wormsim 0.0.1__py3-none-any.whl

wormsim/components/mechanism/x86_64/exc_syn_advance.c

@@ -0,0 +1,587 @@
+/* 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__exc_syn_advance
+#define _nrn_initial _nrn_initial__exc_syn_advance
+#define nrn_cur _nrn_cur__exc_syn_advance
+#define _nrn_current _nrn_current__exc_syn_advance
+#define nrn_jacob _nrn_jacob__exc_syn_advance
+#define nrn_state _nrn_state__exc_syn_advance
+#define _net_receive _net_receive__exc_syn_advance 
+#define rates rates__exc_syn_advance 
+#define states states__exc_syn_advance 
+ 
+#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 weight _p[0]
+#define conductance _p[1]
+#define delta _p[2]
+#define k _p[3]
+#define Vth _p[4]
+#define erev _p[5]
+#define vpre _p[6]
+#define i _p[7]
+#define s _p[8]
+#define inf _p[9]
+#define tau _p[10]
+#define Ds _p[11]
+#define v _p[12]
+#define _g _p[13]
+#define _nd_area  *_ppvar[0]._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 double _hoc_rates();
+ 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 Prop* nrn_point_prop_;
+ static int _pointtype;
+ static void* _hoc_create_pnt(_ho) Object* _ho; { void* create_point_process();
+ return create_point_process(_pointtype, _ho);
+}
+ static void _hoc_destroy_pnt();
+ static double _hoc_loc_pnt(_vptr) void* _vptr; {double loc_point_process();
+ return loc_point_process(_pointtype, _vptr);
+}
+ static double _hoc_has_loc(_vptr) void* _vptr; {double has_loc_point();
+ return has_loc_point(_vptr);
+}
+ static double _hoc_get_loc_pnt(_vptr)void* _vptr; {
+ double get_loc_point_process(); return (get_loc_point_process(_vptr));
+}
+ extern void _nrn_setdata_reg(int, void(*)(Prop*));
+ static void _setdata(Prop* _prop) {
+ _extcall_prop = _prop;
+ }
+ static void _hoc_setdata(void* _vptr) { Prop* _prop;
+ _prop = ((Point_process*)_vptr)->_prop;
+   _setdata(_prop);
+ }
+ /* connect user functions to hoc names */
+ static VoidFunc hoc_intfunc[] = {
+ 0,0
+};
+ static Member_func _member_func[] = {
+ "loc", _hoc_loc_pnt,
+ "has_loc", _hoc_has_loc,
+ "get_loc", _hoc_get_loc_pnt,
+ "rates", _hoc_rates,
+ 0, 0
+};
+ /* declare global and static user variables */
+ /* some parameters have upper and lower limits */
+ static HocParmLimits _hoc_parm_limits[] = {
+ 0,0,0
+};
+ static HocParmUnits _hoc_parm_units[] = {
+ "conductance", "uS",
+ "delta", "mV",
+ "k", "kHz",
+ "Vth", "mV",
+ "erev", "mV",
+ "vpre", "mV",
+ "i", "nA",
+ 0,0
+};
+ static double delta_t = 0.01;
+ static double s0 = 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 void _hoc_destroy_pnt(_vptr) void* _vptr; {
+   destroy_point_process(_vptr);
+}
+ 
+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[2]._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",
+"exc_syn_advance",
+ "weight",
+ "conductance",
+ "delta",
+ "k",
+ "Vth",
+ "erev",
+ 0,
+ "vpre",
+ "i",
+ 0,
+ "s",
+ 0,
+ 0};
+ 
+extern Prop* need_memb(Symbol*);
+
+static void nrn_alloc(Prop* _prop) {
+	Prop *prop_ion;
+	double *_p; Datum *_ppvar;
+  if (nrn_point_prop_) {
+	_prop->_alloc_seq = nrn_point_prop_->_alloc_seq;
+	_p = nrn_point_prop_->param;
+	_ppvar = nrn_point_prop_->dparam;
+ }else{
+ 	_p = nrn_prop_data_alloc(_mechtype, 14, _prop);
+ 	/*initialize range parameters*/
+ 	weight = 1;
+ 	conductance = 0.00049;
+ 	delta = 5;
+ 	k = 0.5;
+ 	Vth = 0;
+ 	erev = 30;
+  }
+ 	_prop->param = _p;
+ 	_prop->param_size = 14;
+  if (!nrn_point_prop_) {
+ 	_ppvar = nrn_prop_datum_alloc(_mechtype, 3, _prop);
+  }
+ 	_prop->dparam = _ppvar;
+ 	/*connect ionic variables to this model*/
+ 
+}
+ static void _initlists();
+  /* some states have an absolute tolerance */
+ static Symbol** _atollist;
+ static HocStateTolerance _hoc_state_tol[] = {
+ 0,0
+};
+ 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 _exc_syn_advance_reg() {
+	int _vectorized = 1;
+  _initlists();
+ 	_pointtype = point_register_mech(_mechanism,
+	 nrn_alloc,nrn_cur, nrn_jacob, nrn_state, nrn_init,
+	 hoc_nrnpointerindex, 1,
+	 _hoc_create_pnt, _hoc_destroy_pnt, _member_func);
+ _mechtype = nrn_get_mechtype(_mechanism[1]);
+     _nrn_setdata_reg(_mechtype, _setdata);
+ #if NMODL_TEXT
+  hoc_reg_nmodl_text(_mechtype, nmodl_file_text);
+  hoc_reg_nmodl_filename(_mechtype, nmodl_filename);
+#endif
+  hoc_register_prop_size(_mechtype, 14, 3);
+  hoc_register_dparam_semantics(_mechtype, 0, "area");
+  hoc_register_dparam_semantics(_mechtype, 1, "pntproc");
+  hoc_register_dparam_semantics(_mechtype, 2, "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 exc_syn_advance /home/zjj/8TB/robot_arm/project/BAAIWorm_v1/eworm/components/mechanism/modfile/exc_syn_advance.mod\n");
+ hoc_register_limits(_mechtype, _hoc_parm_limits);
+ hoc_register_units(_mechtype, _hoc_parm_units);
+ }
+static int _reset;
+static char *modelname = "excitatory to excitatory synapse";
+
+static int error;
+static int _ninits = 0;
+static int _match_recurse=1;
+static void _modl_cleanup(){ _match_recurse=1;}
+static int rates(_threadargsproto_);
+ 
+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; {
+   rates ( _threadargs_ ) ;
+   Ds = ( inf - s ) / tau ;
+   }
+ return _reset;
+}
+ static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
+ rates ( _threadargs_ ) ;
+ Ds = Ds  / (1. - dt*( ( ( ( - 1.0 ) ) ) / tau )) ;
+  return 0;
+}
+ /*END CVODE*/
+ static int states (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) { {
+   rates ( _threadargs_ ) ;
+    s = s + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / tau)))*(- ( ( ( inf ) ) / tau ) / ( ( ( ( - 1.0 ) ) ) / tau ) - s) ;
+   }
+  return 0;
+}
+ 
+static int  rates ( _threadargsproto_ ) {
+   inf = 1.0 / ( 1.0 + exp ( ( Vth - vpre ) / delta ) ) ;
+   tau = ( 1.0 - inf ) / k ;
+    return 0; }
+ 
+static double _hoc_rates(void* _vptr) {
+ double _r;
+   double* _p; Datum* _ppvar; Datum* _thread; _NrnThread* _nt;
+   _p = ((Point_process*)_vptr)->_prop->param;
+  _ppvar = ((Point_process*)_vptr)->_prop->dparam;
+  _thread = _extcall_thread;
+  _nt = (_NrnThread*)((Point_process*)_vptr)->_vnt;
+ _r = 1.;
+ rates ( _p, _ppvar, _thread, _nt );
+ return(_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);
+     _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);
+ _ode_matsol_instance1(_threadargs_);
+ }}
+
+static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
+  int _i; double _save;{
+  s = s0;
+ {
+   rates ( _threadargs_ ) ;
+   s = 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;
+ initmodel(_p, _ppvar, _thread, _nt);
+}
+}
+
+static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
+   i = weight * conductance * s * ( v - erev ) ;
+   }
+ _current += i;
+
+} 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);
+  }
+ _g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
+ 	{ _rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
+ 	}
+ _g = (_g - _rhs)/.001;
+ _g *=  1.e2/(_nd_area);
+ _rhs *= 1.e2/(_nd_area);
+#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;
+{
+ {   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] = &(s) - _p;  _dlist1[0] = &(Ds) - _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/exc_syn_advance.mod";
+static const char* nmodl_file_text = 
+  "COMMENT\n"
+  "Based on NMODL code for neuron_to_neuron_exc_syn\n"
+  "\n"
+  "Code and comments have been normalized--that is,\n"
+  "they are now of the usual form employed in \n"
+  "NMODL-specified synaptic mechanisms.\n"
+  "\n"
+  "Oddities that save neither storage nor time, \n"
+  "or preclude use with adaptive integration, \n"
+  "or deliberately introduce errors in an attempt\n"
+  "to save a few CPU cycles, have been removed.\n"
+  "\n"
+  "Unused variables and parameters have also been removed.\n"
+  "\n"
+  "vpre is now a POINTER.\n"
+  "\n"
+  "In the INITIAL block, the completely unnecessary repeat\n"
+  "execution of procedure rates() has been removed, \n"
+  "and the state variable s is now set to the correct \n"
+  "initial value.\n"
+  "\n"
+  "The value of the current i is now calculated in the\n"
+  "BREAKPOINT block, instead of being calculated as a \n"
+  "side-effect of calling rates().\n"
+  "ENDCOMMENT\n"
+  "\n"
+  "TITLE excitatory to excitatory synapse\n"
+  "\n"
+  "NEURON {\n"
+  "    POINT_PROCESS exc_syn_advance\n"
+  "    NONSPECIFIC_CURRENT i\n"
+  "    RANGE weight, conductance, i, vpre\n"
+  "    RANGE delta, k, Vth, erev\n"
+  "}\n"
+  "\n"
+  "UNITS {\n"
+  "    (nA) = (nanoamp)\n"
+  "    (uA) = (microamp)\n"
+  "    (mA) = (milliamp)\n"
+  "    (A) = (amp)\n"
+  "    (mV) = (millivolt)\n"
+  "    (mS) = (millisiemens)\n"
+  "    (uS) = (microsiemens)\n"
+  "    (molar) = (1/liter)\n"
+  "    (kHz) = (kilohertz)\n"
+  "    (mM) = (millimolar)\n"
+  "    (um) = (micrometer)\n"
+  "    (umol) = (micromole)\n"
+  "    (S) = (siemens)\n"
+  "}\n"
+  "\n"
+  "PARAMETER {\n"
+  "    weight = 1\n"
+  "    conductance = 4.9E-4 (uS)\n"
+  "    delta = 5 (mV)\n"
+  "    k = 0.5 (kHz)\n"
+  "    Vth = 0 (mV)\n"
+  "    erev = 30 (mV) : -10\n"
+  "}\n"
+  "\n"
+  "ASSIGNED {\n"
+  "    v (mV)\n"
+  "    vpre (mV)\n"
+  "    inf\n"
+  "    tau (ms)\n"
+  "    i (nA)\n"
+  "}\n"
+  "\n"
+  "STATE {\n"
+  "    s  \n"
+  "}\n"
+  "\n"
+  "INITIAL {\n"
+  "    rates()\n"
+  "    s = inf : NTC original code did not properly initialize s\n"
+  "}\n"
+  "\n"
+  "BREAKPOINT {\n"
+  "    SOLVE states METHOD cnexp\n"
+  "    i = weight * conductance * s * (v - erev)\n"
+  "}\n"
+  "\n"
+  "DERIVATIVE states {\n"
+  "    rates()\n"
+  "    s' = (inf - s)/tau\n"
+  "}\n"
+  "\n"
+  "PROCEDURE rates() {\n"
+  "    inf = 1/( 1 + exp((Vth - vpre)/delta) )\n"
+  "    tau = (1 - inf)/k\n"
+  "}\n"
+  ;
+#endif