#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stddef.h>
#include <stdexcept>
#include "LUT.h"
#include "ODEint.h"
#include <math.h>
#include <assert.h>
#include <functional>
#include "basics.h"
#include "target.h"
#include "ion_type.h"
#include "ION_IF_sv.h"

Include dependency graph for ION_IF.h:

This graph shows which files directly or indirectly include this file:

Classes
struct	limpet::tc_grp
	time constant groups More...

struct	limpet::ts
	time stepper More...

struct	limpet::SV_TAB
	array of stat variable structures More...

struct	limpet::cell_geom

struct	limpet::IMPinfo

class	limpet::IonIfBase
	Represents the ionic model and plug-in (IMP) data structure. More...

class	limpet::IonIf< T >
	Child class of IonIfBase specialized for each ionic model type. More...

class	limpet::IonIf< T >::LimpetArray< S >
	Utility class for handling arrays of data used by IMPs. More...

Namespaces
	limpet

Macros
#define	M_PI 3.14159265358979323846264338327

#define	heav(x) ( (x)<0 ? 0 : 1)

#define	sign(x) ( (x)<0 ? -1 : 1 )

#define	square(x) ((x)*(x))

#define	cube(x) ((x)(x)(x))

#define	MPI_RESTORE_IMP_POLL_BUFSIZE_TAG 10

#define	MPI_RESTORE_IMP_SNDRCV_BUFFER_TAG 11

#define	MPI_DUMP_IMP_POLL_BUFSIZE_TAG 20

#define	MPI_DUMP_IMP_SNDRCV_BUFFER_TAG 21

#define	MPI_DUMP_SVS_POLL_BUFSIZE_TAG 30

#define	MPI_DUMP_SVS_SNDRCV_BUFFER_TAG 31

#define	NDEF 0
	definition of cell geometry More...

#define	CHANGE_PARAM(T, P, V, F)

Functions
void	limpet::initialize_ts (ts tstp, int ng, int skp, double dt)

void	limpet::update_ts (ts *ptstp)

void	limpet::SV_alloc (SV_TAB *psv, int numSeg, int struct_size)

void	limpet::SV_free (SV_TAB *psv)

void	limpet::free_sv_table (void *)

void	limpet::print_IMPs (void)

bool	limpet::flag_set (const char flags, const char target)

void	limpet::print_models (bool)

float	limpet::modify_param (float a, char *expr)

int	limpet::process_param_mod (char pstr, char par, char *mod)

char *	limpet::get_typename (int type)

bool	limpet::verify_flags (const char flags, const char given)

int	limpet::load_ionic_module (const char *)

char *	limpet::get_next_list (char *lst, char delimiter)

SVputfcn	limpet::getPutSV (SVgetfcn)

Macro Definition Documentation

◆ CHANGE_PARAM

#define CHANGE_PARAM	(	T,
		P,
		V,
		F
	)

Value:

do { \
  ((T##_Params *)P)->V = modify_param( ((T##_Params *)P)->V, F ); \
  log_msg( _nc_logf,0, 0, " %-20s modifier: %-15s value: %g",\
  #V,F,(float)((T##_Params *)P)->V);} while (0)

Definition at line 936 of file ION_IF.h.

◆ cube

#define cube ( x ) ((x)*(x)*(x))

Definition at line 58 of file ION_IF.h.

◆ heav

#define heav ( x ) ( (x)<0 ? 0 : 1)

Definition at line 55 of file ION_IF.h.

◆ M_PI

#define M_PI 3.14159265358979323846264338327

Definition at line 51 of file ION_IF.h.

◆ MPI_DUMP_IMP_POLL_BUFSIZE_TAG

#define MPI_DUMP_IMP_POLL_BUFSIZE_TAG 20

Definition at line 63 of file ION_IF.h.

◆ MPI_DUMP_IMP_SNDRCV_BUFFER_TAG

#define MPI_DUMP_IMP_SNDRCV_BUFFER_TAG 21

Definition at line 64 of file ION_IF.h.

◆ MPI_DUMP_SVS_POLL_BUFSIZE_TAG

#define MPI_DUMP_SVS_POLL_BUFSIZE_TAG 30

Definition at line 65 of file ION_IF.h.

◆ MPI_DUMP_SVS_SNDRCV_BUFFER_TAG

#define MPI_DUMP_SVS_SNDRCV_BUFFER_TAG 31

Definition at line 66 of file ION_IF.h.

◆ MPI_RESTORE_IMP_POLL_BUFSIZE_TAG

#define MPI_RESTORE_IMP_POLL_BUFSIZE_TAG 10

Definition at line 61 of file ION_IF.h.

◆ MPI_RESTORE_IMP_SNDRCV_BUFFER_TAG

#define MPI_RESTORE_IMP_SNDRCV_BUFFER_TAG 11

Definition at line 62 of file ION_IF.h.

◆ NDEF

#define NDEF 0

definition of cell geometry

Each ionic model is based on an underlying cell geometry. Several factors depend on the geometry like conversion factors how currents crossing the membrane translate into a change in ionic concentration. This structure is defined to provide a standardized mechanisms to define cell geometry and subdomain fractions to compute all dependent factors automatically. These factors can be accessed by plugins to derive factors for concentration updates.

Definition at line 112 of file ION_IF.h.

◆ sign

#define sign ( x ) ( (x)<0 ? -1 : 1 )

Definition at line 56 of file ION_IF.h.

◆ square

#define square ( x ) ((x)*(x))

Definition at line 57 of file ION_IF.h.

Classes

Namespaces

Macros

Functions