#include <pthread.h>
#include <matrix2.h>

Classes
struct	OcPtrVector_

struct	ReactSet

struct	ReactGridData

struct	CurrentData

struct	SpeciesIndexList

struct	ICSReactions

struct	ReactionVariables

struct	TaskList

struct	TaskQueue

Macros
#define	v_get_val(x, i) ((x)->ve[(i)])

#define	m_get_val(A, i, j) ((A)->me[(i)][(j)])

#define	SPECIES_ABSENT -1

#define	PREFETCH 4

Typedefs
typedef void(*	fptr) (void)

typedef struct OcPtrVector_	OcPtrVector

typedef struct SpeciesIndexList	SpeciesIndexList

typedef struct ICSReactions	ICSReactions

typedef struct TaskList	TaskList

typedef struct TaskQueue	TaskQueue

Functions
void	set_num_threads (const int)

void	_fadvance (void)

void	_fadvance_fixed_step_3D (void)

int	get_num_threads (void)

void	ecs_set_adi_tort (ECS_Grid_node *)

void	ecs_set_adi_vol (ECS_Grid_node *)

void	ecs_set_adi_homogeneous (ECS_Grid_node *)

void	dg_transfer_data (AdiLineData const, double const, int const, int const, int const)

void	ecs_run_threaded_dg_adi (const int, const int, ECS_Grid_node , ECSAdiDirection , const int)

ReactGridData *	create_threaded_reactions (const int)

void *	do_reactions (void *)

void	current_reaction (double *states)

void	run_threaded_deltas (ICS_Grid_node g, ICSAdiDirection ics_adi_dir)

void	run_threaded_ics_dg_adi (ICS_Grid_node g, ICSAdiDirection ics_adi_dir)

void	ics_dg_adi_x (ICS_Grid_node g, int, int, int, double, double , double , double , double , double , double *)

void	ics_dg_adi_y (ICS_Grid_node g, int, int, int, double, double , double , double , double , double , double *)

void	ics_dg_adi_z (ICS_Grid_node g, int, int, int, double, double , double , double , double , double , double *)

void	ics_dg_adi_x_inhom (ICS_Grid_node g, int, int, int, double, double , double , double , double , double , double *)

void	ics_dg_adi_y_inhom (ICS_Grid_node g, int, int, int, double, double , double , double , double , double , double *)

void	ics_dg_adi_z_inhom (ICS_Grid_node g, int, int, int, double, double , double , double , double , double , double *)

void	_rhs_variable_step (const double , double )

void	_ode_reinit (double *)

int	ode_count (const int)

void	scatter_concentrations (void)

int	find (const int, const int, const int, const int, const int)

void	_ics_hybrid_helper (ICS_Grid_node *)

void	_ics_variable_hybrid_helper (ICS_Grid_node , const double , double const, const double , double *const)

void	_ics_rhs_variable_step_helper (ICS_Grid_node , double const const, double *)

void	_rhs_variable_step_helper (Grid_node , double const const, double *)

void	ics_ode_solve (double, double , const double )

void	ics_ode_solve_helper (ICS_Grid_node , double, double )

void	_rhs_variable_step_helper_tort (Grid_node , double const const, double *)

void	_rhs_variable_step_helper_vol (Grid_node , double const const, double *)

void	set_num_threads_3D (int n)

void	_rhs_variable_step_ecs (const double , double )

void	clear_rates_ecs ()

void	do_ics_reactions (double , double , double , double )

void	get_all_reaction_rates (double , double , double *)

void	_ecs_ode_reinit (double *)

void	do_currents (Grid_node , double , double, int)

void	TaskQueue_add_task (TaskQueue , void (task)(void args), void , void )

void *	TaskQueue_exe_tasks (void *)

void	start_threads (const int)

void	TaskQueue_sync (TaskQueue *)

void	ecs_atolscale (double *)

void	apply_node_flux3D (Grid_node , double, double )

Macro Definition Documentation

◆ m_get_val

#define m_get_val	(	A,
		i,
		j
	)	((A)->me[(i)][(j)])

Definition at line 5 of file rxd.h.

◆ PREFETCH

#define PREFETCH 4

Definition at line 7 of file rxd.h.

◆ SPECIES_ABSENT

#define SPECIES_ABSENT -1

Definition at line 6 of file rxd.h.

◆ v_get_val

#define v_get_val	(	x,
		i
	)	((x)->ve[(i)])

Definition at line 4 of file rxd.h.

Typedef Documentation

◆ fptr

typedef void(* fptr) (void)

Definition at line 9 of file rxd.h.

◆ ICSReactions

typedef struct ICSReactions ICSReactions

◆ OcPtrVector

typedef struct OcPtrVector_ OcPtrVector

◆ SpeciesIndexList

typedef struct SpeciesIndexList SpeciesIndexList

◆ TaskList

typedef struct TaskList TaskList

◆ TaskQueue

typedef struct TaskQueue TaskQueue

Function Documentation

◆ _ecs_ode_reinit()

void _ecs_ode_reinit ( double * )

Definition at line 711 of file rxd_extracellular.cpp.

◆ _fadvance()

void _fadvance ( void )

Definition at line 1338 of file rxd.cpp.

◆ _fadvance_fixed_step_3D()

void _fadvance_fixed_step_3D ( void )

Definition at line 637 of file rxd_extracellular.cpp.

◆ _ics_hybrid_helper()

void _ics_hybrid_helper ( ICS_Grid_node * )

Definition at line 1361 of file rxd_intracellular.cpp.

◆ _ics_rhs_variable_step_helper()

void _ics_rhs_variable_step_helper	(	ICS_Grid_node *	,
		double const *	const,
		double *
	)

Definition at line 800 of file rxd_intracellular.cpp.

◆ _ics_variable_hybrid_helper()

void _ics_variable_hybrid_helper	(	ICS_Grid_node *	,
		const double *	,
		double *	const,
		const double *	,
		double *	const
	)

Definition at line 1416 of file rxd_intracellular.cpp.

◆ _ode_reinit()

void _ode_reinit ( double * )

Definition at line 1382 of file rxd.cpp.

◆ _rhs_variable_step()

void _rhs_variable_step	(	const double *	,
		double *
	)

Definition at line 1407 of file rxd.cpp.

◆ _rhs_variable_step_ecs()

void _rhs_variable_step_ecs	(	const double *	,
		double *
	)

Definition at line 733 of file rxd_extracellular.cpp.

◆ _rhs_variable_step_helper()

void _rhs_variable_step_helper	(	Grid_node *	,
		double const *	const,
		double *
	)

Definition at line 808 of file rxd_extracellular.cpp.

◆ _rhs_variable_step_helper_tort()

void _rhs_variable_step_helper_tort	(	Grid_node *	,
		double const *	const,
		double *
	)

Definition at line 762 of file rxd_vol.cpp.

◆ _rhs_variable_step_helper_vol()

void _rhs_variable_step_helper_vol	(	Grid_node *	,
		double const *	const,
		double *
	)

Definition at line 870 of file rxd_vol.cpp.

◆ apply_node_flux3D()

void apply_node_flux3D	(	Grid_node *	,
		double	,
		double *
	)

◆ clear_rates_ecs()

void clear_rates_ecs ( )

Definition at line 64 of file rxd_extracellular.cpp.

◆ create_threaded_reactions()

ReactGridData* create_threaded_reactions ( const int )

Definition at line 231 of file rxd_extracellular.cpp.

◆ current_reaction()

void current_reaction ( double * states )

◆ dg_transfer_data()

void dg_transfer_data	(	AdiLineData *	const,
		double *	const,
		int	const,
		int	const,
		int	const
	)

◆ do_currents()

void do_currents	(	Grid_node *	,
		double *	,
		double	,
		int
	)

◆ do_ics_reactions()

void do_ics_reactions	(	double *	,
		double *	,
		double *	,
		double *
	)

Definition at line 2009 of file rxd.cpp.

◆ do_reactions()

void* do_reactions ( void * )

◆ ecs_atolscale()

void ecs_atolscale ( double * )

Definition at line 696 of file rxd_extracellular.cpp.

◆ ecs_run_threaded_dg_adi()

void ecs_run_threaded_dg_adi	(	const int	,
		const int	,
		ECS_Grid_node *	,
		ECSAdiDirection *	,
		const int
	)

Definition at line 1342 of file rxd_extracellular.cpp.

◆ ecs_set_adi_homogeneous()

void ecs_set_adi_homogeneous ( ECS_Grid_node * )

Definition at line 1371 of file rxd_extracellular.cpp.

◆ ecs_set_adi_tort()

void ecs_set_adi_tort ( ECS_Grid_node * )

Definition at line 748 of file rxd_vol.cpp.

◆ ecs_set_adi_vol()

void ecs_set_adi_vol ( ECS_Grid_node * )

Definition at line 412 of file rxd_vol.cpp.

◆ find()

int find	(	const int	,
		const int	,
		const int	,
		const int	,
		const int
	)

◆ get_all_reaction_rates()

void get_all_reaction_rates	(	double *	,
		double *	,
		double *
	)

Definition at line 2019 of file rxd.cpp.

◆ get_num_threads()

int get_num_threads ( void )

Definition at line 1333 of file rxd.cpp.

◆ ics_dg_adi_x()

void ics_dg_adi_x	(	ICS_Grid_node *	g,
		int	,
		int	,
		int	,
		double	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *
	)

Definition at line 450 of file rxd_intracellular.cpp.

◆ ics_dg_adi_x_inhom()

void ics_dg_adi_x_inhom	(	ICS_Grid_node *	g,
		int	,
		int	,
		int	,
		double	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *
	)

Definition at line 253 of file rxd_intracellular.cpp.

◆ ics_dg_adi_y()

void ics_dg_adi_y	(	ICS_Grid_node *	g,
		int	,
		int	,
		int	,
		double	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *
	)

Definition at line 518 of file rxd_intracellular.cpp.

◆ ics_dg_adi_y_inhom()

void ics_dg_adi_y_inhom	(	ICS_Grid_node *	g,
		int	,
		int	,
		int	,
		double	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *
	)

Definition at line 325 of file rxd_intracellular.cpp.

◆ ics_dg_adi_z()

void ics_dg_adi_z	(	ICS_Grid_node *	g,
		int	,
		int	,
		int	,
		double	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *
	)

Definition at line 581 of file rxd_intracellular.cpp.

◆ ics_dg_adi_z_inhom()

void ics_dg_adi_z_inhom	(	ICS_Grid_node *	g,
		int	,
		int	,
		int	,
		double	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *	,
		double *
	)

Definition at line 388 of file rxd_intracellular.cpp.

◆ ics_ode_solve()

void ics_ode_solve	(	double	,
		double *	,
		const double *
	)

Definition at line 958 of file rxd_extracellular.cpp.

◆ ics_ode_solve_helper()

void ics_ode_solve_helper	(	ICS_Grid_node *	,
		double	,
		double *
	)

Definition at line 1276 of file rxd_intracellular.cpp.

◆ ode_count()

int ode_count ( const int )

Definition at line 685 of file rxd_extracellular.cpp.

◆ run_threaded_deltas()

void run_threaded_deltas	(	ICS_Grid_node *	g,
		ICSAdiDirection *	ics_adi_dir
	)

Definition at line 233 of file rxd_intracellular.cpp.

◆ run_threaded_ics_dg_adi()

void run_threaded_ics_dg_adi	(	ICS_Grid_node *	g,
		ICSAdiDirection *	ics_adi_dir
	)

◆ scatter_concentrations()

void scatter_concentrations ( void )

Definition at line 669 of file rxd_extracellular.cpp.

◆ set_num_threads()

void set_num_threads ( const int )

Definition at line 1287 of file rxd.cpp.

◆ set_num_threads_3D()

void set_num_threads_3D ( int n )

Definition at line 49 of file rxd_extracellular.cpp.

◆ start_threads()

void start_threads ( const int )

Definition at line 1188 of file rxd.cpp.

◆ TaskQueue_add_task()

void TaskQueue_add_task	(	TaskQueue *	,
		void ()(void *args)	task,
		void *	,
		void *
	)

◆ TaskQueue_exe_tasks()

void* TaskQueue_exe_tasks ( void * )

Definition at line 1242 of file rxd.cpp.

◆ TaskQueue_sync()

void TaskQueue_sync ( TaskQueue * )

Definition at line 1324 of file rxd.cpp.

Classes

Macros

Typedefs

Functions