#include <grids.h>

Inheritance diagram for ICS_Grid_node:

Public Member Functions
	ICS_Grid_node ()

	~ICS_Grid_node ()

	ICS_Grid_node (PyHocObject , long, long , long , long, long , long, long , long, double , double , double, bool, double, double )

void	divide_x_work (const int nthreads)

void	divide_y_work (const int nthreads)

void	divide_z_work (const int nthreads)

void	set_num_threads (const int n)

void	do_grid_currents (double *, double, int)

void	apply_node_flux3D (double dt, double *states)

void	volume_setup ()

int	dg_adi ()

void	variable_step_diffusion (const double states, double ydot)

void	variable_step_ode_solve (double *RHS, double dt)

void	hybrid_connections ()

void	variable_step_hybrid_connections (const double cvode_states_3d, double const ydot_3d, const double cvode_states_1d, double const ydot_1d)

void	scatter_grid_concentrations ()

void	run_threaded_ics_dg_adi (struct ICSAdiDirection *)

void	set_diffusion (double *, int)

void	do_multicompartment_reactions (double *)

void	initialize_multicompartment_reaction ()

void	clear_multicompartment_reaction ()

int	add_multicompartment_reaction (int, int *, int)

double *	set_rxd_currents (int, int , PyHocObject *)

Public Member Functions inherited from Grid_node
int	insert (int grid_list_index)

virtual	~Grid_node ()

Public Attributes
double *	_ics_alphas

long *	_neighbors

long *	_sorted_x_lines

long *	_sorted_y_lines

long *	_sorted_z_lines

long	_x_lines_length

long	_y_lines_length

long	_z_lines_length

long	_line_length_max

long	_num_nodes

long *	_nodes_per_thread

struct ICSAdiGridData *	ics_tasks

struct ICSAdiDirection *	ics_adi_dir_x

struct ICSAdiDirection *	ics_adi_dir_y

struct ICSAdiDirection *	ics_adi_dir_z

Public Attributes inherited from Grid_node
Grid_node *	next

double *	states

double *	states_x

double *	states_y

double *	states_z

double *	states_cur

int	size_x

int	size_y

int	size_z

double	dc_x

double	dc_y

double	dc_z

double	dx

double	dy

double	dz

bool	diffusable

bool	hybrid

BoundaryConditions *	bc

Hybrid_data *	hybrid_data

Concentration_Pair *	concentration_list

Current_Triple *	current_list

ssize_t	num_concentrations

ssize_t	num_currents

int	num_all_currents

int *	proc_offsets

int *	proc_num_currents

int *	proc_flux_offsets

int *	proc_num_fluxes

long *	current_dest

double *	all_currents

unsigned char	VARIABLE_ECS_VOLUME

double *	permeability

double *	alpha

double(*	get_alpha )(double *, int)

double(*	get_permeability )(double *, int)

double	atolscale

int64_t *	ics_surface_nodes_per_seg

int64_t *	ics_surface_nodes_per_seg_start_indices

std::vector< neuron::container::data_handle< double > >	ics_concentration_seg_handles

double **	ics_current_seg_ptrs

double *	ics_scale_factors

int	node_flux_count

long *	node_flux_idx

double *	node_flux_scale

PyObject **	node_flux_src

Detailed Description

Definition at line 250 of file grids.h.

Constructor & Destructor Documentation

◆ ICS_Grid_node() [1/2]

ICS_Grid_node::ICS_Grid_node ( )

Definition at line 233 of file grids.cpp.

◆ ~ICS_Grid_node()

ICS_Grid_node::~ICS_Grid_node ( )

Definition at line 1744 of file grids.cpp.

◆ ICS_Grid_node() [2/2]

ICS_Grid_node::ICS_Grid_node	(	PyHocObject *	my_states,
		long	num_nodes,
		long *	neighbors,
		long *	x_line_defs,
		long	x_lines_length,
		long *	y_line_defs,
		long	y_lines_length,
		long *	z_line_defs,
		long	z_lines_length,
		double *	dc,
		double *	dcgrid,
		double	dx,
		bool	is_diffusable,
		double	atolscale,
		double *	ics_alphas
	)

Definition at line 234 of file grids.cpp.

Member Function Documentation

◆ add_multicompartment_reaction()

int ICS_Grid_node::add_multicompartment_reaction	(	int	,
		int *	,
		int
	)

◆ apply_node_flux3D()

void ICS_Grid_node::apply_node_flux3D	(	double	dt,
		double *	states
	)

virtual

Implements Grid_node.

Definition at line 1638 of file grids.cpp.

◆ clear_multicompartment_reaction()

void ICS_Grid_node::clear_multicompartment_reaction ( )

◆ dg_adi()

int ICS_Grid_node::dg_adi ( )

virtual

Implements Grid_node.

Definition at line 1679 of file grids.cpp.

◆ divide_x_work()

void ICS_Grid_node::divide_x_work ( const int nthreads )

Definition at line 1302 of file grids.cpp.

◆ divide_y_work()

void ICS_Grid_node::divide_y_work ( const int nthreads )

Definition at line 1399 of file grids.cpp.

◆ divide_z_work()

void ICS_Grid_node::divide_z_work ( const int nthreads )

Definition at line 1496 of file grids.cpp.

◆ do_grid_currents()

void ICS_Grid_node::do_grid_currents	(	double *	output,
		double	dt,
		int
	)

virtual

Implements Grid_node.

Definition at line 1647 of file grids.cpp.

◆ do_multicompartment_reactions()

void ICS_Grid_node::do_multicompartment_reactions ( double * )

◆ hybrid_connections()

void ICS_Grid_node::hybrid_connections ( )

virtual

Implements Grid_node.

Definition at line 1717 of file grids.cpp.

◆ initialize_multicompartment_reaction()

void ICS_Grid_node::initialize_multicompartment_reaction ( )

◆ run_threaded_ics_dg_adi()

void ICS_Grid_node::run_threaded_ics_dg_adi ( struct ICSAdiDirection * ics_adi_dir )

Definition at line 775 of file rxd_intracellular.cpp.

◆ scatter_grid_concentrations()

void ICS_Grid_node::scatter_grid_concentrations ( )

virtual

Implements Grid_node.

Definition at line 1728 of file grids.cpp.

◆ set_diffusion()

void ICS_Grid_node::set_diffusion	(	double *	dc,
		int	length
	)

virtual

Implements Grid_node.

Definition at line 556 of file grids.cpp.

◆ set_num_threads()

void ICS_Grid_node::set_num_threads ( const int n )

virtual

Implements Grid_node.

Definition at line 1595 of file grids.cpp.

◆ set_rxd_currents()

double* ICS_Grid_node::set_rxd_currents	(	int	,
		int *	,
		PyHocObject **
	)

◆ variable_step_diffusion()

void ICS_Grid_node::variable_step_diffusion	(	const double *	states,
		double *	ydot
	)

virtual

Implements Grid_node.

Definition at line 1692 of file grids.cpp.

◆ variable_step_hybrid_connections()

void ICS_Grid_node::variable_step_hybrid_connections	(	const double *	cvode_states_3d,
		double *const	ydot_3d,
		const double *	cvode_states_1d,
		double *const	ydot_1d
	)

virtual

Implements Grid_node.

Definition at line 1721 of file grids.cpp.

◆ variable_step_ode_solve()

void ICS_Grid_node::variable_step_ode_solve	(	double *	RHS,
		double	dt
	)

virtual

Implements Grid_node.

Definition at line 1711 of file grids.cpp.

◆ volume_setup()

void ICS_Grid_node::volume_setup ( )

virtual

Implements Grid_node.

Definition at line 1667 of file grids.cpp.

Member Data Documentation

◆ _ics_alphas

double* ICS_Grid_node::_ics_alphas

Definition at line 255 of file grids.h.

◆ _line_length_max

long ICS_Grid_node::_line_length_max

Definition at line 272 of file grids.h.

◆ _neighbors

long* ICS_Grid_node::_neighbors

Definition at line 258 of file grids.h.

◆ _nodes_per_thread

long* ICS_Grid_node::_nodes_per_thread

Definition at line 278 of file grids.h.

◆ _num_nodes

long ICS_Grid_node::_num_nodes

Definition at line 275 of file grids.h.

◆ _sorted_x_lines

long* ICS_Grid_node::_sorted_x_lines

Definition at line 262 of file grids.h.

◆ _sorted_y_lines

long* ICS_Grid_node::_sorted_y_lines

Definition at line 263 of file grids.h.

◆ _sorted_z_lines

long* ICS_Grid_node::_sorted_z_lines

Definition at line 264 of file grids.h.

◆ _x_lines_length

long ICS_Grid_node::_x_lines_length

Definition at line 267 of file grids.h.

◆ _y_lines_length

long ICS_Grid_node::_y_lines_length

Definition at line 268 of file grids.h.

◆ _z_lines_length

long ICS_Grid_node::_z_lines_length

Definition at line 269 of file grids.h.

◆ ics_adi_dir_x

struct ICSAdiDirection* ICS_Grid_node::ics_adi_dir_x

Definition at line 282 of file grids.h.

◆ ics_adi_dir_y

struct ICSAdiDirection* ICS_Grid_node::ics_adi_dir_y

Definition at line 283 of file grids.h.

◆ ics_adi_dir_z

struct ICSAdiDirection* ICS_Grid_node::ics_adi_dir_z

Definition at line 284 of file grids.h.

◆ ics_tasks

struct ICSAdiGridData* ICS_Grid_node::ics_tasks

Definition at line 281 of file grids.h.

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

/home/docs/checkouts/readthedocs.org/user_builds/nrn/checkouts/3466/src/nrnpython/grids.h
/home/docs/checkouts/readthedocs.org/user_builds/nrn/checkouts/3466/src/nrnpython/grids.cpp
/home/docs/checkouts/readthedocs.org/user_builds/nrn/checkouts/3466/src/nrnpython/rxd_intracellular.cpp

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ICS_Grid_node() [1/2]

◆ ~ICS_Grid_node()

◆ ICS_Grid_node() [2/2]

Member Function Documentation

◆ add_multicompartment_reaction()

◆ apply_node_flux3D()

◆ clear_multicompartment_reaction()

◆ dg_adi()

◆ divide_x_work()

◆ divide_y_work()

◆ divide_z_work()

◆ do_grid_currents()

◆ do_multicompartment_reactions()

◆ hybrid_connections()

◆ initialize_multicompartment_reaction()

◆ run_threaded_ics_dg_adi()

◆ scatter_grid_concentrations()

◆ set_diffusion()

◆ set_num_threads()

◆ set_rxd_currents()

◆ variable_step_diffusion()

◆ variable_step_hybrid_connections()

◆ variable_step_ode_solve()

◆ volume_setup()

Member Data Documentation

◆ _ics_alphas

◆ _line_length_max

◆ _neighbors

◆ _nodes_per_thread

◆ _num_nodes

◆ _sorted_x_lines

◆ _sorted_y_lines

◆ _sorted_z_lines

◆ _x_lines_length

◆ _y_lines_length

◆ _z_lines_length

◆ ics_adi_dir_x

◆ ics_adi_dir_y

◆ ics_adi_dir_z

◆ ics_tasks