treeset.c File Reference

#include <../../nrnconf.h>
#include <stdio.h>
#include <errno.h>
#include <math.h>
#include "section.h"
#include "membfunc.h"
#include "neuron.h"
#include "parse.h"
#include "nrnmpiuse.h"
#include "multisplit.h"
#include "spmatrix.h"
#include "multicore.c"
#include <nrnpthread.h>
#include <nrnmpi.h>

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Defines
#define	PI   3.14159265358979323846
#define	NODE_DATA   0
Functions
double	chkarg ()
double	nrn_ra ()
double	nrnmpi_wtime ()
char *	secname ()
double	nrn_arc_position ()
Symbol *	hoc_table_lookup ()
void	nrn_cachevec ()
int	linmod_extra_eqn_count ()
void	linmod_alloc ()
void	linmod_rhs ()
void	linmod_lhs ()
void	nrn_rhs (NrnThread *_nt)
void	nrn_lhs (NrnThread *_nt)
void *	setup_tree_matrix (NrnThread *_nt)
Prop *	need_memb (Symbol *sym)
Prop *	prop_alloc (Prop **pp, int type, Node *nd)
Prop *	prop_alloc_disallow (Prop **pp, short type, Node *nd)
void	prop_free (Prop **pp)
	single_prop_free (Prop *p)
void	nrn_area_ri (Section *sec)
Node *	nrn_parent_node (Node *nd)
	connection_coef ()
	ForAllSections (sec)
	ClassicalNODEA (nd)
	for (j=1;j< sec->nnode;j++)
void	nrn_shape_update ()
int	recalc_diam ()
int	area ()
int	ri ()
	node_data ()
	nrn_complain (double *pp)
	fprintf (stderr,"Don't know the location of params at %lx\n",(long) pp)
	nrn_matrix_node_free ()
int	nrn_modeltype ()
int	nrn_method_consistent ()
	nrn_matrix_node_alloc ()
void	nrn_cachevec (int b)
Variables
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	section_count
Section **	secorder
short *	nrn_is_artificial_
Template **	nrn_pnt_template_
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)

---

Define Documentation

#define NODE_DATA   0

#define PI   3.14159265358979323846

---

Function Documentation

int area

(

)

References chk_access(), getarg(), node_index(), node_ptr(), NODEAREA, nrn_area_ri(), Section::pnode, Section::recalc_area_, ret, sec, and x.

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double chkarg

(

)

ClassicalNODEA

(

nd

)

connection_coef

(

)

References area, assert, ForAllSections, hoc_warning(), nd, nrn_area_ri(), nrn_area_ri_nocount_, recalc_diam_count_, sec, section_count, setup_topology(), and tree_changed.

Referenced by recalc_diam().

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for

(

j

= 1; j < sec->nnode; j++

)

References area, ClassicalNODEA, nd, NODEAREA, and sec.

ForAllSections

(

sec

)

References ClassicalNODEB, nd, NODEAREA, and sec.

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

Referenced by SaveState::check(), SaveState::checkacell(), SaveState::checknet(), SaveState::checknode(), Codraw_plt(), Codraw_preamble(), errcheck(), BBSImpl::execute_helper(), Fig_plt(), for(), Fprint(), hardplot_file(), hoc_audit_command(), hoc_audit_from_emacs(), hoc_audit_from_hoc_main1(), hoc_delete_symbol(), hoc_errno_check(), hoc_Exp(), hoc_object_component(), hoc_on_init_register(), hoc_retrieve_audit(), hoc_sred(), hoc_xopen_from_audit(), hplot(), icur(), initcode(), ion_reg(), ivocmain(), make_pointprocess(), need_memb(), nrn_cache_prop_realloc(), nrn_cacheline_alloc(), nrn_complain(), nrn_errno_check(), nrn_pushsec(), nrn_thread_stat(), nrnpy_pyrun(), nrnpython_start(), plprint(), MultiSplitControl::pmatf(), OcFile::print(), register_mech(), tplot(), tstkchk_actual(), SaveState::write(), SaveState::writenet(), and xred().

Symbol* hoc_table_lookup

(

)

void linmod_alloc

(

)

int linmod_extra_eqn_count

(

)

void linmod_lhs

(

)

References i, LinearModelAddition::lhs(), and m.

Referenced by nrn_lhs().

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void linmod_rhs

(

)

Prop* need_memb

(

Symbol*

sym

)

References fprintf(), hoc_execerror(), m, Prop::next, prop_alloc(), and type.

Referenced by KSChan::alloc().

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node_data

(

)

References nrn_area_ri_count_, recalc_diam_count_, and ret.

double nrn_arc_position

(

)

void nrn_area_ri

(

Section *

sec

)

References assert, diam_changed, Prop::dparam, e, hoc_execerror(), MORPHOLOGY, nd, Prop::next, Section::nnode, NODEAREA, nrn_area_ri_count_, nrn_area_ri_nocount_, nrn_ra(), Prop::param, PI, Section::pnode, Node::prop, Section::prop, Section::recalc_area_, secname(), section_length(), Prop::type, and Datum::val.

Referenced by area(), connection_coef(), and node_ptr().

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void nrn_cachevec

(

int

b

)

References tree_changed, use_cachevec, and use_sparse13.

void nrn_cachevec

(

)

Referenced by MultiSplitControl::multisplit(), and nrn_method_consistent().

nrn_complain

(

double*

pp

)

References ForAllSections, fprintf(), Prop::next, Section::nnode, nrn_arc_position(), Prop::param, Section::pnode, Node::prop, and secname().

Referenced by icur().

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void nrn_lhs

(

NrnThread *

_nt

)

References Node::_a_matelm, Node::_b_matelm, NrnThread::_sp13mat, NrnThread::_v_node, NrnThread::_v_parent, NrnThread::_v_parent_index, activclamp_lhs(), activsynapse_lhs(), assert, CAP, diam_changed, NrnThread::end, hoc_warning(), i, i1, i2, NrnThreadMembList::index, Memb_func::jacob, linmod_lhs(), memb_func, NrnThreadMembList::ml, NrnThread::ncell, nd, NrnThreadMembList::next, NODEA, NODEB, NODED, nrn_cap_jacob(), nrn_errno_check(), nrn_thread_error(), s, NrnThread::tml, use_cachevec, and use_sparse13.

Referenced by Imp::setmat1(), and setup_tree_matrix().

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nrn_matrix_node_alloc

(

)

References Node::_a_matelm, NrnThread::_actual_a, NrnThread::_actual_b, NrnThread::_actual_d, NrnThread::_actual_rhs, Node::_b_matelm, Node::_d, NrnThread::_ecell_memb_list, Node::_rhs, NrnThread::_sp13mat, NrnThread::_v_node, NrnThread::_v_parent, assert, b, cvode_active_, ecalloc, NrnThread::end, Node::eqn_index_, err, FOR_THREADS, hoc_execerror(), linmod_alloc(), linmod_extra_eqn_count(), Memb_list::nodecount, nrn_matrix_cnt_, nrn_matrix_node_free(), nrn_method_consistent(), nrn_threads, nrn_use_daspk_, use_sparse13, v_setup_vectors(), and v_structure_change.

Referenced by recalc_diam().

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nrn_matrix_node_free

(

)

References NrnThread::_actual_a, NrnThread::_actual_b, NrnThread::_actual_d, NrnThread::_actual_rhs, NrnThread::_sp13mat, diam_changed, and FOR_THREADS.

Referenced by LinearModelAddition::LinearModelAddition(), MultiSplitControl::multisplit(), nrn_matrix_node_alloc(), and LinearModelAddition::~LinearModelAddition().

int nrn_method_consistent

(

)

References cvode_active_, nrn_cachevec(), nrn_modeltype(), nrn_use_daspk(), nrn_use_daspk_, type, and use_sparse13.

Referenced by nrn_matrix_node_alloc().

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int nrn_modeltype

(

)

References NrnThread::_ecell_memb_list, FOR_THREADS, hoc_table_lookup(), linmod_extra_eqn_count(), nrn_global_ncell, s, Symbol::template, type, Symbol::u, and v_setup_vectors().

Referenced by nrn_method_consistent().

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Node* nrn_parent_node

(

Node *

nd

)

References Node::_classical_parent.

double nrn_ra

(

)

void nrn_rhs

(

NrnThread *

_nt

)

References NrnThread::_actual_rhs, NrnThread::_sp13mat, NrnThread::_v_node, NrnThread::_v_parent, NrnThread::_v_parent_index, activclamp_rhs(), activstim_rhs(), activsynapse_rhs(), BEFORE_BREAKPOINT, Memb_func::current, diam_changed, NrnThread::end, hoc_warning(), i, i1, i2, NrnThread::id, NrnThreadMembList::index, linmod_rhs(), memb_func, NrnThreadMembList::ml, NrnThread::ncell, nd, NrnThreadMembList::next, NODEA, NODEB, NODERHS, NODEV, nrn_ba(), nrn_errno_check(), nrn_mech_wtime_, nrn_thread_error(), nrnmpi_wtime(), recalc_diam(), s, NrnThread::tml, use_cachevec, and use_sparse13.

Referenced by NonLinImp::compute(), Imp::setmat1(), and setup_tree_matrix().

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void nrn_shape_update

(

)

References diam_change_cnt, diam_changed, hoc_Item::next, recalc_diam(), section_list, setup_topology(), tree_changed, v_setup_vectors(), and v_structure_change.

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double nrnmpi_wtime

(

)

References nrn_timeus().

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

References Prop::_alloc_seq, Memb_func::alloc, assert, Prop::dparam, emalloc, memb_func, Prop::next, Prop::ob, Prop::param, Prop::param_size, Prop::type, and v_structure_change.

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

References prop_alloc().

Referenced by nrn_loc_point_process().

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void prop_free

(

Prop **

pp

)

References Prop::next, and single_prop_free().

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int recalc_diam

(

)

References clamp_prepare(), connection_coef(), diam_change_cnt, diam_changed, nrn_matrix_node_alloc(), stim_prepare(), synapse_prepare(), and v_setup_vectors().

Referenced by Imp::check(), MultiSplitControl::exchange_setup(), fadvance(), fcurrent(), nrn_rhs(), nrn_shape_update(), and verify_structure().

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int ri

(

)

References area, chk_access(), getarg(), node_ptr(), and ret.

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char* secname

(

)

void* setup_tree_matrix

(

NrnThread *

_nt

)

References nrn_lhs(), and nrn_rhs().

Referenced by fcurrent(), and nrn_finitialize().

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single_prop_free

(

Prop*

p

)

References CABLESECTION, clear_point_process_struct(), hoc_obj_unref(), notify_freed_val_array(), nrn_prop_data_free(), nrn_prop_datum_free(), pnt_map, and v_structure_change.

Referenced by NrnProperty::NrnProperty(), prop_free(), and NrnPropertyImpl::~NrnPropertyImpl().

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---

Variable Documentation

area = NODEAREA(sec->parentnode)

int diam_changed

Symlist* hoc_built_in_symlist

nd = sec->pnode[0]

Node* nrn_alloc_node_

int nrn_area_ri_count_

Referenced by node_data(), and nrn_area_ri().

nrn_area_ri_nocount_ = 0

Referenced by connection_coef(), and nrn_area_ri().

int* nrn_dparam_ptr_end_

Referenced by hoc_last_init(), and register_mech().

int* nrn_dparam_ptr_start_

Referenced by hoc_last_init(), and register_mech().

short* nrn_is_artificial_

int nrn_matrix_cnt_ = 0

Referenced by nrn_matrix_node_alloc().

double* nrn_mech_wtime_

Referenced by nonvint(), and nrn_rhs().

void(* nrn_multisplit_setup_)()

Referenced by MultiSplitControl::multisplit(), MultiSplitControl::multisplit_clear(), nrn_fixed_step(), and nrn_fixed_step_group().

Template** nrn_pnt_template_

int* nrn_prop_dparam_size_

Referenced by hoc_last_init(), hoc_register_dparam_size(), and register_mech().

int nrn_shape_changed_

int nrn_use_daspk_ = 0

Referenced by linmod_init(), nrn_matrix_node_alloc(), and nrn_method_consistent().

int recalc_diam_count_

Referenced by connection_coef(), and node_data().

Section** secorder

int section_count

int tree_changed

int use_cachevec

Referenced by bksub(), nrn_cachevec(), nrn_cap_jacob(), nrn_capacity_current(), nrn_lhs(), nrn_rhs(), and MultiSplitControl::v_setup().

int use_sparse13 = 0

Referenced by nrn_cachevec(), nrn_finitialize(), nrn_lhs(), nrn_matrix_node_alloc(), nrn_method_consistent(), nrn_print_matrix(), nrn_rhs(), nrn_solve(), and MultiSplitControl::v_setup().