kinetic.cpp File Reference

#include <../../nmodlconf.h>
#include <stdlib.h>
#include "modl.h"
#include "parse1.hpp"
#include "symbol.h"

Go to the source code of this file.

Classes
struct	Rterm
struct	Reaction
struct	Rlist

Macros
#define	Glass   1
#define	CVODE_FLAG   if (0)
#define	NOT_CVODE_FLAG   if (1)
#define	MAXKINBLK   20

Typedefs
typedef struct Rterm	Rterm
typedef struct Reaction	Reaction
typedef struct Rlist	Rlist

Functions
int	genconservterms (int eqnum, Reaction *r, int fn, Rlist *rlst)
int	number_states (Symbol *fun, Rlist **prlst, Rlist **pclst)
void	kinlist (Symbol *fun, Rlist *rlst)
void	genderivterms (Reaction *r, int type, int n)
void	genmatterms (Reaction *r, int fn)
static int	sparsedeclared (int i)
char *	qconcat (Item *q1, Item *q2)
void	reactname (Item *q1, Item *lastok, Item *q2)
void	leftreact ()
void	massagereaction (Item *qREACTION, Item *qREACT1, Item *qlpar, Item *qcomma, Item *qrpar)
void	flux (Item *qREACTION, Item *qdir, Item *qlast)
void	massagekinetic (Item *q1, Item *q2, Item *q3, Item *q4, int sensused)
void	fixrlst (Rlist *rlst)
void	kinetic_intmethod (Symbol *fun, char *meth)
void	genfluxterm (Reaction *r, int type, int n)
void	kinetic_implicit (Symbol *fun, char *dt, char *mname)
void	massageconserve (Item *q1, Item *q3, Item *q5)
void	check_block (int standard, int actual, char *mes)
void	massagecompart (Item *qexp, Item *qb1, Item *qb2, Symbol *indx)
void	massageldifus (Item *qexp, Item *qb1, Item *qb2, Symbol *indx)
void	kin_vect1 (Item *q1, Item *q2, Item *q4)
void	kin_vect2 ()
void	kin_vect3 (Item *q1, Item *q2, Item *q4)
void	ostmt_start ()
void	see_ostmt ()
void	see_astmt (Item *q1, Item *q2)
void	vectorize_if_else_stmt (int blocktype)

Variables
int	numlist
int	thread_data_index
List *	thread_cleanup_list
Symbol *	indepsym
static Rterm *	rterm = (Rterm*) 0
static Rterm *	lterm
static Reaction *	reactlist = (Reaction*) 0
static Reaction *	conslist = (Reaction*) 0
static List *	done_list
static List *	done_list1
static Rlist *	rlist = (Rlist*) 0
static Rlist *	clist = (Rlist*) 0
static List *	compartlist
List *	ldifuslist
int	sens_parm
static int	nstate_ [MAXKINBLK]
static int	sparse_declared_ [10]
static int	ncons
static int	linmat
static List *	kvect
static int	astmt_state
static Item *	astmt_last

Macro Definition Documentation

CVODE_FLAG

#define CVODE_FLAG   if (0)

Definition at line 38 of file kinetic.cpp.

Glass

#define Glass   1

Definition at line 3 of file kinetic.cpp.

MAXKINBLK

#define MAXKINBLK   20

Definition at line 106 of file kinetic.cpp.

NOT_CVODE_FLAG

#define NOT_CVODE_FLAG   if (1)

Definition at line 39 of file kinetic.cpp.

Typedef Documentation

Reaction

typedef struct Reaction Reaction

Rlist

typedef struct Rlist Rlist

Rterm

typedef struct Rterm Rterm

Function Documentation

check_block()

void check_block	(	int	standard,
		int	actual,
		char *	mes
	)

Definition at line 1209 of file kinetic.cpp.

fixrlst()

void fixrlst

(

Rlist *

rlst

)

Definition at line 501 of file kinetic.cpp.

flux()

void flux	(	Item *	qREACTION,
		Item *	qdir,
		Item *	qlast
	)

Definition at line 220 of file kinetic.cpp.

genconservterms()

int genconservterms	(	int	eqnum,
		Reaction *	r,
		int	fn,
		Rlist *	rlst
	)

Definition at line 1070 of file kinetic.cpp.

genderivterms()

void genderivterms	(	Reaction *	r,
		int	type,
		int	n
	)

Definition at line 555 of file kinetic.cpp.

genfluxterm()

void genfluxterm	(	Reaction *	r,
		int	type,
		int	n
	)

Definition at line 630 of file kinetic.cpp.

genmatterms()

void genmatterms	(	Reaction *	r,
		int	fn
	)

Definition at line 960 of file kinetic.cpp.

kin_vect1()

void kin_vect1	(	Item *	q1,
		Item *	q2,
		Item *	q4
	)

Definition at line 1342 of file kinetic.cpp.

kin_vect2()

void kin_vect2

(

)

Definition at line 1351 of file kinetic.cpp.

kin_vect3()

void kin_vect3	(	Item *	q1,
		Item *	q2,
		Item *	q4
	)

Definition at line 1366 of file kinetic.cpp.

kinetic_implicit()

void kinetic_implicit	(	Symbol *	fun,
		char *	dt,
		char *	mname
	)

Definition at line 692 of file kinetic.cpp.

kinetic_intmethod()

void kinetic_intmethod	(	Symbol *	fun,
		char *	meth
	)

Definition at line 511 of file kinetic.cpp.

kinlist()

void kinlist	(	Symbol *	fun,
		Rlist *	rlst
	)

Definition at line 1171 of file kinetic.cpp.

leftreact()

void leftreact

(

)

Definition at line 192 of file kinetic.cpp.

massagecompart()

void massagecompart	(	Item *	qexp,
		Item *	qb1,
		Item *	qb2,
		Symbol *	indx
	)

Definition at line 1237 of file kinetic.cpp.

massageconserve()

void massageconserve	(	Item *	q1,
		Item *	q3,
		Item *	q5
	)

Definition at line 1040 of file kinetic.cpp.

massagekinetic()

void massagekinetic	(	Item *	q1,
		Item *	q2,
		Item *	q3,
		Item *	q4,
		int	sensused
	)

Definition at line 298 of file kinetic.cpp.

massageldifus()

void massageldifus	(	Item *	qexp,
		Item *	qb1,
		Item *	qb2,
		Symbol *	indx
	)

Definition at line 1274 of file kinetic.cpp.

massagereaction()

void massagereaction	(	Item *	qREACTION,
		Item *	qREACT1,
		Item *	qlpar,
		Item *	qcomma,
		Item *	qrpar
	)

Definition at line 199 of file kinetic.cpp.

number_states()

int number_states	(	Symbol *	fun,
		Rlist **	prlst,
		Rlist **	pclst
	)

Definition at line 1136 of file kinetic.cpp.

ostmt_start()

void ostmt_start

(

)

Definition at line 1406 of file kinetic.cpp.

qconcat()

char* qconcat	(	Item *	q1,
		Item *	q2
	)

Definition at line 124 of file kinetic.cpp.

reactname()

void reactname	(	Item *	q1,
		Item *	lastok,
		Item *	q2
	)

Definition at line 153 of file kinetic.cpp.

see_astmt()

void see_astmt	(	Item *	q1,
		Item *	q2
	)

Definition at line 1421 of file kinetic.cpp.

see_ostmt()

void see_ostmt

(

)

Definition at line 1410 of file kinetic.cpp.

sparsedeclared()

static int sparsedeclared ( int  i )

static

Definition at line 119 of file kinetic.cpp.

vectorize_if_else_stmt()

void vectorize_if_else_stmt

(

int

blocktype

)

Definition at line 1435 of file kinetic.cpp.

Variable Documentation

astmt_last

Item* astmt_last

static

Definition at line 1404 of file kinetic.cpp.

astmt_state

int astmt_state

static

Definition at line 1403 of file kinetic.cpp.

clist

Rlist* clist = (Rlist*) 0

static

Definition at line 75 of file kinetic.cpp.

compartlist

List* compartlist

static

Definition at line 77 of file kinetic.cpp.

conslist

Reaction* conslist = (Reaction*) 0

static

Definition at line 58 of file kinetic.cpp.

done_list

List* done_list

static

Definition at line 59 of file kinetic.cpp.

done_list1

List* done_list1

static

Definition at line 60 of file kinetic.cpp.

indepsym

Symbol* indepsym

extern

Definition at line 11 of file declare.cpp.

kvect

List* kvect

static

Definition at line 1340 of file kinetic.cpp.

ldifuslist

List* ldifuslist

Definition at line 82 of file kinetic.cpp.

linmat

int linmat

static

Definition at line 691 of file kinetic.cpp.

lterm

Rterm * lterm

static

Definition at line 49 of file kinetic.cpp.

ncons

int ncons

static

Definition at line 509 of file kinetic.cpp.

nstate_

int nstate_[MAXKINBLK]

static

Definition at line 107 of file kinetic.cpp.

numlist

int numlist

extern

Definition at line 16 of file deriv.cpp.

reactlist

Reaction* reactlist = (Reaction*) 0

static

Definition at line 57 of file kinetic.cpp.

rlist

Rlist* rlist = (Rlist*) 0

static

Definition at line 74 of file kinetic.cpp.

rterm

Rterm* rterm = (Rterm*) 0

static

Definition at line 49 of file kinetic.cpp.

sens_parm

int sens_parm

extern

Definition at line 104 of file sens.cpp.

sparse_declared_

int sparse_declared_[10]

static

Definition at line 118 of file kinetic.cpp.

thread_cleanup_list

List* thread_cleanup_list

extern

Definition at line 127 of file nocpout.cpp.

thread_data_index

int thread_data_index

extern

Definition at line 126 of file nocpout.cpp.