kdr.c

/* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "mech_api.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
 
#if METHOD3
extern int _method3;
#endif

#if !NRNGPU
#undef exp
#define exp hoc_Exp
extern double hoc_Exp(double);
#endif
 
#define nrn_init _nrn_init__kdr
#define _nrn_initial _nrn_initial__kdr
#define nrn_cur _nrn_cur__kdr
#define _nrn_current _nrn_current__kdr
#define nrn_jacob _nrn_jacob__kdr
#define nrn_state _nrn_state__kdr
#define _net_receive _net_receive__kdr 
#define rate rate__kdr 
#define states states__kdr 
 
#define _threadargscomma_ _p, _ppvar, _thread, _nt,
#define _threadargsprotocomma_ double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt,
#define _threadargs_ _p, _ppvar, _thread, _nt
#define _threadargsproto_ double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt
 	/*SUPPRESS 761*/
	/*SUPPRESS 762*/
	/*SUPPRESS 763*/
	/*SUPPRESS 765*/
	 extern double *getarg();
 /* Thread safe. No static _p or _ppvar. */
 
#define t _nt->_t
#define dt _nt->_dt
#define gkdrbar _p[0]
#define gkdrbar_columnindex 0
#define ik _p[1]
#define ik_columnindex 1
#define gk _p[2]
#define gk_columnindex 2
#define n _p[3]
#define n_columnindex 3
#define Dn _p[4]
#define Dn_columnindex 4
#define inf _p[5]
#define inf_columnindex 5
#define tau _p[6]
#define tau_columnindex 6
#define ek _p[7]
#define ek_columnindex 7
#define ki _p[8]
#define ki_columnindex 8
#define ko _p[9]
#define ko_columnindex 9
#define v _p[10]
#define v_columnindex 10
#define _g _p[11]
#define _g_columnindex 11
#define _ion_ki	*_ppvar[0]._pval
#define _ion_ko	*_ppvar[1]._pval
#define _ion_ik	*_ppvar[2]._pval
#define _ion_dikdv	*_ppvar[3]._pval
 
#if MAC
#if !defined(v)
#define v _mlhv
#endif
#if !defined(h)
#define h _mlhh
#endif
#endif
 
#if defined(__cplusplus)
extern "C" {
#endif
 static int hoc_nrnpointerindex =  -1;
 static Datum* _extcall_thread;
 static Prop* _extcall_prop;
 /* external NEURON variables */
 /* declaration of user functions */
 static void _hoc_alf(void);
 static void _hoc_bet(void);
 static void _hoc_rate(void);
 static int _mechtype;
extern void _nrn_cacheloop_reg(int, int);
extern void hoc_register_prop_size(int, int, int);
extern void hoc_register_limits(int, HocParmLimits*);
extern void hoc_register_units(int, HocParmUnits*);
extern void nrn_promote(Prop*, int, int);
extern Memb_func* memb_func;
 
#define NMODL_TEXT 1
#if NMODL_TEXT
static const char* nmodl_file_text;
static const char* nmodl_filename;
extern void hoc_reg_nmodl_text(int, const char*);
extern void hoc_reg_nmodl_filename(int, const char*);
#endif

 extern void _nrn_setdata_reg(int, void(*)(Prop*));
 static void _setdata(Prop* _prop) {
 _extcall_prop = _prop;
 }
 static void _hoc_setdata() {
 Prop *_prop, *hoc_getdata_range(int);
 _prop = hoc_getdata_range(_mechtype);
   _setdata(_prop);
 hoc_retpushx(1.);
}
 /* connect user functions to hoc names */
 static VoidFunc hoc_intfunc[] = {
 "setdata_kdr", _hoc_setdata,
 "alf_kdr", _hoc_alf,
 "bet_kdr", _hoc_bet,
 "rate_kdr", _hoc_rate,
 0, 0
};
#define alf alf_kdr
#define bet bet_kdr
 extern double alf( _threadargsprotocomma_ double );
 extern double bet( _threadargsprotocomma_ double );
 /* declare global and static user variables */
 /* some parameters have upper and lower limits */
 static HocParmLimits _hoc_parm_limits[] = {
 "gkdrbar_kdr", 0, 1e+09,
 0,0,0
};
 static HocParmUnits _hoc_parm_units[] = {
 "gkdrbar_kdr", "mho/cm2",
 "ik_kdr", "mA/cm2",
 "gk_kdr", "mho/cm2",
 0,0
};
 static double delta_t = 1;
 static double n0 = 0;
 /* connect global user variables to hoc */
 static DoubScal hoc_scdoub[] = {
 0,0
};
 static DoubVec hoc_vdoub[] = {
 0,0,0
};
 static double _sav_indep;
 static void nrn_alloc(Prop*);
static void  nrn_init(NrnThread*, _Memb_list*, int);
static void nrn_state(NrnThread*, _Memb_list*, int);
 static void nrn_cur(NrnThread*, _Memb_list*, int);
static void  nrn_jacob(NrnThread*, _Memb_list*, int);
 
static int _ode_count(int);
static void _ode_map(int, double**, double**, double*, Datum*, double*, int);
static void _ode_spec(NrnThread*, _Memb_list*, int);
static void _ode_matsol(NrnThread*, _Memb_list*, int);
 
#define _cvode_ieq _ppvar[4]._i
 static void _ode_matsol_instance1(_threadargsproto_);
 /* connect range variables in _p that hoc is supposed to know about */
 static const char *_mechanism[] = {
 "7.7.0",
"kdr",
 "gkdrbar_kdr",
 0,
 "ik_kdr",
 "gk_kdr",
 0,
 "n_kdr",
 0,
 0};
 static Symbol* _k_sym;
 
extern Prop* need_memb(Symbol*);

static void nrn_alloc(Prop* _prop) {
	Prop *prop_ion;
	double *_p; Datum *_ppvar;
 	_p = nrn_prop_data_alloc(_mechtype, 12, _prop);
 	/*initialize range parameters*/
 	gkdrbar = 0.0338;
 	_prop->param = _p;
 	_prop->param_size = 12;
 	_ppvar = nrn_prop_datum_alloc(_mechtype, 5, _prop);
 	_prop->dparam = _ppvar;
 	/*connect ionic variables to this model*/
 prop_ion = need_memb(_k_sym);
 nrn_promote(prop_ion, 1, 0);
 	_ppvar[0]._pval = &prop_ion->param[1]; /* ki */
 	_ppvar[1]._pval = &prop_ion->param[2]; /* ko */
 	_ppvar[2]._pval = &prop_ion->param[3]; /* ik */
 	_ppvar[3]._pval = &prop_ion->param[4]; /* _ion_dikdv */
 
}
 static void _initlists();
  /* some states have an absolute tolerance */
 static Symbol** _atollist;
 static HocStateTolerance _hoc_state_tol[] = {
 0,0
};
 static void _update_ion_pointer(Datum*);
 extern Symbol* hoc_lookup(const char*);
extern void _nrn_thread_reg(int, int, void(*)(Datum*));
extern void _nrn_thread_table_reg(int, void(*)(double*, Datum*, Datum*, NrnThread*, int));
extern void hoc_register_tolerance(int, HocStateTolerance*, Symbol***);
extern void _cvode_abstol( Symbol**, double*, int);

 void _kdr_reg() {
	int _vectorized = 1;
  _initlists();
 	ion_reg("k", -10000.);
 	_k_sym = hoc_lookup("k_ion");
 	register_mech(_mechanism, nrn_alloc,nrn_cur, nrn_jacob, nrn_state, nrn_init, hoc_nrnpointerindex, 1);
 _mechtype = nrn_get_mechtype(_mechanism[1]);
     _nrn_setdata_reg(_mechtype, _setdata);
     _nrn_thread_reg(_mechtype, 2, _update_ion_pointer);
 #if NMODL_TEXT
  hoc_reg_nmodl_text(_mechtype, nmodl_file_text);
  hoc_reg_nmodl_filename(_mechtype, nmodl_filename);
#endif
  hoc_register_prop_size(_mechtype, 12, 5);
  hoc_register_dparam_semantics(_mechtype, 0, "k_ion");
  hoc_register_dparam_semantics(_mechtype, 1, "k_ion");
  hoc_register_dparam_semantics(_mechtype, 2, "k_ion");
  hoc_register_dparam_semantics(_mechtype, 3, "k_ion");
  hoc_register_dparam_semantics(_mechtype, 4, "cvodeieq");
 	hoc_register_cvode(_mechtype, _ode_count, _ode_map, _ode_spec, _ode_matsol);
 	hoc_register_tolerance(_mechtype, _hoc_state_tol, &_atollist);
 	hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
 	ivoc_help("help ?1 kdr kdr.mod\n");
 hoc_register_limits(_mechtype, _hoc_parm_limits);
 hoc_register_units(_mechtype, _hoc_parm_units);
 }
static int _reset;
static char *modelname = "";

static int error;
static int _ninits = 0;
static int _match_recurse=1;
static void _modl_cleanup(){ _match_recurse=1;}
static int rate(_threadargsprotocomma_ double);
 
static int _ode_spec1(_threadargsproto_);
/*static int _ode_matsol1(_threadargsproto_);*/
 static int _slist1[1], _dlist1[1];
 static int states(_threadargsproto_);
 
/*CVODE*/
 static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
   rate ( _threadargscomma_ v ) ;
   Dn = ( inf - n ) / tau ;
   }
 return _reset;
}
 static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
 rate ( _threadargscomma_ v ) ;
 Dn = Dn  / (1. - dt*( ( ( ( - 1.0 ) ) ) / tau )) ;
  return 0;
}
 /*END CVODE*/
 static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
   rate ( _threadargscomma_ v ) ;
    n = n + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / tau)))*(- ( ( ( inf ) ) / tau ) / ( ( ( ( - 1.0 ) ) ) / tau ) - n) ;
   }
  return 0;
}
 
double alf ( _threadargsprotocomma_ double _lv ) {
   double _lalf;
 double _lva ;
 _lva = _lv - 13.0 ;
   if ( fabs ( _lva ) < 1e-04 ) {
     _lva = _lva + 0.0001 ;
     _lalf = ( - 0.018 * _lva ) / ( - 1.0 + exp ( - ( _lva / 25.0 ) ) ) ;
     }
   else {
     _lalf = ( - 0.018 * ( _lv - 13.0 ) ) / ( - 1.0 + exp ( - ( ( _lv - 13.0 ) / 25.0 ) ) ) ;
     }
   
return _lalf;
 }
 
static void _hoc_alf(void) {
  double _r;
   double* _p; Datum* _ppvar; Datum* _thread; NrnThread* _nt;
   if (_extcall_prop) {_p = _extcall_prop->param; _ppvar = _extcall_prop->dparam;}else{ _p = (double*)0; _ppvar = (Datum*)0; }
  _thread = _extcall_thread;
  _nt = nrn_threads;
 _r =  alf ( _p, _ppvar, _thread, _nt, *getarg(1) );
 hoc_retpushx(_r);
}
 
double bet ( _threadargsprotocomma_ double _lv ) {
   double _lbet;
 double _lvb ;
 _lvb = _lv - 23.0 ;
   if ( fabs ( _lvb ) < 1e-04 ) {
     _lvb = _lvb + 0.0001 ;
     _lbet = ( 0.0054 * _lvb ) / ( - 1.0 + exp ( _lvb / 12.0 ) ) ;
     }
   else {
     _lbet = ( 0.0054 * ( _lv - 23.0 ) ) / ( - 1.0 + exp ( ( _lv - 23.0 ) / 12.0 ) ) ;
     }
   
return _lbet;
 }
 
static void _hoc_bet(void) {
  double _r;
   double* _p; Datum* _ppvar; Datum* _thread; NrnThread* _nt;
   if (_extcall_prop) {_p = _extcall_prop->param; _ppvar = _extcall_prop->dparam;}else{ _p = (double*)0; _ppvar = (Datum*)0; }
  _thread = _extcall_thread;
  _nt = nrn_threads;
 _r =  bet ( _p, _ppvar, _thread, _nt, *getarg(1) );
 hoc_retpushx(_r);
}
 
static int  rate ( _threadargsprotocomma_ double _lv ) {
   double _lq10 , _lsum , _laa , _lab ;
 _laa = alf ( _threadargscomma_ _lv ) ;
   _lab = bet ( _threadargscomma_ _lv ) ;
   _lsum = _laa + _lab ;
   inf = _laa / _lsum ;
   tau = 1.0 / ( _lsum ) ;
    return 0; }
 
static void _hoc_rate(void) {
  double _r;
   double* _p; Datum* _ppvar; Datum* _thread; NrnThread* _nt;
   if (_extcall_prop) {_p = _extcall_prop->param; _ppvar = _extcall_prop->dparam;}else{ _p = (double*)0; _ppvar = (Datum*)0; }
  _thread = _extcall_thread;
  _nt = nrn_threads;
 _r = 1.;
 rate ( _p, _ppvar, _thread, _nt, *getarg(1) );
 hoc_retpushx(_r);
}
 
static int _ode_count(int _type){ return 1;}
 
static void _ode_spec(NrnThread* _nt, _Memb_list* _ml, int _type) {
   double* _p; Datum* _ppvar; Datum* _thread;
   Node* _nd; double _v; int _iml, _cntml;
  _cntml = _ml->_nodecount;
  _thread = _ml->_thread;
  for (_iml = 0; _iml < _cntml; ++_iml) {
    _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
    _nd = _ml->_nodelist[_iml];
    v = NODEV(_nd);
  ki = _ion_ki;
  ko = _ion_ko;
     _ode_spec1 (_p, _ppvar, _thread, _nt);
  }}
 
static void _ode_map(int _ieq, double** _pv, double** _pvdot, double* _pp, Datum* _ppd, double* _atol, int _type) { 
	double* _p; Datum* _ppvar;
 	int _i; _p = _pp; _ppvar = _ppd;
	_cvode_ieq = _ieq;
	for (_i=0; _i < 1; ++_i) {
		_pv[_i] = _pp + _slist1[_i];  _pvdot[_i] = _pp + _dlist1[_i];
		_cvode_abstol(_atollist, _atol, _i);
	}
 }
 
static void _ode_matsol_instance1(_threadargsproto_) {
 _ode_matsol1 (_p, _ppvar, _thread, _nt);
 }
 
static void _ode_matsol(NrnThread* _nt, _Memb_list* _ml, int _type) {
   double* _p; Datum* _ppvar; Datum* _thread;
   Node* _nd; double _v; int _iml, _cntml;
  _cntml = _ml->_nodecount;
  _thread = _ml->_thread;
  for (_iml = 0; _iml < _cntml; ++_iml) {
    _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
    _nd = _ml->_nodelist[_iml];
    v = NODEV(_nd);
  ki = _ion_ki;
  ko = _ion_ko;
 _ode_matsol_instance1(_threadargs_);
 }}
 extern void nrn_update_ion_pointer(Symbol*, Datum*, int, int);
 static void _update_ion_pointer(Datum* _ppvar) {
   nrn_update_ion_pointer(_k_sym, _ppvar, 0, 1);
   nrn_update_ion_pointer(_k_sym, _ppvar, 1, 2);
   nrn_update_ion_pointer(_k_sym, _ppvar, 2, 3);
   nrn_update_ion_pointer(_k_sym, _ppvar, 3, 4);
 }

static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
  int _i; double _save;{
  n = n0;
 {
   rate ( _threadargscomma_ v ) ;
   n = inf ;
   }
 
}
}

static void nrn_init(NrnThread* _nt, _Memb_list* _ml, int _type){
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; double _v; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
 v = _v;
  ki = _ion_ki;
  ko = _ion_ko;
 initmodel(_p, _ppvar, _thread, _nt);
 }
}

static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
   gk = gkdrbar * n * n * n * n ;
   ek = 25.0 * log ( ko / ki ) ;
   ik = gk * ( v - ek ) ;
   }
 _current += ik;

} return _current;
}

static void nrn_cur(NrnThread* _nt, _Memb_list* _ml, int _type) {
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
  ki = _ion_ki;
  ko = _ion_ko;
 _g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
 	{ double _dik;
  _dik = ik;
 _rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
  _ion_dikdv += (_dik - ik)/.001 ;
 	}
 _g = (_g - _rhs)/.001;
  _ion_ik += ik ;
#if CACHEVEC
  if (use_cachevec) {
	VEC_RHS(_ni[_iml]) -= _rhs;
  }else
#endif
  {
	NODERHS(_nd) -= _rhs;
  }
 
}
 
}

static void nrn_jacob(NrnThread* _nt, _Memb_list* _ml, int _type) {
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml];
#if CACHEVEC
  if (use_cachevec) {
	VEC_D(_ni[_iml]) += _g;
  }else
#endif
  {
     _nd = _ml->_nodelist[_iml];
	NODED(_nd) += _g;
  }
 
}
 
}

static void nrn_state(NrnThread* _nt, _Memb_list* _ml, int _type) {
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; double _v = 0.0; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
 _nd = _ml->_nodelist[_iml];
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
 v=_v;
{
  ki = _ion_ki;
  ko = _ion_ko;
 {   states(_p, _ppvar, _thread, _nt);
  } }}

}

static void terminal(){}

static void _initlists(){
 double _x; double* _p = &_x;
 int _i; static int _first = 1;
  if (!_first) return;
 _slist1[0] = n_columnindex;  _dlist1[0] = Dn_columnindex;
_first = 0;
}

#if defined(__cplusplus)
} /* extern "C" */
#endif

#if NMODL_TEXT
static const char* nmodl_filename = "kdr.mod";
static const char* nmodl_file_text = 
  ": Delayed rectifier K+ channel\n"
  "\n"
  "NEURON {\n"
  "	SUFFIX kdr\n"
  "	USEION k READ ki, ko WRITE ik\n"
  "	RANGE gkdrbar, ik, gk\n"
  "	\n"
  "}\n"
  "\n"
  "UNITS {\n"
  "	(mA) = (milliamp)\n"
  "	(mV) = (millivolt)\n"
  "	\n"
  "}\n"
  "\n"
  "INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}\n"
  "PARAMETER {\n"
  "	v (mV)\n"
  "	dt (ms)\n"
  "	gkdrbar= 0.0338 (mho/cm2) <0,1e9>\n"
  "	\n"
  "	\n"
  "}\n"
  "\n"
  "STATE {\n"
  "	n\n"
  "}\n"
  "\n"
  "ASSIGNED {\n"
  "	ik (mA/cm2)\n"
  "	inf\n"
  "	tau (ms)\n"
  "	gk (mho/cm2)\n"
  "	ek (mV)\n"
  "	ki (mM)\n"
  "	ko (mM)\n"
  "\n"
  "}\n"
  "\n"
  "\n"
  "INITIAL {\n"
  "	rate(v)\n"
  "	n = inf\n"
  "}\n"
  "\n"
  "BREAKPOINT {\n"
  "	SOLVE states METHOD cnexp\n"
  "	gk= gkdrbar*n*n*n*n\n"
  "	ek = 25 * log(ko/ki)\n"
  "	ik = gk*(v-ek)\n"
  "	\n"
  "}\n"
  "\n"
  "DERIVATIVE states {\n"
  "	rate(v)\n"
  "	n' = (inf-n)/tau\n"
  "}\n"
  "\n"
  "UNITSOFF\n"
  "\n"
  "FUNCTION alf(v){ LOCAL va \n"
  "	\n"
  "	   va=v-13\n"
  "	if (fabs(va)<1e-04){\n"
  "	   va=va+0.0001\n"
  "		alf= (-0.018*va)/(-1+exp(-(va/25)))\n"
  "	} else {\n"
  "	  	alf = (-0.018*(v-13))/(-1+exp(-((v-13)/25)))\n"
  "	}\n"
  "}\n"
  "\n"
  "\n"
  "FUNCTION bet(v) { LOCAL vb \n"
  "	\n"
  "	  vb=v-23\n"
  "	if (fabs(vb)<1e-04){\n"
  "	  vb=vb+0.0001\n"
  "		bet= (0.0054*vb)/(-1+exp(vb/12))\n"
  "	} else {\n"
  "	  	bet = (0.0054*(v-23))/(-1+exp((v-23)/12))\n"
  "	}\n"
  "}	\n"
  "\n"
  "\n"
  "\n"
  "\n"
  "\n"
  "\n"
  "PROCEDURE rate(v (mV)) {LOCAL q10, sum, aa, ab\n"
  "	\n"
  "	aa=alf(v) ab=bet(v) \n"
  "	\n"
  "	sum = aa+ab\n"
  "	inf = aa/sum\n"
  "	tau = 1/(sum)\n"
  "	\n"
  "	\n"
  "}\n"
  "\n"
  "UNITSON	\n"
  "\n"
  "\n"
  "\n"
  ;
#endif