treeset.cpp File Reference

#include <../../nrnconf.h>
#include <stdio.h>
#include <errno.h>
#include <math.h>
#include <string>
#include "section.h"
#include "membfunc.h"
#include "neuron.h"
#include "parse.hpp"
#include "nrnmpi.h"
#include "multisplit.h"
#include "spmatrix.h"
#include "nonvintblock.h"
#include "nrndae_c.h"
#include "utils/profile/profiler_interface.h"
#include "multicore.cpp"

Go to the source code of this file.

Macros
#define	UPDATE_VEC_AREA(nd)   if (nd->_nt && nd->_nt->_actual_area) { nd->_nt->_actual_area[(nd)->v_node_index] = NODEAREA(nd);}
#define	PI   3.14159265358979323846
#define	NODE_DATA   0

Functions
spREAL *	spGetElement (char *, int, int)
double	chkarg (int, double low, double high)
double	nrn_ra (Section *)
double	nrnmpi_wtime ()
void	nrn_define_shape ()
void	nrn_partrans_update_ptrs ()
static void	nrn_recalc_node_ptrs ()
void	nrn_rhs (NrnThread *_nt)
void	nrn_lhs (NrnThread *_nt)
void *	setup_tree_matrix (NrnThread *_nt)
Prop *	prop_alloc (Prop **, int, Node *)
Prop *	need_memb (Symbol *sym)
Prop *	prop_alloc_disallow (Prop **pp, short type, Node *nd)
void	prop_free (Prop **pp)
void	single_prop_free (Prop *p)
static double	diam_from_list (Section *sec, int inode, Prop *p, double rparent)
void	nrn_area_ri (Section *sec)
Node *	nrn_parent_node (Node *nd)
void	connection_coef (void)
	ForAllSections (sec) if(!sec -> parentsec)
	ClassicalNODEA (nd)
	for (j=1;j< sec->nnode;j++)
	ClassicalNODEB (nd)
	ext_con_coef ()
void	nrn_shape_update_always (void)
void	nrn_shape_update (void)
static void	nrn_matrix_node_alloc (void)
void	recalc_diam (void)
void	area (void)
void	ri (void)
void	pt3dconst (void)
void	nrn_pt3dstyle0 (Section *sec)
void	nrn_pt3dstyle1 (Section *sec, double x, double y, double z)
void	pt3dstyle (void)
void	pt3dclear (void)
static void	nrn_pt3dbufchk (Section *sec, int n)
static void	nrn_pt3dmodified (Section *sec, int i0)
void	nrn_pt3dclear (Section *sec, int req)
void	nrn_pt3dinsert (Section *sec, int i0, double x, double y, double z, double d)
void	pt3dinsert (void)
void	nrn_pt3dchange1 (Section *sec, int i, double d)
void	nrn_pt3dchange2 (Section *sec, int i, double x, double y, double z, double diam)
void	pt3dchange (void)
void	nrn_pt3dremove (Section *sec, int i0)
void	pt3dremove (void)
void	nrn_diam_change (Section *sec)
void	nrn_length_change (Section *sec, double d)
int	can_change_morph (Section *sec)
static void	stor_pt3d_vec (Section *sec, IvocVect *xv, IvocVect *yv, IvocVect *zv, IvocVect *dv)
void	pt3dadd (void)
void	n3d (void)
void	x3d (void)
void	y3d (void)
void	z3d (void)
void	arc3d (void)
void	diam3d (void)
void	spine3d (void)
void	stor_pt3d (Section *sec, double x, double y, double z, double d)
void	setSpineArea (void)
void	getSpineArea (void)
void	define_shape (void)
static void	nrn_translate_shape (Section *sec, float x, float y, float z)
void	v_setup_vectors (void)
void	node_data (void)
void	nrn_complain (double *pp)
	fprintf (stderr, "Don't know the location of params at %p\, pp)
void	nrn_matrix_node_free (void)
int	nrn_modeltype (void)
int	nrn_method_consistent (void)
void	nrn_cachevec (int b)
void	nrn_old_thread_save (void)
double *	nrn_recalc_ptr (double *old)
void	nrn_register_recalc_ptr_callback (Pfrv f)
void	nrn_recalc_ptrs (double *(*r)(double *))

Variables
int	cvode_active_
int	nrn_shape_changed_
double *	nrn_mech_wtime_
int	diam_changed
int	tree_changed
Symlist *	hoc_built_in_symlist
int *	nrn_prop_dparam_size_
int *	nrn_dparam_ptr_start_
int *	nrn_dparam_ptr_end_
void(*	nrn_multisplit_setup_ )()
int	use_cachevec
int	nrn_matrix_cnt_ = 0
int	use_sparse13 = 0
int	nrn_use_daspk_ = 0
int	v_structure_change
int	structure_change_cnt
int	diam_change_cnt
int	nrn_node_ptr_change_cnt_
int	section_count
Section **	secorder
short *	nrn_is_artificial_
cTemplate **	nrn_pnt_template_
static Prop **	current_prop_list
static int	disallow_needmemb = 0
Section *	nrn_pnt_sec_for_need_
Node *	nrn_alloc_node_
int	recalc_diam_count_
int	nrn_area_ri_nocount_ = 0
int	nrn_area_ri_count_
	nd = sec->pnode[0]
	area = NODEAREA(sec->parentnode)
j< sec->	nnode
	j
static int	pt3dconst_
static double	spinearea =0.
static int	n_recalc_ptr_callback
static void(*	recalc_ptr_callback [20])()
static int	recalc_cnt_
static double **	recalc_ptr_new_vp_
static double **	recalc_ptr_old_vp_
static int	n_old_thread_
static int *	old_actual_v_size_
static double **	old_actual_v_
static double **	old_actual_area_
static double *(*	recalc_ptr_ )(double *)

Macro Definition Documentation

NODE_DATA

#define NODE_DATA   0

Definition at line 1779 of file treeset.cpp.

PI

#define PI   3.14159265358979323846

Definition at line 768 of file treeset.cpp.

UPDATE_VEC_AREA

#define UPDATE_VEC_AREA

(

nd

)

if (nd->_nt && nd->_nt->_actual_area) { nd->_nt->_actual_area[(nd)->v_node_index] = NODEAREA(nd);}

Definition at line 59 of file treeset.cpp.

Function Documentation

arc3d()

void arc3d

(

void

)

Definition at line 1317 of file treeset.cpp.

area()

void area

(

void

)

Definition at line 952 of file treeset.cpp.

can_change_morph()

int can_change_morph

(

Section *

sec

)

Definition at line 1245 of file treeset.cpp.

chkarg()

double chkarg	(	int	,
		double	low,
		double	high
	)

Definition at line 608 of file code2.cpp.

ClassicalNODEA()

ClassicalNODEA

(

nd

)

ClassicalNODEB()

ClassicalNODEB

(

nd

)

connection_coef()

void connection_coef

(

void

)

Definition at line 834 of file treeset.cpp.

define_shape()

void define_shape

(

void

)

Definition at line 1378 of file treeset.cpp.

diam3d()

void diam3d

(

void

)

Definition at line 1326 of file treeset.cpp.

diam_from_list()

static double diam_from_list ( Section *  sec, int  inode, Prop *  p, double  rparent  )

static

Definition at line 1496 of file treeset.cpp.

ext_con_coef()

ext_con_coef

(

)

Definition at line 507 of file extcelln.cpp.

for()

for

(

j

= 1; j < sec->nnode; j++

)

Definition at line 897 of file treeset.cpp.

ForAllSections()

ForAllSections

(

sec

)

-> parentsec)

Definition at line 874 of file treeset.cpp.

fprintf()

fprintf	(	stderr	,
		"Don't know the location of params at %p\	,
		pp
	)

getSpineArea()

void getSpineArea

(

void

)

Definition at line 1374 of file treeset.cpp.

n3d()

void n3d

(

void

)

Definition at line 1284 of file treeset.cpp.

need_memb()

Prop* need_memb

(

Symbol *

sym

)

Definition at line 638 of file treeset.cpp.

node_data()

void node_data

(

void

)

Definition at line 1872 of file treeset.cpp.

nrn_area_ri()

void nrn_area_ri

(

Section *

sec

)

Definition at line 773 of file treeset.cpp.

nrn_cachevec()

void nrn_cachevec

(

int

b

)

Definition at line 2108 of file treeset.cpp.

nrn_complain()

void nrn_complain

(

double *

pp

)

Definition at line 1879 of file treeset.cpp.

nrn_define_shape()

void nrn_define_shape

(

void

)

Definition at line 1411 of file treeset.cpp.

nrn_diam_change()

void nrn_diam_change

(

Section *

sec

)

Definition at line 1201 of file treeset.cpp.

nrn_length_change()

void nrn_length_change	(	Section *	sec,
		double	d
	)

Definition at line 1220 of file treeset.cpp.

nrn_lhs()

void nrn_lhs

(

NrnThread *

_nt

)

Definition at line 484 of file treeset.cpp.

nrn_matrix_node_alloc()

static void nrn_matrix_node_alloc ( void  )

static

Definition at line 1999 of file treeset.cpp.

nrn_matrix_node_free()

void nrn_matrix_node_free

(

void

)

Definition at line 1901 of file treeset.cpp.

nrn_method_consistent()

int nrn_method_consistent

(

void

)

Definition at line 1964 of file treeset.cpp.

nrn_modeltype()

int nrn_modeltype

(

void

)

Definition at line 1934 of file treeset.cpp.

nrn_old_thread_save()

void nrn_old_thread_save

(

void

)

Definition at line 2140 of file treeset.cpp.

nrn_parent_node()

Node* nrn_parent_node

(

Node *

nd

)

Definition at line 830 of file treeset.cpp.

nrn_partrans_update_ptrs()

void nrn_partrans_update_ptrs

(

)

Definition at line 345 of file partrans.cpp.

nrn_pt3dbufchk()

static void nrn_pt3dbufchk ( Section *  sec, int  n  )

static

Definition at line 1062 of file treeset.cpp.

nrn_pt3dchange1()

void nrn_pt3dchange1	(	Section *	sec,
		int	i,
		double	d
	)

Definition at line 1149 of file treeset.cpp.

nrn_pt3dchange2()

void nrn_pt3dchange2	(	Section *	sec,
		int	i,
		double	x,
		double	y,
		double	z,
		double	diam
	)

Definition at line 1156 of file treeset.cpp.

nrn_pt3dclear()

void nrn_pt3dclear	(	Section *	sec,
		int	req
	)

Definition at line 1103 of file treeset.cpp.

nrn_pt3dinsert()

void nrn_pt3dinsert	(	Section *	sec,
		int	i0,
		double	x,
		double	y,
		double	z,
		double	d
	)

Definition at line 1120 of file treeset.cpp.

nrn_pt3dmodified()

static void nrn_pt3dmodified ( Section *  sec, int  i0  )

static

Definition at line 1075 of file treeset.cpp.

nrn_pt3dremove()

void nrn_pt3dremove	(	Section *	sec,
		int	i0
	)

Definition at line 1177 of file treeset.cpp.

nrn_pt3dstyle0()

void nrn_pt3dstyle0

(

Section *

sec

)

Definition at line 993 of file treeset.cpp.

nrn_pt3dstyle1()

void nrn_pt3dstyle1	(	Section *	sec,
		double	x,
		double	y,
		double	z
	)

Definition at line 1002 of file treeset.cpp.

nrn_ra()

double nrn_ra

(

Section *

)

Definition at line 392 of file cabcode.cpp.

nrn_recalc_node_ptrs()

void nrn_recalc_node_ptrs ( void  )

static

Definition at line 2193 of file treeset.cpp.

nrn_recalc_ptr()

double* nrn_recalc_ptr

(

double *

old

)

Definition at line 2158 of file treeset.cpp.

nrn_recalc_ptrs()

void nrn_recalc_ptrs

(

double *(*)(double *)

r

)

Definition at line 2178 of file treeset.cpp.

nrn_register_recalc_ptr_callback()

void nrn_register_recalc_ptr_callback

(

Pfrv

f

)

Definition at line 2170 of file treeset.cpp.

nrn_rhs()

void nrn_rhs

(

NrnThread *

_nt

)

Definition at line 355 of file treeset.cpp.

nrn_shape_update()

void nrn_shape_update

(

void

)

Definition at line 932 of file treeset.cpp.

nrn_shape_update_always()

void nrn_shape_update_always

(

void

)

Definition at line 915 of file treeset.cpp.

nrn_translate_shape()

static void nrn_translate_shape ( Section *  sec, float  x, float  y, float  z  )

static

Definition at line 1383 of file treeset.cpp.

nrnmpi_wtime()

double nrnmpi_wtime

(

)

Definition at line 171 of file nrnmpi.cpp.

prop_alloc()

Prop* prop_alloc	(	Prop **	pp,
		int	type,
		Node *	nd
	)

Definition at line 688 of file treeset.cpp.

prop_alloc_disallow()

Prop* prop_alloc_disallow	(	Prop **	pp,
		short	type,
		Node *	nd
	)

Definition at line 716 of file treeset.cpp.

prop_free()

void prop_free

(

Prop **

pp

)

Definition at line 724 of file treeset.cpp.

pt3dadd()

void pt3dadd

(

void

)

Definition at line 1268 of file treeset.cpp.

pt3dchange()

void pt3dchange

(

void

)

Definition at line 1164 of file treeset.cpp.

pt3dclear()

void pt3dclear

(

void

)

Definition at line 1050 of file treeset.cpp.

pt3dconst()

void pt3dconst

(

void

)

Definition at line 985 of file treeset.cpp.

pt3dinsert()

void pt3dinsert

(

void

)

Definition at line 1139 of file treeset.cpp.

pt3dremove()

void pt3dremove

(

void

)

Definition at line 1191 of file treeset.cpp.

pt3dstyle()

void pt3dstyle

(

void

)

Definition at line 1014 of file treeset.cpp.

recalc_diam()

void recalc_diam

(

void

)

Definition at line 940 of file treeset.cpp.

ri()

void ri

(

void

)

Definition at line 968 of file treeset.cpp.

setSpineArea()

void setSpineArea

(

void

)

Definition at line 1368 of file treeset.cpp.

setup_tree_matrix()

void* setup_tree_matrix

(

NrnThread *

_nt

)

Definition at line 614 of file treeset.cpp.

single_prop_free()

void single_prop_free

(

Prop *

p

)

Definition at line 736 of file treeset.cpp.

spGetElement()

spREAL* spGetElement	(	char *	,
		int	,
		int
	)

Definition at line 195 of file spbuild.c.

spine3d()

void spine3d

(

void

)

Definition at line 1337 of file treeset.cpp.

stor_pt3d()

void stor_pt3d	(	Section *	sec,
		double	x,
		double	y,
		double	z,
		double	d
	)

Definition at line 1352 of file treeset.cpp.

stor_pt3d_vec()

static void stor_pt3d_vec ( Section *  sec, IvocVect *  xv, IvocVect *  yv, IvocVect *  zv, IvocVect *  dv  )

static

Definition at line 1250 of file treeset.cpp.

v_setup_vectors()

void v_setup_vectors

(

void

)

Definition at line 1623 of file treeset.cpp.

x3d()

void x3d

(

void

)

Definition at line 1290 of file treeset.cpp.

y3d()

void y3d

(

void

)

Definition at line 1299 of file treeset.cpp.

z3d()

void z3d

(

void

)

Definition at line 1308 of file treeset.cpp.

Variable Documentation

area

area = NODEAREA(sec->parentnode)

Definition at line 894 of file treeset.cpp.

current_prop_list

Prop** current_prop_list

static

Definition at line 628 of file treeset.cpp.

cvode_active_

int cvode_active_

Definition at line 158 of file fadvance.cpp.

diam_change_cnt

int diam_change_cnt

Definition at line 80 of file treeset.cpp.

diam_changed

int diam_changed

Definition at line 23 of file cabcode.cpp.

disallow_needmemb

int disallow_needmemb = 0

static

Definition at line 630 of file treeset.cpp.

hoc_built_in_symlist

Symlist* hoc_built_in_symlist

Definition at line 39 of file symbol.cpp.

j

j

Initial value:

{
            nd = sec->pnode[j]

Definition at line 905 of file treeset.cpp.

n_old_thread_

int n_old_thread_

static

Definition at line 2133 of file treeset.cpp.

n_recalc_ptr_callback

int n_recalc_ptr_callback

static

Definition at line 2129 of file treeset.cpp.

nd

nd = sec->pnode[0]

Definition at line 893 of file treeset.cpp.

nnode

j< sec-> nnode

Definition at line 905 of file treeset.cpp.

nrn_alloc_node_

Node* nrn_alloc_node_

Definition at line 686 of file treeset.cpp.

nrn_area_ri_count_

int nrn_area_ri_count_

Definition at line 772 of file treeset.cpp.

nrn_area_ri_nocount_

nrn_area_ri_nocount_ = 0

Definition at line 772 of file treeset.cpp.

nrn_dparam_ptr_end_

int* nrn_dparam_ptr_end_

Definition at line 181 of file init.cpp.

nrn_dparam_ptr_start_

int* nrn_dparam_ptr_start_

Definition at line 180 of file init.cpp.

nrn_is_artificial_

short* nrn_is_artificial_

Definition at line 231 of file init.cpp.

nrn_matrix_cnt_

int nrn_matrix_cnt_ = 0

Definition at line 68 of file treeset.cpp.

nrn_mech_wtime_

double* nrn_mech_wtime_

Definition at line 29 of file treeset.cpp.

nrn_multisplit_setup_

void(* nrn_multisplit_setup_) ()

Definition at line 46 of file treeset.cpp.

nrn_node_ptr_change_cnt_

int nrn_node_ptr_change_cnt_

Definition at line 82 of file treeset.cpp.

nrn_pnt_sec_for_need_

Section* nrn_pnt_sec_for_need_

Definition at line 633 of file treeset.cpp.

nrn_pnt_template_

cTemplate** nrn_pnt_template_

Definition at line 169 of file init.cpp.

nrn_prop_dparam_size_

int* nrn_prop_dparam_size_

Definition at line 179 of file init.cpp.

nrn_shape_changed_

int nrn_shape_changed_

Definition at line 28 of file treeset.cpp.

nrn_use_daspk_

int nrn_use_daspk_ = 0

Definition at line 70 of file treeset.cpp.

old_actual_area_

double** old_actual_area_

static

Definition at line 2136 of file treeset.cpp.

old_actual_v_

double** old_actual_v_

static

Definition at line 2135 of file treeset.cpp.

old_actual_v_size_

int* old_actual_v_size_

static

Definition at line 2134 of file treeset.cpp.

pt3dconst_

int pt3dconst_

static

Definition at line 983 of file treeset.cpp.

recalc_cnt_

int recalc_cnt_

static

Definition at line 2131 of file treeset.cpp.

recalc_diam_count_

int recalc_diam_count_

Definition at line 772 of file treeset.cpp.

recalc_ptr_

double*(* recalc_ptr_) (double *)

static

Definition at line 2156 of file treeset.cpp.

recalc_ptr_callback

void(* recalc_ptr_callback[20])()

static

Definition at line 2130 of file treeset.cpp.

recalc_ptr_new_vp_

double** recalc_ptr_new_vp_

static

Definition at line 2132 of file treeset.cpp.

recalc_ptr_old_vp_

double ** recalc_ptr_old_vp_

static

Definition at line 2132 of file treeset.cpp.

secorder

Section** secorder

Definition at line 77 of file solve.cpp.

section_count

int section_count

Definition at line 76 of file solve.cpp.

spinearea

double spinearea =0.

static

Definition at line 1366 of file treeset.cpp.

structure_change_cnt

int structure_change_cnt

Definition at line 79 of file treeset.cpp.

tree_changed

int tree_changed

Definition at line 19 of file cabcode.cpp.

use_cachevec

int use_cachevec

Definition at line 61 of file treeset.cpp.

use_sparse13

int use_sparse13 = 0

Definition at line 69 of file treeset.cpp.

v_structure_change

int v_structure_change

Definition at line 78 of file treeset.cpp.