#include <stdio.h>
#include <assert.h>
#include <nrnmpi.h>
#include "nrn_pyhocobject.h"
#include "nrnwrap_Python.h"

Classes
struct	Hybrid_data

struct	Concentration_Pair

struct	Current_Triple

struct	Reaction

struct	AdiLineData

struct	BoundaryConditions

class	Grid_node

class	ECS_Grid_node

struct	ECSAdiDirection

struct	ECSAdiGridData

class	ICS_Grid_node

struct	ICSAdiDirection

struct	ICSAdiGridData

Macros
#define	IDX(x, y, z) ((z) + (y) g->size_z + (x) g->size_z * g->size_y)

#define	INDEX(x, y, z) ((z) + (y) grid->size_z + (x) grid->size_z * grid->size_y)

#define	ALPHA(x, y, z) (g->get_alpha(g->alpha, IDX(x, y, z)))

#define	VOLFRAC(idx) (g->get_alpha(g->alpha, idx))

#define	TORT(idx) (g->get_permeability(g->permeability, idx))

#define	PERM(x, y, z) (g->get_permeability(g->permeability, IDX(x, y, z)))

#define	SQ(x) ((x) * (x))

#define	CU(x) ((x) * (x) * (x))

#define	TRUE 1

#define	FALSE 0

#define	TORTUOSITY 2

#define	VOLUME_FRACTION 3

#define	ICS_ALPHA 4

#define	NEUMANN 0

#define	DIRICHLET 1

#define	MAX(a, b) ((a) > (b) ? (a) : (b))

#define	MIN(a, b) ((a) < (b) ? (a) : (b))

Typedefs
using	ReactionRate = void(double , double , double *, double , double , double , double , double *, double)

using	ECSReactionRate = void(double , double , double , double )

Functions
void	make_dt_ptr (PyHocObject *my_dt_ptr)

int	ECS_insert (int grid_list_index, PyHocObject my_states, int my_num_states_x, int my_num_states_y, int my_num_states_z, double my_dc_x, double my_dc_y, double my_dc_z, double my_dx, double my_dy, double my_dz, PyHocObject my_alpha, PyHocObject *my_permeability, int, double, double)

Grid_node *	ICS_make_Grid (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 dcs, double dx, bool is_diffusable, double atolscale, double *ics_alphas)

int	ICS_insert (int grid_list_index, 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 dcs, double dx, bool is_diffusable, double atolscale, double *ics_alphas)

int	ICS_insert_inhom (int grid_list_index, 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 dcs, double dx, bool is_diffusable, double atolscale, double *ics_alphas)

int	set_diffusion (int, int, double *, int)

int	remove (Grid_node *head, Grid_node find)

void	empty_list (int list_index)

void	apply_node_flux (int, long , double , PyObject *, double, double )

Variables
double *	dt_ptr

double *	t_ptr

Grid_node *	Parallel_grids [100]

Macro Definition Documentation

◆ ALPHA

#define ALPHA	(	x,
		y,
		z
	)	(g->get_alpha(g->alpha, IDX(x, y, z)))

Definition at line 16 of file grids.h.

◆ CU

#define CU ( x ) ((x) * (x) * (x))

Definition at line 21 of file grids.h.

◆ DIRICHLET

#define DIRICHLET 1

Definition at line 29 of file grids.h.

◆ FALSE

#define FALSE 0

Definition at line 23 of file grids.h.

◆ ICS_ALPHA

#define ICS_ALPHA 4

Definition at line 26 of file grids.h.

◆ IDX

#define IDX	(	x,
		y,
		z
	)	((z) + (y) g->size_z + (x) g->size_z * g->size_y)

Definition at line 14 of file grids.h.

◆ INDEX

#define INDEX	(	x,
		y,
		z
	)	((z) + (y) grid->size_z + (x) grid->size_z * grid->size_y)

Definition at line 15 of file grids.h.

◆ MAX

#define MAX	(	a,
		b
	)	((a) > (b) ? (a) : (b))

Definition at line 31 of file grids.h.

◆ MIN

#define MIN	(	a,
		b
	)	((a) < (b) ? (a) : (b))

Definition at line 32 of file grids.h.

◆ NEUMANN

#define NEUMANN 0

Definition at line 28 of file grids.h.

◆ PERM

#define PERM	(	x,
		y,
		z
	)	(g->get_permeability(g->permeability, IDX(x, y, z)))

Definition at line 19 of file grids.h.

◆ SQ

#define SQ ( x ) ((x) * (x))

Definition at line 20 of file grids.h.

◆ TORT

#define TORT ( idx ) (g->get_permeability(g->permeability, idx))

Definition at line 18 of file grids.h.

◆ TORTUOSITY

#define TORTUOSITY 2

Definition at line 24 of file grids.h.

◆ TRUE

#define TRUE 1

Definition at line 22 of file grids.h.

◆ VOLFRAC

#define VOLFRAC ( idx ) (g->get_alpha(g->alpha, idx))

Definition at line 17 of file grids.h.

◆ VOLUME_FRACTION

#define VOLUME_FRACTION 3

Definition at line 25 of file grids.h.

Typedef Documentation

◆ ECSReactionRate

using ECSReactionRate = void(double*, double*, double*, double*)

Definition at line 58 of file grids.h.

◆ ReactionRate

using ReactionRate = void(double**, double**, double**, double*, double*, double*, double*, double**, double)

Definition at line 56 of file grids.h.

Function Documentation

◆ apply_node_flux()

void apply_node_flux	(	int	n,
		long *	index,
		double *	scale,
		PyObject **	source,
		double	dt,
		double *	states
	)

Definition at line 314 of file rxd.cpp.

◆ ECS_insert()

int ECS_insert	(	int	grid_list_index,
		PyHocObject *	my_states,
		int	my_num_states_x,
		int	my_num_states_y,
		int	my_num_states_z,
		double	my_dc_x,
		double	my_dc_y,
		double	my_dc_z,
		double	my_dx,
		double	my_dy,
		double	my_dz,
		PyHocObject *	my_alpha,
		PyHocObject *	my_permeability,
		int	bc,
		double	bc_value,
		double	atolscale
	)

Definition at line 198 of file grids.cpp.

◆ empty_list()

void empty_list ( int list_index )

Definition at line 801 of file grids.cpp.

◆ ICS_insert()

int ICS_insert	(	int	grid_list_index,
		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 *	dcs,
		double	dx,
		bool	is_diffusable,
		double	atolscale,
		double *	ics_alphas
	)

Definition at line 385 of file grids.cpp.

◆ ICS_insert_inhom()

int ICS_insert_inhom	(	int	grid_list_index,
		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 *	dcs,
		double	dx,
		bool	is_diffusable,
		double	atolscale,
		double *	ics_alphas
	)

Definition at line 419 of file grids.cpp.

◆ ICS_make_Grid()

Grid_node* ICS_make_Grid	(	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 *	dcs,
		double	dx,
		bool	is_diffusable,
		double	atolscale,
		double *	ics_alphas
	)

◆ make_dt_ptr()

void make_dt_ptr ( PyHocObject * my_dt_ptr )

◆ remove()

int remove	(	Grid_node **	head,
		Grid_node *	find
	)

Definition at line 769 of file grids.cpp.

◆ set_diffusion()

int set_diffusion	(	int	grid_list_index,
		int	grid_id,
		double *	dc,
		int	length
	)

Definition at line 453 of file grids.cpp.

Variable Documentation

◆ dt_ptr

double* dt_ptr

extern

Definition at line 15 of file grids.cpp.

◆ Parallel_grids

Grid_node* Parallel_grids[100]

extern

Definition at line 17 of file grids.cpp.

◆ t_ptr

double* t_ptr

extern

Definition at line 16 of file grids.cpp.

Classes

Macros

Typedefs

Functions

Variables

Macro Definition Documentation

◆ ALPHA

◆ CU

◆ DIRICHLET

◆ FALSE

◆ ICS_ALPHA

◆ IDX

◆ INDEX

◆ MAX

◆ MIN

◆ NEUMANN

◆ PERM

◆ SQ

◆ TORT

◆ TORTUOSITY

◆ TRUE

◆ VOLFRAC

◆ VOLUME_FRACTION

Typedef Documentation

◆ ECSReactionRate

◆ ReactionRate

Function Documentation

◆ apply_node_flux()

◆ ECS_insert()

◆ empty_list()

◆ ICS_insert()

◆ ICS_insert_inhom()

◆ ICS_make_Grid()

◆ make_dt_ptr()

◆ remove()

◆ set_diffusion()

Variable Documentation

◆ dt_ptr

◆ Parallel_grids

◆ t_ptr