/* Created by Language version: 7.7.0 */ /* VECTORIZED */ #define NRN_VECTORIZED 1 #include #include #include #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 = 5; static constexpr auto number_of_floating_point_variables = 10; namespace { template using _nrn_mechanism_std_vector = std::vector; using _nrn_model_sorted_token = neuron::model_sorted_token; using _nrn_mechanism_cache_range = neuron::cache::MechanismRange; using _nrn_mechanism_cache_instance = neuron::cache::MechanismInstance; using _nrn_non_owning_id_without_container = neuron::container::non_owning_identifier_without_container; template using _nrn_mechanism_field = neuron::mechanism::field; template void _nrn_mechanism_register_data_fields(Args&&... args) { neuron::mechanism::register_data_fields(std::forward(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__SK_E2 #define _nrn_initial _nrn_initial__SK_E2 #define nrn_cur _nrn_cur__SK_E2 #define _nrn_current _nrn_current__SK_E2 #define nrn_jacob _nrn_jacob__SK_E2 #define nrn_state _nrn_state__SK_E2 #define _net_receive _net_receive__SK_E2 #define rates rates__SK_E2 #define states states__SK_E2 #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 gSK_E2bar _ml->template fpfield<0>(_iml) #define gSK_E2bar_columnindex 0 #define ik _ml->template fpfield<1>(_iml) #define ik_columnindex 1 #define gSK_E2 _ml->template fpfield<2>(_iml) #define gSK_E2_columnindex 2 #define z _ml->template fpfield<3>(_iml) #define z_columnindex 3 #define ek _ml->template fpfield<4>(_iml) #define ek_columnindex 4 #define cai _ml->template fpfield<5>(_iml) #define cai_columnindex 5 #define zInf _ml->template fpfield<6>(_iml) #define zInf_columnindex 6 #define Dz _ml->template fpfield<7>(_iml) #define Dz_columnindex 7 #define v _ml->template fpfield<8>(_iml) #define v_columnindex 8 #define _g _ml->template fpfield<9>(_iml) #define _g_columnindex 9 #define _ion_ek *(_ml->dptr_field<0>(_iml)) #define _p_ion_ek static_cast>(_ppvar[0]) #define _ion_ik *(_ml->dptr_field<1>(_iml)) #define _p_ion_ik static_cast>(_ppvar[1]) #define _ion_dikdv *(_ml->dptr_field<2>(_iml)) #define _ion_cai *(_ml->dptr_field<3>(_iml)) #define _p_ion_cai static_cast>(_ppvar[3]) #define _ion_cao *(_ml->dptr_field<4>(_iml)) #define _p_ion_cao static_cast>(_ppvar[4]) /* Thread safe. No static _ml, _iml or _ppvar. */ static int hoc_nrnpointerindex = -1; static _nrn_mechanism_std_vector _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 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_SK_E2", _hoc_setdata}, {"rates_SK_E2", _hoc_rates}, {0, 0} }; /* Direct Python call wrappers to density mechanism functions.*/ static double _npy_rates(Prop*); static NPyDirectMechFunc npy_direct_func_proc[] = { {"rates", _npy_rates}, {0, 0} }; /* declare global and static user variables */ #define gind 0 #define _gth 0 #define zTau zTau_SK_E2 double zTau = 1; /* some parameters have upper and lower limits */ static HocParmLimits _hoc_parm_limits[] = { {0, 0, 0} }; static HocParmUnits _hoc_parm_units[] = { {"zTau_SK_E2", "ms"}, {"gSK_E2bar_SK_E2", "mho/cm2"}, {"ik_SK_E2", "mA/cm2"}, {"gSK_E2_SK_E2", "S/cm2"}, {0, 0} }; static double delta_t = 0.01; static double z0 = 0; /* connect global user variables to hoc */ static DoubScal hoc_scdoub[] = { {"zTau_SK_E2", &zTau_SK_E2}, {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*, neuron::container::data_handle*, 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[5].literal_value() 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", "SK_E2", "gSK_E2bar_SK_E2", 0, "ik_SK_E2", "gSK_E2_SK_E2", 0, "z_SK_E2", 0, 0}; static Symbol* _k_sym; static Symbol* _ca_sym; /* Used by NrnProperty */ static _nrn_mechanism_std_vector _parm_default{ 0.098377, /* gSK_E2bar */ }; extern Prop* need_memb(Symbol*); static void nrn_alloc(Prop* _prop) { Prop *prop_ion{}; Datum *_ppvar{}; _ppvar = nrn_prop_datum_alloc(_mechtype, 6, _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) == 10); /*initialize range parameters*/ gSK_E2bar = _parm_default[0]; /* 0.098377 */ assert(_nrn_mechanism_get_num_vars(_prop) == 10); _nrn_mechanism_access_dparam(_prop) = _ppvar; /*connect ionic variables to this model*/ prop_ion = need_memb(_k_sym); nrn_promote(prop_ion, 0, 1); _ppvar[0] = _nrn_mechanism_get_param_handle(prop_ion, 0); /* ek */ _ppvar[1] = _nrn_mechanism_get_param_handle(prop_ion, 3); /* ik */ _ppvar[2] = _nrn_mechanism_get_param_handle(prop_ion, 4); /* _ion_dikdv */ prop_ion = need_memb(_ca_sym); nrn_promote(prop_ion, 1, 0); _ppvar[3] = _nrn_mechanism_get_param_handle(prop_ion, 1); /* cai */ _ppvar[4] = _nrn_mechanism_get_param_handle(prop_ion, 2); /* cao */ } 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 _SK_E2_reg() { int _vectorized = 1; _initlists(); ion_reg("k", -10000.); ion_reg("ca", -10000.); _k_sym = hoc_lookup("k_ion"); _ca_sym = hoc_lookup("ca_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{"gSK_E2bar"} /* 0 */, _nrn_mechanism_field{"ik"} /* 1 */, _nrn_mechanism_field{"gSK_E2"} /* 2 */, _nrn_mechanism_field{"z"} /* 3 */, _nrn_mechanism_field{"ek"} /* 4 */, _nrn_mechanism_field{"cai"} /* 5 */, _nrn_mechanism_field{"zInf"} /* 6 */, _nrn_mechanism_field{"Dz"} /* 7 */, _nrn_mechanism_field{"v"} /* 8 */, _nrn_mechanism_field{"_g"} /* 9 */, _nrn_mechanism_field{"_ion_ek", "k_ion"} /* 0 */, _nrn_mechanism_field{"_ion_ik", "k_ion"} /* 1 */, _nrn_mechanism_field{"_ion_dikdv", "k_ion"} /* 2 */, _nrn_mechanism_field{"_ion_cai", "ca_ion"} /* 3 */, _nrn_mechanism_field{"_ion_cao", "ca_ion"} /* 4 */, _nrn_mechanism_field{"_cvode_ieq", "cvodeieq"} /* 5 */); hoc_register_prop_size(_mechtype, 10, 6); 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, "ca_ion"); hoc_register_dparam_semantics(_mechtype, 4, "ca_ion"); hoc_register_dparam_semantics(_mechtype, 5, "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 SK_E2 /home/qh4os/neurenv/mech/SK_E2.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[1], _dlist1[1]; static int states(_internalthreadargsproto_); /*CVODE*/ static int _ode_spec1 (_internalthreadargsproto_) {int _reset = 0; { rates ( _threadargscomma_ cai ) ; Dz = ( zInf - z ) / zTau ; } return _reset; } static int _ode_matsol1 (_internalthreadargsproto_) { rates ( _threadargscomma_ cai ) ; Dz = Dz / (1. - dt*( ( ( ( - 1.0 ) ) ) / zTau )) ; return 0; } /*END CVODE*/ static int states (_internalthreadargsproto_) { { rates ( _threadargscomma_ cai ) ; z = z + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / zTau)))*(- ( ( ( zInf ) ) / zTau ) / ( ( ( ( - 1.0 ) ) ) / zTau ) - z) ; } return 0; } static int rates ( _internalthreadargsprotocomma_ double _lca ) { if ( _lca < 1e-7 ) { _lca = _lca + 1e-07 ; } zInf = 1.0 / ( 1.0 + pow( ( 0.00043 / _lca ) , 4.8 ) ) ; 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(); } _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(); } _nt = nrn_threads; _r = 1.; rates ( _threadargscomma_ *getarg(1) ); return(_r); } static int _ode_count(int _type){ return 1;} 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(); } for (_iml = 0; _iml < _cntml; ++_iml) { _ppvar = _ml_arg->_pdata[_iml]; _nd = _ml_arg->_nodelist[_iml]; v = NODEV(_nd); ek = _ion_ek; cai = _ion_cai; _ode_spec1 (_threadargs_); }} static void _ode_map(Prop* _prop, int _ieq, neuron::container::data_handle* _pv, neuron::container::data_handle* _pvdot, double* _atol, int _type) { Datum* _ppvar; _ppvar = _nrn_mechanism_access_dparam(_prop); _cvode_ieq = _ieq; for (int _i=0; _i < 1; ++_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(); } for (_iml = 0; _iml < _cntml; ++_iml) { _ppvar = _ml_arg->_pdata[_iml]; _nd = _ml_arg->_nodelist[_iml]; v = NODEV(_nd); ek = _ion_ek; cai = _ion_cai; _ode_matsol_instance1(_threadargs_); }} static void initmodel(_internalthreadargsproto_) { int _i; double _save;{ z = z0; { rates ( _threadargscomma_ cai ) ; z = zInf ; } } } 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(); } for (_iml = 0; _iml < _cntml; ++_iml) { _ppvar = _ml_arg->_pdata[_iml]; _v = _vec_v[_ni[_iml]]; v = _v; ek = _ion_ek; cai = _ion_cai; initmodel(_threadargs_); } } static double _nrn_current(_internalthreadargsprotocomma_ double _v) { double _current=0.; v=_v; { { gSK_E2 = gSK_E2bar * z ; ik = gSK_E2 * ( v - ek ) ; } _current += ik; } 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(); } for (_iml = 0; _iml < _cntml; ++_iml) { _ppvar = _ml_arg->_pdata[_iml]; _v = _vec_v[_ni[_iml]]; ek = _ion_ek; cai = _ion_cai; auto const _g_local = _nrn_current(_threadargscomma_ _v + .001); { double _dik; _dik = ik; _rhs = _nrn_current(_threadargscomma_ _v); _ion_dikdv += (_dik - ik)/.001 ; } _g = (_g_local - _rhs)/.001; _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(); } 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(); } 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; { ek = _ion_ek; cai = _ion_cai; { states(_threadargs_); } }} } static void terminal(){} static void _initlists(){ int _i; static int _first = 1; if (!_first) return; _slist1[0] = {z_columnindex, 0}; _dlist1[0] = {Dz_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/SK_E2.mod"; const char* nmodl_file_text = ":Comment : L6\n" ": SK-type calcium-activated potassium current\n" ": Reference : Kohler et al. 1996\n" "\n" "NEURON {\n" " SUFFIX SK_E2\n" " USEION k READ ek WRITE ik\n" " USEION ca READ cai\n" " RANGE gSK_E2bar, gSK_E2, ik\n" "}\n" "\n" "UNITS {\n" " (mV) = (millivolt)\n" " (mA) = (milliamp)\n" " (mM) = (milli/liter)\n" "}\n" "\n" "PARAMETER {\n" " v (mV)\n" " gSK_E2bar = 0.098377 (mho/cm2)\n" " zTau = 1 (ms)\n" " ek (mV)\n" " cai (mM)\n" "}\n" "\n" "ASSIGNED {\n" " zInf\n" " ik (mA/cm2)\n" " gSK_E2 (S/cm2)\n" " celsius (degC)\n" "}\n" "\n" "STATE {\n" " z FROM 0 TO 1\n" "}\n" "\n" "BREAKPOINT {\n" " SOLVE states METHOD cnexp\n" " gSK_E2 = gSK_E2bar * z\n" " ik = gSK_E2 * (v - ek)\n" "}\n" "\n" "DERIVATIVE states {\n" " rates(cai)\n" " z' = (zInf - z) / zTau\n" "}\n" "\n" "PROCEDURE rates(ca(mM)) {\n" " if(ca < 1e-7){\n" " ca = ca + 1e-07\n" " }\n" " zInf = 1/(1 + (0.00043 / ca)^4.8)\n" "}\n" "\n" "INITIAL {\n" " rates(cai)\n" " z = zInf\n" "}\n" ; hoc_reg_nmodl_filename(mech_type, nmodl_filename); hoc_reg_nmodl_text(mech_type, nmodl_file_text); } #endif