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neurenv/mech/x86_64/hhqt.cpp
Connell Paxton a0a907245a Added additional files
2026-07-11 18:20:01 -04:00

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/* 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
#define _pval pval
// clang-format off
#include "md1redef.h"
#include "section_fwd.hpp"
#include "nrniv_mf.h"
#include "md2redef.h"
#include "nrnconf.h"
// clang-format on
#include "neuron/cache/mechanism_range.hpp"
static constexpr auto number_of_datum_variables = 6;
static constexpr auto number_of_floating_point_variables = 25;
namespace {
template <typename T>
using _nrn_mechanism_std_vector = std::vector<T>;
using _nrn_model_sorted_token = neuron::model_sorted_token;
using _nrn_mechanism_cache_range = neuron::cache::MechanismRange<number_of_floating_point_variables, number_of_datum_variables>;
using _nrn_mechanism_cache_instance = neuron::cache::MechanismInstance<number_of_floating_point_variables, number_of_datum_variables>;
using _nrn_non_owning_id_without_container = neuron::container::non_owning_identifier_without_container;
template <typename T>
using _nrn_mechanism_field = neuron::mechanism::field<T>;
template <typename... Args>
void _nrn_mechanism_register_data_fields(Args&&... args) {
neuron::mechanism::register_data_fields(std::forward<Args>(args)...);
}
}
#if !NRNGPU
#undef exp
#define exp hoc_Exp
#if NRN_ENABLE_ARCH_INDEP_EXP_POW
#undef pow
#define pow hoc_pow
#endif
#endif
#define nrn_init _nrn_init__hhqt
#define _nrn_initial _nrn_initial__hhqt
#define nrn_cur _nrn_cur__hhqt
#define _nrn_current _nrn_current__hhqt
#define nrn_jacob _nrn_jacob__hhqt
#define nrn_state _nrn_state__hhqt
#define _net_receive _net_receive__hhqt
#define rates rates__hhqt
#define states states__hhqt
#define _threadargscomma_ _ml, _iml, _ppvar, _thread, _globals, _nt,
#define _threadargsprotocomma_ Memb_list* _ml, size_t _iml, Datum* _ppvar, Datum* _thread, double* _globals, NrnThread* _nt,
#define _internalthreadargsprotocomma_ _nrn_mechanism_cache_range* _ml, size_t _iml, Datum* _ppvar, Datum* _thread, double* _globals, NrnThread* _nt,
#define _threadargs_ _ml, _iml, _ppvar, _thread, _globals, _nt
#define _threadargsproto_ Memb_list* _ml, size_t _iml, Datum* _ppvar, Datum* _thread, double* _globals, NrnThread* _nt
#define _internalthreadargsproto_ _nrn_mechanism_cache_range* _ml, size_t _iml, Datum* _ppvar, Datum* _thread, double* _globals, NrnThread* _nt
/*SUPPRESS 761*/
/*SUPPRESS 762*/
/*SUPPRESS 763*/
/*SUPPRESS 765*/
extern double *hoc_getarg(int);
#define t _nt->_t
#define dt _nt->_dt
#define gnabar _ml->template fpfield<0>(_iml)
#define gnabar_columnindex 0
#define gkbar _ml->template fpfield<1>(_iml)
#define gkbar_columnindex 1
#define gl _ml->template fpfield<2>(_iml)
#define gl_columnindex 2
#define el _ml->template fpfield<3>(_iml)
#define el_columnindex 3
#define gna _ml->template fpfield<4>(_iml)
#define gna_columnindex 4
#define gk _ml->template fpfield<5>(_iml)
#define gk_columnindex 5
#define il _ml->template fpfield<6>(_iml)
#define il_columnindex 6
#define m _ml->template fpfield<7>(_iml)
#define m_columnindex 7
#define h _ml->template fpfield<8>(_iml)
#define h_columnindex 8
#define n _ml->template fpfield<9>(_iml)
#define n_columnindex 9
#define ena _ml->template fpfield<10>(_iml)
#define ena_columnindex 10
#define ek _ml->template fpfield<11>(_iml)
#define ek_columnindex 11
#define ina _ml->template fpfield<12>(_iml)
#define ina_columnindex 12
#define ik _ml->template fpfield<13>(_iml)
#define ik_columnindex 13
#define minf _ml->template fpfield<14>(_iml)
#define minf_columnindex 14
#define hinf _ml->template fpfield<15>(_iml)
#define hinf_columnindex 15
#define ninf _ml->template fpfield<16>(_iml)
#define ninf_columnindex 16
#define mtau _ml->template fpfield<17>(_iml)
#define mtau_columnindex 17
#define htau _ml->template fpfield<18>(_iml)
#define htau_columnindex 18
#define ntau _ml->template fpfield<19>(_iml)
#define ntau_columnindex 19
#define Dm _ml->template fpfield<20>(_iml)
#define Dm_columnindex 20
#define Dh _ml->template fpfield<21>(_iml)
#define Dh_columnindex 21
#define Dn _ml->template fpfield<22>(_iml)
#define Dn_columnindex 22
#define v _ml->template fpfield<23>(_iml)
#define v_columnindex 23
#define _g _ml->template fpfield<24>(_iml)
#define _g_columnindex 24
#define _ion_ena *(_ml->dptr_field<0>(_iml))
#define _p_ion_ena static_cast<neuron::container::data_handle<double>>(_ppvar[0])
#define _ion_ina *(_ml->dptr_field<1>(_iml))
#define _p_ion_ina static_cast<neuron::container::data_handle<double>>(_ppvar[1])
#define _ion_dinadv *(_ml->dptr_field<2>(_iml))
#define _ion_ek *(_ml->dptr_field<3>(_iml))
#define _p_ion_ek static_cast<neuron::container::data_handle<double>>(_ppvar[3])
#define _ion_ik *(_ml->dptr_field<4>(_iml))
#define _p_ion_ik static_cast<neuron::container::data_handle<double>>(_ppvar[4])
#define _ion_dikdv *(_ml->dptr_field<5>(_iml))
/* Thread safe. No static _ml, _iml or _ppvar. */
static int hoc_nrnpointerindex = -1;
static _nrn_mechanism_std_vector<Datum> _extcall_thread;
static Prop* _extcall_prop;
/* _prop_id kind of shadows _extcall_prop to allow validity checking. */
static _nrn_non_owning_id_without_container _prop_id{};
/* external NEURON variables */
extern double celsius;
/* declaration of user functions */
static void _hoc_rates(void);
static void _hoc_vtrap(void);
static int _mechtype;
extern void _nrn_cacheloop_reg(int, int);
extern void hoc_register_limits(int, HocParmLimits*);
extern void hoc_register_units(int, HocParmUnits*);
extern void nrn_promote(Prop*, int, int);
#define NMODL_TEXT 1
#if NMODL_TEXT
static void register_nmodl_text_and_filename(int mechtype);
#endif
static void _hoc_setdata();
/* connect user functions to hoc names */
static VoidFunc hoc_intfunc[] = {
{"setdata_hhqt", _hoc_setdata},
{"rates_hhqt", _hoc_rates},
{"vtrap_hhqt", _hoc_vtrap},
{0, 0}
};
/* Direct Python call wrappers to density mechanism functions.*/
static double _npy_rates(Prop*);
static double _npy_vtrap(Prop*);
static NPyDirectMechFunc npy_direct_func_proc[] = {
{"rates", _npy_rates},
{"vtrap", _npy_vtrap},
{0, 0}
};
#define vtrap vtrap_hhqt
extern double vtrap( _internalthreadargsprotocomma_ double , double );
/* declare global and static user variables */
#define gind 0
#define _gth 0
/* some parameters have upper and lower limits */
static HocParmLimits _hoc_parm_limits[] = {
{"gl_hhqt", 0, 1e+09},
{"gkbar_hhqt", 0, 1e+09},
{"gnabar_hhqt", 0, 1e+09},
{0, 0, 0}
};
static HocParmUnits _hoc_parm_units[] = {
{"gnabar_hhqt", "S/cm2"},
{"gkbar_hhqt", "S/cm2"},
{"gl_hhqt", "S/cm2"},
{"el_hhqt", "mV"},
{"gna_hhqt", "S/cm2"},
{"gk_hhqt", "S/cm2"},
{"il_hhqt", "mA/cm2"},
{0, 0}
};
static double delta_t = 0.01;
static double h0 = 0;
static double m0 = 0;
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;
extern void _nrn_setdata_reg(int, void(*)(Prop*));
static void _setdata(Prop* _prop) {
_extcall_prop = _prop;
_prop_id = _nrn_get_prop_id(_prop);
}
static void _hoc_setdata() {
Prop *_prop, *hoc_getdata_range(int);
_prop = hoc_getdata_range(_mechtype);
_setdata(_prop);
hoc_retpushx(1.);
}
static void nrn_alloc(Prop*);
static void nrn_init(_nrn_model_sorted_token const&, NrnThread*, Memb_list*, int);
static void nrn_state(_nrn_model_sorted_token const&, NrnThread*, Memb_list*, int);
static void nrn_cur(_nrn_model_sorted_token const&, NrnThread*, Memb_list*, int);
static void nrn_jacob(_nrn_model_sorted_token const&, NrnThread*, Memb_list*, int);
static int _ode_count(int);
static void _ode_map(Prop*, int, neuron::container::data_handle<double>*, neuron::container::data_handle<double>*, double*, int);
static void _ode_spec(_nrn_model_sorted_token const&, NrnThread*, Memb_list*, int);
static void _ode_matsol(_nrn_model_sorted_token const&, NrnThread*, Memb_list*, int);
#define _cvode_ieq _ppvar[6].literal_value<int>()
static void _ode_matsol_instance1(_internalthreadargsproto_);
/* connect range variables in _p that hoc is supposed to know about */
static const char *_mechanism[] = {
"7.7.0",
"hhqt",
"gnabar_hhqt",
"gkbar_hhqt",
"gl_hhqt",
"el_hhqt",
0,
"gna_hhqt",
"gk_hhqt",
"il_hhqt",
0,
"m_hhqt",
"h_hhqt",
"n_hhqt",
0,
0};
static Symbol* _na_sym;
static Symbol* _k_sym;
/* Used by NrnProperty */
static _nrn_mechanism_std_vector<double> _parm_default{
0.12, /* gnabar */
0.036, /* gkbar */
0.0003, /* gl */
-54.3, /* el */
};
extern Prop* need_memb(Symbol*);
static void nrn_alloc(Prop* _prop) {
Prop *prop_ion{};
Datum *_ppvar{};
_ppvar = nrn_prop_datum_alloc(_mechtype, 7, _prop);
_nrn_mechanism_access_dparam(_prop) = _ppvar;
_nrn_mechanism_cache_instance _ml_real{_prop};
auto* const _ml = &_ml_real;
size_t const _iml{};
assert(_nrn_mechanism_get_num_vars(_prop) == 25);
/*initialize range parameters*/
gnabar = _parm_default[0]; /* 0.12 */
gkbar = _parm_default[1]; /* 0.036 */
gl = _parm_default[2]; /* 0.0003 */
el = _parm_default[3]; /* -54.3 */
assert(_nrn_mechanism_get_num_vars(_prop) == 25);
_nrn_mechanism_access_dparam(_prop) = _ppvar;
/*connect ionic variables to this model*/
prop_ion = need_memb(_na_sym);
nrn_promote(prop_ion, 0, 1);
_ppvar[0] = _nrn_mechanism_get_param_handle(prop_ion, 0); /* ena */
_ppvar[1] = _nrn_mechanism_get_param_handle(prop_ion, 3); /* ina */
_ppvar[2] = _nrn_mechanism_get_param_handle(prop_ion, 4); /* _ion_dinadv */
prop_ion = need_memb(_k_sym);
nrn_promote(prop_ion, 0, 1);
_ppvar[3] = _nrn_mechanism_get_param_handle(prop_ion, 0); /* ek */
_ppvar[4] = _nrn_mechanism_get_param_handle(prop_ion, 3); /* ik */
_ppvar[5] = _nrn_mechanism_get_param_handle(prop_ion, 4); /* _ion_dikdv */
}
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*));
void _nrn_thread_table_reg(int, nrn_thread_table_check_t);
extern void hoc_register_tolerance(int, HocStateTolerance*, Symbol***);
extern void _cvode_abstol( Symbol**, double*, int);
extern "C" void _hhqt_reg() {
int _vectorized = 1;
_initlists();
ion_reg("na", -10000.);
ion_reg("k", -10000.);
_na_sym = hoc_lookup("na_ion");
_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]);
hoc_register_parm_default(_mechtype, &_parm_default);
hoc_register_npy_direct(_mechtype, npy_direct_func_proc);
_nrn_setdata_reg(_mechtype, _setdata);
#if NMODL_TEXT
register_nmodl_text_and_filename(_mechtype);
#endif
_nrn_mechanism_register_data_fields(_mechtype,
_nrn_mechanism_field<double>{"gnabar"} /* 0 */,
_nrn_mechanism_field<double>{"gkbar"} /* 1 */,
_nrn_mechanism_field<double>{"gl"} /* 2 */,
_nrn_mechanism_field<double>{"el"} /* 3 */,
_nrn_mechanism_field<double>{"gna"} /* 4 */,
_nrn_mechanism_field<double>{"gk"} /* 5 */,
_nrn_mechanism_field<double>{"il"} /* 6 */,
_nrn_mechanism_field<double>{"m"} /* 7 */,
_nrn_mechanism_field<double>{"h"} /* 8 */,
_nrn_mechanism_field<double>{"n"} /* 9 */,
_nrn_mechanism_field<double>{"ena"} /* 10 */,
_nrn_mechanism_field<double>{"ek"} /* 11 */,
_nrn_mechanism_field<double>{"ina"} /* 12 */,
_nrn_mechanism_field<double>{"ik"} /* 13 */,
_nrn_mechanism_field<double>{"minf"} /* 14 */,
_nrn_mechanism_field<double>{"hinf"} /* 15 */,
_nrn_mechanism_field<double>{"ninf"} /* 16 */,
_nrn_mechanism_field<double>{"mtau"} /* 17 */,
_nrn_mechanism_field<double>{"htau"} /* 18 */,
_nrn_mechanism_field<double>{"ntau"} /* 19 */,
_nrn_mechanism_field<double>{"Dm"} /* 20 */,
_nrn_mechanism_field<double>{"Dh"} /* 21 */,
_nrn_mechanism_field<double>{"Dn"} /* 22 */,
_nrn_mechanism_field<double>{"v"} /* 23 */,
_nrn_mechanism_field<double>{"_g"} /* 24 */,
_nrn_mechanism_field<double*>{"_ion_ena", "na_ion"} /* 0 */,
_nrn_mechanism_field<double*>{"_ion_ina", "na_ion"} /* 1 */,
_nrn_mechanism_field<double*>{"_ion_dinadv", "na_ion"} /* 2 */,
_nrn_mechanism_field<double*>{"_ion_ek", "k_ion"} /* 3 */,
_nrn_mechanism_field<double*>{"_ion_ik", "k_ion"} /* 4 */,
_nrn_mechanism_field<double*>{"_ion_dikdv", "k_ion"} /* 5 */,
_nrn_mechanism_field<int>{"_cvode_ieq", "cvodeieq"} /* 6 */);
hoc_register_prop_size(_mechtype, 25, 7);
hoc_register_dparam_semantics(_mechtype, 0, "na_ion");
hoc_register_dparam_semantics(_mechtype, 1, "na_ion");
hoc_register_dparam_semantics(_mechtype, 2, "na_ion");
hoc_register_dparam_semantics(_mechtype, 3, "k_ion");
hoc_register_dparam_semantics(_mechtype, 4, "k_ion");
hoc_register_dparam_semantics(_mechtype, 5, "k_ion");
hoc_register_dparam_semantics(_mechtype, 6, "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 hhqt /home/qh4os/neurenv/mech/hhqt.mod\n");
hoc_register_limits(_mechtype, _hoc_parm_limits);
hoc_register_units(_mechtype, _hoc_parm_units);
}
static int _reset;
static const char *modelname = "";
static int error;
static int _ninits = 0;
static int _match_recurse=1;
static void _modl_cleanup(){ _match_recurse=1;}
static int rates(_internalthreadargsprotocomma_ double);
static int _ode_spec1(_internalthreadargsproto_);
/*static int _ode_matsol1(_internalthreadargsproto_);*/
static neuron::container::field_index _slist1[3], _dlist1[3];
static int states(_internalthreadargsproto_);
/*CVODE*/
static int _ode_spec1 (_internalthreadargsproto_) {int _reset = 0; {
rates ( _threadargscomma_ v ) ;
Dm = ( minf - m ) / mtau ;
Dh = ( hinf - h ) / htau ;
Dn = ( ninf - n ) / ntau ;
}
return _reset;
}
static int _ode_matsol1 (_internalthreadargsproto_) {
rates ( _threadargscomma_ v ) ;
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mtau )) ;
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / htau )) ;
Dn = Dn / (1. - dt*( ( ( ( - 1.0 ) ) ) / ntau )) ;
return 0;
}
/*END CVODE*/
static int states (_internalthreadargsproto_) { {
rates ( _threadargscomma_ v ) ;
m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / mtau)))*(- ( ( ( minf ) ) / mtau ) / ( ( ( ( - 1.0 ) ) ) / mtau ) - m) ;
h = h + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / htau)))*(- ( ( ( hinf ) ) / htau ) / ( ( ( ( - 1.0 ) ) ) / htau ) - h) ;
n = n + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / ntau)))*(- ( ( ( ninf ) ) / ntau ) / ( ( ( ( - 1.0 ) ) ) / ntau ) - n) ;
}
return 0;
}
static int rates ( _internalthreadargsprotocomma_ double _lv ) {
double _lalpha , _lbeta , _lsum , _lq10 ;
_lq10 = pow( 3.0 , ( ( celsius - 6.3 ) / 10.0 ) ) ;
_lalpha = .1 * vtrap ( _threadargscomma_ - ( _lv + 40.0 ) , 10.0 ) ;
_lbeta = 4.0 * exp ( - ( _lv + 65.0 ) / 18.0 ) ;
_lsum = _lalpha + _lbeta ;
mtau = 1.0 / ( _lq10 * _lsum ) ;
minf = _lalpha / _lsum ;
_lalpha = .07 * exp ( - ( _lv + 65.0 ) / 20.0 ) ;
_lbeta = 1.0 / ( exp ( - ( _lv + 35.0 ) / 10.0 ) + 1.0 ) ;
_lsum = _lalpha + _lbeta ;
htau = 1.0 / ( _lq10 * _lsum ) ;
hinf = _lalpha / _lsum ;
_lalpha = .01 * vtrap ( _threadargscomma_ - ( _lv + 55.0 ) , 10.0 ) ;
_lbeta = .125 * exp ( - ( _lv + 65.0 ) / 80.0 ) ;
_lsum = _lalpha + _lbeta ;
ntau = 1.0 / ( _lq10 * _lsum ) ;
ninf = _lalpha / _lsum ;
return 0; }
static void _hoc_rates(void) {
double _r;
Datum* _ppvar; Datum* _thread; NrnThread* _nt;
Prop* _local_prop = _prop_id ? _extcall_prop : nullptr;
_nrn_mechanism_cache_instance _ml_real{_local_prop};
auto* const _ml = &_ml_real;
size_t const _iml{};
_ppvar = _local_prop ? _nrn_mechanism_access_dparam(_local_prop) : nullptr;
_thread = _extcall_thread.data();
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
_nt = nrn_threads;
_r = 1.;
rates ( _threadargscomma_ *getarg(1) );
hoc_retpushx(_r);
}
static double _npy_rates(Prop* _prop) {
double _r{0.0};
Datum* _ppvar; Datum* _thread; NrnThread* _nt;
_nrn_mechanism_cache_instance _ml_real{_prop};
auto* const _ml = &_ml_real;
size_t const _iml{};
_ppvar = _nrn_mechanism_access_dparam(_prop);
_thread = _extcall_thread.data();
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
_nt = nrn_threads;
_r = 1.;
rates ( _threadargscomma_ *getarg(1) );
return(_r);
}
double vtrap ( _internalthreadargsprotocomma_ double _lx , double _ly ) {
double _lvtrap;
if ( fabs ( _lx / _ly ) < 1e-6 ) {
_lvtrap = _ly * ( 1.0 - _lx / _ly / 2.0 ) ;
}
else {
_lvtrap = _lx / ( exp ( _lx / _ly ) - 1.0 ) ;
}
return _lvtrap;
}
static void _hoc_vtrap(void) {
double _r;
Datum* _ppvar; Datum* _thread; NrnThread* _nt;
Prop* _local_prop = _prop_id ? _extcall_prop : nullptr;
_nrn_mechanism_cache_instance _ml_real{_local_prop};
auto* const _ml = &_ml_real;
size_t const _iml{};
_ppvar = _local_prop ? _nrn_mechanism_access_dparam(_local_prop) : nullptr;
_thread = _extcall_thread.data();
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
_nt = nrn_threads;
_r = vtrap ( _threadargscomma_ *getarg(1) , *getarg(2) );
hoc_retpushx(_r);
}
static double _npy_vtrap(Prop* _prop) {
double _r{0.0};
Datum* _ppvar; Datum* _thread; NrnThread* _nt;
_nrn_mechanism_cache_instance _ml_real{_prop};
auto* const _ml = &_ml_real;
size_t const _iml{};
_ppvar = _nrn_mechanism_access_dparam(_prop);
_thread = _extcall_thread.data();
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
_nt = nrn_threads;
_r = vtrap ( _threadargscomma_ *getarg(1) , *getarg(2) );
return(_r);
}
static int _ode_count(int _type){ return 3;}
static void _ode_spec(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
Datum* _ppvar;
size_t _iml; _nrn_mechanism_cache_range* _ml; Node* _nd{};
double _v{};
int _cntml;
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _type};
_ml = &_lmr;
_cntml = _ml_arg->_nodecount;
Datum *_thread{_ml_arg->_thread};
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
for (_iml = 0; _iml < _cntml; ++_iml) {
_ppvar = _ml_arg->_pdata[_iml];
_nd = _ml_arg->_nodelist[_iml];
v = NODEV(_nd);
ena = _ion_ena;
ek = _ion_ek;
_ode_spec1 (_threadargs_);
}}
static void _ode_map(Prop* _prop, int _ieq, neuron::container::data_handle<double>* _pv, neuron::container::data_handle<double>* _pvdot, double* _atol, int _type) {
Datum* _ppvar;
_ppvar = _nrn_mechanism_access_dparam(_prop);
_cvode_ieq = _ieq;
for (int _i=0; _i < 3; ++_i) {
_pv[_i] = _nrn_mechanism_get_param_handle(_prop, _slist1[_i]);
_pvdot[_i] = _nrn_mechanism_get_param_handle(_prop, _dlist1[_i]);
_cvode_abstol(_atollist, _atol, _i);
}
}
static void _ode_matsol_instance1(_internalthreadargsproto_) {
_ode_matsol1 (_threadargs_);
}
static void _ode_matsol(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
Datum* _ppvar;
size_t _iml; _nrn_mechanism_cache_range* _ml; Node* _nd{};
double _v{};
int _cntml;
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _type};
_ml = &_lmr;
_cntml = _ml_arg->_nodecount;
Datum *_thread{_ml_arg->_thread};
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
for (_iml = 0; _iml < _cntml; ++_iml) {
_ppvar = _ml_arg->_pdata[_iml];
_nd = _ml_arg->_nodelist[_iml];
v = NODEV(_nd);
ena = _ion_ena;
ek = _ion_ek;
_ode_matsol_instance1(_threadargs_);
}}
static void initmodel(_internalthreadargsproto_) {
int _i; double _save;{
h = h0;
m = m0;
n = n0;
{
rates ( _threadargscomma_ v ) ;
m = minf ;
h = hinf ;
n = ninf ;
}
}
}
static void nrn_init(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _type};
auto* const _vec_v = _nt->node_voltage_storage();
auto* const _ml = &_lmr;
Datum* _ppvar; Datum* _thread;
Node *_nd; double _v; int* _ni; int _iml, _cntml;
_ni = _ml_arg->_nodeindices;
_cntml = _ml_arg->_nodecount;
_thread = _ml_arg->_thread;
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
for (_iml = 0; _iml < _cntml; ++_iml) {
_ppvar = _ml_arg->_pdata[_iml];
_v = _vec_v[_ni[_iml]];
v = _v;
ena = _ion_ena;
ek = _ion_ek;
initmodel(_threadargs_);
}
}
static double _nrn_current(_internalthreadargsprotocomma_ double _v) {
double _current=0.; v=_v;
{ {
gna = gnabar * m * m * m * h ;
ina = gna * ( v - ena ) ;
gk = gkbar * n * n * n * n ;
ik = gk * ( v - ek ) ;
il = gl * ( v - el ) ;
}
_current += ina;
_current += ik;
_current += il;
} return _current;
}
static void nrn_cur(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _type};
auto const _vec_rhs = _nt->node_rhs_storage();
auto const _vec_sav_rhs = _nt->node_sav_rhs_storage();
auto const _vec_v = _nt->node_voltage_storage();
auto* const _ml = &_lmr;
Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
_ni = _ml_arg->_nodeindices;
_cntml = _ml_arg->_nodecount;
_thread = _ml_arg->_thread;
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
for (_iml = 0; _iml < _cntml; ++_iml) {
_ppvar = _ml_arg->_pdata[_iml];
_v = _vec_v[_ni[_iml]];
ena = _ion_ena;
ek = _ion_ek;
auto const _g_local = _nrn_current(_threadargscomma_ _v + .001);
{ double _dik;
double _dina;
_dina = ina;
_dik = ik;
_rhs = _nrn_current(_threadargscomma_ _v);
_ion_dinadv += (_dina - ina)/.001 ;
_ion_dikdv += (_dik - ik)/.001 ;
}
_g = (_g_local - _rhs)/.001;
_ion_ina += ina ;
_ion_ik += ik ;
_vec_rhs[_ni[_iml]] -= _rhs;
}
}
static void nrn_jacob(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _type};
auto const _vec_d = _nt->node_d_storage();
auto const _vec_sav_d = _nt->node_sav_d_storage();
auto* const _ml = &_lmr;
Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; int _iml, _cntml;
_ni = _ml_arg->_nodeindices;
_cntml = _ml_arg->_nodecount;
_thread = _ml_arg->_thread;
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
for (_iml = 0; _iml < _cntml; ++_iml) {
_vec_d[_ni[_iml]] += _g;
}
}
static void nrn_state(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type) {
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _type};
auto* const _vec_v = _nt->node_voltage_storage();
auto* const _ml = &_lmr;
Datum* _ppvar; Datum* _thread;
Node *_nd; double _v = 0.0; int* _ni;
_ni = _ml_arg->_nodeindices;
size_t _cntml = _ml_arg->_nodecount;
_thread = _ml_arg->_thread;
double* _globals = nullptr;
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
for (size_t _iml = 0; _iml < _cntml; ++_iml) {
_ppvar = _ml_arg->_pdata[_iml];
_nd = _ml_arg->_nodelist[_iml];
_v = _vec_v[_ni[_iml]];
v=_v;
{
ena = _ion_ena;
ek = _ion_ek;
{ states(_threadargs_);
} }}
}
static void terminal(){}
static void _initlists(){
int _i; static int _first = 1;
if (!_first) return;
_slist1[0] = {m_columnindex, 0}; _dlist1[0] = {Dm_columnindex, 0};
_slist1[1] = {h_columnindex, 0}; _dlist1[1] = {Dh_columnindex, 0};
_slist1[2] = {n_columnindex, 0}; _dlist1[2] = {Dn_columnindex, 0};
_first = 0;
}
#if NMODL_TEXT
static void register_nmodl_text_and_filename(int mech_type) {
const char* nmodl_filename = "/home/qh4os/neurenv/mech/hhqt.mod";
const char* nmodl_file_text =
"COMMENT\n"
" This is the original Hodgkin-Huxley treatment for the set of sodium, \n"
" potassium, and leakage channels found in the squid giant axon membrane.\n"
" (\"A quantitative description of membrane current and its application \n"
" conduction and excitation in nerve\" J.Physiol. (Lond.) 117:500-544 (1952).)\n"
" Membrane voltage is in absolute mV and has been reversed in polarity\n"
" from the original HH convention and shifted to reflect a resting potential\n"
" of -65 mV.\n"
" Remember to set a squid-appropriate temperature\n"
" (e.g. in HOC: \"celsius=6.3\" or in Python: \"h.celsius=6.3\").\n"
" See squid.hoc for an example of a simulation using this model.\n"
" SW Jaslove 6 March, 1992\n"
"ENDCOMMENT\n"
"\n"
"NEURON {\n"
" SUFFIX hhqt\n"
" USEION na READ ena WRITE ina\n"
" USEION k READ ek WRITE ik\n"
" NONSPECIFIC_CURRENT il\n"
" RANGE gnabar, gkbar, gl, el, gna, gk\n"
"}\n"
" \n"
"UNITS {\n"
" (mA) = (milliamp)\n"
" (mV) = (millivolt)\n"
" (S) = (siemens)\n"
"}\n"
" \n"
"PARAMETER {\n"
" gnabar = .12 (S/cm2) <0,1e9>\n"
" gkbar = .036 (S/cm2) <0,1e9>\n"
" gl = .0003 (S/cm2) <0,1e9>\n"
" el = -54.3 (mV)\n"
"}\n"
" \n"
"ASSIGNED {\n"
" v (mV)\n"
" ena (mV)\n"
" ek (mV)\n"
" gna (S/cm2)\n"
" gk (S/cm2)\n"
" ina (mA/cm2)\n"
" ik (mA/cm2)\n"
" il (mA/cm2)\n"
" minf hinf ninf\n"
" mtau (ms) htau (ms) ntau (ms)\n"
" celsius (degC)\n"
"}\n"
" \n"
"STATE {\n"
" m h n\n"
"}\n"
" \n"
"BREAKPOINT {\n"
" SOLVE states METHOD cnexp\n"
" gna = gnabar*m*m*m*h\n"
" ina = gna*(v - ena)\n"
" gk = gkbar*n*n*n*n\n"
" ik = gk*(v - ek) \n"
" il = gl*(v - el)\n"
"}\n"
"\n"
"DERIVATIVE states { \n"
" rates(v)\n"
" m' = (minf-m)/mtau\n"
" h' = (hinf-h)/htau\n"
" n' = (ninf-n)/ntau\n"
"}\n"
" \n"
"INITIAL {\n"
" rates(v)\n"
" m = minf\n"
" h = hinf\n"
" n = ninf\n"
"}\n"
"\n"
"PROCEDURE rates(v(mV)) { :Computes rate and other constants at current v.\n"
" :Call once from HOC to initialize inf at resting v.\n"
" LOCAL alpha, beta, sum, q10\n"
" q10 = 3^((celsius - 6.3)/10)\n"
"\n"
"UNITSOFF\n"
" :\"m\" sodium activation system\n"
" alpha = .1*vtrap(-(v+40),10)\n"
" beta = 4*exp(-(v+65)/18)\n"
" sum = alpha + beta\n"
" mtau = 1/(q10*sum)\n"
" minf = alpha/sum\n"
" \n"
" :\"h\" sodium inactivation system\n"
" alpha = .07*exp(-(v+65)/20)\n"
" beta = 1/(exp(-(v+35)/10) + 1)\n"
" sum = alpha + beta\n"
" htau = 1/(q10*sum)\n"
" hinf = alpha/sum\n"
" \n"
" :\"n\" potassium activation system\n"
" alpha = .01*vtrap(-(v+55),10) \n"
" beta = .125*exp(-(v+65)/80)\n"
" sum = alpha + beta\n"
" ntau = 1/(q10*sum)\n"
" ninf = alpha/sum\n"
"}\n"
" \n"
"FUNCTION vtrap(x,y) { :Traps for 0 in denominator of rate eqns.\n"
" if (fabs(x/y) < 1e-6) {\n"
" vtrap = y*(1 - x/y/2)\n"
" }else{\n"
" vtrap = x/(exp(x/y) - 1)\n"
" }\n"
"}\n"
" \n"
"UNITSON\n"
;
hoc_reg_nmodl_filename(mech_type, nmodl_filename);
hoc_reg_nmodl_text(mech_type, nmodl_file_text);
}
#endif
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