rxd_extracellular.cpp File Reference

#include <../../nrnconf.h>
#include <stdio.h>
#include <assert.h>
#include <string.h>
#include "grids.h"
#include "rxd.h"
#include "nrnwrap_Python.h"
#include <cmath>
#include <ocmatrix.h>
#include <cfloat>

Go to the source code of this file.

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

Functions
static void	ecs_refresh_reactions (int)
void	set_num_threads_3D (const int n)
void	clear_rates_ecs (void)
Reaction *	ecs_create_reaction (int list_idx, int num_species, int num_params, int *species_ids, ECSReactionRate f, unsigned char *subregion, uint64_t *mc3d_start_indices, int mc3d_region_size, double *mc3d_mults)
NRN_EXPORT void	ics_register_reaction (int list_idx, int num_species, int num_params, int *species_id, uint64_t *mc3d_start_indices, int mc3d_region_size, double *mc3d_mults, ECSReactionRate f)
NRN_EXPORT void	ecs_register_reaction (int list_idx, int num_species, int num_params, int *species_id, ECSReactionRate f)
void	ecs_register_subregion_reaction_ecs (int list_idx, int num_species, int num_params, int *species_id, unsigned char *my_subregion, ECSReactionRate f)
ReactGridData *	create_threaded_reactions (const int n)
void *	ecs_do_reactions (void *dataptr)
static void	run_threaded_reactions (ReactGridData *tasks)
void	_fadvance_fixed_step_3D (void)
NRN_EXPORT void	scatter_concentrations (void)
int	ode_count (const int offset)
void	ecs_atolscale (double *y)
void	_ecs_ode_reinit (double *y)
void	_rhs_variable_step_ecs (const double *states, double *ydot)
void	_rhs_variable_step_helper (Grid_node *g, double const *const states, double *ydot)
void	ics_ode_solve (double dt, double *RHS, const double *states)
static int	solve_dd_clhs_tridiag (const int N, const double l_diag, const double diag, const double u_diag, const double lbc_diag, const double lbc_u_diag, const double ubc_l_diag, const double ubc_diag, double *const b, double *const c)
static void	ecs_dg_adi_x (ECS_Grid_node *g, const double dt, const int y, const int z, double const *const state, double *const RHS, double *const scratch)
static void	ecs_dg_adi_y (ECS_Grid_node *g, double const dt, int const x, int const z, double const *const state, double *const RHS, double *const scratch)
static void	ecs_dg_adi_z (ECS_Grid_node *g, double const dt, int const x, int const y, double const *const state, double *const RHS, double *const scratch)
static void *	ecs_do_dg_adi (void *dataptr)
void	ecs_run_threaded_dg_adi (const int i, const int j, ECS_Grid_node *g, ECSAdiDirection *ecs_adi_dir, const int n)
void	ecs_set_adi_homogeneous (ECS_Grid_node *g)

Variables
ReactGridData *	threaded_reactions_tasks
int	NUM_THREADS
TaskQueue *	AllTasks
double *	t_ptr
double *	states
Reaction *	ecs_reactions = NULL
int	states_cvode_offset

Macro Definition Documentation

loc

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

Definition at line 12 of file rxd_extracellular.cpp.

Function Documentation

_ecs_ode_reinit()

void _ecs_ode_reinit

(

double *

y

)

Definition at line 638 of file rxd_extracellular.cpp.

_fadvance_fixed_step_3D()

void _fadvance_fixed_step_3D

(

void

)

Definition at line 565 of file rxd_extracellular.cpp.

_rhs_variable_step_ecs()

void _rhs_variable_step_ecs	(	const double *	states,
		double *	ydot
	)

Definition at line 661 of file rxd_extracellular.cpp.

_rhs_variable_step_helper()

void _rhs_variable_step_helper	(	Grid_node *	g,
		double const *const	states,
		double *	ydot
	)

Definition at line 734 of file rxd_extracellular.cpp.

clear_rates_ecs()

void clear_rates_ecs

(

void

)

Definition at line 58 of file rxd_extracellular.cpp.

create_threaded_reactions()

ReactGridData* create_threaded_reactions

(

const int

n

)

Definition at line 225 of file rxd_extracellular.cpp.

ecs_atolscale()

void ecs_atolscale

(

double *

y

)

Definition at line 624 of file rxd_extracellular.cpp.

ecs_create_reaction()

Reaction* ecs_create_reaction	(	int	list_idx,
		int	num_species,
		int	num_params,
		int *	species_ids,
		ECSReactionRate	f,
		unsigned char *	subregion,
		uint64_t *	mc3d_start_indices,
		int	mc3d_region_size,
		double *	mc3d_mults
	)

Definition at line 88 of file rxd_extracellular.cpp.

ecs_dg_adi_x()

static void ecs_dg_adi_x ( ECS_Grid_node *  g, const double  dt, const int  y, const int  z, double const *const  state, double *const  RHS, double *const  scratch  )

static

Definition at line 1040 of file rxd_extracellular.cpp.

ecs_dg_adi_y()

static void ecs_dg_adi_y ( ECS_Grid_node *  g, double const  dt, int const  x, int const  z, double const *const  state, double *const  RHS, double *const  scratch  )

static

Definition at line 1155 of file rxd_extracellular.cpp.

ecs_dg_adi_z()

static void ecs_dg_adi_z ( ECS_Grid_node *  g, double const  dt, int const  x, int const  y, double const *const  state, double *const  RHS, double *const  scratch  )

static

Definition at line 1231 of file rxd_extracellular.cpp.

ecs_do_dg_adi()

static void* ecs_do_dg_adi ( void *  dataptr )

static

Definition at line 1297 of file rxd_extracellular.cpp.

ecs_do_reactions()

void* ecs_do_reactions

(

void *

dataptr

)

Definition at line 276 of file rxd_extracellular.cpp.

ecs_refresh_reactions()

static void ecs_refresh_reactions ( int  n )

static

Definition at line 34 of file rxd_extracellular.cpp.

ecs_register_reaction()

NRN_EXPORT void ecs_register_reaction	(	int	list_idx,
		int	num_species,
		int	num_params,
		int *	species_id,
		ECSReactionRate	f
	)

Definition at line 191 of file rxd_extracellular.cpp.

ecs_register_subregion_reaction_ecs()

void ecs_register_subregion_reaction_ecs	(	int	list_idx,
		int	num_species,
		int	num_params,
		int *	species_id,
		unsigned char *	my_subregion,
		ECSReactionRate	f
	)

Definition at line 208 of file rxd_extracellular.cpp.

ecs_run_threaded_dg_adi()

void ecs_run_threaded_dg_adi	(	const int	i,
		const int	j,
		ECS_Grid_node *	g,
		ECSAdiDirection *	ecs_adi_dir,
		const int	n
	)

Definition at line 1322 of file rxd_extracellular.cpp.

ecs_set_adi_homogeneous()

void ecs_set_adi_homogeneous

(

ECS_Grid_node *

g

)

Definition at line 1354 of file rxd_extracellular.cpp.

ics_ode_solve()

void ics_ode_solve	(	double	dt,
		double *	RHS,
		const double *	states
	)

Definition at line 891 of file rxd_extracellular.cpp.

ics_register_reaction()

NRN_EXPORT void ics_register_reaction	(	int	list_idx,
		int	num_species,
		int	num_params,
		int *	species_id,
		uint64_t *	mc3d_start_indices,
		int	mc3d_region_size,
		double *	mc3d_mults,
		ECSReactionRate	f
	)

Definition at line 165 of file rxd_extracellular.cpp.

ode_count()

int ode_count

(

const int

offset

)

Definition at line 613 of file rxd_extracellular.cpp.

run_threaded_reactions()

static void run_threaded_reactions ( ReactGridData *  tasks )

static

Definition at line 552 of file rxd_extracellular.cpp.

scatter_concentrations()

NRN_EXPORT void scatter_concentrations

(

void

)

Definition at line 596 of file rxd_extracellular.cpp.

set_num_threads_3D()

void set_num_threads_3D

(

const int

n

)

Definition at line 46 of file rxd_extracellular.cpp.

solve_dd_clhs_tridiag()

static int solve_dd_clhs_tridiag ( const int  N, const double  l_diag, const double  diag, const double  u_diag, const double  lbc_diag, const double  lbc_u_diag, const double  ubc_l_diag, const double  ubc_diag, double *const  b, double *const  c  )

static

Definition at line 957 of file rxd_extracellular.cpp.

Variable Documentation

AllTasks

TaskQueue* AllTasks

extern

Definition at line 41 of file rxd.cpp.

ecs_reactions

Reaction* ecs_reactions = NULL

Definition at line 27 of file rxd_extracellular.cpp.

NUM_THREADS

int NUM_THREADS

extern

Definition at line 34 of file rxd.cpp.

states

double* states

extern

Definition at line 75 of file rxd.cpp.

states_cvode_offset

int states_cvode_offset

Definition at line 29 of file rxd_extracellular.cpp.

t_ptr

double* t_ptr

extern

Definition at line 16 of file grids.cpp.

threaded_reactions_tasks

ReactGridData* threaded_reactions_tasks

Definition at line 20 of file rxd_extracellular.cpp.