemented from item_dim.

Definition at line 148 of file c_elegans.cpp.

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std::string c_elegans::type ( ) const

virtual

Implements item.

Definition at line 126 of file c_elegans.cpp.

void c_elegans::update ( )

virtual

Reimplemented from item.

Definition at line 230 of file c_elegans.cpp.

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Member Data Documentation

std::vector<size_t> c_elegans::abl_neur

private

Definition at line 42 of file c_elegans.h.

double c_elegans::ad

private

Definition at line 40 of file c_elegans.h.

sparse_type c_elegans::AEchem_trans

private

Definition at line 36 of file c_elegans.h.

sparse_type c_elegans::AEchem_trans_full

private

Definition at line 36 of file c_elegans.h.

sparse_type c_elegans::ag_full

private

Definition at line 36 of file c_elegans.h.

constexpr size_t c_elegans::al_num = 4

staticprivate

Definition at line 34 of file c_elegans.h.

double c_elegans::ar

private

Definition at line 40 of file c_elegans.h.

double c_elegans::beta

private

Definition at line 40 of file c_elegans.h.

int c_elegans::cur_ind

private

Definition at line 31 of file c_elegans.h.

double c_elegans::cur_inj

private

Definition at line 43 of file c_elegans.h.

constexpr size_t c_elegans::dim_s = dim_v

staticprivate

Definition at line 39 of file c_elegans.h.

constexpr size_t c_elegans::dim_v = num_neur

staticprivate

Definition at line 38 of file c_elegans.h.

double c_elegans::dummy

private

Definition at line 32 of file c_elegans.h.

Array<double, num_neur, 1> c_elegans::Echem

private

Definition at line 37 of file c_elegans.h.

double c_elegans::EchemEx

private

Definition at line 40 of file c_elegans.h.

double c_elegans::EchemInh

private

Definition at line 40 of file c_elegans.h.

Array<double, num_neur, 1> c_elegans::eqS

private

Definition at line 37 of file c_elegans.h.

Array<double, num_neur, 1> c_elegans::eqV

private

Definition at line 37 of file c_elegans.h.

bool c_elegans::first_round

private

Definition at line 45 of file c_elegans.h.

double c_elegans::gchem

private

Definition at line 40 of file c_elegans.h.

double c_elegans::gelec

private

Definition at line 40 of file c_elegans.h.

bool c_elegans::has_gone

private

Definition at line 44 of file c_elegans.h.

std::vector<size_t> c_elegans::inj_nodes

private

Definition at line 41 of file c_elegans.h.

sparse_type c_elegans::laplacian

private

Definition at line 36 of file c_elegans.h.

double c_elegans::memG

private

Definition at line 40 of file c_elegans.h.

double c_elegans::memV

private

Definition at line 40 of file c_elegans.h.

constexpr size_t c_elegans::num_neur = 279

staticprivate

Definition at line 33 of file c_elegans.h.

Array<double, num_neur, 1> c_elegans::sig

private

Definition at line 37 of file c_elegans.h.

double c_elegans::tau

private

Definition at line 40 of file c_elegans.h.

Array<double, num_neur, 1> c_elegans::vmean

private

Definition at line 37 of file c_elegans.h.

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

• rhs/c_elegans.h
• rhs/c_elegans.cpp