486 lines
13 KiB
C
486 lines
13 KiB
C
/* Created by Language version: 7.7.0 */
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/* VECTORIZED */
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#define NRN_VECTORIZED 1
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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#include "mech_api.h"
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#undef PI
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#define nil 0
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#include "md1redef.h"
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#include "section.h"
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#include "nrniv_mf.h"
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#include "md2redef.h"
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#if METHOD3
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extern int _method3;
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#endif
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#if !NRNGPU
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#undef exp
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#define exp hoc_Exp
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extern double hoc_Exp(double);
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#endif
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#define nrn_init _nrn_init__CaDynamics_E2
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#define _nrn_initial _nrn_initial__CaDynamics_E2
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#define nrn_cur _nrn_cur__CaDynamics_E2
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#define _nrn_current _nrn_current__CaDynamics_E2
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#define nrn_jacob _nrn_jacob__CaDynamics_E2
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#define nrn_state _nrn_state__CaDynamics_E2
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#define _net_receive _net_receive__CaDynamics_E2
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#define states states__CaDynamics_E2
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#define _threadargscomma_ _p, _ppvar, _thread, _nt,
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#define _threadargsprotocomma_ double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt,
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#define _threadargs_ _p, _ppvar, _thread, _nt
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#define _threadargsproto_ double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt
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/*SUPPRESS 761*/
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/*SUPPRESS 762*/
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/*SUPPRESS 763*/
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/*SUPPRESS 765*/
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extern double *getarg(int);
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/* Thread safe. No static _p or _ppvar. */
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#define t _nt->_t
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#define dt _nt->_dt
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#define gamma _p[0]
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#define gamma_columnindex 0
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#define decay _p[1]
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#define decay_columnindex 1
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#define depth _p[2]
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#define depth_columnindex 2
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#define minCai _p[3]
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#define minCai_columnindex 3
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#define ica _p[4]
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#define ica_columnindex 4
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#define cai _p[5]
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#define cai_columnindex 5
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#define Dcai _p[6]
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#define Dcai_columnindex 6
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#define v _p[7]
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#define v_columnindex 7
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#define _g _p[8]
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#define _g_columnindex 8
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#define _ion_ica *_ppvar[0]._pval
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#define _ion_cai *_ppvar[1]._pval
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#define _style_ca *((int*)_ppvar[2]._pvoid)
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#if MAC
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#if !defined(v)
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#define v _mlhv
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#endif
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#if !defined(h)
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#define h _mlhh
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#endif
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#endif
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#if defined(__cplusplus)
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extern "C" {
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#endif
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static int hoc_nrnpointerindex = -1;
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static Datum* _extcall_thread;
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static Prop* _extcall_prop;
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/* external NEURON variables */
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/* declaration of user functions */
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static int _mechtype;
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extern void _nrn_cacheloop_reg(int, int);
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extern void hoc_register_prop_size(int, int, int);
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extern void hoc_register_limits(int, HocParmLimits*);
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extern void hoc_register_units(int, HocParmUnits*);
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extern void nrn_promote(Prop*, int, int);
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extern Memb_func* memb_func;
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#define NMODL_TEXT 1
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#if NMODL_TEXT
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static const char* nmodl_file_text;
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static const char* nmodl_filename;
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extern void hoc_reg_nmodl_text(int, const char*);
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extern void hoc_reg_nmodl_filename(int, const char*);
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#endif
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extern void _nrn_setdata_reg(int, void(*)(Prop*));
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static void _setdata(Prop* _prop) {
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_extcall_prop = _prop;
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}
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static void _hoc_setdata() {
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Prop *_prop, *hoc_getdata_range(int);
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_prop = hoc_getdata_range(_mechtype);
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_setdata(_prop);
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hoc_retpushx(1.);
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}
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/* connect user functions to hoc names */
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static VoidFunc hoc_intfunc[] = {
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"setdata_CaDynamics_E2", _hoc_setdata,
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0, 0
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};
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/* declare global and static user variables */
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/* some parameters have upper and lower limits */
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static HocParmLimits _hoc_parm_limits[] = {
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0,0,0
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};
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static HocParmUnits _hoc_parm_units[] = {
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"decay_CaDynamics_E2", "ms",
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"depth_CaDynamics_E2", "um",
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"minCai_CaDynamics_E2", "mM",
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0,0
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};
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static double cai0 = 0;
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static double delta_t = 0.01;
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/* connect global user variables to hoc */
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static DoubScal hoc_scdoub[] = {
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0,0
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};
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static DoubVec hoc_vdoub[] = {
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0,0,0
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};
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static double _sav_indep;
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static void nrn_alloc(Prop*);
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static void nrn_init(NrnThread*, _Memb_list*, int);
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static void nrn_state(NrnThread*, _Memb_list*, int);
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static void nrn_cur(NrnThread*, _Memb_list*, int);
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static void nrn_jacob(NrnThread*, _Memb_list*, int);
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static int _ode_count(int);
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static void _ode_map(int, double**, double**, double*, Datum*, double*, int);
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static void _ode_spec(NrnThread*, _Memb_list*, int);
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static void _ode_matsol(NrnThread*, _Memb_list*, int);
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#define _cvode_ieq _ppvar[3]._i
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static void _ode_matsol_instance1(_threadargsproto_);
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/* connect range variables in _p that hoc is supposed to know about */
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static const char *_mechanism[] = {
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"7.7.0",
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"CaDynamics_E2",
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"gamma_CaDynamics_E2",
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"decay_CaDynamics_E2",
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"depth_CaDynamics_E2",
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"minCai_CaDynamics_E2",
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0,
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0,
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0,
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0};
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static Symbol* _ca_sym;
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extern Prop* need_memb(Symbol*);
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static void nrn_alloc(Prop* _prop) {
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Prop *prop_ion;
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double *_p; Datum *_ppvar;
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_p = nrn_prop_data_alloc(_mechtype, 9, _prop);
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/*initialize range parameters*/
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gamma = 0.001734;
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decay = 103.091;
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depth = 0.1;
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minCai = 0.0001;
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_prop->param = _p;
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_prop->param_size = 9;
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_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
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_prop->dparam = _ppvar;
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/*connect ionic variables to this model*/
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prop_ion = need_memb(_ca_sym);
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nrn_check_conc_write(_prop, prop_ion, 1);
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nrn_promote(prop_ion, 3, 0);
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_ppvar[0]._pval = &prop_ion->param[3]; /* ica */
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_ppvar[1]._pval = &prop_ion->param[1]; /* cai */
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_ppvar[2]._pvoid = (void*)(&(prop_ion->dparam[0]._i)); /* iontype for ca */
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}
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static void _initlists();
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/* some states have an absolute tolerance */
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static Symbol** _atollist;
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static HocStateTolerance _hoc_state_tol[] = {
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0,0
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};
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static void _update_ion_pointer(Datum*);
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extern Symbol* hoc_lookup(const char*);
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extern void _nrn_thread_reg(int, int, void(*)(Datum*));
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extern void _nrn_thread_table_reg(int, void(*)(double*, Datum*, Datum*, NrnThread*, int));
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extern void hoc_register_tolerance(int, HocStateTolerance*, Symbol***);
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extern void _cvode_abstol( Symbol**, double*, int);
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void _CaDynamics_E2_reg() {
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int _vectorized = 1;
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_initlists();
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ion_reg("ca", -10000.);
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_ca_sym = hoc_lookup("ca_ion");
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register_mech(_mechanism, nrn_alloc,nrn_cur, nrn_jacob, nrn_state, nrn_init, hoc_nrnpointerindex, 1);
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_mechtype = nrn_get_mechtype(_mechanism[1]);
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_nrn_setdata_reg(_mechtype, _setdata);
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_nrn_thread_reg(_mechtype, 2, _update_ion_pointer);
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#if NMODL_TEXT
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hoc_reg_nmodl_text(_mechtype, nmodl_file_text);
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hoc_reg_nmodl_filename(_mechtype, nmodl_filename);
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#endif
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hoc_register_prop_size(_mechtype, 9, 4);
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hoc_register_dparam_semantics(_mechtype, 0, "ca_ion");
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hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
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hoc_register_dparam_semantics(_mechtype, 2, "#ca_ion");
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hoc_register_dparam_semantics(_mechtype, 3, "cvodeieq");
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nrn_writes_conc(_mechtype, 0);
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hoc_register_cvode(_mechtype, _ode_count, _ode_map, _ode_spec, _ode_matsol);
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hoc_register_tolerance(_mechtype, _hoc_state_tol, &_atollist);
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hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
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ivoc_help("help ?1 CaDynamics_E2 /mnt/c/neuron/neurenv/mech/CaDynamics_E2.mod\n");
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hoc_register_limits(_mechtype, _hoc_parm_limits);
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hoc_register_units(_mechtype, _hoc_parm_units);
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}
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#define FARADAY _nrnunit_FARADAY[_nrnunit_use_legacy_]
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static double _nrnunit_FARADAY[2] = {0x1.78e555060882cp+16, 96485.3}; /* 96485.3321233100141 */
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static int _reset;
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static char *modelname = "";
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static int error;
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static int _ninits = 0;
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static int _match_recurse=1;
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static void _modl_cleanup(){ _match_recurse=1;}
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static int _ode_spec1(_threadargsproto_);
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/*static int _ode_matsol1(_threadargsproto_);*/
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static int _slist1[1], _dlist1[1];
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static int states(_threadargsproto_);
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/*CVODE*/
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static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
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Dcai = - ( 10000.0 ) * ( ica * gamma / ( 2.0 * FARADAY * depth ) ) - ( cai - minCai ) / decay ;
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}
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return _reset;
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}
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static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
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Dcai = Dcai / (1. - dt*( ( - ( ( 1.0 ) ) / decay ) )) ;
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return 0;
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}
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/*END CVODE*/
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static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
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cai = cai + (1. - exp(dt*(( - ( ( 1.0 ) ) / decay ))))*(- ( ( - ( 10000.0 ) )*( ( ( ( ica )*( gamma ) ) / ( 2.0 * FARADAY * depth ) ) ) - ( ( ( - minCai ) ) ) / decay ) / ( ( - ( ( 1.0 ) ) / decay ) ) - cai) ;
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}
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return 0;
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}
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static int _ode_count(int _type){ return 1;}
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static void _ode_spec(NrnThread* _nt, _Memb_list* _ml, int _type) {
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double* _p; Datum* _ppvar; Datum* _thread;
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Node* _nd; double _v; int _iml, _cntml;
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_cntml = _ml->_nodecount;
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_thread = _ml->_thread;
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for (_iml = 0; _iml < _cntml; ++_iml) {
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_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
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_nd = _ml->_nodelist[_iml];
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v = NODEV(_nd);
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ica = _ion_ica;
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cai = _ion_cai;
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_ode_spec1 (_p, _ppvar, _thread, _nt);
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_ion_cai = cai;
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}}
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static void _ode_map(int _ieq, double** _pv, double** _pvdot, double* _pp, Datum* _ppd, double* _atol, int _type) {
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double* _p; Datum* _ppvar;
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int _i; _p = _pp; _ppvar = _ppd;
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_cvode_ieq = _ieq;
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for (_i=0; _i < 1; ++_i) {
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_pv[_i] = _pp + _slist1[_i]; _pvdot[_i] = _pp + _dlist1[_i];
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_cvode_abstol(_atollist, _atol, _i);
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}
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_pv[0] = &(_ion_cai);
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}
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static void _ode_matsol_instance1(_threadargsproto_) {
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_ode_matsol1 (_p, _ppvar, _thread, _nt);
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}
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static void _ode_matsol(NrnThread* _nt, _Memb_list* _ml, int _type) {
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double* _p; Datum* _ppvar; Datum* _thread;
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Node* _nd; double _v; int _iml, _cntml;
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_cntml = _ml->_nodecount;
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_thread = _ml->_thread;
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for (_iml = 0; _iml < _cntml; ++_iml) {
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_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
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_nd = _ml->_nodelist[_iml];
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v = NODEV(_nd);
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ica = _ion_ica;
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cai = _ion_cai;
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_ode_matsol_instance1(_threadargs_);
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}}
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extern void nrn_update_ion_pointer(Symbol*, Datum*, int, int);
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static void _update_ion_pointer(Datum* _ppvar) {
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nrn_update_ion_pointer(_ca_sym, _ppvar, 0, 3);
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nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 1);
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}
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static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
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int _i; double _save;{
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}
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}
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static void nrn_init(NrnThread* _nt, _Memb_list* _ml, int _type){
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double* _p; Datum* _ppvar; Datum* _thread;
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Node *_nd; double _v; int* _ni; int _iml, _cntml;
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#if CACHEVEC
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_ni = _ml->_nodeindices;
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#endif
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_cntml = _ml->_nodecount;
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_thread = _ml->_thread;
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for (_iml = 0; _iml < _cntml; ++_iml) {
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_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
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#if CACHEVEC
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if (use_cachevec) {
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_v = VEC_V(_ni[_iml]);
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}else
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#endif
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{
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_nd = _ml->_nodelist[_iml];
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_v = NODEV(_nd);
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}
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v = _v;
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ica = _ion_ica;
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cai = _ion_cai;
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initmodel(_p, _ppvar, _thread, _nt);
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_ion_cai = cai;
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nrn_wrote_conc(_ca_sym, (&(_ion_cai)) - 1, _style_ca);
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}
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}
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static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{
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} return _current;
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}
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static void nrn_cur(NrnThread* _nt, _Memb_list* _ml, int _type) {
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double* _p; Datum* _ppvar; Datum* _thread;
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Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
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#if CACHEVEC
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_ni = _ml->_nodeindices;
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#endif
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_cntml = _ml->_nodecount;
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_thread = _ml->_thread;
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for (_iml = 0; _iml < _cntml; ++_iml) {
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_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
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#if CACHEVEC
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if (use_cachevec) {
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_v = VEC_V(_ni[_iml]);
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}else
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#endif
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{
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_nd = _ml->_nodelist[_iml];
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_v = NODEV(_nd);
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}
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}
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}
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static void nrn_jacob(NrnThread* _nt, _Memb_list* _ml, int _type) {
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double* _p; Datum* _ppvar; Datum* _thread;
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Node *_nd; int* _ni; int _iml, _cntml;
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#if CACHEVEC
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_ni = _ml->_nodeindices;
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#endif
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_cntml = _ml->_nodecount;
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_thread = _ml->_thread;
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for (_iml = 0; _iml < _cntml; ++_iml) {
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_p = _ml->_data[_iml];
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#if CACHEVEC
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if (use_cachevec) {
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VEC_D(_ni[_iml]) += _g;
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}else
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#endif
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{
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_nd = _ml->_nodelist[_iml];
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NODED(_nd) += _g;
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}
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}
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}
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static void nrn_state(NrnThread* _nt, _Memb_list* _ml, int _type) {
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double* _p; Datum* _ppvar; Datum* _thread;
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Node *_nd; double _v = 0.0; int* _ni; int _iml, _cntml;
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#if CACHEVEC
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_ni = _ml->_nodeindices;
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#endif
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_cntml = _ml->_nodecount;
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_thread = _ml->_thread;
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for (_iml = 0; _iml < _cntml; ++_iml) {
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_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
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_nd = _ml->_nodelist[_iml];
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#if CACHEVEC
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if (use_cachevec) {
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_v = VEC_V(_ni[_iml]);
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}else
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#endif
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{
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_nd = _ml->_nodelist[_iml];
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_v = NODEV(_nd);
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}
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v=_v;
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{
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ica = _ion_ica;
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cai = _ion_cai;
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{ states(_p, _ppvar, _thread, _nt);
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} {
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}
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_ion_cai = cai;
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}}
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}
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static void terminal(){}
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static void _initlists(){
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double _x; double* _p = &_x;
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int _i; static int _first = 1;
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if (!_first) return;
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_slist1[0] = cai_columnindex; _dlist1[0] = Dcai_columnindex;
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_first = 0;
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}
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#if defined(__cplusplus)
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} /* extern "C" */
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#endif
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#if NMODL_TEXT
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static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/CaDynamics_E2.mod";
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static const char* nmodl_file_text =
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":Comment : L6\n"
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": Dynamics that track inside calcium concentration\n"
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": modified from Destexhe et al. 1994\n"
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"\n"
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"NEURON {\n"
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" SUFFIX CaDynamics_E2\n"
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" USEION ca READ ica WRITE cai\n"
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" RANGE decay, gamma, minCai, depth\n"
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"}\n"
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"\n"
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"UNITS {\n"
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" (mV) = (millivolt)\n"
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" (mA) = (milliamp)\n"
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" FARADAY = (faraday) (coulombs)\n"
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" (molar) = (1/liter)\n"
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" (mM) = (millimolar)\n"
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" (um) = (micron)\n"
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"}\n"
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"\n"
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"PARAMETER {\n"
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" gamma = 0.001734 : percent of free calcium (not buffered)\n"
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" decay = 103.091390 (ms) : rate of removal of calcium\n"
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" depth = 0.1 (um) : depth of shell\n"
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" minCai = 1e-4 (mM)\n"
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"}\n"
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"\n"
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"ASSIGNED {ica (mA/cm2)}\n"
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"\n"
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"STATE {\n"
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" cai (mM)\n"
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" }\n"
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"\n"
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"BREAKPOINT { SOLVE states METHOD cnexp }\n"
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"\n"
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"DERIVATIVE states {\n"
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" cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay\n"
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"}\n"
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;
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#endif
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