wormsim 0.0.1__py3-none-any.whl

wormsim/components/mechanism/x86_64/egl2.c

@@ -0,0 +1,569 @@
+/* Created by Language version: 7.7.0 */
+/* VECTORIZED */
+#define NRN_VECTORIZED 1
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include "scoplib_ansi.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__egl2
+#define _nrn_initial _nrn_initial__egl2
+#define nrn_cur _nrn_cur__egl2
+#define _nrn_current _nrn_current__egl2
+#define nrn_jacob _nrn_jacob__egl2
+#define nrn_state _nrn_state__egl2
+#define _net_receive _net_receive__egl2 
+#define setparames setparames__egl2 
+#define states states__egl2 
+ 
+#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 gbegl2 _p[0]
+#define minf _p[1]
+#define tm _p[2]
+#define m _p[3]
+#define ek _p[4]
+#define ik _p[5]
+#define Dm _p[6]
+#define v _p[7]
+#define _g _p[8]
+#define _ion_ek	*_ppvar[0]._pval
+#define _ion_ik	*_ppvar[1]._pval
+#define _ion_dikdv	*_ppvar[2]._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_setparames(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_egl2", _hoc_setdata,
+ "setparames_egl2", _hoc_setparames,
+ 0, 0
+};
+ /* declare global and static user variables */
+#define atm atm_egl2
+ double atm = 1845.8;
+#define btm btm_egl2
+ double btm = -122.6;
+#define ctm ctm_egl2
+ double ctm = 13.8;
+#define dtm dtm_egl2
+ double dtm = 1517.74;
+#define ka ka_egl2
+ double ka = 14.9;
+#define vhm vhm_egl2
+ double vhm = -6.9;
+ /* some parameters have upper and lower limits */
+ static HocParmLimits _hoc_parm_limits[] = {
+ 0,0,0
+};
+ static HocParmUnits _hoc_parm_units[] = {
+ "vhm_egl2", "mV",
+ "ka_egl2", "mV",
+ "atm_egl2", "ms",
+ "btm_egl2", "mV",
+ "ctm_egl2", "mV",
+ "dtm_egl2", "ms",
+ "gbegl2_egl2", "nS/um2",
+ "tm_egl2", "ms",
+ 0,0
+};
+ static double delta_t = 0.01;
+ static double m0 = 0;
+ /* connect global user variables to hoc */
+ static DoubScal hoc_scdoub[] = {
+ "vhm_egl2", &vhm_egl2,
+ "ka_egl2", &ka_egl2,
+ "atm_egl2", &atm_egl2,
+ "btm_egl2", &btm_egl2,
+ "ctm_egl2", &ctm_egl2,
+ "dtm_egl2", &dtm_egl2,
+ 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[3]._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",
+"egl2",
+ "gbegl2_egl2",
+ 0,
+ "minf_egl2",
+ "tm_egl2",
+ 0,
+ "m_egl2",
+ 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, 9, _prop);
+ 	/*initialize range parameters*/
+ 	gbegl2 = 1;
+ 	_prop->param = _p;
+ 	_prop->param_size = 9;
+ 	_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
+ 	_prop->dparam = _ppvar;
+ 	/*connect ionic variables to this model*/
+ prop_ion = need_memb(_k_sym);
+ nrn_promote(prop_ion, 0, 1);
+ 	_ppvar[0]._pval = &prop_ion->param[0]; /* ek */
+ 	_ppvar[1]._pval = &prop_ion->param[3]; /* ik */
+ 	_ppvar[2]._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 _egl2_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, 9, 4);
+  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, "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 egl2 /home/zjj/8TB/robot_arm/project/BAAIWorm_v1/eworm/components/mechanism/modfile/egl2.mod\n");
+ hoc_register_limits(_mechtype, _hoc_parm_limits);
+ hoc_register_units(_mechtype, _hoc_parm_units);
+ }
+static int _reset;
+static char *modelname = "egl2 current for C. elegans neuron model";
+
+static int error;
+static int _ninits = 0;
+static int _match_recurse=1;
+static void _modl_cleanup(){ _match_recurse=1;}
+static int setparames(_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; {
+   setparames ( _threadargscomma_ v ) ;
+   Dm = ( minf - m ) / tm ;
+   }
+ return _reset;
+}
+ static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
+ setparames ( _threadargscomma_ v ) ;
+ Dm = Dm  / (1. - dt*( ( ( ( - 1.0 ) ) ) / tm )) ;
+  return 0;
+}
+ /*END CVODE*/
+ static int states (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) { {
+   setparames ( _threadargscomma_ v ) ;
+    m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / tm)))*(- ( ( ( minf ) ) / tm ) / ( ( ( ( - 1.0 ) ) ) / tm ) - m) ;
+   }
+  return 0;
+}
+ 
+static int  setparames ( _threadargsprotocomma_ double _lv ) {
+   minf = 1.0 / ( 1.0 + exp ( - ( _lv - vhm ) / ka ) ) ;
+   tm = atm / ( 1.0 + exp ( ( _lv - btm ) / ctm ) ) + dtm ;
+    return 0; }
+ 
+static void _hoc_setparames(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.;
+ setparames ( _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);
+  ek = _ion_ek;
+     _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);
+  ek = _ion_ek;
+ _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, 0);
+   nrn_update_ion_pointer(_k_sym, _ppvar, 1, 3);
+   nrn_update_ion_pointer(_k_sym, _ppvar, 2, 4);
+ }
+
+static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
+  int _i; double _save;{
+  m = m0;
+ {
+   setparames ( _threadargscomma_ v ) ;
+   m = minf ;
+   }
+ 
+}
+}
+
+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;
+  ek = _ion_ek;
+ initmodel(_p, _ppvar, _thread, _nt);
+ }
+}
+
+static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
+   ik = gbegl2 * m * ( v + 80.0 ) ;
+   }
+ _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);
+  }
+  ek = _ion_ek;
+ _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;
+{
+  ek = _ion_ek;
+ {   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] = &(m) - _p;  _dlist1[0] = &(Dm) - _p;
+_first = 0;
+}
+
+#if defined(__cplusplus)
+} /* extern "C" */
+#endif
+
+#if NMODL_TEXT
+static const char* nmodl_filename = "/home/zjj/8TB/robot_arm/project/BAAIWorm_v1/eworm/components/mechanism/modfile/egl2.mod";
+static const char* nmodl_file_text = 
+  "TITLE egl2 current for C. elegans neuron model\n"
+  "\n"
+  "\n"
+  "COMMENT\n"
+  "channel type: voltage-gated potassium channel\n"
+  "\n"
+  "patch clamp data from:\n"
+  "Weinshenker, D. , et al. \"Block of an ether-a-go-go-like K(+) channel by imipramine rescues egl-2 excitation defects in Caenorhabditis elegans. \" Journal of Neuroscience the Official Journal of the Society for Neuroscience 19.22(1999):9831.\n"
+  "Figure 3a upper left\n"
+  "\n"
+  "ENDCOMMENT\n"
+  "\n"
+  "\n"
+  "UNITS {\n"
+  "    (nS) = (nanosiemens)\n"
+  "    (mV) = (millivolt)\n"
+  "    (pA) = (picoamp)\n"
+  "    (um) = (micron)\n"
+  "}\n"
+  "\n"
+  "\n"
+  "NEURON {\n"
+  "    SUFFIX egl2\n"
+  "    USEION k READ ek WRITE ik\n"
+  "    RANGE gbegl2, minf, tm, m\n"
+  "}\n"
+  "\n"
+  "\n"
+  "PARAMETER {\n"
+  "    gbegl2 = 1 (nS/um2)\n"
+  "    vhm = -6.9 (mV)\n"
+  "    ka = 14.9 (mV)\n"
+  "    atm = 1845.8 (ms)\n"
+  "    btm = -122.6 (mV)\n"
+  "    ctm = 13.8 (mV)\n"
+  "    dtm = 1517.74 (ms)\n"
+  "}\n"
+  "\n"
+  "\n"
+  "ASSIGNED {\n"
+  "    v (mV)\n"
+  "    ek (mV)\n"
+  "    ik (pA/um2)\n"
+  "    minf\n"
+  "    tm (ms)\n"
+  "}\n"
+  "\n"
+  "\n"
+  "STATE {\n"
+  "    m\n"
+  "}\n"
+  "\n"
+  "\n"
+  "BREAKPOINT {\n"
+  "    SOLVE states METHOD cnexp\n"
+  "    :ik = gbegl2 * m * (v - ek)\n"
+  "    ik = gbegl2 * m * (v + 80) : ek = -80\n"
+  "}\n"
+  "\n"
+  "\n"
+  "INITIAL {\n"
+  "    setparames(v)\n"
+  "    m = minf\n"
+  "}\n"
+  "\n"
+  "\n"
+  "DERIVATIVE states {\n"
+  "    setparames(v)\n"
+  "    m' = (minf - m) / tm\n"
+  "}\n"
+  "\n"
+  "\n"
+  "PROCEDURE setparames(v (mV)) {\n"
+  "    minf = 1 / (1 + exp(-(v - vhm) / ka))\n"
+  "    tm = atm / (1 + exp((v - btm) / ctm)) + dtm\n"
+  "}\n"
+  ;
+#endif