#include <fstream>
#include <sstream>
#include <vector>
#include <set>
#include <cstdlib>
#include "partrans.h"

Classes
struct	core2nrn_callback_t

struct	NrnCoreTransferEvents

Typedefs
typedef void (	CNB) (...)

typedef struct core2nrn_callback_t	core2nrn_callback_t

typedef std::vector< std::pair< int, bool > >	Core2NrnWatchInfoItem

typedef std::vector< Core2NrnWatchInfoItem >	Core2NrnWatchInfo

Enumerations
enum	mech_type { voltage = -1 , i_membrane_ = -2 }

Functions
void	write_memb_mech_types_direct (std::ostream &s)

void	part2_clean ()

int	get_global_int_item (const char *name)

void *	get_global_dbl_item (void p, const char &name, int &size, double *&val)

void	nrnthread_group_ids (int *groupids)

int	nrnthread_dat1 (int tid, int &n_presyn, int &n_netcon, int &output_gid, int &netcon_srcgid, std::vector< int > &netcon_negsrcgid_tid)

int	nrnthread_dat2_1 (int tid, int &ngid, int &n_real_gid, int &nnode, int &ndiam, int &nmech, int &tml_index, int &ml_nodecount, int &nidata, int &nvdata, int &nweight)

int	nrnthread_dat2_2 (int tid, int &v_parent_index, double &a, double &b, double &area, double &v, double &diamvec)

int	nrnthread_dat2_mech (int tid, size_t i, int dsz_inst, int &nodeindices, double &data, int *&pdata, std::vector< int > &pointer2type)

int	nrnthread_dat2_3 (int tid, int nweight, int &output_vindex, double &output_threshold, int &netcon_pnttype, int &netcon_pntindex, double &weights, double &delays)

int	nrnthread_dat2_corepointer (int tid, int &n)

int	nrnthread_dat2_corepointer_mech (int tid, int type, int &icnt, int &dcnt, int &iarray, double &darray)

int	nrnthread_dat2_vecplay (int tid, std::vector< int > &n)

int	nrnthread_dat2_vecplay_inst (int tid, int i, int &vptype, int &mtype, int &ix, int &sz, double &yvec, double &tvec, int &last_index, int &discon_index, int &ubound_index)

int *	datum2int (int type, Memb_list *ml, NrnThread &nt, CellGroup &cg, DatumIndices &di, int ml_vdata_offset, std::vector< int > &pointer2type)

void	nrnthread_get_trajectory_requests (int tid, int &bsize, int &ntrajec, void *&vpr, int &types, int &indices, double &pvars, double *&varrays)

void	nrnthread_trajectory_values (int tid, int n_pr, void **vpr, double t)

void	nrnthread_trajectory_return (int tid, int n_pr, int bsize, int vecsz, void **vpr, double t)

int	nrnthread_all_spike_vectors_return (std::vector< double > &spiketvec, std::vector< int > &spikegidvec)
	NEURON callback used from CORENEURON to transfer all spike vectors after simulation. More...

void	nrnthreads_all_weights_return (std::vector< double * > &weights)
	Copy weights from all coreneuron::NrnThread to NetCon instances. More...

size_t	nrnthreads_type_return (int type, int tid, double &data, double *&mdata)
	Return location for CoreNEURON to copy data into. More...

int	core2nrn_corepointer_mech (int tid, int type, int icnt, int dcnt, int iarray, double darray)

void	core2nrn_clear_queues (double t)
	Initialize queues before transfer Probably aleady clear, but if binq then must be initialized to time. More...

void	core2nrn_NetCon_event (int tid, double td, size_t nc_index)
	Called from CoreNEURON core2nrn_tqueue_item. More...

void	core2nrn_SelfEvent_event (int tid, double td, int tar_type, int tar_index, double flag, size_t nc_index, int is_movable)

void	core2nrn_SelfEvent_event_noweight (int tid, double td, int tar_type, int tar_index, double flag, int is_movable)

void	core2nrn_PreSyn_flag (int tid, std::set< int > presyns_flag_true)

NrnCoreTransferEvents *	nrn2core_transfer_tqueue (int tid)

void	nrn2core_transfer_WATCH (void(*cb)(int, int, int, int, int))

void	nrn_watch_clear ()
	Watch info corenrn->nrn transfer requires all activated WatchCondition be deactivated prior to mirroring the activation that exists on the corenrn side. More...

void	core2nrn_watch_activate (int tid, int type, int wbegin, Core2NrnWatchInfo &)

void	core2nrn_vecplay (int tid, int i_nrn, int last_index, int discon_index, int ubound_index)
	getting one item at a time from CoreNEURON More...

void	core2nrn_vecplay_events ()
	start the vecplay events More...

void	nrn2core_PreSyn_flag (int tid, std::set< int > &presyns_flag_true)

void	nrn2core_patternstim (void **info)

void	map_coreneuron_callbacks (void *handle)
	Populate function pointers by mapping function pointers for callback. More...

Variables
static core2nrn_callback_t	cnbs []

Typedef Documentation

◆ CNB

typedef void*(* CNB) (...)

Definition at line 12 of file nrncore_callbacks.h.

◆ core2nrn_callback_t

typedef struct core2nrn_callback_t core2nrn_callback_t

◆ Core2NrnWatchInfo

typedef std::vector<Core2NrnWatchInfoItem> Core2NrnWatchInfo

Definition at line 163 of file nrncore_callbacks.h.

◆ Core2NrnWatchInfoItem

typedef std::vector<std::pair<int, bool> > Core2NrnWatchInfoItem

Definition at line 162 of file nrncore_callbacks.h.

Enumeration Type Documentation

◆ mech_type

enum mech_type

Enumerator
voltage
i_membrane_

Definition at line 21 of file nrncore_callbacks.h.

Function Documentation

◆ core2nrn_clear_queues()

void core2nrn_clear_queues ( double t )

Initialize queues before transfer Probably aleady clear, but if binq then must be initialized to time.

Definition at line 1023 of file nrncore_callbacks.cpp.

◆ core2nrn_corepointer_mech()

int core2nrn_corepointer_mech	(	int	tid,
		int	type,
		int	icnt,
		int	dcnt,
		int *	iarray,
		double *	darray
	)

Definition at line 503 of file nrncore_callbacks.cpp.

◆ core2nrn_NetCon_event()

void core2nrn_NetCon_event	(	int	tid,
		double	td,
		size_t	nc_index
	)

Called from CoreNEURON core2nrn_tqueue_item.

Definition at line 1030 of file nrncore_callbacks.cpp.

◆ core2nrn_PreSyn_flag()

void core2nrn_PreSyn_flag	(	int	tid,
		std::set< int >	presyns_flag_true
	)

Definition at line 1112 of file nrncore_callbacks.cpp.

◆ core2nrn_SelfEvent_event()

void core2nrn_SelfEvent_event	(	int	tid,
		double	td,
		int	tar_type,
		int	tar_index,
		double	flag,
		size_t	nc_index,
		int	is_movable
	)

Definition at line 1079 of file nrncore_callbacks.cpp.

◆ core2nrn_SelfEvent_event_noweight()

void core2nrn_SelfEvent_event_noweight	(	int	tid,
		double	td,
		int	tar_type,
		int	tar_index,
		double	flag,
		int	is_movable
	)

Definition at line 1100 of file nrncore_callbacks.cpp.

◆ core2nrn_vecplay()

void core2nrn_vecplay	(	int	tid,
		int	i_nrn,
		int	last_index,
		int	discon_index,
		int	ubound_index
	)

getting one item at a time from CoreNEURON

Definition at line 715 of file nrncore_callbacks.cpp.

◆ core2nrn_vecplay_events()

void core2nrn_vecplay_events ( )

start the vecplay events

Definition at line 728 of file nrncore_callbacks.cpp.

◆ core2nrn_watch_activate()

void core2nrn_watch_activate	(	int	tid,
		int	type,
		int	wbegin,
		Core2NrnWatchInfo &	wi
	)

Definition at line 1172 of file nrncore_callbacks.cpp.

◆ datum2int()

int* datum2int	(	int	type,
		Memb_list *	ml,
		NrnThread &	nt,
		CellGroup &	cg,
		DatumIndices &	di,
		int	ml_vdata_offset,
		std::vector< int > &	pointer2type
	)

Definition at line 527 of file nrncore_callbacks.cpp.

◆ get_global_dbl_item()

void* get_global_dbl_item	(	void *	p,
		const char *&	name,
		int &	size,
		double *&	val
	)

Definition at line 85 of file nrncore_callbacks.cpp.

◆ get_global_int_item()

int get_global_int_item ( const char * name )

Definition at line 72 of file nrncore_callbacks.cpp.

◆ map_coreneuron_callbacks()

void map_coreneuron_callbacks ( void * handle )

Populate function pointers by mapping function pointers for callback.

Definition at line 34 of file nrncore_callbacks.cpp.

◆ nrn2core_patternstim()

void nrn2core_patternstim ( void ** info )

Definition at line 1209 of file nrncore_callbacks.cpp.

◆ nrn2core_PreSyn_flag()

void nrn2core_PreSyn_flag	(	int	tid,
		std::set< int > &	presyns_flag_true
	)

Definition at line 1149 of file nrncore_callbacks.cpp.

◆ nrn2core_transfer_tqueue()

NrnCoreTransferEvents* nrn2core_transfer_tqueue ( int tid )

Definition at line 933 of file nrncore_callbacks.cpp.

◆ nrn2core_transfer_WATCH()

void nrn2core_transfer_WATCH ( void(*)(int, int, int, int, int) cb )

Definition at line 6161 of file netcvode.cpp.

◆ nrn_watch_clear()

void nrn_watch_clear ( )

Watch info corenrn->nrn transfer requires all activated WatchCondition be deactivated prior to mirroring the activation that exists on the corenrn side.

Definition at line 2620 of file netcvode.cpp.

◆ nrnthread_all_spike_vectors_return()

int nrnthread_all_spike_vectors_return	(	std::vector< double > &	spiketvec,
		std::vector< int > &	spikegidvec
	)

NEURON callback used from CORENEURON to transfer all spike vectors after simulation.

Parameters

spiketvec	- vector of spikes
spikegidvec	- vector of gids

Returns: 1 if CORENEURON shall drop writing out.dat; 0 otherwise

Definition at line 1329 of file netpar.cpp.

◆ nrnthread_dat1()

int nrnthread_dat1	(	int	tid,
		int &	n_presyn,
		int &	n_netcon,
		int *&	output_gid,
		int *&	netcon_srcgid,
		std::vector< int > &	netcon_negsrcgid_tid
	)

Definition at line 203 of file nrncore_callbacks.cpp.

◆ nrnthread_dat2_1()

int nrnthread_dat2_1	(	int	tid,
		int &	ngid,
		int &	n_real_gid,
		int &	nnode,
		int &	ndiam,
		int &	nmech,
		int *&	tml_index,
		int *&	ml_nodecount,
		int &	nidata,
		int &	nvdata,
		int &	nweight
	)

Definition at line 224 of file nrncore_callbacks.cpp.

◆ nrnthread_dat2_2()

int nrnthread_dat2_2	(	int	tid,
		int *&	v_parent_index,
		double *&	a,
		double *&	b,
		double *&	area,
		double *&	v,
		double *&	diamvec
	)

Definition at line 278 of file nrncore_callbacks.cpp.

◆ nrnthread_dat2_3()

int nrnthread_dat2_3	(	int	tid,
		int	nweight,
		int *&	output_vindex,
		double *&	output_threshold,
		int *&	netcon_pnttype,
		int *&	netcon_pntindex,
		double *&	weights,
		double *&	delays
	)

Definition at line 397 of file nrncore_callbacks.cpp.

◆ nrnthread_dat2_corepointer()

int nrnthread_dat2_corepointer	(	int	tid,
		int &	n
	)

Definition at line 445 of file nrncore_callbacks.cpp.

◆ nrnthread_dat2_corepointer_mech()

int nrnthread_dat2_corepointer_mech	(	int	tid,
		int	type,
		int &	icnt,
		int &	dcnt,
		int *&	iarray,
		double *&	darray
	)

Definition at line 461 of file nrncore_callbacks.cpp.

◆ nrnthread_dat2_mech()

int nrnthread_dat2_mech	(	int	tid,
		size_t	i,
		int	dsz_inst,
		int *&	nodeindices,
		double *&	data,
		int *&	pdata,
		std::vector< int > &	pointer2type
	)

Definition at line 329 of file nrncore_callbacks.cpp.

◆ nrnthread_dat2_vecplay()

int nrnthread_dat2_vecplay	(	int	tid,
		std::vector< int > &	n
	)

Definition at line 633 of file nrncore_callbacks.cpp.

◆ nrnthread_dat2_vecplay_inst()

int nrnthread_dat2_vecplay_inst	(	int	tid,
		int	i,
		int &	vptype,
		int &	mtype,
		int &	ix,
		int &	sz,
		double *&	yvec,
		double *&	tvec,
		int &	last_index,
		int &	discon_index,
		int &	ubound_index
	)

Definition at line 661 of file nrncore_callbacks.cpp.

◆ nrnthread_get_trajectory_requests()

void nrnthread_get_trajectory_requests	(	int	tid,
		int &	bsize,
		int &	ntrajec,
		void **&	vpr,
		int *&	types,
		int *&	indices,
		double **&	pvars,
		double **&	varrays
	)

◆ nrnthread_group_ids()

void nrnthread_group_ids ( int * groupids )

Definition at line 196 of file nrncore_callbacks.cpp.

◆ nrnthread_trajectory_return()

void nrnthread_trajectory_return	(	int	tid,
		int	n_pr,
		int	bsize,
		int	vecsz,
		void **	vpr,
		double	t
	)

Definition at line 6097 of file netcvode.cpp.

◆ nrnthread_trajectory_values()

void nrnthread_trajectory_values	(	int	tid,
		int	n_pr,
		void **	vpr,
		double	t
	)

Definition at line 6054 of file netcvode.cpp.

◆ nrnthreads_all_weights_return()

void nrnthreads_all_weights_return ( std::vector< double * > & weights )

Copy weights from all coreneuron::NrnThread to NetCon instances.

This depends on the CoreNEURON weight order for each thread to be the same as was originally sent from NEURON. See how that order was constructed in CellGroup::mk_cgs_netcon_info.

Definition at line 123 of file nrncore_callbacks.cpp.

◆ nrnthreads_type_return()

size_t nrnthreads_type_return	(	int	type,
		int	tid,
		double *&	data,
		double **&	mdata
	)

Return location for CoreNEURON to copy data into.

The type is mechanism type or special negative type for voltage, i_membrane_, or time. See coreneuron/io/nrn_setup.cpp:stdindex2ptr. We allow coreneuron to copy to NEURON's AoS data as CoreNEURON knows how its data is arranged (SoA and possibly permuted). This function figures out the size (just for sanity check) and data pointer to be returned based on type and thread id. The ARTIFICIAL_CELL type case is special as there is no thread specific Memb_list for those.

Definition at line 151 of file nrncore_callbacks.cpp.

◆ part2_clean()

void part2_clean ( )

Definition at line 590 of file nrncore_callbacks.cpp.

◆ write_memb_mech_types_direct()

void write_memb_mech_types_direct ( std::ostream & s )

Definition at line 49 of file nrncore_callbacks.cpp.

Variable Documentation

◆ cnbs

core2nrn_callback_t cnbs[]

static

Definition at line 186 of file nrncore_callbacks.h.

Classes

Typedefs

Enumerations

Functions

Variables