#include <../../nrnconf.h>
#include <stdio.h>
#include <assert.h>
#include <string.h>
#include "grids.h"
#include <cfloat>
#include "rxd.h"
#include <../nrnoc/section.h>
#include <../nrnoc/nrn_ansi.h>
#include <../nrnoc/multicore.h>
#include "nrnwrap_Python.h"
#include "nrnpython.h"
#include <thread>
#include <vector>
#include "ocmatrix.h"
#include "ivocvect.h"
#include <nanobind/nanobind.h>

Namespaces
	nrn

	nrn::rxd

Functions
static void	ode_solve (double, double , double )

static void	free_zvi_child ()

static void	transfer_to_legacy ()

static void *	allocopy (void *src, size_t size)

NRN_EXPORT void	rxd_set_no_diffusion ()

NRN_EXPORT void	free_curr_ptrs ()

NRN_EXPORT void	free_conc_ptrs ()

NRN_EXPORT void	rxd_setup_curr_ptrs (int num_currents, int curr_index, double curr_scale, PyHocObject **curr_ptrs)

NRN_EXPORT void	rxd_setup_conc_ptrs (int conc_count, int conc_index, PyHocObject *conc_ptrs)

NRN_EXPORT void	rxd_include_node_flux3D (int grid_count, int grid_counts, int grids, long index, double scales, PyObject **sources)

NRN_EXPORT void	rxd_include_node_flux1D (int n, long index, double scales, PyObject **sources)

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

static void	apply_node_flux1D (double dt, double *states)

NRN_EXPORT void	rxd_set_euler_matrix (int nrow, int nnonzero, long nonzero_i, long nonzero_j, double nonzero_values, double c_diagonal)

static void	add_currents (double *result)

static void	mul (int nnonzero, long nonzero_i, long nonzero_j, const double nonzero_values, const double v, double *result)

NRN_EXPORT void	set_setup (fptr *setup_fn)

NRN_EXPORT void	set_initialize (fptr *initialize_fn)

NRN_EXPORT void	set_setup_matrices (fptr *setup_matrices)

NRN_EXPORT void	set_setup_units (fptr *setup_units)

static void	nrn_tree_solve (double a, double b, double c, double dbase, double rhs, long pindex, long n, double dt)

static void	ode_abs_tol (double *p1)

static void	free_currents ()

NRN_EXPORT void	setup_currents (int num_currents, int num_fluxes, int num_species, int node_idxs, double scales, PyHocObject ptrs, int mapped, int *mapped_ecs)

static void	_currents (double *rhs)

NRN_EXPORT int	rxd_nonvint_block (int method, int size, double p1, double p2, int)

NRN_EXPORT void	register_rate (int nspecies, int nparam, int nregions, int nseg, int sidx, int necs, int necsparam, int ecs_ids, int ecsidx, int nmult, double mult, PyHocObject *vptrs, ReactionRate f)

NRN_EXPORT void	clear_rates ()

NRN_EXPORT void	species_atolscale (int id, double scale, int len, int *idx)

NRN_EXPORT void	remove_species_atolscale (int id)

NRN_EXPORT void	setup_solver (double my_states, int my_num_states, long zvi, int num_zvi)

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

void	TaskQueue_exe_tasks (std::size_t thread_index, TaskQueue *q)

NRN_EXPORT void	set_num_threads (const int n)

void	TaskQueue_sync (TaskQueue *q)

NRN_EXPORT int	get_num_threads (void)

void	_fadvance (void)

void	_ode_reinit (double *y)

void	_rhs_variable_step (const double p1, double p2)

void	get_reaction_rates (ICSReactions react, double states, double rates, double ydot)

void	solve_reaction (ICSReactions react, double states, double bval, double cvode_states, double *cvode_b)

void	do_ics_reactions (double states, double b, double cvode_states, double cvode_b)

void	get_all_reaction_rates (double states, double rates, double *ydot)

Variables
PyTypeObject *	hocobject_type

int	structure_change_cnt

int	states_cvode_offset

int	prev_structure_change_cnt = 0

unsigned char	initialized = FALSE

NrnThread *	nrn_threads

int	NUM_THREADS = 1

std::vector< std::thread >	nrn::rxd::Threads

TaskQueue	nrn::rxd::task_queue

TaskQueue *	AllTasks {&nrn::rxd::task_queue}

double *	dt_ptr

double *	t_ptr

fptr *	_setup

fptr *	_initialize

fptr *	_setup_matrices

fptr *	_setup_units

unsigned char	diffusion = FALSE

int	_rxd_euler_nrow = 0

int	_rxd_euler_nnonzero = 0

int	_rxd_num_zvi = 0

long *	_rxd_euler_nonzero_i = NULL

long *	_rxd_euler_nonzero_j = NULL

double *	_rxd_euler_nonzero_values = NULL

long *	_rxd_zero_volume_indices = NULL

double *	_rxd_a = NULL

double *	_rxd_b = NULL

double *	_rxd_c = NULL

double *	_rxd_d = NULL

long *	_rxd_p = NULL

unsigned int *	_rxd_zvi_child_count = NULL

long **	_rxd_zvi_child = NULL

static int	_cvode_offset

static int	_ecs_count

ICSReactions *	_reactions = NULL

SpeciesIndexList *	species_indices = NULL

double *	states

unsigned int	num_states = 0

int	_num_reactions = 0

int	_curr_count

int *	_curr_indices = NULL

double *	_curr_scales = NULL

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

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

int	_conc_count

int *	_conc_indices = NULL

int	_memb_curr_total = 0

int	_memb_curr_nodes = 0

int	_memb_count = 0

double *	_rxd_flux_scale

double *	_rxd_induced_currents_scale

int *	_cur_node_indices

int *	_memb_species_count

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

int **	_memb_cur_charges

int ***	_memb_cur_mapped

int ***	_memb_cur_mapped_ecs

double *	_rxd_induced_currents = NULL

ECS_Grid_node **	_rxd_induced_currents_grid = NULL

unsigned char	_membrane_flux = FALSE

int *	_membrane_lookup

int	_node_flux_count = 0

long *	_node_flux_idx = NULL

double *	_node_flux_scale = NULL

PyObject **	_node_flux_src = NULL

Function Documentation

◆ _currents()

static void _currents ( double * rhs )

static

Definition at line 743 of file rxd.cpp.

◆ _fadvance()

void _fadvance ( void )

Definition at line 1268 of file rxd.cpp.

◆ _ode_reinit()

void _ode_reinit ( double * y )

Definition at line 1317 of file rxd.cpp.

◆ _rhs_variable_step()

void _rhs_variable_step	(	const double *	p1,
		double *	p2
	)

Definition at line 1336 of file rxd.cpp.

◆ add_currents()

static void add_currents ( double * result )

static

Definition at line 443 of file rxd.cpp.

◆ allocopy()

static void* allocopy	(	void *	src,
		size_t	size
	)

inlinestatic

Definition at line 139 of file rxd.cpp.

◆ 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.

◆ apply_node_flux1D()

static void apply_node_flux1D	(	double	dt,
		double *	states
	)

static

Definition at line 354 of file rxd.cpp.

◆ clear_rates()

NRN_EXPORT void clear_rates ( )

Definition at line 1013 of file rxd.cpp.

◆ do_ics_reactions()

void do_ics_reactions	(	double *	states,
		double *	b,
		double *	cvode_states,
		double *	cvode_b
	)

Definition at line 1752 of file rxd.cpp.

◆ free_conc_ptrs()

NRN_EXPORT void free_conc_ptrs ( )

Definition at line 171 of file rxd.cpp.

◆ free_curr_ptrs()

NRN_EXPORT void free_curr_ptrs ( )

Definition at line 160 of file rxd.cpp.

◆ free_currents()

static void free_currents ( )

static

Definition at line 610 of file rxd.cpp.

◆ free_zvi_child()

static void free_zvi_child ( )

static

Definition at line 117 of file rxd.cpp.

◆ get_all_reaction_rates()

void get_all_reaction_rates	(	double *	states,
		double *	rates,
		double *	ydot
	)

Definition at line 1760 of file rxd.cpp.

◆ get_num_threads()

NRN_EXPORT int get_num_threads ( void )

Definition at line 1263 of file rxd.cpp.

◆ get_reaction_rates()

void get_reaction_rates	(	ICSReactions *	react,
		double *	states,
		double *	rates,
		double *	ydot
	)

Definition at line 1433 of file rxd.cpp.

◆ mul()

static void mul	(	int	nnonzero,
		long *	nonzero_i,
		long *	nonzero_j,
		const double *	nonzero_values,
		const double *	v,
		double *	result
	)

static

Definition at line 464 of file rxd.cpp.

◆ nrn_tree_solve()

static void nrn_tree_solve	(	double *	a,
		double *	b,
		double *	c,
		double *	dbase,
		double *	rhs,
		long *	pindex,
		long	n,
		double	dt
	)

static

Definition at line 498 of file rxd.cpp.

◆ ode_abs_tol()

static void ode_abs_tol ( double * p1 )

static

Definition at line 595 of file rxd.cpp.

◆ ode_solve()

static void ode_solve	(	double	dt,
		double *	p1,
		double *	p2
	)

static

Definition at line 556 of file rxd.cpp.

◆ register_rate()

NRN_EXPORT void register_rate	(	int	nspecies,
		int	nparam,
		int	nregions,
		int	nseg,
		int *	sidx,
		int	necs,
		int	necsparam,
		int *	ecs_ids,
		int *	ecsidx,
		int	nmult,
		double *	mult,
		PyHocObject **	vptrs,
		ReactionRate *	f
	)

Definition at line 855 of file rxd.cpp.

◆ remove_species_atolscale()

NRN_EXPORT void remove_species_atolscale ( int id )

Definition at line 1104 of file rxd.cpp.

◆ rxd_include_node_flux1D()

NRN_EXPORT void rxd_include_node_flux1D	(	int	n,
		long *	index,
		double *	scales,
		PyObject **	sources
	)

Definition at line 296 of file rxd.cpp.

◆ rxd_include_node_flux3D()

NRN_EXPORT void rxd_include_node_flux3D	(	int	grid_count,
		int *	grid_counts,
		int *	grids,
		long *	index,
		double *	scales,
		PyObject **	sources
	)

Definition at line 212 of file rxd.cpp.

◆ rxd_nonvint_block()

NRN_EXPORT int rxd_nonvint_block	(	int	method,
		int	size,
		double *	p1,
		double *	p2,
		int
	)

Definition at line 775 of file rxd.cpp.

◆ rxd_set_euler_matrix()

NRN_EXPORT void rxd_set_euler_matrix	(	int	nrow,
		int	nnonzero,
		long *	nonzero_i,
		long *	nonzero_j,
		double *	nonzero_values,
		double *	c_diagonal
	)

Definition at line 358 of file rxd.cpp.

◆ rxd_set_no_diffusion()

NRN_EXPORT void rxd_set_no_diffusion ( )

Definition at line 145 of file rxd.cpp.

◆ rxd_setup_conc_ptrs()

NRN_EXPORT void rxd_setup_conc_ptrs	(	int	conc_count,
		int *	conc_index,
		PyHocObject **	conc_ptrs
	)

Definition at line 198 of file rxd.cpp.

◆ rxd_setup_curr_ptrs()

NRN_EXPORT void rxd_setup_curr_ptrs	(	int	num_currents,
		int *	curr_index,
		double *	curr_scale,
		PyHocObject **	curr_ptrs
	)

Definition at line 180 of file rxd.cpp.

◆ set_initialize()

NRN_EXPORT void set_initialize ( fptr * initialize_fn )

Definition at line 484 of file rxd.cpp.

◆ set_num_threads()

NRN_EXPORT void set_num_threads ( const int n )

Definition at line 1209 of file rxd.cpp.

◆ set_setup()

NRN_EXPORT void set_setup ( fptr * setup_fn )

Definition at line 480 of file rxd.cpp.

◆ set_setup_matrices()

NRN_EXPORT void set_setup_matrices ( fptr * setup_matrices )

Definition at line 489 of file rxd.cpp.

◆ set_setup_units()

NRN_EXPORT void set_setup_units ( fptr * setup_units )

Definition at line 493 of file rxd.cpp.

◆ setup_currents()

NRN_EXPORT void setup_currents	(	int	num_currents,
		int	num_fluxes,
		int *	num_species,
		int *	node_idxs,
		double *	scales,
		PyHocObject **	ptrs,
		int *	mapped,
		int *	mapped_ecs
	)

Definition at line 633 of file rxd.cpp.

◆ setup_solver()

NRN_EXPORT void setup_solver	(	double *	my_states,
		int	my_num_states,
		long *	zvi,
		int	num_zvi
	)

Definition at line 1120 of file rxd.cpp.

◆ solve_reaction()

void solve_reaction	(	ICSReactions *	react,
		double *	states,
		double *	bval,
		double *	cvode_states,
		double *	cvode_b
	)

Definition at line 1524 of file rxd.cpp.

◆ species_atolscale()

NRN_EXPORT void species_atolscale	(	int	id,
		double	scale,
		int	len,
		int *	idx
	)

Definition at line 1079 of file rxd.cpp.

◆ TaskQueue_add_task()

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

Definition at line 1142 of file rxd.cpp.

◆ TaskQueue_exe_tasks()

void TaskQueue_exe_tasks	(	std::size_t	thread_index,
		TaskQueue *	q
	)

Definition at line 1171 of file rxd.cpp.

◆ TaskQueue_sync()

void TaskQueue_sync ( TaskQueue * q )

Definition at line 1257 of file rxd.cpp.

◆ transfer_to_legacy()

static void transfer_to_legacy ( )

static

Definition at line 131 of file rxd.cpp.

Variable Documentation

◆ _conc_count

int _conc_count

Definition at line 82 of file rxd.cpp.

◆ _conc_indices

int* _conc_indices = NULL

Definition at line 83 of file rxd.cpp.

◆ _conc_ptrs

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

Definition at line 81 of file rxd.cpp.

◆ _cur_node_indices

int* _cur_node_indices

Definition at line 93 of file rxd.cpp.

◆ _curr_count

int _curr_count

Definition at line 78 of file rxd.cpp.

◆ _curr_indices

int* _curr_indices = NULL

Definition at line 79 of file rxd.cpp.

◆ _curr_ptrs

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

Definition at line 81 of file rxd.cpp.

◆ _curr_scales

double* _curr_scales = NULL

Definition at line 80 of file rxd.cpp.

◆ _cvode_offset

int _cvode_offset

static

Definition at line 65 of file rxd.cpp.

◆ _ecs_count

int _ecs_count

static

Definition at line 66 of file rxd.cpp.

◆ _initialize

fptr * _initialize

Definition at line 48 of file rxd.cpp.

◆ _memb_count

int _memb_count = 0

Definition at line 90 of file rxd.cpp.

◆ _memb_cur_charges

int** _memb_cur_charges

Definition at line 102 of file rxd.cpp.

◆ _memb_cur_mapped

int*** _memb_cur_mapped

Definition at line 103 of file rxd.cpp.

◆ _memb_cur_mapped_ecs

int*** _memb_cur_mapped_ecs

Definition at line 104 of file rxd.cpp.

◆ _memb_cur_ptrs

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

Definition at line 101 of file rxd.cpp.

◆ _memb_curr_nodes

int _memb_curr_nodes = 0

Definition at line 88 of file rxd.cpp.

◆ _memb_curr_total

int _memb_curr_total = 0

Definition at line 86 of file rxd.cpp.

◆ _memb_species_count

int* _memb_species_count

Definition at line 96 of file rxd.cpp.

◆ _membrane_flux

unsigned char _membrane_flux = FALSE

Definition at line 109 of file rxd.cpp.

◆ _membrane_lookup

int* _membrane_lookup

Definition at line 110 of file rxd.cpp.

◆ _node_flux_count

int _node_flux_count = 0

Definition at line 112 of file rxd.cpp.

◆ _node_flux_idx

long* _node_flux_idx = NULL

Definition at line 113 of file rxd.cpp.

◆ _node_flux_scale

double* _node_flux_scale = NULL

Definition at line 114 of file rxd.cpp.

◆ _node_flux_src

PyObject** _node_flux_src = NULL

Definition at line 115 of file rxd.cpp.

◆ _num_reactions

int _num_reactions = 0

Definition at line 77 of file rxd.cpp.

◆ _reactions

ICSReactions* _reactions = NULL

Definition at line 69 of file rxd.cpp.

◆ _rxd_a

double* _rxd_a = NULL

Definition at line 58 of file rxd.cpp.

◆ _rxd_b

double* _rxd_b = NULL

Definition at line 59 of file rxd.cpp.

◆ _rxd_c

double* _rxd_c = NULL

Definition at line 60 of file rxd.cpp.

◆ _rxd_d

double* _rxd_d = NULL

Definition at line 61 of file rxd.cpp.

◆ _rxd_euler_nnonzero

int _rxd_euler_nnonzero = 0

Definition at line 53 of file rxd.cpp.

◆ _rxd_euler_nonzero_i

long* _rxd_euler_nonzero_i = NULL

Definition at line 54 of file rxd.cpp.

◆ _rxd_euler_nonzero_j

long* _rxd_euler_nonzero_j = NULL

Definition at line 55 of file rxd.cpp.

◆ _rxd_euler_nonzero_values

double* _rxd_euler_nonzero_values = NULL

Definition at line 56 of file rxd.cpp.

◆ _rxd_euler_nrow

int _rxd_euler_nrow = 0

Definition at line 53 of file rxd.cpp.

◆ _rxd_flux_scale

double* _rxd_flux_scale

Definition at line 91 of file rxd.cpp.

◆ _rxd_induced_currents

double* _rxd_induced_currents = NULL

Definition at line 106 of file rxd.cpp.

◆ _rxd_induced_currents_grid

ECS_Grid_node** _rxd_induced_currents_grid = NULL

Definition at line 107 of file rxd.cpp.

◆ _rxd_induced_currents_scale

double* _rxd_induced_currents_scale

Definition at line 92 of file rxd.cpp.

◆ _rxd_num_zvi

int _rxd_num_zvi = 0

Definition at line 53 of file rxd.cpp.

◆ _rxd_p

long* _rxd_p = NULL

Definition at line 62 of file rxd.cpp.

◆ _rxd_zero_volume_indices

long* _rxd_zero_volume_indices = NULL

Definition at line 57 of file rxd.cpp.

◆ _rxd_zvi_child

long** _rxd_zvi_child = NULL

Definition at line 64 of file rxd.cpp.

◆ _rxd_zvi_child_count

unsigned int* _rxd_zvi_child_count = NULL

Definition at line 63 of file rxd.cpp.

◆ _setup

fptr* _setup

Definition at line 48 of file rxd.cpp.

◆ _setup_matrices

fptr * _setup_matrices

Definition at line 48 of file rxd.cpp.

◆ _setup_units

fptr * _setup_units

Definition at line 48 of file rxd.cpp.

◆ AllTasks

TaskQueue* AllTasks {&nrn::rxd::task_queue}

Definition at line 41 of file rxd.cpp.

◆ diffusion

unsigned char diffusion = FALSE

Definition at line 52 of file rxd.cpp.

◆ dt_ptr

double* dt_ptr

extern

Definition at line 15 of file grids.cpp.

◆ hocobject_type

PyTypeObject* hocobject_type

extern

Definition at line 130 of file nrnpy_hoc.cpp.

◆ initialized

unsigned char initialized = FALSE

Definition at line 28 of file rxd.cpp.

◆ nrn_threads

NrnThread* nrn_threads

extern

Definition at line 49 of file rxd.cpp.

◆ num_states

unsigned int num_states = 0

Definition at line 76 of file rxd.cpp.

◆ NUM_THREADS

int NUM_THREADS = 1

Definition at line 34 of file rxd.cpp.

◆ prev_structure_change_cnt

int prev_structure_change_cnt = 0

Definition at line 27 of file rxd.cpp.

◆ species_indices

SpeciesIndexList* species_indices = NULL

Definition at line 72 of file rxd.cpp.

◆ states

double* states

Definition at line 75 of file rxd.cpp.

◆ states_cvode_offset

int states_cvode_offset

extern

Definition at line 29 of file rxd_extracellular.cpp.

◆ structure_change_cnt

int structure_change_cnt

extern

Definition at line 66 of file treeset.cpp.

◆ t_ptr

double* t_ptr

extern

Definition at line 16 of file grids.cpp.

Namespaces

Functions

Variables

Function Documentation

◆ _currents()

◆ _fadvance()

◆ _ode_reinit()

◆ _rhs_variable_step()

◆ add_currents()

◆ allocopy()

◆ apply_node_flux()

◆ apply_node_flux1D()

◆ clear_rates()

◆ do_ics_reactions()

◆ free_conc_ptrs()

◆ free_curr_ptrs()

◆ free_currents()

◆ free_zvi_child()

◆ get_all_reaction_rates()

◆ get_num_threads()

◆ get_reaction_rates()

◆ mul()

◆ nrn_tree_solve()

◆ ode_abs_tol()

◆ ode_solve()

◆ register_rate()

◆ remove_species_atolscale()

◆ rxd_include_node_flux1D()

◆ rxd_include_node_flux3D()

◆ rxd_nonvint_block()

◆ rxd_set_euler_matrix()

◆ rxd_set_no_diffusion()

◆ rxd_setup_conc_ptrs()

◆ rxd_setup_curr_ptrs()

◆ set_initialize()

◆ set_num_threads()

◆ set_setup()

◆ set_setup_matrices()

◆ set_setup_units()

◆ setup_currents()

◆ setup_solver()

◆ solve_reaction()

◆ species_atolscale()

◆ TaskQueue_add_task()

◆ TaskQueue_exe_tasks()

◆ TaskQueue_sync()

◆ transfer_to_legacy()

Variable Documentation

◆ _conc_count

◆ _conc_indices

◆ _conc_ptrs

◆ _cur_node_indices

◆ _curr_count

◆ _curr_indices

◆ _curr_ptrs

◆ _curr_scales

◆ _cvode_offset

◆ _ecs_count

◆ _initialize

◆ _memb_count

◆ _memb_cur_charges

◆ _memb_cur_mapped

◆ _memb_cur_mapped_ecs

◆ _memb_cur_ptrs

◆ _memb_curr_nodes

◆ _memb_curr_total

◆ _memb_species_count

◆ _membrane_flux

◆ _membrane_lookup

◆ _node_flux_count

◆ _node_flux_idx

◆ _node_flux_scale

◆ _node_flux_src

◆ _num_reactions

◆ _reactions

◆ _rxd_a

◆ _rxd_b

◆ _rxd_c

◆ _rxd_d

◆ _rxd_euler_nnonzero