369 lines
11 KiB
C++
369 lines
11 KiB
C++
/* Created by Language version: 7.7.0 */
|
|
/* NOT VECTORIZED */
|
|
#define NRN_VECTORIZED 0
|
|
#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"
|
|
#include <vector>
|
|
using std::size_t;
|
|
static auto& std_cerr_stream = std::cerr;
|
|
static constexpr auto number_of_datum_variables = 2;
|
|
static constexpr auto number_of_floating_point_variables = 6;
|
|
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__xtra
|
|
#define _nrn_initial _nrn_initial__xtra
|
|
#define nrn_cur _nrn_cur__xtra
|
|
#define _nrn_current _nrn_current__xtra
|
|
#define nrn_jacob _nrn_jacob__xtra
|
|
#define nrn_state _nrn_state__xtra
|
|
#define _net_receive _net_receive__xtra
|
|
|
|
#define _threadargscomma_ /**/
|
|
#define _threadargsprotocomma_ /**/
|
|
#define _internalthreadargsprotocomma_ /**/
|
|
#define _threadargs_ /**/
|
|
#define _threadargsproto_ /**/
|
|
#define _internalthreadargsproto_ /**/
|
|
/*SUPPRESS 761*/
|
|
/*SUPPRESS 762*/
|
|
/*SUPPRESS 763*/
|
|
/*SUPPRESS 765*/
|
|
extern double *hoc_getarg(int);
|
|
|
|
#define t nrn_threads->_t
|
|
#define dt nrn_threads->_dt
|
|
#define es _ml->template fpfield<0>(_iml)
|
|
#define es_columnindex 0
|
|
#define x _ml->template fpfield<1>(_iml)
|
|
#define x_columnindex 1
|
|
#define y _ml->template fpfield<2>(_iml)
|
|
#define y_columnindex 2
|
|
#define z _ml->template fpfield<3>(_iml)
|
|
#define z_columnindex 3
|
|
#define type _ml->template fpfield<4>(_iml)
|
|
#define type_columnindex 4
|
|
#define order _ml->template fpfield<5>(_iml)
|
|
#define order_columnindex 5
|
|
#define ex *_ppvar[0].get<double*>()
|
|
#define _p_ex _ppvar[0].literal_value<void*>()
|
|
#define area (*(_ml->dptr_field<1>(_iml)))
|
|
static _nrn_mechanism_cache_instance _ml_real{nullptr};
|
|
static _nrn_mechanism_cache_range *_ml{&_ml_real};
|
|
static size_t _iml{0};
|
|
static Datum *_ppvar;
|
|
static int hoc_nrnpointerindex = 0;
|
|
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 */
|
|
/* declaration of user functions */
|
|
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_xtra", _hoc_setdata},
|
|
{0, 0}
|
|
};
|
|
|
|
/* Direct Python call wrappers to density mechanism functions.*/
|
|
|
|
static NPyDirectMechFunc npy_direct_func_proc[] = {
|
|
{0, 0}
|
|
};
|
|
/* declare global and static user variables */
|
|
#define gind 0
|
|
#define _gth 0
|
|
#define stim stim_xtra
|
|
double stim = 0;
|
|
/* some parameters have upper and lower limits */
|
|
static HocParmLimits _hoc_parm_limits[] = {
|
|
{0, 0, 0}
|
|
};
|
|
static HocParmUnits _hoc_parm_units[] = {
|
|
{"stim_xtra", "unitless"},
|
|
{"es_xtra", "mV"},
|
|
{"x_xtra", "1"},
|
|
{"y_xtra", "1"},
|
|
{"z_xtra", "1"},
|
|
{"type_xtra", "1"},
|
|
{"order_xtra", "1"},
|
|
{"ex_xtra", "millivolts"},
|
|
{0, 0}
|
|
};
|
|
static double v = 0;
|
|
/* connect global user variables to hoc */
|
|
static DoubScal hoc_scdoub[] = {
|
|
{"stim_xtra", &stim_xtra},
|
|
{0, 0}
|
|
};
|
|
static DoubVec hoc_vdoub[] = {
|
|
{0, 0, 0}
|
|
};
|
|
static double _sav_indep;
|
|
static void _ba1(Node*_nd, Datum* _ppd, Datum* _thread, NrnThread* _nt, Memb_list* _ml, size_t _iml, _nrn_model_sorted_token const&);
|
|
extern void _nrn_setdata_reg(int, void(*)(Prop*));
|
|
static void _setdata(Prop* _prop) {
|
|
_extcall_prop = _prop;
|
|
_prop_id = _nrn_get_prop_id(_prop);
|
|
neuron::legacy::set_globals_from_prop(_prop, _ml_real, _ml, _iml);
|
|
_ppvar = _nrn_mechanism_access_dparam(_prop);
|
|
Node * _node = _nrn_mechanism_access_node(_prop);
|
|
v = _nrn_mechanism_access_voltage(_node);
|
|
}
|
|
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);
|
|
/* connect range variables in _p that hoc is supposed to know about */
|
|
static const char *_mechanism[] = {
|
|
"7.7.0",
|
|
"xtra",
|
|
"es_xtra",
|
|
"x_xtra",
|
|
"y_xtra",
|
|
"z_xtra",
|
|
"type_xtra",
|
|
"order_xtra",
|
|
0,
|
|
0,
|
|
0,
|
|
"ex_xtra",
|
|
0};
|
|
extern Node* nrn_alloc_node_;
|
|
|
|
/* Used by NrnProperty */
|
|
static _nrn_mechanism_std_vector<double> _parm_default{
|
|
0, /* es */
|
|
0, /* x */
|
|
0, /* y */
|
|
0, /* z */
|
|
0, /* type */
|
|
0, /* order */
|
|
};
|
|
|
|
|
|
extern Prop* need_memb(Symbol*);
|
|
static void nrn_alloc(Prop* _prop) {
|
|
Prop *prop_ion{};
|
|
Datum *_ppvar{};
|
|
_ppvar = nrn_prop_datum_alloc(_mechtype, 2, _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) == 6);
|
|
/*initialize range parameters*/
|
|
es = _parm_default[0]; /* 0 */
|
|
x = _parm_default[1]; /* 0 */
|
|
y = _parm_default[2]; /* 0 */
|
|
z = _parm_default[3]; /* 0 */
|
|
type = _parm_default[4]; /* 0 */
|
|
order = _parm_default[5]; /* 0 */
|
|
assert(_nrn_mechanism_get_num_vars(_prop) == 6);
|
|
_nrn_mechanism_access_dparam(_prop) = _ppvar;
|
|
/*connect ionic variables to this model*/
|
|
_ppvar[1] = _nrn_mechanism_get_area_handle(nrn_alloc_node_);
|
|
|
|
}
|
|
static void _initlists();
|
|
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 _xtra_reg() {
|
|
int _vectorized = 0;
|
|
_initlists();
|
|
register_mech(_mechanism, nrn_alloc,nullptr, nullptr, nullptr, nrn_init, hoc_nrnpointerindex, 0);
|
|
_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>{"es"} /* 0 */,
|
|
_nrn_mechanism_field<double>{"x"} /* 1 */,
|
|
_nrn_mechanism_field<double>{"y"} /* 2 */,
|
|
_nrn_mechanism_field<double>{"z"} /* 3 */,
|
|
_nrn_mechanism_field<double>{"type"} /* 4 */,
|
|
_nrn_mechanism_field<double>{"order"} /* 5 */,
|
|
_nrn_mechanism_field<double*>{"ex", "pointer"} /* 0 */,
|
|
_nrn_mechanism_field<double*>{"area", "area"} /* 1 */);
|
|
hoc_register_prop_size(_mechtype, 6, 2);
|
|
hoc_register_dparam_semantics(_mechtype, 0, "pointer");
|
|
hoc_register_dparam_semantics(_mechtype, 1, "area");
|
|
hoc_reg_ba(_mechtype, _ba1, 11);
|
|
|
|
hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
|
|
ivoc_help("help ?1 xtra /home/qh4os/neurenv/mech/xtra.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;}
|
|
/* BEFORE BREAKPOINT */
|
|
static void _ba1(Node*_nd, Datum* _ppd, Datum* _thread, NrnThread* _nt, Memb_list* _ml_arg, size_t _iml, _nrn_model_sorted_token const& _sorted_token) {
|
|
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _ml_arg->_type()}; auto* const _ml = &_lmr;
|
|
double* _globals = nullptr;
|
|
if (gind != 0 && _thread != nullptr) { _globals = _thread[_gth].get<double*>(); }
|
|
_ppvar = _ppd;
|
|
v = NODEV(_nd);
|
|
ex = stim * es ;
|
|
}
|
|
|
|
static void initmodel() {
|
|
int _i; double _save;_ninits++;
|
|
{
|
|
{
|
|
ex = stim * es ;
|
|
}
|
|
|
|
}
|
|
}
|
|
|
|
static void nrn_init(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
|
|
Node *_nd; double _v; int* _ni; int _cntml;
|
|
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _type};
|
|
auto* const _vec_v = _nt->node_voltage_storage();
|
|
_ml = &_lmr;
|
|
_ni = _ml_arg->_nodeindices;
|
|
_cntml = _ml_arg->_nodecount;
|
|
for (_iml = 0; _iml < _cntml; ++_iml) {
|
|
_ppvar = _ml_arg->_pdata[_iml];
|
|
_v = _vec_v[_ni[_iml]];
|
|
v = _v;
|
|
initmodel();
|
|
}}
|
|
|
|
static double _nrn_current(double _v){double _current=0.;v=_v;{
|
|
} return _current;
|
|
}
|
|
|
|
static void nrn_state(_nrn_model_sorted_token const& _sorted_token, NrnThread* _nt, Memb_list* _ml_arg, int _type){
|
|
Node *_nd; double _v = 0.0; int* _ni; int _cntml;
|
|
_nrn_mechanism_cache_range _lmr{_sorted_token, *_nt, *_ml_arg, _type};
|
|
auto* const _vec_v = _nt->node_voltage_storage();
|
|
_ml = &_lmr;
|
|
_ni = _ml_arg->_nodeindices;
|
|
_cntml = _ml_arg->_nodecount;
|
|
for (_iml = 0; _iml < _cntml; ++_iml) {
|
|
_ppvar = _ml_arg->_pdata[_iml];
|
|
_nd = _ml_arg->_nodelist[_iml];
|
|
_v = _vec_v[_ni[_iml]];
|
|
v=_v;
|
|
{
|
|
}}
|
|
|
|
}
|
|
|
|
static void terminal(){}
|
|
|
|
static void _initlists() {
|
|
int _i; static int _first = 1;
|
|
if (!_first) return;
|
|
_first = 0;
|
|
}
|
|
|
|
#if NMODL_TEXT
|
|
static void register_nmodl_text_and_filename(int mech_type) {
|
|
const char* nmodl_filename = "/home/qh4os/neurenv/mech/xtra.mod";
|
|
const char* nmodl_file_text =
|
|
": $Id: xtra.mod,v 1.4 2014/08/18 23:15:25 ted Exp ted $\n"
|
|
": 2018/05/20 Modified by Aman Aberra \n"
|
|
"\n"
|
|
"NEURON {\n"
|
|
" SUFFIX xtra\n"
|
|
" RANGE es : (es = max amplitude of the potential) \n"
|
|
" RANGE x, y, z, type, order\n"
|
|
" GLOBAL stim : (stim = normalized waveform)\n"
|
|
" POINTER ex \n"
|
|
"}\n"
|
|
"\n"
|
|
"PARAMETER { \n"
|
|
" es = 0 (mV)\n"
|
|
" x = 0 (1) : spatial coords\n"
|
|
" y = 0 (1)\n"
|
|
" z = 0 (1) \n"
|
|
" type = 0 (1) : numbering system for morphological category of section - unassigned is 0\n"
|
|
" order = 0 (1) : order of branch/collateral. \n"
|
|
"}\n"
|
|
"\n"
|
|
"ASSIGNED {\n"
|
|
" v (millivolts)\n"
|
|
" ex (millivolts)\n"
|
|
" stim (unitless) \n"
|
|
" area (micron2)\n"
|
|
"}\n"
|
|
"\n"
|
|
"INITIAL {\n"
|
|
" ex = stim*es \n"
|
|
"}\n"
|
|
"\n"
|
|
"\n"
|
|
"BEFORE BREAKPOINT { : before each cy' = f(y,t) setup\n"
|
|
" ex = stim*es\n"
|
|
"}\n"
|
|
"\n"
|
|
;
|
|
hoc_reg_nmodl_filename(mech_type, nmodl_filename);
|
|
hoc_reg_nmodl_text(mech_type, nmodl_file_text);
|
|
}
|
|
#endif
|