added built mechanisms
This commit is contained in:
parent
66dcb51e86
commit
edc98e38e4
26
flake.lock
generated
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26
flake.lock
generated
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@ -0,0 +1,26 @@
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{
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"nodes": {
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"nixpkgs": {
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"locked": {
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"lastModified": 1770667721,
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"narHash": "sha256-vz7gbwsMH9iQxywSIfZAQ4V9m+N+Z9v5+F3XdN8Zn8g=",
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||||
"owner": "NixOS",
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||||
"repo": "nixpkgs",
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||||
"rev": "47617cf6e75b32d7bcacc8539e6ba379afda99d9",
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"type": "github"
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},
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"original": {
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"owner": "NixOS",
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"repo": "nixpkgs",
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"type": "github"
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}
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},
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"root": {
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"inputs": {
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"nixpkgs": "nixpkgs"
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}
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}
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},
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"root": "root",
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"version": 7
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}
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BIN
x86_64/.libs/libnrnmech.so
Normal file
BIN
x86_64/.libs/libnrnmech.so
Normal file
Binary file not shown.
587
x86_64/Ca.c
Normal file
587
x86_64/Ca.c
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@ -0,0 +1,587 @@
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/* Created by Language version: 7.7.0 */
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/* VECTORIZED */
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#define NRN_VECTORIZED 1
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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#include "mech_api.h"
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#undef PI
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#define nil 0
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#include "md1redef.h"
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#include "section.h"
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#include "nrniv_mf.h"
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#include "md2redef.h"
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#if METHOD3
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extern int _method3;
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#endif
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#if !NRNGPU
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#undef exp
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#define exp hoc_Exp
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extern double hoc_Exp(double);
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#endif
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#define nrn_init _nrn_init__Ca
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#define _nrn_initial _nrn_initial__Ca
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#define nrn_cur _nrn_cur__Ca
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#define _nrn_current _nrn_current__Ca
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#define nrn_jacob _nrn_jacob__Ca
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#define nrn_state _nrn_state__Ca
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#define _net_receive _net_receive__Ca
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#define rates rates__Ca
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#define states states__Ca
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#define _threadargscomma_ _p, _ppvar, _thread, _nt,
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#define _threadargsprotocomma_ double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt,
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#define _threadargs_ _p, _ppvar, _thread, _nt
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#define _threadargsproto_ double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt
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/*SUPPRESS 761*/
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/*SUPPRESS 762*/
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/*SUPPRESS 763*/
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/*SUPPRESS 765*/
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extern double *getarg(int);
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/* Thread safe. No static _p or _ppvar. */
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#define t _nt->_t
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#define dt _nt->_dt
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#define gCabar _p[0]
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#define gCabar_columnindex 0
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#define ica _p[1]
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#define ica_columnindex 1
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#define gCa _p[2]
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#define gCa_columnindex 2
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#define m _p[3]
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#define m_columnindex 3
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#define h _p[4]
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#define h_columnindex 4
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#define eca _p[5]
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#define eca_columnindex 5
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#define mInf _p[6]
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#define mInf_columnindex 6
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#define mTau _p[7]
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#define mTau_columnindex 7
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#define mAlpha _p[8]
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#define mAlpha_columnindex 8
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#define mBeta _p[9]
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#define mBeta_columnindex 9
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#define hInf _p[10]
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#define hInf_columnindex 10
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#define hTau _p[11]
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#define hTau_columnindex 11
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#define hAlpha _p[12]
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#define hAlpha_columnindex 12
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#define hBeta _p[13]
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#define hBeta_columnindex 13
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#define Dm _p[14]
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#define Dm_columnindex 14
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#define Dh _p[15]
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#define Dh_columnindex 15
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#define v _p[16]
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#define v_columnindex 16
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#define _g _p[17]
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#define _g_columnindex 17
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#define _ion_eca *_ppvar[0]._pval
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#define _ion_ica *_ppvar[1]._pval
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#define _ion_dicadv *_ppvar[2]._pval
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#if MAC
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#if !defined(v)
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#define v _mlhv
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#endif
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#if !defined(h)
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#define h _mlhh
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#endif
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#endif
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#if defined(__cplusplus)
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extern "C" {
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#endif
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static int hoc_nrnpointerindex = -1;
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static Datum* _extcall_thread;
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static Prop* _extcall_prop;
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/* external NEURON variables */
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/* declaration of user functions */
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static void _hoc_rates(void);
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static int _mechtype;
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extern void _nrn_cacheloop_reg(int, int);
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extern void hoc_register_prop_size(int, int, int);
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extern void hoc_register_limits(int, HocParmLimits*);
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extern void hoc_register_units(int, HocParmUnits*);
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extern void nrn_promote(Prop*, int, int);
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extern Memb_func* memb_func;
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#define NMODL_TEXT 1
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#if NMODL_TEXT
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static const char* nmodl_file_text;
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static const char* nmodl_filename;
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extern void hoc_reg_nmodl_text(int, const char*);
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extern void hoc_reg_nmodl_filename(int, const char*);
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#endif
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extern void _nrn_setdata_reg(int, void(*)(Prop*));
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static void _setdata(Prop* _prop) {
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_extcall_prop = _prop;
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}
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static void _hoc_setdata() {
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Prop *_prop, *hoc_getdata_range(int);
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_prop = hoc_getdata_range(_mechtype);
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_setdata(_prop);
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hoc_retpushx(1.);
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}
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/* connect user functions to hoc names */
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static VoidFunc hoc_intfunc[] = {
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"setdata_Ca", _hoc_setdata,
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"rates_Ca", _hoc_rates,
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0, 0
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};
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/* declare global and static user variables */
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/* some parameters have upper and lower limits */
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static HocParmLimits _hoc_parm_limits[] = {
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0,0,0
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};
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static HocParmUnits _hoc_parm_units[] = {
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"gCabar_Ca", "S/cm2",
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"ica_Ca", "mA/cm2",
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"gCa_Ca", "S/cm2",
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0,0
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};
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static double delta_t = 0.01;
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static double h0 = 0;
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static double m0 = 0;
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/* connect global user variables to hoc */
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static DoubScal hoc_scdoub[] = {
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0,0
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};
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static DoubVec hoc_vdoub[] = {
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0,0,0
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};
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static double _sav_indep;
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static void nrn_alloc(Prop*);
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static void nrn_init(NrnThread*, _Memb_list*, int);
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static void nrn_state(NrnThread*, _Memb_list*, int);
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static void nrn_cur(NrnThread*, _Memb_list*, int);
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static void nrn_jacob(NrnThread*, _Memb_list*, int);
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static int _ode_count(int);
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static void _ode_map(int, double**, double**, double*, Datum*, double*, int);
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static void _ode_spec(NrnThread*, _Memb_list*, int);
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static void _ode_matsol(NrnThread*, _Memb_list*, int);
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#define _cvode_ieq _ppvar[3]._i
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static void _ode_matsol_instance1(_threadargsproto_);
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/* connect range variables in _p that hoc is supposed to know about */
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static const char *_mechanism[] = {
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"7.7.0",
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"Ca",
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"gCabar_Ca",
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0,
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"ica_Ca",
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"gCa_Ca",
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0,
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"m_Ca",
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"h_Ca",
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0,
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0};
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static Symbol* _ca_sym;
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extern Prop* need_memb(Symbol*);
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static void nrn_alloc(Prop* _prop) {
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Prop *prop_ion;
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double *_p; Datum *_ppvar;
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_p = nrn_prop_data_alloc(_mechtype, 18, _prop);
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/*initialize range parameters*/
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gCabar = 1e-05;
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_prop->param = _p;
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_prop->param_size = 18;
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_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
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_prop->dparam = _ppvar;
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/*connect ionic variables to this model*/
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prop_ion = need_memb(_ca_sym);
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nrn_promote(prop_ion, 0, 1);
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_ppvar[0]._pval = &prop_ion->param[0]; /* eca */
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_ppvar[1]._pval = &prop_ion->param[3]; /* ica */
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_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dicadv */
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}
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static void _initlists();
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/* some states have an absolute tolerance */
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static Symbol** _atollist;
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static HocStateTolerance _hoc_state_tol[] = {
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0,0
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};
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static void _update_ion_pointer(Datum*);
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extern Symbol* hoc_lookup(const char*);
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extern void _nrn_thread_reg(int, int, void(*)(Datum*));
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extern void _nrn_thread_table_reg(int, void(*)(double*, Datum*, Datum*, NrnThread*, int));
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extern void hoc_register_tolerance(int, HocStateTolerance*, Symbol***);
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extern void _cvode_abstol( Symbol**, double*, int);
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void _Ca_reg() {
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int _vectorized = 1;
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_initlists();
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ion_reg("ca", -10000.);
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_ca_sym = hoc_lookup("ca_ion");
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register_mech(_mechanism, nrn_alloc,nrn_cur, nrn_jacob, nrn_state, nrn_init, hoc_nrnpointerindex, 1);
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_mechtype = nrn_get_mechtype(_mechanism[1]);
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_nrn_setdata_reg(_mechtype, _setdata);
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_nrn_thread_reg(_mechtype, 2, _update_ion_pointer);
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#if NMODL_TEXT
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hoc_reg_nmodl_text(_mechtype, nmodl_file_text);
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hoc_reg_nmodl_filename(_mechtype, nmodl_filename);
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#endif
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hoc_register_prop_size(_mechtype, 18, 4);
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hoc_register_dparam_semantics(_mechtype, 0, "ca_ion");
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hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
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hoc_register_dparam_semantics(_mechtype, 2, "ca_ion");
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hoc_register_dparam_semantics(_mechtype, 3, "cvodeieq");
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hoc_register_cvode(_mechtype, _ode_count, _ode_map, _ode_spec, _ode_matsol);
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hoc_register_tolerance(_mechtype, _hoc_state_tol, &_atollist);
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hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
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ivoc_help("help ?1 Ca /mnt/c/neuron/neurenv/mech/Ca.mod\n");
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hoc_register_limits(_mechtype, _hoc_parm_limits);
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hoc_register_units(_mechtype, _hoc_parm_units);
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}
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static int _reset;
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static char *modelname = "";
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static int error;
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static int _ninits = 0;
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static int _match_recurse=1;
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static void _modl_cleanup(){ _match_recurse=1;}
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static int rates(_threadargsproto_);
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static int _ode_spec1(_threadargsproto_);
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/*static int _ode_matsol1(_threadargsproto_);*/
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static int _slist1[2], _dlist1[2];
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static int states(_threadargsproto_);
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/*CVODE*/
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static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
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rates ( _threadargs_ ) ;
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Dm = ( mInf - m ) / mTau ;
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Dh = ( hInf - h ) / hTau ;
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}
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return _reset;
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}
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static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
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rates ( _threadargs_ ) ;
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Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
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Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
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return 0;
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}
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/*END CVODE*/
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static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
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rates ( _threadargs_ ) ;
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m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / mTau)))*(- ( ( ( mInf ) ) / mTau ) / ( ( ( ( - 1.0 ) ) ) / mTau ) - m) ;
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h = h + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / hTau)))*(- ( ( ( hInf ) ) / hTau ) / ( ( ( ( - 1.0 ) ) ) / hTau ) - h) ;
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}
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||||
return 0;
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||||
}
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||||
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||||
static int rates ( _threadargsproto_ ) {
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||||
if ( ( v == - 27.0 ) ) {
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v = v + 0.0001 ;
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}
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mAlpha = ( 0.055 * ( - 27.0 - v ) ) / ( exp ( ( - 27.0 - v ) / 3.8 ) - 1.0 ) ;
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mBeta = ( 0.94 * exp ( ( - 75.0 - v ) / 17.0 ) ) ;
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mInf = mAlpha / ( mAlpha + mBeta ) ;
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mTau = 1.0 / ( mAlpha + mBeta ) ;
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hAlpha = ( 0.000457 * exp ( ( - 13.0 - v ) / 50.0 ) ) ;
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hBeta = ( 0.0065 / ( exp ( ( - v - 15.0 ) / 28.0 ) + 1.0 ) ) ;
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||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
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||||
hTau = 1.0 / ( hAlpha + hBeta ) ;
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||||
return 0; }
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||||
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||||
static void _hoc_rates(void) {
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||||
double _r;
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||||
double* _p; Datum* _ppvar; Datum* _thread; NrnThread* _nt;
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||||
if (_extcall_prop) {_p = _extcall_prop->param; _ppvar = _extcall_prop->dparam;}else{ _p = (double*)0; _ppvar = (Datum*)0; }
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||||
_thread = _extcall_thread;
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||||
_nt = nrn_threads;
|
||||
_r = 1.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
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||||
hoc_retpushx(_r);
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||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
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||||
|
||||
static void _ode_spec(NrnThread* _nt, _Memb_list* _ml, int _type) {
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||||
double* _p; Datum* _ppvar; Datum* _thread;
|
||||
Node* _nd; double _v; int _iml, _cntml;
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||||
_cntml = _ml->_nodecount;
|
||||
_thread = _ml->_thread;
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||||
for (_iml = 0; _iml < _cntml; ++_iml) {
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||||
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
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||||
_nd = _ml->_nodelist[_iml];
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||||
v = NODEV(_nd);
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||||
eca = _ion_eca;
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||||
_ode_spec1 (_p, _ppvar, _thread, _nt);
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||||
}}
|
||||
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||||
static void _ode_map(int _ieq, double** _pv, double** _pvdot, double* _pp, Datum* _ppd, double* _atol, int _type) {
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||||
double* _p; Datum* _ppvar;
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||||
int _i; _p = _pp; _ppvar = _ppd;
|
||||
_cvode_ieq = _ieq;
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||||
for (_i=0; _i < 2; ++_i) {
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||||
_pv[_i] = _pp + _slist1[_i]; _pvdot[_i] = _pp + _dlist1[_i];
|
||||
_cvode_abstol(_atollist, _atol, _i);
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||||
}
|
||||
}
|
||||
|
||||
static void _ode_matsol_instance1(_threadargsproto_) {
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||||
_ode_matsol1 (_p, _ppvar, _thread, _nt);
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||||
}
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||||
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||||
static void _ode_matsol(NrnThread* _nt, _Memb_list* _ml, int _type) {
|
||||
double* _p; Datum* _ppvar; Datum* _thread;
|
||||
Node* _nd; double _v; int _iml, _cntml;
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||||
_cntml = _ml->_nodecount;
|
||||
_thread = _ml->_thread;
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||||
for (_iml = 0; _iml < _cntml; ++_iml) {
|
||||
_p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
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||||
_nd = _ml->_nodelist[_iml];
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||||
v = NODEV(_nd);
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||||
eca = _ion_eca;
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||||
_ode_matsol_instance1(_threadargs_);
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||||
}}
|
||||
extern void nrn_update_ion_pointer(Symbol*, Datum*, int, int);
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||||
static void _update_ion_pointer(Datum* _ppvar) {
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
eca = _ion_eca;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gCa = gCabar * m * m * h ;
|
||||
ica = gCa * ( v - eca ) ;
|
||||
}
|
||||
_current += ica;
|
||||
|
||||
} 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);
|
||||
}
|
||||
eca = _ion_eca;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dica;
|
||||
_dica = ica;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dicadv += (_dica - ica)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ica += ica ;
|
||||
#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;
|
||||
{
|
||||
eca = _ion_eca;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/Ca.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment :\n"
|
||||
":Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX Ca\n"
|
||||
" USEION ca READ eca WRITE ica\n"
|
||||
" RANGE gCabar, gCa, ica \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gCabar = 0.00001 (S/cm2) \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" eca (mV)\n"
|
||||
" ica (mA/cm2)\n"
|
||||
" gCa (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE { \n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gCa = gCabar*m*m*h\n"
|
||||
" ica = gCa*(v-eca)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" UNITSOFF\n"
|
||||
" if((v == -27) ){ \n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) \n"
|
||||
" mBeta = (0.94*exp((-75-v)/17))\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
" mTau = 1/(mAlpha + mBeta)\n"
|
||||
" hAlpha = (0.000457*exp((-13-v)/50))\n"
|
||||
" hBeta = (0.0065/(exp((-v-15)/28)+1))\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" hTau = 1/(hAlpha + hBeta)\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/Ca.o
Normal file
BIN
x86_64/Ca.o
Normal file
Binary file not shown.
485
x86_64/CaDynamics_E2.c
Normal file
485
x86_64/CaDynamics_E2.c
Normal file
@ -0,0 +1,485 @@
|
||||
/* 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
|
||||
#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__CaDynamics_E2
|
||||
#define _nrn_initial _nrn_initial__CaDynamics_E2
|
||||
#define nrn_cur _nrn_cur__CaDynamics_E2
|
||||
#define _nrn_current _nrn_current__CaDynamics_E2
|
||||
#define nrn_jacob _nrn_jacob__CaDynamics_E2
|
||||
#define nrn_state _nrn_state__CaDynamics_E2
|
||||
#define _net_receive _net_receive__CaDynamics_E2
|
||||
#define states states__CaDynamics_E2
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gamma _p[0]
|
||||
#define gamma_columnindex 0
|
||||
#define decay _p[1]
|
||||
#define decay_columnindex 1
|
||||
#define depth _p[2]
|
||||
#define depth_columnindex 2
|
||||
#define minCai _p[3]
|
||||
#define minCai_columnindex 3
|
||||
#define ica _p[4]
|
||||
#define ica_columnindex 4
|
||||
#define cai _p[5]
|
||||
#define cai_columnindex 5
|
||||
#define Dcai _p[6]
|
||||
#define Dcai_columnindex 6
|
||||
#define v _p[7]
|
||||
#define v_columnindex 7
|
||||
#define _g _p[8]
|
||||
#define _g_columnindex 8
|
||||
#define _ion_ica *_ppvar[0]._pval
|
||||
#define _ion_cai *_ppvar[1]._pval
|
||||
#define _style_ca *((int*)_ppvar[2]._pvoid)
|
||||
|
||||
#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 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_CaDynamics_E2", _hoc_setdata,
|
||||
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[] = {
|
||||
"decay_CaDynamics_E2", "ms",
|
||||
"depth_CaDynamics_E2", "um",
|
||||
"minCai_CaDynamics_E2", "mM",
|
||||
0,0
|
||||
};
|
||||
static double cai0 = 0;
|
||||
static double delta_t = 0.01;
|
||||
/* 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 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",
|
||||
"CaDynamics_E2",
|
||||
"gamma_CaDynamics_E2",
|
||||
"decay_CaDynamics_E2",
|
||||
"depth_CaDynamics_E2",
|
||||
"minCai_CaDynamics_E2",
|
||||
0,
|
||||
0,
|
||||
0,
|
||||
0};
|
||||
static Symbol* _ca_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*/
|
||||
gamma = 0.001734;
|
||||
decay = 103.091;
|
||||
depth = 0.1;
|
||||
minCai = 0.0001;
|
||||
_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(_ca_sym);
|
||||
nrn_check_conc_write(_prop, prop_ion, 1);
|
||||
nrn_promote(prop_ion, 3, 0);
|
||||
_ppvar[0]._pval = &prop_ion->param[3]; /* ica */
|
||||
_ppvar[1]._pval = &prop_ion->param[1]; /* cai */
|
||||
_ppvar[2]._pvoid = (void*)(&(prop_ion->dparam[0]._i)); /* iontype for ca */
|
||||
|
||||
}
|
||||
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 _CaDynamics_E2_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("ca", -10000.);
|
||||
_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]);
|
||||
_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, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 2, "#ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 3, "cvodeieq");
|
||||
nrn_writes_conc(_mechtype, 0);
|
||||
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 CaDynamics_E2 /mnt/c/neuron/neurenv/mech/CaDynamics_E2.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
|
||||
#define FARADAY _nrnunit_FARADAY[_nrnunit_use_legacy_]
|
||||
static double _nrnunit_FARADAY[2] = {0x1.78e555060882cp+16, 96485.3}; /* 96485.3321233100141 */
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
static int error;
|
||||
static int _ninits = 0;
|
||||
static int _match_recurse=1;
|
||||
static void _modl_cleanup(){ _match_recurse=1;}
|
||||
|
||||
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; {
|
||||
Dcai = - ( 10000.0 ) * ( ica * gamma / ( 2.0 * FARADAY * depth ) ) - ( cai - minCai ) / decay ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
Dcai = Dcai / (1. - dt*( ( - ( ( 1.0 ) ) / decay ) )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
cai = cai + (1. - exp(dt*(( - ( ( 1.0 ) ) / decay ))))*(- ( ( - ( 10000.0 ) )*( ( ( ( ica )*( gamma ) ) / ( 2.0 * FARADAY * depth ) ) ) - ( ( ( - minCai ) ) ) / decay ) / ( ( - ( ( 1.0 ) ) / decay ) ) - cai) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
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);
|
||||
ica = _ion_ica;
|
||||
cai = _ion_cai;
|
||||
_ode_spec1 (_p, _ppvar, _thread, _nt);
|
||||
_ion_cai = cai;
|
||||
}}
|
||||
|
||||
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);
|
||||
}
|
||||
_pv[0] = &(_ion_cai);
|
||||
}
|
||||
|
||||
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);
|
||||
ica = _ion_ica;
|
||||
cai = _ion_cai;
|
||||
_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(_ca_sym, _ppvar, 0, 3);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 1);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ica = _ion_ica;
|
||||
cai = _ion_cai;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
_ion_cai = cai;
|
||||
nrn_wrote_conc(_ca_sym, (&(_ion_cai)) - 1, _style_ca);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{
|
||||
} 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);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
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;
|
||||
{
|
||||
ica = _ion_ica;
|
||||
cai = _ion_cai;
|
||||
{ states(_p, _ppvar, _thread, _nt);
|
||||
} {
|
||||
}
|
||||
_ion_cai = cai;
|
||||
}}
|
||||
|
||||
}
|
||||
|
||||
static void terminal(){}
|
||||
|
||||
static void _initlists(){
|
||||
double _x; double* _p = &_x;
|
||||
int _i; static int _first = 1;
|
||||
if (!_first) return;
|
||||
_slist1[0] = cai_columnindex; _dlist1[0] = Dcai_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/CaDynamics_E2.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
": Dynamics that track inside calcium concentration\n"
|
||||
": modified from Destexhe et al. 1994\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX CaDynamics_E2\n"
|
||||
" USEION ca READ ica WRITE cai\n"
|
||||
" RANGE decay, gamma, minCai, depth\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
" FARADAY = (faraday) (coulombs)\n"
|
||||
" (molar) = (1/liter)\n"
|
||||
" (mM) = (millimolar)\n"
|
||||
" (um) = (micron)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gamma = 0.001734 : percent of free calcium (not buffered)\n"
|
||||
" decay = 103.091390 (ms) : rate of removal of calcium\n"
|
||||
" depth = 0.1 (um) : depth of shell\n"
|
||||
" minCai = 1e-4 (mM)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {ica (mA/cm2)}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" cai (mM)\n"
|
||||
" }\n"
|
||||
"\n"
|
||||
"BREAKPOINT { SOLVE states METHOD cnexp }\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/CaDynamics_E2.o
Normal file
BIN
x86_64/CaDynamics_E2.o
Normal file
Binary file not shown.
485
x86_64/CaDynamics_E2_soma.c
Normal file
485
x86_64/CaDynamics_E2_soma.c
Normal file
@ -0,0 +1,485 @@
|
||||
/* 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
|
||||
#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__CaDynamics_E2_soma
|
||||
#define _nrn_initial _nrn_initial__CaDynamics_E2_soma
|
||||
#define nrn_cur _nrn_cur__CaDynamics_E2_soma
|
||||
#define _nrn_current _nrn_current__CaDynamics_E2_soma
|
||||
#define nrn_jacob _nrn_jacob__CaDynamics_E2_soma
|
||||
#define nrn_state _nrn_state__CaDynamics_E2_soma
|
||||
#define _net_receive _net_receive__CaDynamics_E2_soma
|
||||
#define states states__CaDynamics_E2_soma
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gamma _p[0]
|
||||
#define gamma_columnindex 0
|
||||
#define decay _p[1]
|
||||
#define decay_columnindex 1
|
||||
#define depth _p[2]
|
||||
#define depth_columnindex 2
|
||||
#define minCai _p[3]
|
||||
#define minCai_columnindex 3
|
||||
#define ica _p[4]
|
||||
#define ica_columnindex 4
|
||||
#define cai _p[5]
|
||||
#define cai_columnindex 5
|
||||
#define Dcai _p[6]
|
||||
#define Dcai_columnindex 6
|
||||
#define v _p[7]
|
||||
#define v_columnindex 7
|
||||
#define _g _p[8]
|
||||
#define _g_columnindex 8
|
||||
#define _ion_ica *_ppvar[0]._pval
|
||||
#define _ion_cai *_ppvar[1]._pval
|
||||
#define _style_ca *((int*)_ppvar[2]._pvoid)
|
||||
|
||||
#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 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_CaDynamics_E2_soma", _hoc_setdata,
|
||||
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[] = {
|
||||
"decay_CaDynamics_E2_soma", "ms",
|
||||
"depth_CaDynamics_E2_soma", "um",
|
||||
"minCai_CaDynamics_E2_soma", "mM",
|
||||
0,0
|
||||
};
|
||||
static double cai0 = 0;
|
||||
static double delta_t = 0.01;
|
||||
/* 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 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",
|
||||
"CaDynamics_E2_soma",
|
||||
"gamma_CaDynamics_E2_soma",
|
||||
"decay_CaDynamics_E2_soma",
|
||||
"depth_CaDynamics_E2_soma",
|
||||
"minCai_CaDynamics_E2_soma",
|
||||
0,
|
||||
0,
|
||||
0,
|
||||
0};
|
||||
static Symbol* _ca_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*/
|
||||
gamma = 0.000996;
|
||||
decay = 873.499;
|
||||
depth = 0.1;
|
||||
minCai = 0.0001;
|
||||
_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(_ca_sym);
|
||||
nrn_check_conc_write(_prop, prop_ion, 1);
|
||||
nrn_promote(prop_ion, 3, 0);
|
||||
_ppvar[0]._pval = &prop_ion->param[3]; /* ica */
|
||||
_ppvar[1]._pval = &prop_ion->param[1]; /* cai */
|
||||
_ppvar[2]._pvoid = (void*)(&(prop_ion->dparam[0]._i)); /* iontype for ca */
|
||||
|
||||
}
|
||||
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 _CaDynamics_E2_soma_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("ca", -10000.);
|
||||
_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]);
|
||||
_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, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 2, "#ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 3, "cvodeieq");
|
||||
nrn_writes_conc(_mechtype, 0);
|
||||
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 CaDynamics_E2_soma /mnt/c/neuron/neurenv/mech/CaDynamics_E2_soma.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
|
||||
#define FARADAY _nrnunit_FARADAY[_nrnunit_use_legacy_]
|
||||
static double _nrnunit_FARADAY[2] = {0x1.78e555060882cp+16, 96485.3}; /* 96485.3321233100141 */
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
static int error;
|
||||
static int _ninits = 0;
|
||||
static int _match_recurse=1;
|
||||
static void _modl_cleanup(){ _match_recurse=1;}
|
||||
|
||||
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; {
|
||||
Dcai = - ( 10000.0 ) * ( ica * gamma / ( 2.0 * FARADAY * depth ) ) - ( cai - minCai ) / decay ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
Dcai = Dcai / (1. - dt*( ( - ( ( 1.0 ) ) / decay ) )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
cai = cai + (1. - exp(dt*(( - ( ( 1.0 ) ) / decay ))))*(- ( ( - ( 10000.0 ) )*( ( ( ( ica )*( gamma ) ) / ( 2.0 * FARADAY * depth ) ) ) - ( ( ( - minCai ) ) ) / decay ) / ( ( - ( ( 1.0 ) ) / decay ) ) - cai) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
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);
|
||||
ica = _ion_ica;
|
||||
cai = _ion_cai;
|
||||
_ode_spec1 (_p, _ppvar, _thread, _nt);
|
||||
_ion_cai = cai;
|
||||
}}
|
||||
|
||||
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);
|
||||
}
|
||||
_pv[0] = &(_ion_cai);
|
||||
}
|
||||
|
||||
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);
|
||||
ica = _ion_ica;
|
||||
cai = _ion_cai;
|
||||
_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(_ca_sym, _ppvar, 0, 3);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 1);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ica = _ion_ica;
|
||||
cai = _ion_cai;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
_ion_cai = cai;
|
||||
nrn_wrote_conc(_ca_sym, (&(_ion_cai)) - 1, _style_ca);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{
|
||||
} 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);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
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;
|
||||
{
|
||||
ica = _ion_ica;
|
||||
cai = _ion_cai;
|
||||
{ states(_p, _ppvar, _thread, _nt);
|
||||
} {
|
||||
}
|
||||
_ion_cai = cai;
|
||||
}}
|
||||
|
||||
}
|
||||
|
||||
static void terminal(){}
|
||||
|
||||
static void _initlists(){
|
||||
double _x; double* _p = &_x;
|
||||
int _i; static int _first = 1;
|
||||
if (!_first) return;
|
||||
_slist1[0] = cai_columnindex; _dlist1[0] = Dcai_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/CaDynamics_E2_soma.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
": Dynamics that track inside calcium concentration\n"
|
||||
": modified from Destexhe et al. 1994\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX CaDynamics_E2_soma\n"
|
||||
" USEION ca READ ica WRITE cai\n"
|
||||
" RANGE decay, gamma, minCai, depth\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
" FARADAY = (faraday) (coulombs)\n"
|
||||
" (molar) = (1/liter)\n"
|
||||
" (mM) = (millimolar)\n"
|
||||
" (um) = (micron)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gamma = 0.000996 : percent of free calcium (not buffered)\n"
|
||||
" decay = 873.498863 (ms) : rate of removal of calcium\n"
|
||||
" depth = 0.1 (um) : depth of shell\n"
|
||||
" minCai = 1e-4 (mM)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {ica (mA/cm2)}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" cai (mM)\n"
|
||||
" }\n"
|
||||
"\n"
|
||||
"BREAKPOINT { SOLVE states METHOD cnexp }\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/CaDynamics_E2_soma.o
Normal file
BIN
x86_64/CaDynamics_E2_soma.o
Normal file
Binary file not shown.
585
x86_64/Ca_HVA.c
Normal file
585
x86_64/Ca_HVA.c
Normal file
@ -0,0 +1,585 @@
|
||||
/* 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
|
||||
#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__Ca_HVA
|
||||
#define _nrn_initial _nrn_initial__Ca_HVA
|
||||
#define nrn_cur _nrn_cur__Ca_HVA
|
||||
#define _nrn_current _nrn_current__Ca_HVA
|
||||
#define nrn_jacob _nrn_jacob__Ca_HVA
|
||||
#define nrn_state _nrn_state__Ca_HVA
|
||||
#define _net_receive _net_receive__Ca_HVA
|
||||
#define rates rates__Ca_HVA
|
||||
#define states states__Ca_HVA
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gCa_HVAbar _p[0]
|
||||
#define gCa_HVAbar_columnindex 0
|
||||
#define ica _p[1]
|
||||
#define ica_columnindex 1
|
||||
#define m _p[2]
|
||||
#define m_columnindex 2
|
||||
#define h _p[3]
|
||||
#define h_columnindex 3
|
||||
#define eca _p[4]
|
||||
#define eca_columnindex 4
|
||||
#define gCa _p[5]
|
||||
#define gCa_columnindex 5
|
||||
#define mInf _p[6]
|
||||
#define mInf_columnindex 6
|
||||
#define mTau _p[7]
|
||||
#define mTau_columnindex 7
|
||||
#define mAlpha _p[8]
|
||||
#define mAlpha_columnindex 8
|
||||
#define mBeta _p[9]
|
||||
#define mBeta_columnindex 9
|
||||
#define hInf _p[10]
|
||||
#define hInf_columnindex 10
|
||||
#define hTau _p[11]
|
||||
#define hTau_columnindex 11
|
||||
#define hAlpha _p[12]
|
||||
#define hAlpha_columnindex 12
|
||||
#define hBeta _p[13]
|
||||
#define hBeta_columnindex 13
|
||||
#define Dm _p[14]
|
||||
#define Dm_columnindex 14
|
||||
#define Dh _p[15]
|
||||
#define Dh_columnindex 15
|
||||
#define v _p[16]
|
||||
#define v_columnindex 16
|
||||
#define _g _p[17]
|
||||
#define _g_columnindex 17
|
||||
#define _ion_eca *_ppvar[0]._pval
|
||||
#define _ion_ica *_ppvar[1]._pval
|
||||
#define _ion_dicadv *_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_rates(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_Ca_HVA", _hoc_setdata,
|
||||
"rates_Ca_HVA", _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[] = {
|
||||
"gCa_HVAbar_Ca_HVA", "S/cm2",
|
||||
"ica_Ca_HVA", "mA/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"Ca_HVA",
|
||||
"gCa_HVAbar_Ca_HVA",
|
||||
0,
|
||||
"ica_Ca_HVA",
|
||||
0,
|
||||
"m_Ca_HVA",
|
||||
"h_Ca_HVA",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _ca_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, 18, _prop);
|
||||
/*initialize range parameters*/
|
||||
gCa_HVAbar = 0.000684;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 18;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_ca_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* eca */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ica */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dicadv */
|
||||
|
||||
}
|
||||
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 _Ca_HVA_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("ca", -10000.);
|
||||
_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]);
|
||||
_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, 18, 4);
|
||||
hoc_register_dparam_semantics(_mechtype, 0, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 2, "ca_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 Ca_HVA /mnt/c/neuron/neurenv/mech/Ca_HVA.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
if ( ( v == - 27.0 ) ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.055 * ( - 27.0 - v ) ) / ( exp ( ( - 27.0 - v ) / 3.8 ) - 1.0 ) ;
|
||||
mBeta = ( 0.94 * exp ( ( - 75.0 - v ) / 17.0 ) ) ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
mTau = 1.0 / ( mAlpha + mBeta ) ;
|
||||
hAlpha = ( 0.000457 * exp ( ( - 13.0 - v ) / 50.0 ) ) ;
|
||||
hBeta = ( 0.0065 / ( exp ( ( - v - 15.0 ) / 28.0 ) + 1.0 ) ) ;
|
||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
|
||||
hTau = 1.0 / ( hAlpha + hBeta ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
eca = _ion_eca;
|
||||
_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 < 2; ++_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);
|
||||
eca = _ion_eca;
|
||||
_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(_ca_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
eca = _ion_eca;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gCa = gCa_HVAbar * m * m * h ;
|
||||
ica = gCa * ( v - eca ) ;
|
||||
}
|
||||
_current += ica;
|
||||
|
||||
} 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);
|
||||
}
|
||||
eca = _ion_eca;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dica;
|
||||
_dica = ica;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dicadv += (_dica - ica)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ica += ica ;
|
||||
#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;
|
||||
{
|
||||
eca = _ion_eca;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/Ca_HVA.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX Ca_HVA\n"
|
||||
" USEION ca READ eca WRITE ica\n"
|
||||
" RANGE gCa_HVAbar, gCa_HVA, ica \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gCa_HVAbar = 0.000684 (S/cm2) \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" eca (mV)\n"
|
||||
" ica (mA/cm2)\n"
|
||||
" gCa (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE { \n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gCa = gCa_HVAbar*m*m*h\n"
|
||||
" ica = gCa*(v-eca)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" UNITSOFF\n"
|
||||
" if((v == -27) ){ \n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) \n"
|
||||
" mBeta = (0.94*exp((-75-v)/17))\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
" mTau = 1/(mAlpha + mBeta)\n"
|
||||
" hAlpha = (0.000457*exp((-13-v)/50))\n"
|
||||
" hBeta = (0.0065/(exp((-v-15)/28)+1))\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" hTau = 1/(hAlpha + hBeta)\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/Ca_HVA.o
Normal file
BIN
x86_64/Ca_HVA.o
Normal file
Binary file not shown.
585
x86_64/Ca_HVA_soma.c
Normal file
585
x86_64/Ca_HVA_soma.c
Normal file
@ -0,0 +1,585 @@
|
||||
/* 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
|
||||
#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__Ca_HVA_soma
|
||||
#define _nrn_initial _nrn_initial__Ca_HVA_soma
|
||||
#define nrn_cur _nrn_cur__Ca_HVA_soma
|
||||
#define _nrn_current _nrn_current__Ca_HVA_soma
|
||||
#define nrn_jacob _nrn_jacob__Ca_HVA_soma
|
||||
#define nrn_state _nrn_state__Ca_HVA_soma
|
||||
#define _net_receive _net_receive__Ca_HVA_soma
|
||||
#define rates rates__Ca_HVA_soma
|
||||
#define states states__Ca_HVA_soma
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gCa_HVAbar _p[0]
|
||||
#define gCa_HVAbar_columnindex 0
|
||||
#define ica _p[1]
|
||||
#define ica_columnindex 1
|
||||
#define m _p[2]
|
||||
#define m_columnindex 2
|
||||
#define h _p[3]
|
||||
#define h_columnindex 3
|
||||
#define eca _p[4]
|
||||
#define eca_columnindex 4
|
||||
#define gCa _p[5]
|
||||
#define gCa_columnindex 5
|
||||
#define mInf _p[6]
|
||||
#define mInf_columnindex 6
|
||||
#define mTau _p[7]
|
||||
#define mTau_columnindex 7
|
||||
#define mAlpha _p[8]
|
||||
#define mAlpha_columnindex 8
|
||||
#define mBeta _p[9]
|
||||
#define mBeta_columnindex 9
|
||||
#define hInf _p[10]
|
||||
#define hInf_columnindex 10
|
||||
#define hTau _p[11]
|
||||
#define hTau_columnindex 11
|
||||
#define hAlpha _p[12]
|
||||
#define hAlpha_columnindex 12
|
||||
#define hBeta _p[13]
|
||||
#define hBeta_columnindex 13
|
||||
#define Dm _p[14]
|
||||
#define Dm_columnindex 14
|
||||
#define Dh _p[15]
|
||||
#define Dh_columnindex 15
|
||||
#define v _p[16]
|
||||
#define v_columnindex 16
|
||||
#define _g _p[17]
|
||||
#define _g_columnindex 17
|
||||
#define _ion_eca *_ppvar[0]._pval
|
||||
#define _ion_ica *_ppvar[1]._pval
|
||||
#define _ion_dicadv *_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_rates(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_Ca_HVA_soma", _hoc_setdata,
|
||||
"rates_Ca_HVA_soma", _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[] = {
|
||||
"gCa_HVAbar_Ca_HVA_soma", "S/cm2",
|
||||
"ica_Ca_HVA_soma", "mA/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"Ca_HVA_soma",
|
||||
"gCa_HVAbar_Ca_HVA_soma",
|
||||
0,
|
||||
"ica_Ca_HVA_soma",
|
||||
0,
|
||||
"m_Ca_HVA_soma",
|
||||
"h_Ca_HVA_soma",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _ca_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, 18, _prop);
|
||||
/*initialize range parameters*/
|
||||
gCa_HVAbar = 0.000459;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 18;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_ca_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* eca */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ica */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dicadv */
|
||||
|
||||
}
|
||||
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 _Ca_HVA_soma_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("ca", -10000.);
|
||||
_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]);
|
||||
_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, 18, 4);
|
||||
hoc_register_dparam_semantics(_mechtype, 0, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 2, "ca_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 Ca_HVA_soma /mnt/c/neuron/neurenv/mech/Ca_HVA_soma.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
if ( ( v == - 27.0 ) ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.055 * ( - 27.0 - v ) ) / ( exp ( ( - 27.0 - v ) / 3.8 ) - 1.0 ) ;
|
||||
mBeta = ( 0.94 * exp ( ( - 75.0 - v ) / 17.0 ) ) ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
mTau = 1.0 / ( mAlpha + mBeta ) ;
|
||||
hAlpha = ( 0.000457 * exp ( ( - 13.0 - v ) / 50.0 ) ) ;
|
||||
hBeta = ( 0.0065 / ( exp ( ( - v - 15.0 ) / 28.0 ) + 1.0 ) ) ;
|
||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
|
||||
hTau = 1.0 / ( hAlpha + hBeta ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
eca = _ion_eca;
|
||||
_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 < 2; ++_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);
|
||||
eca = _ion_eca;
|
||||
_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(_ca_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
eca = _ion_eca;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gCa = gCa_HVAbar * m * m * h ;
|
||||
ica = gCa * ( v - eca ) ;
|
||||
}
|
||||
_current += ica;
|
||||
|
||||
} 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);
|
||||
}
|
||||
eca = _ion_eca;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dica;
|
||||
_dica = ica;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dicadv += (_dica - ica)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ica += ica ;
|
||||
#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;
|
||||
{
|
||||
eca = _ion_eca;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/Ca_HVA_soma.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX Ca_HVA_soma\n"
|
||||
" USEION ca READ eca WRITE ica\n"
|
||||
" RANGE gCa_HVAbar, gCa_HVA, ica \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gCa_HVAbar = 0.000459 (S/cm2) \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" eca (mV)\n"
|
||||
" ica (mA/cm2)\n"
|
||||
" gCa (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE { \n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gCa = gCa_HVAbar*m*m*h\n"
|
||||
" ica = gCa*(v-eca)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" UNITSOFF\n"
|
||||
" if((v == -27) ){ \n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) \n"
|
||||
" mBeta = (0.94*exp((-75-v)/17))\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
" mTau = 1/(mAlpha + mBeta)\n"
|
||||
" hAlpha = (0.000457*exp((-13-v)/50))\n"
|
||||
" hBeta = (0.0065/(exp((-v-15)/28)+1))\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" hTau = 1/(hAlpha + hBeta)\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/Ca_HVA_soma.o
Normal file
BIN
x86_64/Ca_HVA_soma.o
Normal file
Binary file not shown.
578
x86_64/Ca_LVAst.c
Normal file
578
x86_64/Ca_LVAst.c
Normal file
@ -0,0 +1,578 @@
|
||||
/* 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
|
||||
#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__Ca_LVAst
|
||||
#define _nrn_initial _nrn_initial__Ca_LVAst
|
||||
#define nrn_cur _nrn_cur__Ca_LVAst
|
||||
#define _nrn_current _nrn_current__Ca_LVAst
|
||||
#define nrn_jacob _nrn_jacob__Ca_LVAst
|
||||
#define nrn_state _nrn_state__Ca_LVAst
|
||||
#define _net_receive _net_receive__Ca_LVAst
|
||||
#define rates rates__Ca_LVAst
|
||||
#define states states__Ca_LVAst
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gCa_LVAstbar _p[0]
|
||||
#define gCa_LVAstbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ica _p[2]
|
||||
#define ica_columnindex 2
|
||||
#define gCa_LVAst _p[3]
|
||||
#define gCa_LVAst_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define eca _p[6]
|
||||
#define eca_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define hInf _p[9]
|
||||
#define hInf_columnindex 9
|
||||
#define hTau _p[10]
|
||||
#define hTau_columnindex 10
|
||||
#define Dm _p[11]
|
||||
#define Dm_columnindex 11
|
||||
#define Dh _p[12]
|
||||
#define Dh_columnindex 12
|
||||
#define v _p[13]
|
||||
#define v_columnindex 13
|
||||
#define _g _p[14]
|
||||
#define _g_columnindex 14
|
||||
#define _ion_eca *_ppvar[0]._pval
|
||||
#define _ion_ica *_ppvar[1]._pval
|
||||
#define _ion_dicadv *_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 */
|
||||
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_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_Ca_LVAst", _hoc_setdata,
|
||||
"rates_Ca_LVAst", _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[] = {
|
||||
"gCa_LVAstbar_Ca_LVAst", "S/cm2",
|
||||
"ica_Ca_LVAst", "mA/cm2",
|
||||
"gCa_LVAst_Ca_LVAst", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"Ca_LVAst",
|
||||
"gCa_LVAstbar_Ca_LVAst",
|
||||
"celsius_Ca_LVAst",
|
||||
0,
|
||||
"ica_Ca_LVAst",
|
||||
"gCa_LVAst_Ca_LVAst",
|
||||
0,
|
||||
"m_Ca_LVAst",
|
||||
"h_Ca_LVAst",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _ca_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, 15, _prop);
|
||||
/*initialize range parameters*/
|
||||
gCa_LVAstbar = 7e-06;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 15;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_ca_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* eca */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ica */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dicadv */
|
||||
|
||||
}
|
||||
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 _Ca_LVAst_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("ca", -10000.);
|
||||
_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]);
|
||||
_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, 15, 4);
|
||||
hoc_register_dparam_semantics(_mechtype, 0, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 2, "ca_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 Ca_LVAst /mnt/c/neuron/neurenv/mech/Ca_LVAst.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
v = v + 10.0 ;
|
||||
mInf = 1.0000 / ( 1.0 + exp ( ( v - - 30.000 ) / - 6.0 ) ) ;
|
||||
mTau = ( 5.0000 + 20.0000 / ( 1.0 + exp ( ( v - - 25.000 ) / 5.0 ) ) ) / _lqt ;
|
||||
hInf = 1.0000 / ( 1.0 + exp ( ( v - - 80.000 ) / 6.4 ) ) ;
|
||||
hTau = ( 20.0000 + 50.0000 / ( 1.0 + exp ( ( v - - 40.000 ) / 7.0 ) ) ) / _lqt ;
|
||||
v = v - 10.0 ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
eca = _ion_eca;
|
||||
_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 < 2; ++_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);
|
||||
eca = _ion_eca;
|
||||
_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(_ca_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
eca = _ion_eca;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gCa_LVAst = gCa_LVAstbar * m * m * h ;
|
||||
ica = gCa_LVAst * ( v - eca ) ;
|
||||
}
|
||||
_current += ica;
|
||||
|
||||
} 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);
|
||||
}
|
||||
eca = _ion_eca;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dica;
|
||||
_dica = ica;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dicadv += (_dica - ica)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ica += ica ;
|
||||
#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;
|
||||
{
|
||||
eca = _ion_eca;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/Ca_LVAst.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Comment : LVA ca channel. Note: mtau is an approximation from the plots\n"
|
||||
":Reference : : Avery and Johnston 1996, tau from Randall 1997\n"
|
||||
":Comment: shifted by -10 mv to correct for junction potential\n"
|
||||
":Comment: corrected rates using q10 = 2.3, target temperature 35, orginal 21\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX Ca_LVAst\n"
|
||||
" USEION ca READ eca WRITE ica\n"
|
||||
" RANGE gCa_LVAstbar, gCa_LVAst, ica, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gCa_LVAstbar = 0.000007 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" eca (mV)\n"
|
||||
" ica (mA/cm2)\n"
|
||||
" gCa_LVAst (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gCa_LVAst = gCa_LVAstbar*m*m*h\n"
|
||||
" ica = gCa_LVAst*(v-eca)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" v = v + 10\n"
|
||||
" mInf = 1.0000/(1+ exp((v - -30.000)/-6))\n"
|
||||
" mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt\n"
|
||||
" hInf = 1.0000/(1+ exp((v - -80.000)/6.4))\n"
|
||||
" hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt\n"
|
||||
" v = v - 10\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/Ca_LVAst.o
Normal file
BIN
x86_64/Ca_LVAst.o
Normal file
Binary file not shown.
578
x86_64/Ca_LVAst_soma.c
Normal file
578
x86_64/Ca_LVAst_soma.c
Normal file
@ -0,0 +1,578 @@
|
||||
/* 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
|
||||
#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__Ca_LVAst_soma
|
||||
#define _nrn_initial _nrn_initial__Ca_LVAst_soma
|
||||
#define nrn_cur _nrn_cur__Ca_LVAst_soma
|
||||
#define _nrn_current _nrn_current__Ca_LVAst_soma
|
||||
#define nrn_jacob _nrn_jacob__Ca_LVAst_soma
|
||||
#define nrn_state _nrn_state__Ca_LVAst_soma
|
||||
#define _net_receive _net_receive__Ca_LVAst_soma
|
||||
#define rates rates__Ca_LVAst_soma
|
||||
#define states states__Ca_LVAst_soma
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gCa_LVAstbar _p[0]
|
||||
#define gCa_LVAstbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ica _p[2]
|
||||
#define ica_columnindex 2
|
||||
#define gCa_LVAst _p[3]
|
||||
#define gCa_LVAst_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define eca _p[6]
|
||||
#define eca_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define hInf _p[9]
|
||||
#define hInf_columnindex 9
|
||||
#define hTau _p[10]
|
||||
#define hTau_columnindex 10
|
||||
#define Dm _p[11]
|
||||
#define Dm_columnindex 11
|
||||
#define Dh _p[12]
|
||||
#define Dh_columnindex 12
|
||||
#define v _p[13]
|
||||
#define v_columnindex 13
|
||||
#define _g _p[14]
|
||||
#define _g_columnindex 14
|
||||
#define _ion_eca *_ppvar[0]._pval
|
||||
#define _ion_ica *_ppvar[1]._pval
|
||||
#define _ion_dicadv *_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 */
|
||||
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_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_Ca_LVAst_soma", _hoc_setdata,
|
||||
"rates_Ca_LVAst_soma", _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[] = {
|
||||
"gCa_LVAstbar_Ca_LVAst_soma", "S/cm2",
|
||||
"ica_Ca_LVAst_soma", "mA/cm2",
|
||||
"gCa_LVAst_Ca_LVAst_soma", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"Ca_LVAst_soma",
|
||||
"gCa_LVAstbar_Ca_LVAst_soma",
|
||||
"celsius_Ca_LVAst_soma",
|
||||
0,
|
||||
"ica_Ca_LVAst_soma",
|
||||
"gCa_LVAst_Ca_LVAst_soma",
|
||||
0,
|
||||
"m_Ca_LVAst_soma",
|
||||
"h_Ca_LVAst_soma",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _ca_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, 15, _prop);
|
||||
/*initialize range parameters*/
|
||||
gCa_LVAstbar = 0.005592;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 15;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_ca_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* eca */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ica */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dicadv */
|
||||
|
||||
}
|
||||
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 _Ca_LVAst_soma_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("ca", -10000.);
|
||||
_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]);
|
||||
_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, 15, 4);
|
||||
hoc_register_dparam_semantics(_mechtype, 0, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
|
||||
hoc_register_dparam_semantics(_mechtype, 2, "ca_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 Ca_LVAst_soma /mnt/c/neuron/neurenv/mech/Ca_LVAst_soma.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
v = v + 10.0 ;
|
||||
mInf = 1.0000 / ( 1.0 + exp ( ( v - - 30.000 ) / - 6.0 ) ) ;
|
||||
mTau = ( 5.0000 + 20.0000 / ( 1.0 + exp ( ( v - - 25.000 ) / 5.0 ) ) ) / _lqt ;
|
||||
hInf = 1.0000 / ( 1.0 + exp ( ( v - - 80.000 ) / 6.4 ) ) ;
|
||||
hTau = ( 20.0000 + 50.0000 / ( 1.0 + exp ( ( v - - 40.000 ) / 7.0 ) ) ) / _lqt ;
|
||||
v = v - 10.0 ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
eca = _ion_eca;
|
||||
_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 < 2; ++_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);
|
||||
eca = _ion_eca;
|
||||
_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(_ca_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
eca = _ion_eca;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gCa_LVAst = gCa_LVAstbar * m * m * h ;
|
||||
ica = gCa_LVAst * ( v - eca ) ;
|
||||
}
|
||||
_current += ica;
|
||||
|
||||
} 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);
|
||||
}
|
||||
eca = _ion_eca;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dica;
|
||||
_dica = ica;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dicadv += (_dica - ica)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ica += ica ;
|
||||
#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;
|
||||
{
|
||||
eca = _ion_eca;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/Ca_LVAst_soma.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Comment : LVA ca channel. Note: mtau is an approximation from the plots\n"
|
||||
":Reference : : Avery and Johnston 1996, tau from Randall 1997\n"
|
||||
":Comment: shifted by -10 mv to correct for junction potential\n"
|
||||
":Comment: corrected rates using q10 = 2.3, target temperature 35, orginal 21\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX Ca_LVAst_soma\n"
|
||||
" USEION ca READ eca WRITE ica\n"
|
||||
" RANGE gCa_LVAstbar, gCa_LVAst, ica, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gCa_LVAstbar = 0.005592 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" eca (mV)\n"
|
||||
" ica (mA/cm2)\n"
|
||||
" gCa_LVAst (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gCa_LVAst = gCa_LVAstbar*m*m*h\n"
|
||||
" ica = gCa_LVAst*(v-eca)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" v = v + 10\n"
|
||||
" mInf = 1.0000/(1+ exp((v - -30.000)/-6))\n"
|
||||
" mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt\n"
|
||||
" hInf = 1.0000/(1+ exp((v - -80.000)/6.4))\n"
|
||||
" hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt\n"
|
||||
" v = v - 10\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/Ca_LVAst_soma.o
Normal file
BIN
x86_64/Ca_LVAst_soma.o
Normal file
Binary file not shown.
523
x86_64/Ih.c
Normal file
523
x86_64/Ih.c
Normal file
@ -0,0 +1,523 @@
|
||||
/* 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
|
||||
#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__Ih
|
||||
#define _nrn_initial _nrn_initial__Ih
|
||||
#define nrn_cur _nrn_cur__Ih
|
||||
#define _nrn_current _nrn_current__Ih
|
||||
#define nrn_jacob _nrn_jacob__Ih
|
||||
#define nrn_state _nrn_state__Ih
|
||||
#define _net_receive _net_receive__Ih
|
||||
#define rates rates__Ih
|
||||
#define states states__Ih
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gIhbar _p[0]
|
||||
#define gIhbar_columnindex 0
|
||||
#define ihcn _p[1]
|
||||
#define ihcn_columnindex 1
|
||||
#define gIh _p[2]
|
||||
#define gIh_columnindex 2
|
||||
#define m _p[3]
|
||||
#define m_columnindex 3
|
||||
#define mInf _p[4]
|
||||
#define mInf_columnindex 4
|
||||
#define mTau _p[5]
|
||||
#define mTau_columnindex 5
|
||||
#define mAlpha _p[6]
|
||||
#define mAlpha_columnindex 6
|
||||
#define mBeta _p[7]
|
||||
#define mBeta_columnindex 7
|
||||
#define Dm _p[8]
|
||||
#define Dm_columnindex 8
|
||||
#define v _p[9]
|
||||
#define v_columnindex 9
|
||||
#define _g _p[10]
|
||||
#define _g_columnindex 10
|
||||
|
||||
#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_rates(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_Ih", _hoc_setdata,
|
||||
"rates_Ih", _hoc_rates,
|
||||
0, 0
|
||||
};
|
||||
/* declare global and static user variables */
|
||||
#define ehcn ehcn_Ih
|
||||
double ehcn = -45;
|
||||
/* some parameters have upper and lower limits */
|
||||
static HocParmLimits _hoc_parm_limits[] = {
|
||||
0,0,0
|
||||
};
|
||||
static HocParmUnits _hoc_parm_units[] = {
|
||||
"ehcn_Ih", "mV",
|
||||
"gIhbar_Ih", "S/cm2",
|
||||
"ihcn_Ih", "mA/cm2",
|
||||
"gIh_Ih", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double m0 = 0;
|
||||
/* connect global user variables to hoc */
|
||||
static DoubScal hoc_scdoub[] = {
|
||||
"ehcn_Ih", &ehcn_Ih,
|
||||
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[0]._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",
|
||||
"Ih",
|
||||
"gIhbar_Ih",
|
||||
0,
|
||||
"ihcn_Ih",
|
||||
"gIh_Ih",
|
||||
0,
|
||||
"m_Ih",
|
||||
0,
|
||||
0};
|
||||
|
||||
extern Prop* need_memb(Symbol*);
|
||||
|
||||
static void nrn_alloc(Prop* _prop) {
|
||||
Prop *prop_ion;
|
||||
double *_p; Datum *_ppvar;
|
||||
_p = nrn_prop_data_alloc(_mechtype, 11, _prop);
|
||||
/*initialize range parameters*/
|
||||
gIhbar = 8e-05;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 11;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 1, _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 _Ih_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
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);
|
||||
#if NMODL_TEXT
|
||||
hoc_reg_nmodl_text(_mechtype, nmodl_file_text);
|
||||
hoc_reg_nmodl_filename(_mechtype, nmodl_filename);
|
||||
#endif
|
||||
hoc_register_prop_size(_mechtype, 11, 1);
|
||||
hoc_register_dparam_semantics(_mechtype, 0, "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 Ih /mnt/c/neuron/neurenv/mech/Ih.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / mTau)))*(- ( ( ( mInf ) ) / mTau ) / ( ( ( ( - 1.0 ) ) ) / mTau ) - m) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
if ( v == - 154.9 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = 0.001 * 6.43 * ( v + 154.9 ) / ( exp ( ( v + 154.9 ) / 11.9 ) - 1.0 ) ;
|
||||
mBeta = 0.001 * 193.0 * exp ( v / 33.1 ) ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
mTau = 1.0 / ( mAlpha + mBeta ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
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);
|
||||
_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;{
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
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;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gIh = gIhbar * m ;
|
||||
ihcn = gIh * ( v - ehcn ) ;
|
||||
}
|
||||
_current += ihcn;
|
||||
|
||||
} 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;
|
||||
#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] = m_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/Ih.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference : : Kole,Hallermann,and Stuart, J. Neurosci. 2006\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX Ih\n"
|
||||
" NONSPECIFIC_CURRENT ihcn\n"
|
||||
" RANGE gIhbar, gIh, ihcn \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gIhbar = 0.00008 (S/cm2) \n"
|
||||
" ehcn = -45.0 (mV)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ihcn (mA/cm2)\n"
|
||||
" gIh (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE { \n"
|
||||
" m\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gIh = gIhbar*m\n"
|
||||
" ihcn = gIh*(v-ehcn)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" UNITSOFF\n"
|
||||
" if(v == -154.9){\n"
|
||||
" v = v + 0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1)\n"
|
||||
" mBeta = 0.001*193*exp(v/33.1)\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
" mTau = 1/(mAlpha + mBeta)\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/Ih.o
Normal file
BIN
x86_64/Ih.o
Normal file
Binary file not shown.
557
x86_64/Im.c
Normal file
557
x86_64/Im.c
Normal file
@ -0,0 +1,557 @@
|
||||
/* 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
|
||||
#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__Im
|
||||
#define _nrn_initial _nrn_initial__Im
|
||||
#define nrn_cur _nrn_cur__Im
|
||||
#define _nrn_current _nrn_current__Im
|
||||
#define nrn_jacob _nrn_jacob__Im
|
||||
#define nrn_state _nrn_state__Im
|
||||
#define _net_receive _net_receive__Im
|
||||
#define rates rates__Im
|
||||
#define states states__Im
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gImbar _p[0]
|
||||
#define gImbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ik _p[2]
|
||||
#define ik_columnindex 2
|
||||
#define gIm _p[3]
|
||||
#define gIm_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define ek _p[5]
|
||||
#define ek_columnindex 5
|
||||
#define mInf _p[6]
|
||||
#define mInf_columnindex 6
|
||||
#define mTau _p[7]
|
||||
#define mTau_columnindex 7
|
||||
#define mAlpha _p[8]
|
||||
#define mAlpha_columnindex 8
|
||||
#define mBeta _p[9]
|
||||
#define mBeta_columnindex 9
|
||||
#define Dm _p[10]
|
||||
#define Dm_columnindex 10
|
||||
#define v _p[11]
|
||||
#define v_columnindex 11
|
||||
#define _g _p[12]
|
||||
#define _g_columnindex 12
|
||||
#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 */
|
||||
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_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_Im", _hoc_setdata,
|
||||
"rates_Im", _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[] = {
|
||||
"gImbar_Im", "S/cm2",
|
||||
"ik_Im", "mA/cm2",
|
||||
"gIm_Im", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double m0 = 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 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",
|
||||
"Im",
|
||||
"gImbar_Im",
|
||||
"celsius_Im",
|
||||
0,
|
||||
"ik_Im",
|
||||
"gIm_Im",
|
||||
0,
|
||||
"m_Im",
|
||||
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, 13, _prop);
|
||||
/*initialize range parameters*/
|
||||
gImbar = 0.001;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 13;
|
||||
_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 _Im_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, 13, 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 Im /mnt/c/neuron/neurenv/mech/Im.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / mTau)))*(- ( ( ( mInf ) ) / mTau ) / ( ( ( ( - 1.0 ) ) ) / mTau ) - m) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
mAlpha = 3.3e-3 * exp ( 2.5 * 0.04 * ( v - - 35.0 ) ) ;
|
||||
mBeta = 3.3e-3 * exp ( - 2.5 * 0.04 * ( v - - 35.0 ) ) ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
mTau = ( 1.0 / ( mAlpha + mBeta ) ) / _lqt ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
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;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
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;{ {
|
||||
gIm = gImbar * m ;
|
||||
ik = gIm * ( v - ek ) ;
|
||||
}
|
||||
_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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/Im.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones\n"
|
||||
":Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX Im\n"
|
||||
" USEION k READ ek WRITE ik\n"
|
||||
" RANGE gImbar, gIm, ik, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gImbar = 0.001000 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ek (mV)\n"
|
||||
" ik (mA/cm2)\n"
|
||||
" gIm (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE { \n"
|
||||
" m\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gIm = gImbar*m\n"
|
||||
" ik = gIm*(v-ek)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35))\n"
|
||||
" mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35))\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
" mTau = (1/(mAlpha + mBeta))/qt\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/Im.o
Normal file
BIN
x86_64/Im.o
Normal file
Binary file not shown.
588
x86_64/K_Pst.c
Normal file
588
x86_64/K_Pst.c
Normal file
@ -0,0 +1,588 @@
|
||||
/* 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
|
||||
#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__K_Pst
|
||||
#define _nrn_initial _nrn_initial__K_Pst
|
||||
#define nrn_cur _nrn_cur__K_Pst
|
||||
#define _nrn_current _nrn_current__K_Pst
|
||||
#define nrn_jacob _nrn_jacob__K_Pst
|
||||
#define nrn_state _nrn_state__K_Pst
|
||||
#define _net_receive _net_receive__K_Pst
|
||||
#define rates rates__K_Pst
|
||||
#define states states__K_Pst
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gK_Pstbar _p[0]
|
||||
#define gK_Pstbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ik _p[2]
|
||||
#define ik_columnindex 2
|
||||
#define gK_Pst _p[3]
|
||||
#define gK_Pst_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ek _p[6]
|
||||
#define ek_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define hInf _p[9]
|
||||
#define hInf_columnindex 9
|
||||
#define hTau _p[10]
|
||||
#define hTau_columnindex 10
|
||||
#define Dm _p[11]
|
||||
#define Dm_columnindex 11
|
||||
#define Dh _p[12]
|
||||
#define Dh_columnindex 12
|
||||
#define v _p[13]
|
||||
#define v_columnindex 13
|
||||
#define _g _p[14]
|
||||
#define _g_columnindex 14
|
||||
#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 */
|
||||
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_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_K_Pst", _hoc_setdata,
|
||||
"rates_K_Pst", _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[] = {
|
||||
"gK_Pstbar_K_Pst", "S/cm2",
|
||||
"ik_K_Pst", "mA/cm2",
|
||||
"gK_Pst_K_Pst", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"K_Pst",
|
||||
"gK_Pstbar_K_Pst",
|
||||
"celsius_K_Pst",
|
||||
0,
|
||||
"ik_K_Pst",
|
||||
"gK_Pst_K_Pst",
|
||||
0,
|
||||
"m_K_Pst",
|
||||
"h_K_Pst",
|
||||
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, 15, _prop);
|
||||
/*initialize range parameters*/
|
||||
gK_Pstbar = 0.957198;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 15;
|
||||
_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 _K_Pst_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, 15, 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 K_Pst /mnt/c/neuron/neurenv/mech/K_Pst.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
v = v + 10.0 ;
|
||||
mInf = ( 1.0 / ( 1.0 + exp ( - ( v + 1.0 ) / 12.0 ) ) ) ;
|
||||
if ( v < - 50.0 ) {
|
||||
mTau = ( 1.25 + 175.03 * exp ( - v * - 0.026 ) ) / _lqt ;
|
||||
}
|
||||
else {
|
||||
mTau = ( ( 1.25 + 13.0 * exp ( - v * 0.026 ) ) ) / _lqt ;
|
||||
}
|
||||
hInf = 1.0 / ( 1.0 + exp ( - ( v + 54.0 ) / - 11.0 ) ) ;
|
||||
hTau = ( 360.0 + ( 1010.0 + 24.0 * ( v + 55.0 ) ) * exp ( - pow( ( ( v + 75.0 ) / 48.0 ) , 2.0 ) ) ) / _lqt ;
|
||||
v = v - 10.0 ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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 < 2; ++_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;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;{ {
|
||||
gK_Pst = gK_Pstbar * m * m * h ;
|
||||
ik = gK_Pst * ( v - ek ) ;
|
||||
}
|
||||
_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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/K_Pst.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Comment : The persistent component of the K current\n"
|
||||
":Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000\n"
|
||||
":Comment : shifted -10 mv to correct for junction potential\n"
|
||||
":Comment: corrected rates using q10 = 2.3, target temperature 35, orginal 21\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra** \n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX K_Pst\n"
|
||||
" USEION k READ ek WRITE ik\n"
|
||||
" RANGE gK_Pstbar, gK_Pst, ik, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gK_Pstbar = 0.957198 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ek (mV)\n"
|
||||
" ik (mA/cm2)\n"
|
||||
" gK_Pst (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gK_Pst = gK_Pstbar*m*m*h\n"
|
||||
" ik = gK_Pst*(v-ek)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10)\n"
|
||||
" UNITSOFF\n"
|
||||
" v = v + 10\n"
|
||||
" mInf = (1/(1 + exp(-(v+1)/12)))\n"
|
||||
" if(v<-50){\n"
|
||||
" mTau = (1.25+175.03*exp(-v * -0.026))/qt\n"
|
||||
" }else{\n"
|
||||
" mTau = ((1.25+13*exp(-v*0.026)))/qt\n"
|
||||
" }\n"
|
||||
" hInf = 1/(1 + exp(-(v+54)/-11))\n"
|
||||
" hTau = (360+(1010+24*(v+55))*exp(-((v+75)/48)^2))/qt\n"
|
||||
" v = v - 10\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/K_Pst.o
Normal file
BIN
x86_64/K_Pst.o
Normal file
Binary file not shown.
578
x86_64/K_Tst.c
Normal file
578
x86_64/K_Tst.c
Normal file
@ -0,0 +1,578 @@
|
||||
/* 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
|
||||
#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__K_Tst
|
||||
#define _nrn_initial _nrn_initial__K_Tst
|
||||
#define nrn_cur _nrn_cur__K_Tst
|
||||
#define _nrn_current _nrn_current__K_Tst
|
||||
#define nrn_jacob _nrn_jacob__K_Tst
|
||||
#define nrn_state _nrn_state__K_Tst
|
||||
#define _net_receive _net_receive__K_Tst
|
||||
#define rates rates__K_Tst
|
||||
#define states states__K_Tst
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gK_Tstbar _p[0]
|
||||
#define gK_Tstbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ik _p[2]
|
||||
#define ik_columnindex 2
|
||||
#define gK_Tst _p[3]
|
||||
#define gK_Tst_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ek _p[6]
|
||||
#define ek_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define hInf _p[9]
|
||||
#define hInf_columnindex 9
|
||||
#define hTau _p[10]
|
||||
#define hTau_columnindex 10
|
||||
#define Dm _p[11]
|
||||
#define Dm_columnindex 11
|
||||
#define Dh _p[12]
|
||||
#define Dh_columnindex 12
|
||||
#define v _p[13]
|
||||
#define v_columnindex 13
|
||||
#define _g _p[14]
|
||||
#define _g_columnindex 14
|
||||
#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 */
|
||||
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_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_K_Tst", _hoc_setdata,
|
||||
"rates_K_Tst", _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[] = {
|
||||
"gK_Tstbar_K_Tst", "S/cm2",
|
||||
"ik_K_Tst", "mA/cm2",
|
||||
"gK_Tst_K_Tst", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"K_Tst",
|
||||
"gK_Tstbar_K_Tst",
|
||||
"celsius_K_Tst",
|
||||
0,
|
||||
"ik_K_Tst",
|
||||
"gK_Tst_K_Tst",
|
||||
0,
|
||||
"m_K_Tst",
|
||||
"h_K_Tst",
|
||||
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, 15, _prop);
|
||||
/*initialize range parameters*/
|
||||
gK_Tstbar = 0.029456;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 15;
|
||||
_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 _K_Tst_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, 15, 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 K_Tst /mnt/c/neuron/neurenv/mech/K_Tst.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
v = v + 10.0 ;
|
||||
mInf = 1.0 / ( 1.0 + exp ( - ( v + 0.0 ) / 19.0 ) ) ;
|
||||
mTau = ( 0.34 + 0.92 * exp ( - pow( ( ( v + 71.0 ) / 59.0 ) , 2.0 ) ) ) / _lqt ;
|
||||
hInf = 1.0 / ( 1.0 + exp ( - ( v + 66.0 ) / - 10.0 ) ) ;
|
||||
hTau = ( 8.0 + 49.0 * exp ( - pow( ( ( v + 73.0 ) / 23.0 ) , 2.0 ) ) ) / _lqt ;
|
||||
v = v - 10.0 ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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 < 2; ++_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;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;{ {
|
||||
gK_Tst = gK_Tstbar * ( pow( m , 4.0 ) ) * h ;
|
||||
ik = gK_Tst * ( v - ek ) ;
|
||||
}
|
||||
_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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/K_Tst.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Comment : The transient component of the K current\n"
|
||||
":Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000\n"
|
||||
":Comment : shifted -10 mv to correct for junction potential\n"
|
||||
":Comment: corrected rates using q10 = 2.3, target temperature 35, orginal 21\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX K_Tst\n"
|
||||
" USEION k READ ek WRITE ik\n"
|
||||
" RANGE gK_Tstbar, gK_Tst, ik, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gK_Tstbar = 0.029456 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ek (mV)\n"
|
||||
" ik (mA/cm2)\n"
|
||||
" gK_Tst (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gK_Tst = gK_Tstbar*(m^4)*h\n"
|
||||
" ik = gK_Tst*(v-ek)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10)\n"
|
||||
" UNITSOFF\n"
|
||||
" v = v + 10\n"
|
||||
" mInf = 1/(1 + exp(-(v+0)/19))\n"
|
||||
" mTau = (0.34+0.92*exp(-((v+71)/59)^2))/qt\n"
|
||||
" hInf = 1/(1 + exp(-(v+66)/-10))\n"
|
||||
" hTau = (8+49*exp(-((v+73)/23)^2))/qt\n"
|
||||
" v = v - 10\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/K_Tst.o
Normal file
BIN
x86_64/K_Tst.o
Normal file
Binary file not shown.
605
x86_64/NaTa_t.c
Normal file
605
x86_64/NaTa_t.c
Normal file
@ -0,0 +1,605 @@
|
||||
/* 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
|
||||
#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__NaTa_t
|
||||
#define _nrn_initial _nrn_initial__NaTa_t
|
||||
#define nrn_cur _nrn_cur__NaTa_t
|
||||
#define _nrn_current _nrn_current__NaTa_t
|
||||
#define nrn_jacob _nrn_jacob__NaTa_t
|
||||
#define nrn_state _nrn_state__NaTa_t
|
||||
#define _net_receive _net_receive__NaTa_t
|
||||
#define rates rates__NaTa_t
|
||||
#define states states__NaTa_t
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gNaTa_tbar _p[0]
|
||||
#define gNaTa_tbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ina _p[2]
|
||||
#define ina_columnindex 2
|
||||
#define gNaTa_t _p[3]
|
||||
#define gNaTa_t_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ena _p[6]
|
||||
#define ena_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define mAlpha _p[9]
|
||||
#define mAlpha_columnindex 9
|
||||
#define mBeta _p[10]
|
||||
#define mBeta_columnindex 10
|
||||
#define hInf _p[11]
|
||||
#define hInf_columnindex 11
|
||||
#define hTau _p[12]
|
||||
#define hTau_columnindex 12
|
||||
#define hAlpha _p[13]
|
||||
#define hAlpha_columnindex 13
|
||||
#define hBeta _p[14]
|
||||
#define hBeta_columnindex 14
|
||||
#define Dm _p[15]
|
||||
#define Dm_columnindex 15
|
||||
#define Dh _p[16]
|
||||
#define Dh_columnindex 16
|
||||
#define v _p[17]
|
||||
#define v_columnindex 17
|
||||
#define _g _p[18]
|
||||
#define _g_columnindex 18
|
||||
#define _ion_ena *_ppvar[0]._pval
|
||||
#define _ion_ina *_ppvar[1]._pval
|
||||
#define _ion_dinadv *_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 */
|
||||
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_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_NaTa_t", _hoc_setdata,
|
||||
"rates_NaTa_t", _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[] = {
|
||||
"gNaTa_tbar_NaTa_t", "S/cm2",
|
||||
"ina_NaTa_t", "mA/cm2",
|
||||
"gNaTa_t_NaTa_t", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"NaTa_t",
|
||||
"gNaTa_tbar_NaTa_t",
|
||||
"celsius_NaTa_t",
|
||||
0,
|
||||
"ina_NaTa_t",
|
||||
"gNaTa_t_NaTa_t",
|
||||
0,
|
||||
"m_NaTa_t",
|
||||
"h_NaTa_t",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _na_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, 19, _prop);
|
||||
/*initialize range parameters*/
|
||||
gNaTa_tbar = 3.28876;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 19;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_na_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* ena */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ina */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dinadv */
|
||||
|
||||
}
|
||||
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 _NaTa_t_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("na", -10000.);
|
||||
_na_sym = hoc_lookup("na_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, 19, 4);
|
||||
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, "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 NaTa_t /mnt/c/neuron/neurenv/mech/NaTa_t.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
if ( v == - 38.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.182 * ( v - - 38.0 ) ) / ( 1.0 - ( exp ( - ( v - - 38.0 ) / 6.0 ) ) ) ;
|
||||
mBeta = ( 0.124 * ( - v - 38.0 ) ) / ( 1.0 - ( exp ( - ( - v - 38.0 ) / 6.0 ) ) ) ;
|
||||
mTau = ( 1.0 / ( mAlpha + mBeta ) ) / _lqt ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
if ( v == - 66.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
hAlpha = ( - 0.015 * ( v - - 66.0 ) ) / ( 1.0 - ( exp ( ( v - - 66.0 ) / 6.0 ) ) ) ;
|
||||
hBeta = ( - 0.015 * ( - v - 66.0 ) ) / ( 1.0 - ( exp ( ( - v - 66.0 ) / 6.0 ) ) ) ;
|
||||
hTau = ( 1.0 / ( hAlpha + hBeta ) ) / _lqt ;
|
||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
ena = _ion_ena;
|
||||
_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 < 2; ++_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);
|
||||
ena = _ion_ena;
|
||||
_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(_na_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ena = _ion_ena;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gNaTa_t = gNaTa_tbar * m * m * m * h ;
|
||||
ina = gNaTa_t * ( v - ena ) ;
|
||||
}
|
||||
_current += ina;
|
||||
|
||||
} 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);
|
||||
}
|
||||
ena = _ion_ena;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dina;
|
||||
_dina = ina;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dinadv += (_dina - ina)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ina += ina ;
|
||||
#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;
|
||||
{
|
||||
ena = _ion_ena;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/NaTa_t.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference :Colbert and Pan 2002\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX NaTa_t\n"
|
||||
" USEION na READ ena WRITE ina\n"
|
||||
" RANGE gNaTa_tbar, gNaTa_t, ina, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gNaTa_tbar = 3.288755 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ena (mV)\n"
|
||||
" ina (mA/cm2)\n"
|
||||
" gNaTa_t (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gNaTa_t = gNaTa_tbar*m*m*m*h\n"
|
||||
" ina = gNaTa_t*(v-ena)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" if(v == -38){\n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6)))\n"
|
||||
" mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6)))\n"
|
||||
" mTau = (1/(mAlpha + mBeta))/qt\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
"\n"
|
||||
" if(v == -66){\n"
|
||||
" v = v + 0.0001\n"
|
||||
" }\n"
|
||||
"\n"
|
||||
" hAlpha = (-0.015 * (v- -66))/(1-(exp((v- -66)/6)))\n"
|
||||
" hBeta = (-0.015 * (-v -66))/(1-(exp((-v -66)/6)))\n"
|
||||
" hTau = (1/(hAlpha + hBeta))/qt\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/NaTa_t.o
Normal file
BIN
x86_64/NaTa_t.o
Normal file
Binary file not shown.
605
x86_64/NaTa_t_myel.c
Normal file
605
x86_64/NaTa_t_myel.c
Normal file
@ -0,0 +1,605 @@
|
||||
/* 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
|
||||
#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__NaTa_t_myel
|
||||
#define _nrn_initial _nrn_initial__NaTa_t_myel
|
||||
#define nrn_cur _nrn_cur__NaTa_t_myel
|
||||
#define _nrn_current _nrn_current__NaTa_t_myel
|
||||
#define nrn_jacob _nrn_jacob__NaTa_t_myel
|
||||
#define nrn_state _nrn_state__NaTa_t_myel
|
||||
#define _net_receive _net_receive__NaTa_t_myel
|
||||
#define rates rates__NaTa_t_myel
|
||||
#define states states__NaTa_t_myel
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gNaTa_tbar _p[0]
|
||||
#define gNaTa_tbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ina _p[2]
|
||||
#define ina_columnindex 2
|
||||
#define gNaTa_t _p[3]
|
||||
#define gNaTa_t_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ena _p[6]
|
||||
#define ena_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define mAlpha _p[9]
|
||||
#define mAlpha_columnindex 9
|
||||
#define mBeta _p[10]
|
||||
#define mBeta_columnindex 10
|
||||
#define hInf _p[11]
|
||||
#define hInf_columnindex 11
|
||||
#define hTau _p[12]
|
||||
#define hTau_columnindex 12
|
||||
#define hAlpha _p[13]
|
||||
#define hAlpha_columnindex 13
|
||||
#define hBeta _p[14]
|
||||
#define hBeta_columnindex 14
|
||||
#define Dm _p[15]
|
||||
#define Dm_columnindex 15
|
||||
#define Dh _p[16]
|
||||
#define Dh_columnindex 16
|
||||
#define v _p[17]
|
||||
#define v_columnindex 17
|
||||
#define _g _p[18]
|
||||
#define _g_columnindex 18
|
||||
#define _ion_ena *_ppvar[0]._pval
|
||||
#define _ion_ina *_ppvar[1]._pval
|
||||
#define _ion_dinadv *_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 */
|
||||
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_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_NaTa_t_myel", _hoc_setdata,
|
||||
"rates_NaTa_t_myel", _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[] = {
|
||||
"gNaTa_tbar_NaTa_t_myel", "S/cm2",
|
||||
"ina_NaTa_t_myel", "mA/cm2",
|
||||
"gNaTa_t_NaTa_t_myel", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"NaTa_t_myel",
|
||||
"gNaTa_tbar_NaTa_t_myel",
|
||||
"celsius_NaTa_t_myel",
|
||||
0,
|
||||
"ina_NaTa_t_myel",
|
||||
"gNaTa_t_NaTa_t_myel",
|
||||
0,
|
||||
"m_NaTa_t_myel",
|
||||
"h_NaTa_t_myel",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _na_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, 19, _prop);
|
||||
/*initialize range parameters*/
|
||||
gNaTa_tbar = 6.57751;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 19;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_na_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* ena */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ina */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dinadv */
|
||||
|
||||
}
|
||||
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 _NaTa_t_myel_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("na", -10000.);
|
||||
_na_sym = hoc_lookup("na_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, 19, 4);
|
||||
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, "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 NaTa_t_myel /mnt/c/neuron/neurenv/mech/NaTa_t_myel.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
if ( v == - 38.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.182 * ( v - - 38.0 ) ) / ( 1.0 - ( exp ( - ( v - - 38.0 ) / 6.0 ) ) ) ;
|
||||
mBeta = ( 0.124 * ( - v - 38.0 ) ) / ( 1.0 - ( exp ( - ( - v - 38.0 ) / 6.0 ) ) ) ;
|
||||
mTau = ( 1.0 / ( mAlpha + mBeta ) ) / _lqt ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
if ( v == - 66.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
hAlpha = ( - 0.015 * ( v - - 66.0 ) ) / ( 1.0 - ( exp ( ( v - - 66.0 ) / 6.0 ) ) ) ;
|
||||
hBeta = ( - 0.015 * ( - v - 66.0 ) ) / ( 1.0 - ( exp ( ( - v - 66.0 ) / 6.0 ) ) ) ;
|
||||
hTau = ( 1.0 / ( hAlpha + hBeta ) ) / _lqt ;
|
||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
ena = _ion_ena;
|
||||
_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 < 2; ++_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);
|
||||
ena = _ion_ena;
|
||||
_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(_na_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ena = _ion_ena;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gNaTa_t = gNaTa_tbar * m * m * m * h ;
|
||||
ina = gNaTa_t * ( v - ena ) ;
|
||||
}
|
||||
_current += ina;
|
||||
|
||||
} 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);
|
||||
}
|
||||
ena = _ion_ena;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dina;
|
||||
_dina = ina;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dinadv += (_dina - ina)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ina += ina ;
|
||||
#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;
|
||||
{
|
||||
ena = _ion_ena;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/NaTa_t_myel.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference :Colbert and Pan 2002\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX NaTa_t_myel\n"
|
||||
" USEION na READ ena WRITE ina\n"
|
||||
" RANGE gNaTa_tbar, gNaTa_t, ina, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gNaTa_tbar = 6.577510 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ena (mV)\n"
|
||||
" ina (mA/cm2)\n"
|
||||
" gNaTa_t (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gNaTa_t = gNaTa_tbar*m*m*m*h\n"
|
||||
" ina = gNaTa_t*(v-ena)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" if(v == -38){\n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6)))\n"
|
||||
" mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6)))\n"
|
||||
" mTau = (1/(mAlpha + mBeta))/qt\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
"\n"
|
||||
" if(v == -66){\n"
|
||||
" v = v + 0.0001\n"
|
||||
" }\n"
|
||||
"\n"
|
||||
" hAlpha = (-0.015 * (v- -66))/(1-(exp((v- -66)/6)))\n"
|
||||
" hBeta = (-0.015 * (-v -66))/(1-(exp((-v -66)/6)))\n"
|
||||
" hTau = (1/(hAlpha + hBeta))/qt\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/NaTa_t_myel.o
Normal file
BIN
x86_64/NaTa_t_myel.o
Normal file
Binary file not shown.
605
x86_64/NaTa_t_nor.c
Normal file
605
x86_64/NaTa_t_nor.c
Normal file
@ -0,0 +1,605 @@
|
||||
/* 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
|
||||
#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__NaTa_t_nor
|
||||
#define _nrn_initial _nrn_initial__NaTa_t_nor
|
||||
#define nrn_cur _nrn_cur__NaTa_t_nor
|
||||
#define _nrn_current _nrn_current__NaTa_t_nor
|
||||
#define nrn_jacob _nrn_jacob__NaTa_t_nor
|
||||
#define nrn_state _nrn_state__NaTa_t_nor
|
||||
#define _net_receive _net_receive__NaTa_t_nor
|
||||
#define rates rates__NaTa_t_nor
|
||||
#define states states__NaTa_t_nor
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gNaTa_tbar _p[0]
|
||||
#define gNaTa_tbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ina _p[2]
|
||||
#define ina_columnindex 2
|
||||
#define gNaTa_t _p[3]
|
||||
#define gNaTa_t_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ena _p[6]
|
||||
#define ena_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define mAlpha _p[9]
|
||||
#define mAlpha_columnindex 9
|
||||
#define mBeta _p[10]
|
||||
#define mBeta_columnindex 10
|
||||
#define hInf _p[11]
|
||||
#define hInf_columnindex 11
|
||||
#define hTau _p[12]
|
||||
#define hTau_columnindex 12
|
||||
#define hAlpha _p[13]
|
||||
#define hAlpha_columnindex 13
|
||||
#define hBeta _p[14]
|
||||
#define hBeta_columnindex 14
|
||||
#define Dm _p[15]
|
||||
#define Dm_columnindex 15
|
||||
#define Dh _p[16]
|
||||
#define Dh_columnindex 16
|
||||
#define v _p[17]
|
||||
#define v_columnindex 17
|
||||
#define _g _p[18]
|
||||
#define _g_columnindex 18
|
||||
#define _ion_ena *_ppvar[0]._pval
|
||||
#define _ion_ina *_ppvar[1]._pval
|
||||
#define _ion_dinadv *_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 */
|
||||
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_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_NaTa_t_nor", _hoc_setdata,
|
||||
"rates_NaTa_t_nor", _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[] = {
|
||||
"gNaTa_tbar_NaTa_t_nor", "S/cm2",
|
||||
"ina_NaTa_t_nor", "mA/cm2",
|
||||
"gNaTa_t_NaTa_t_nor", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"NaTa_t_nor",
|
||||
"gNaTa_tbar_NaTa_t_nor",
|
||||
"celsius_NaTa_t_nor",
|
||||
0,
|
||||
"ina_NaTa_t_nor",
|
||||
"gNaTa_t_NaTa_t_nor",
|
||||
0,
|
||||
"m_NaTa_t_nor",
|
||||
"h_NaTa_t_nor",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _na_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, 19, _prop);
|
||||
/*initialize range parameters*/
|
||||
gNaTa_tbar = 6.57751;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 19;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_na_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* ena */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ina */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dinadv */
|
||||
|
||||
}
|
||||
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 _NaTa_t_nor_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("na", -10000.);
|
||||
_na_sym = hoc_lookup("na_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, 19, 4);
|
||||
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, "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 NaTa_t_nor /mnt/c/neuron/neurenv/mech/NaTa_t_nor.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
if ( v == - 38.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.182 * ( v - - 38.0 ) ) / ( 1.0 - ( exp ( - ( v - - 38.0 ) / 6.0 ) ) ) ;
|
||||
mBeta = ( 0.124 * ( - v - 38.0 ) ) / ( 1.0 - ( exp ( - ( - v - 38.0 ) / 6.0 ) ) ) ;
|
||||
mTau = ( 1.0 / ( mAlpha + mBeta ) ) / _lqt ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
if ( v == - 66.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
hAlpha = ( - 0.015 * ( v - - 66.0 ) ) / ( 1.0 - ( exp ( ( v - - 66.0 ) / 6.0 ) ) ) ;
|
||||
hBeta = ( - 0.015 * ( - v - 66.0 ) ) / ( 1.0 - ( exp ( ( - v - 66.0 ) / 6.0 ) ) ) ;
|
||||
hTau = ( 1.0 / ( hAlpha + hBeta ) ) / _lqt ;
|
||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
ena = _ion_ena;
|
||||
_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 < 2; ++_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);
|
||||
ena = _ion_ena;
|
||||
_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(_na_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ena = _ion_ena;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gNaTa_t = gNaTa_tbar * m * m * m * h ;
|
||||
ina = gNaTa_t * ( v - ena ) ;
|
||||
}
|
||||
_current += ina;
|
||||
|
||||
} 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);
|
||||
}
|
||||
ena = _ion_ena;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dina;
|
||||
_dina = ina;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dinadv += (_dina - ina)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ina += ina ;
|
||||
#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;
|
||||
{
|
||||
ena = _ion_ena;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/NaTa_t_nor.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference :Colbert and Pan 2002\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX NaTa_t_nor\n"
|
||||
" USEION na READ ena WRITE ina\n"
|
||||
" RANGE gNaTa_tbar, gNaTa_t, ina, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gNaTa_tbar = 6.577510 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ena (mV)\n"
|
||||
" ina (mA/cm2)\n"
|
||||
" gNaTa_t (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gNaTa_t = gNaTa_tbar*m*m*m*h\n"
|
||||
" ina = gNaTa_t*(v-ena)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" if(v == -38){\n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6)))\n"
|
||||
" mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6)))\n"
|
||||
" mTau = (1/(mAlpha + mBeta))/qt\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
"\n"
|
||||
" if(v == -66){\n"
|
||||
" v = v + 0.0001\n"
|
||||
" }\n"
|
||||
"\n"
|
||||
" hAlpha = (-0.015 * (v- -66))/(1-(exp((v- -66)/6)))\n"
|
||||
" hBeta = (-0.015 * (-v -66))/(1-(exp((-v -66)/6)))\n"
|
||||
" hTau = (1/(hAlpha + hBeta))/qt\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/NaTa_t_nor.o
Normal file
BIN
x86_64/NaTa_t_nor.o
Normal file
Binary file not shown.
605
x86_64/NaTs2_t.c
Normal file
605
x86_64/NaTs2_t.c
Normal file
@ -0,0 +1,605 @@
|
||||
/* 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
|
||||
#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__NaTs2_t
|
||||
#define _nrn_initial _nrn_initial__NaTs2_t
|
||||
#define nrn_cur _nrn_cur__NaTs2_t
|
||||
#define _nrn_current _nrn_current__NaTs2_t
|
||||
#define nrn_jacob _nrn_jacob__NaTs2_t
|
||||
#define nrn_state _nrn_state__NaTs2_t
|
||||
#define _net_receive _net_receive__NaTs2_t
|
||||
#define rates rates__NaTs2_t
|
||||
#define states states__NaTs2_t
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gNaTs2_tbar _p[0]
|
||||
#define gNaTs2_tbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ina _p[2]
|
||||
#define ina_columnindex 2
|
||||
#define gNaTs2_t _p[3]
|
||||
#define gNaTs2_t_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ena _p[6]
|
||||
#define ena_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define mAlpha _p[9]
|
||||
#define mAlpha_columnindex 9
|
||||
#define mBeta _p[10]
|
||||
#define mBeta_columnindex 10
|
||||
#define hInf _p[11]
|
||||
#define hInf_columnindex 11
|
||||
#define hTau _p[12]
|
||||
#define hTau_columnindex 12
|
||||
#define hAlpha _p[13]
|
||||
#define hAlpha_columnindex 13
|
||||
#define hBeta _p[14]
|
||||
#define hBeta_columnindex 14
|
||||
#define Dm _p[15]
|
||||
#define Dm_columnindex 15
|
||||
#define Dh _p[16]
|
||||
#define Dh_columnindex 16
|
||||
#define v _p[17]
|
||||
#define v_columnindex 17
|
||||
#define _g _p[18]
|
||||
#define _g_columnindex 18
|
||||
#define _ion_ena *_ppvar[0]._pval
|
||||
#define _ion_ina *_ppvar[1]._pval
|
||||
#define _ion_dinadv *_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 */
|
||||
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_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_NaTs2_t", _hoc_setdata,
|
||||
"rates_NaTs2_t", _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[] = {
|
||||
"gNaTs2_tbar_NaTs2_t", "S/cm2",
|
||||
"ina_NaTs2_t", "mA/cm2",
|
||||
"gNaTs2_t_NaTs2_t", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"NaTs2_t",
|
||||
"gNaTs2_tbar_NaTs2_t",
|
||||
"celsius_NaTs2_t",
|
||||
0,
|
||||
"ina_NaTs2_t",
|
||||
"gNaTs2_t_NaTs2_t",
|
||||
0,
|
||||
"m_NaTs2_t",
|
||||
"h_NaTs2_t",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _na_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, 19, _prop);
|
||||
/*initialize range parameters*/
|
||||
gNaTs2_tbar = 1e-05;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 19;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_na_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* ena */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ina */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dinadv */
|
||||
|
||||
}
|
||||
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 _NaTs2_t_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("na", -10000.);
|
||||
_na_sym = hoc_lookup("na_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, 19, 4);
|
||||
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, "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 NaTs2_t /mnt/c/neuron/neurenv/mech/NaTs2_t.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
if ( v == - 32.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.182 * ( v - - 32.0 ) ) / ( 1.0 - ( exp ( - ( v - - 32.0 ) / 6.0 ) ) ) ;
|
||||
mBeta = ( 0.124 * ( - v - 32.0 ) ) / ( 1.0 - ( exp ( - ( - v - 32.0 ) / 6.0 ) ) ) ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
mTau = ( 1.0 / ( mAlpha + mBeta ) ) / _lqt ;
|
||||
if ( v == - 60.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
hAlpha = ( - 0.015 * ( v - - 60.0 ) ) / ( 1.0 - ( exp ( ( v - - 60.0 ) / 6.0 ) ) ) ;
|
||||
hBeta = ( - 0.015 * ( - v - 60.0 ) ) / ( 1.0 - ( exp ( ( - v - 60.0 ) / 6.0 ) ) ) ;
|
||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
|
||||
hTau = ( 1.0 / ( hAlpha + hBeta ) ) / _lqt ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
ena = _ion_ena;
|
||||
_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 < 2; ++_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);
|
||||
ena = _ion_ena;
|
||||
_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(_na_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ena = _ion_ena;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gNaTs2_t = gNaTs2_tbar * m * m * m * h ;
|
||||
ina = gNaTs2_t * ( v - ena ) ;
|
||||
}
|
||||
_current += ina;
|
||||
|
||||
} 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);
|
||||
}
|
||||
ena = _ion_ena;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dina;
|
||||
_dina = ina;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dinadv += (_dina - ina)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ina += ina ;
|
||||
#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;
|
||||
{
|
||||
ena = _ion_ena;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/NaTs2_t.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference :Colbert and Pan 2002\n"
|
||||
":comment: took the NaTa and shifted both activation/inactivation by 6 mv\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX NaTs2_t\n"
|
||||
" USEION na READ ena WRITE ina\n"
|
||||
" RANGE gNaTs2_tbar, gNaTs2_t, ina, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gNaTs2_tbar = 0.00001 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ena (mV)\n"
|
||||
" ina (mA/cm2)\n"
|
||||
" gNaTs2_t (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gNaTs2_t = gNaTs2_tbar*m*m*m*h\n"
|
||||
" ina = gNaTs2_t*(v-ena)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" if(v == -32){\n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.182 * (v- -32))/(1-(exp(-(v- -32)/6)))\n"
|
||||
" mBeta = (0.124 * (-v -32))/(1-(exp(-(-v -32)/6)))\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
" mTau = (1/(mAlpha + mBeta))/qt\n"
|
||||
"\n"
|
||||
" if(v == -60){\n"
|
||||
" v = v + 0.0001\n"
|
||||
" }\n"
|
||||
" hAlpha = (-0.015 * (v- -60))/(1-(exp((v- -60)/6)))\n"
|
||||
" hBeta = (-0.015 * (-v -60))/(1-(exp((-v -60)/6)))\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" hTau = (1/(hAlpha + hBeta))/qt\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/NaTs2_t.o
Normal file
BIN
x86_64/NaTs2_t.o
Normal file
Binary file not shown.
605
x86_64/NaTs2_t_apic.c
Normal file
605
x86_64/NaTs2_t_apic.c
Normal file
@ -0,0 +1,605 @@
|
||||
/* 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
|
||||
#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__NaTs2_t_apic
|
||||
#define _nrn_initial _nrn_initial__NaTs2_t_apic
|
||||
#define nrn_cur _nrn_cur__NaTs2_t_apic
|
||||
#define _nrn_current _nrn_current__NaTs2_t_apic
|
||||
#define nrn_jacob _nrn_jacob__NaTs2_t_apic
|
||||
#define nrn_state _nrn_state__NaTs2_t_apic
|
||||
#define _net_receive _net_receive__NaTs2_t_apic
|
||||
#define rates rates__NaTs2_t_apic
|
||||
#define states states__NaTs2_t_apic
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gNaTs2_tbar _p[0]
|
||||
#define gNaTs2_tbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ina _p[2]
|
||||
#define ina_columnindex 2
|
||||
#define gNaTs2_t _p[3]
|
||||
#define gNaTs2_t_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ena _p[6]
|
||||
#define ena_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define mAlpha _p[9]
|
||||
#define mAlpha_columnindex 9
|
||||
#define mBeta _p[10]
|
||||
#define mBeta_columnindex 10
|
||||
#define hInf _p[11]
|
||||
#define hInf_columnindex 11
|
||||
#define hTau _p[12]
|
||||
#define hTau_columnindex 12
|
||||
#define hAlpha _p[13]
|
||||
#define hAlpha_columnindex 13
|
||||
#define hBeta _p[14]
|
||||
#define hBeta_columnindex 14
|
||||
#define Dm _p[15]
|
||||
#define Dm_columnindex 15
|
||||
#define Dh _p[16]
|
||||
#define Dh_columnindex 16
|
||||
#define v _p[17]
|
||||
#define v_columnindex 17
|
||||
#define _g _p[18]
|
||||
#define _g_columnindex 18
|
||||
#define _ion_ena *_ppvar[0]._pval
|
||||
#define _ion_ina *_ppvar[1]._pval
|
||||
#define _ion_dinadv *_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 */
|
||||
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_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_NaTs2_t_apic", _hoc_setdata,
|
||||
"rates_NaTs2_t_apic", _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[] = {
|
||||
"gNaTs2_tbar_NaTs2_t_apic", "S/cm2",
|
||||
"ina_NaTs2_t_apic", "mA/cm2",
|
||||
"gNaTs2_t_NaTs2_t_apic", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"NaTs2_t_apic",
|
||||
"gNaTs2_tbar_NaTs2_t_apic",
|
||||
"celsius_NaTs2_t_apic",
|
||||
0,
|
||||
"ina_NaTs2_t_apic",
|
||||
"gNaTs2_t_NaTs2_t_apic",
|
||||
0,
|
||||
"m_NaTs2_t_apic",
|
||||
"h_NaTs2_t_apic",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _na_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, 19, _prop);
|
||||
/*initialize range parameters*/
|
||||
gNaTs2_tbar = 0.02569;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 19;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_na_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* ena */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ina */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dinadv */
|
||||
|
||||
}
|
||||
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 _NaTs2_t_apic_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("na", -10000.);
|
||||
_na_sym = hoc_lookup("na_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, 19, 4);
|
||||
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, "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 NaTs2_t_apic /mnt/c/neuron/neurenv/mech/NaTs2_t_apic.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
if ( v == - 32.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.182 * ( v - - 32.0 ) ) / ( 1.0 - ( exp ( - ( v - - 32.0 ) / 6.0 ) ) ) ;
|
||||
mBeta = ( 0.124 * ( - v - 32.0 ) ) / ( 1.0 - ( exp ( - ( - v - 32.0 ) / 6.0 ) ) ) ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
mTau = ( 1.0 / ( mAlpha + mBeta ) ) / _lqt ;
|
||||
if ( v == - 60.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
hAlpha = ( - 0.015 * ( v - - 60.0 ) ) / ( 1.0 - ( exp ( ( v - - 60.0 ) / 6.0 ) ) ) ;
|
||||
hBeta = ( - 0.015 * ( - v - 60.0 ) ) / ( 1.0 - ( exp ( ( - v - 60.0 ) / 6.0 ) ) ) ;
|
||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
|
||||
hTau = ( 1.0 / ( hAlpha + hBeta ) ) / _lqt ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
ena = _ion_ena;
|
||||
_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 < 2; ++_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);
|
||||
ena = _ion_ena;
|
||||
_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(_na_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ena = _ion_ena;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gNaTs2_t = gNaTs2_tbar * m * m * m * h ;
|
||||
ina = gNaTs2_t * ( v - ena ) ;
|
||||
}
|
||||
_current += ina;
|
||||
|
||||
} 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);
|
||||
}
|
||||
ena = _ion_ena;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dina;
|
||||
_dina = ina;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dinadv += (_dina - ina)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ina += ina ;
|
||||
#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;
|
||||
{
|
||||
ena = _ion_ena;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/NaTs2_t_apic.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference :Colbert and Pan 2002\n"
|
||||
":comment: took the NaTa and shifted both activation/inactivation by 6 mv\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX NaTs2_t_apic\n"
|
||||
" USEION na READ ena WRITE ina\n"
|
||||
" RANGE gNaTs2_tbar, gNaTs2_t, ina, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gNaTs2_tbar = 0.025690 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ena (mV)\n"
|
||||
" ina (mA/cm2)\n"
|
||||
" gNaTs2_t (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gNaTs2_t = gNaTs2_tbar*m*m*m*h\n"
|
||||
" ina = gNaTs2_t*(v-ena)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" if(v == -32){\n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.182 * (v- -32))/(1-(exp(-(v- -32)/6)))\n"
|
||||
" mBeta = (0.124 * (-v -32))/(1-(exp(-(-v -32)/6)))\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
" mTau = (1/(mAlpha + mBeta))/qt\n"
|
||||
"\n"
|
||||
" if(v == -60){\n"
|
||||
" v = v + 0.0001\n"
|
||||
" }\n"
|
||||
" hAlpha = (-0.015 * (v- -60))/(1-(exp((v- -60)/6)))\n"
|
||||
" hBeta = (-0.015 * (-v -60))/(1-(exp((-v -60)/6)))\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" hTau = (1/(hAlpha + hBeta))/qt\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/NaTs2_t_apic.o
Normal file
BIN
x86_64/NaTs2_t_apic.o
Normal file
Binary file not shown.
605
x86_64/NaTs2_t_soma.c
Normal file
605
x86_64/NaTs2_t_soma.c
Normal file
@ -0,0 +1,605 @@
|
||||
/* 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
|
||||
#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__NaTs2_t_soma
|
||||
#define _nrn_initial _nrn_initial__NaTs2_t_soma
|
||||
#define nrn_cur _nrn_cur__NaTs2_t_soma
|
||||
#define _nrn_current _nrn_current__NaTs2_t_soma
|
||||
#define nrn_jacob _nrn_jacob__NaTs2_t_soma
|
||||
#define nrn_state _nrn_state__NaTs2_t_soma
|
||||
#define _net_receive _net_receive__NaTs2_t_soma
|
||||
#define rates rates__NaTs2_t_soma
|
||||
#define states states__NaTs2_t_soma
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gNaTs2_tbar _p[0]
|
||||
#define gNaTs2_tbar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ina _p[2]
|
||||
#define ina_columnindex 2
|
||||
#define gNaTs2_t _p[3]
|
||||
#define gNaTs2_t_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ena _p[6]
|
||||
#define ena_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define mAlpha _p[9]
|
||||
#define mAlpha_columnindex 9
|
||||
#define mBeta _p[10]
|
||||
#define mBeta_columnindex 10
|
||||
#define hInf _p[11]
|
||||
#define hInf_columnindex 11
|
||||
#define hTau _p[12]
|
||||
#define hTau_columnindex 12
|
||||
#define hAlpha _p[13]
|
||||
#define hAlpha_columnindex 13
|
||||
#define hBeta _p[14]
|
||||
#define hBeta_columnindex 14
|
||||
#define Dm _p[15]
|
||||
#define Dm_columnindex 15
|
||||
#define Dh _p[16]
|
||||
#define Dh_columnindex 16
|
||||
#define v _p[17]
|
||||
#define v_columnindex 17
|
||||
#define _g _p[18]
|
||||
#define _g_columnindex 18
|
||||
#define _ion_ena *_ppvar[0]._pval
|
||||
#define _ion_ina *_ppvar[1]._pval
|
||||
#define _ion_dinadv *_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 */
|
||||
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_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_NaTs2_t_soma", _hoc_setdata,
|
||||
"rates_NaTs2_t_soma", _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[] = {
|
||||
"gNaTs2_tbar_NaTs2_t_soma", "S/cm2",
|
||||
"ina_NaTs2_t_soma", "mA/cm2",
|
||||
"gNaTs2_t_NaTs2_t_soma", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"NaTs2_t_soma",
|
||||
"gNaTs2_tbar_NaTs2_t_soma",
|
||||
"celsius_NaTs2_t_soma",
|
||||
0,
|
||||
"ina_NaTs2_t_soma",
|
||||
"gNaTs2_t_NaTs2_t_soma",
|
||||
0,
|
||||
"m_NaTs2_t_soma",
|
||||
"h_NaTs2_t_soma",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _na_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, 19, _prop);
|
||||
/*initialize range parameters*/
|
||||
gNaTs2_tbar = 0.976885;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 19;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_na_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* ena */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ina */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dinadv */
|
||||
|
||||
}
|
||||
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 _NaTs2_t_soma_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("na", -10000.);
|
||||
_na_sym = hoc_lookup("na_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, 19, 4);
|
||||
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, "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 NaTs2_t_soma /mnt/c/neuron/neurenv/mech/NaTs2_t_soma.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
if ( v == - 32.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.182 * ( v - - 32.0 ) ) / ( 1.0 - ( exp ( - ( v - - 32.0 ) / 6.0 ) ) ) ;
|
||||
mBeta = ( 0.124 * ( - v - 32.0 ) ) / ( 1.0 - ( exp ( - ( - v - 32.0 ) / 6.0 ) ) ) ;
|
||||
mInf = mAlpha / ( mAlpha + mBeta ) ;
|
||||
mTau = ( 1.0 / ( mAlpha + mBeta ) ) / _lqt ;
|
||||
if ( v == - 60.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
hAlpha = ( - 0.015 * ( v - - 60.0 ) ) / ( 1.0 - ( exp ( ( v - - 60.0 ) / 6.0 ) ) ) ;
|
||||
hBeta = ( - 0.015 * ( - v - 60.0 ) ) / ( 1.0 - ( exp ( ( - v - 60.0 ) / 6.0 ) ) ) ;
|
||||
hInf = hAlpha / ( hAlpha + hBeta ) ;
|
||||
hTau = ( 1.0 / ( hAlpha + hBeta ) ) / _lqt ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
ena = _ion_ena;
|
||||
_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 < 2; ++_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);
|
||||
ena = _ion_ena;
|
||||
_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(_na_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ena = _ion_ena;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gNaTs2_t = gNaTs2_tbar * m * m * m * h ;
|
||||
ina = gNaTs2_t * ( v - ena ) ;
|
||||
}
|
||||
_current += ina;
|
||||
|
||||
} 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);
|
||||
}
|
||||
ena = _ion_ena;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dina;
|
||||
_dina = ina;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dinadv += (_dina - ina)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ina += ina ;
|
||||
#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;
|
||||
{
|
||||
ena = _ion_ena;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/NaTs2_t_soma.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference :Colbert and Pan 2002\n"
|
||||
":comment: took the NaTa and shifted both activation/inactivation by 6 mv\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX NaTs2_t_soma\n"
|
||||
" USEION na READ ena WRITE ina\n"
|
||||
" RANGE gNaTs2_tbar, gNaTs2_t, ina, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gNaTs2_tbar = 0.976885 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ena (mV)\n"
|
||||
" ina (mA/cm2)\n"
|
||||
" gNaTs2_t (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gNaTs2_t = gNaTs2_tbar*m*m*m*h\n"
|
||||
" ina = gNaTs2_t*(v-ena)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10) \n"
|
||||
" UNITSOFF\n"
|
||||
" if(v == -32){\n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.182 * (v- -32))/(1-(exp(-(v- -32)/6)))\n"
|
||||
" mBeta = (0.124 * (-v -32))/(1-(exp(-(-v -32)/6)))\n"
|
||||
" mInf = mAlpha/(mAlpha + mBeta)\n"
|
||||
" mTau = (1/(mAlpha + mBeta))/qt\n"
|
||||
"\n"
|
||||
" if(v == -60){\n"
|
||||
" v = v + 0.0001\n"
|
||||
" }\n"
|
||||
" hAlpha = (-0.015 * (v- -60))/(1-(exp((v- -60)/6)))\n"
|
||||
" hBeta = (-0.015 * (-v -60))/(1-(exp((-v -60)/6)))\n"
|
||||
" hInf = hAlpha/(hAlpha + hBeta)\n"
|
||||
" hTau = (1/(hAlpha + hBeta))/qt\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/NaTs2_t_soma.o
Normal file
BIN
x86_64/NaTs2_t_soma.o
Normal file
Binary file not shown.
614
x86_64/Nap_Et2.c
Normal file
614
x86_64/Nap_Et2.c
Normal file
@ -0,0 +1,614 @@
|
||||
/* 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
|
||||
#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__Nap_Et2
|
||||
#define _nrn_initial _nrn_initial__Nap_Et2
|
||||
#define nrn_cur _nrn_cur__Nap_Et2
|
||||
#define _nrn_current _nrn_current__Nap_Et2
|
||||
#define nrn_jacob _nrn_jacob__Nap_Et2
|
||||
#define nrn_state _nrn_state__Nap_Et2
|
||||
#define _net_receive _net_receive__Nap_Et2
|
||||
#define rates rates__Nap_Et2
|
||||
#define states states__Nap_Et2
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gNap_Et2bar _p[0]
|
||||
#define gNap_Et2bar_columnindex 0
|
||||
#define celsius _p[1]
|
||||
#define celsius_columnindex 1
|
||||
#define ina _p[2]
|
||||
#define ina_columnindex 2
|
||||
#define gNap_Et2 _p[3]
|
||||
#define gNap_Et2_columnindex 3
|
||||
#define m _p[4]
|
||||
#define m_columnindex 4
|
||||
#define h _p[5]
|
||||
#define h_columnindex 5
|
||||
#define ena _p[6]
|
||||
#define ena_columnindex 6
|
||||
#define mInf _p[7]
|
||||
#define mInf_columnindex 7
|
||||
#define mTau _p[8]
|
||||
#define mTau_columnindex 8
|
||||
#define mAlpha _p[9]
|
||||
#define mAlpha_columnindex 9
|
||||
#define mBeta _p[10]
|
||||
#define mBeta_columnindex 10
|
||||
#define hInf _p[11]
|
||||
#define hInf_columnindex 11
|
||||
#define hTau _p[12]
|
||||
#define hTau_columnindex 12
|
||||
#define hAlpha _p[13]
|
||||
#define hAlpha_columnindex 13
|
||||
#define hBeta _p[14]
|
||||
#define hBeta_columnindex 14
|
||||
#define Dm _p[15]
|
||||
#define Dm_columnindex 15
|
||||
#define Dh _p[16]
|
||||
#define Dh_columnindex 16
|
||||
#define v _p[17]
|
||||
#define v_columnindex 17
|
||||
#define _g _p[18]
|
||||
#define _g_columnindex 18
|
||||
#define _ion_ena *_ppvar[0]._pval
|
||||
#define _ion_ina *_ppvar[1]._pval
|
||||
#define _ion_dinadv *_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 */
|
||||
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_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_Nap_Et2", _hoc_setdata,
|
||||
"rates_Nap_Et2", _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[] = {
|
||||
"gNap_Et2bar_Nap_Et2", "S/cm2",
|
||||
"ina_Nap_Et2", "mA/cm2",
|
||||
"gNap_Et2_Nap_Et2", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double h0 = 0;
|
||||
static double m0 = 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 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",
|
||||
"Nap_Et2",
|
||||
"gNap_Et2bar_Nap_Et2",
|
||||
"celsius_Nap_Et2",
|
||||
0,
|
||||
"ina_Nap_Et2",
|
||||
"gNap_Et2_Nap_Et2",
|
||||
0,
|
||||
"m_Nap_Et2",
|
||||
"h_Nap_Et2",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _na_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, 19, _prop);
|
||||
/*initialize range parameters*/
|
||||
gNap_Et2bar = 0.000671;
|
||||
celsius = 35;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 19;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_na_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* ena */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ina */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dinadv */
|
||||
|
||||
}
|
||||
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 _Nap_Et2_reg() {
|
||||
int _vectorized = 1;
|
||||
_initlists();
|
||||
ion_reg("na", -10000.);
|
||||
_na_sym = hoc_lookup("na_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, 19, 4);
|
||||
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, "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 Nap_Et2 /mnt/c/neuron/neurenv/mech/Nap_Et2.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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[2], _dlist1[2];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
Dh = ( hInf - h ) / hTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / hTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
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) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
double _lqt ;
|
||||
_lqt = pow( 2.3 , ( ( celsius - 21.0 ) / 10.0 ) ) ;
|
||||
mInf = 1.0 / ( 1.0 + exp ( ( v - - 52.6 ) / - 4.6 ) ) ;
|
||||
if ( v == - 38.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
mAlpha = ( 0.182 * ( v - - 38.0 ) ) / ( 1.0 - ( exp ( - ( v - - 38.0 ) / 6.0 ) ) ) ;
|
||||
mBeta = ( 0.124 * ( - v - 38.0 ) ) / ( 1.0 - ( exp ( - ( - v - 38.0 ) / 6.0 ) ) ) ;
|
||||
mTau = 6.0 * ( 1.0 / ( mAlpha + mBeta ) ) / _lqt ;
|
||||
if ( v == - 17.0 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
if ( v == - 64.4 ) {
|
||||
v = v + 0.0001 ;
|
||||
}
|
||||
hInf = 1.0 / ( 1.0 + exp ( ( v - - 48.8 ) / 10.0 ) ) ;
|
||||
hAlpha = - 2.88e-6 * ( v + 17.0 ) / ( 1.0 - exp ( ( v + 17.0 ) / 4.63 ) ) ;
|
||||
hBeta = 6.94e-6 * ( v + 64.4 ) / ( 1.0 - exp ( - ( v + 64.4 ) / 2.63 ) ) ;
|
||||
hTau = ( 1.0 / ( hAlpha + hBeta ) ) / _lqt ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 2;}
|
||||
|
||||
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);
|
||||
ena = _ion_ena;
|
||||
_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 < 2; ++_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);
|
||||
ena = _ion_ena;
|
||||
_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(_na_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 2, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
m = mInf ;
|
||||
h = hInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ena = _ion_ena;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
|
||||
gNap_Et2 = gNap_Et2bar * m * m * m * h ;
|
||||
ina = gNap_Et2 * ( v - ena ) ;
|
||||
}
|
||||
_current += ina;
|
||||
|
||||
} 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);
|
||||
}
|
||||
ena = _ion_ena;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dina;
|
||||
_dina = ina;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dinadv += (_dina - ina)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ina += ina ;
|
||||
#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;
|
||||
{
|
||||
ena = _ion_ena;
|
||||
{ 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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/Nap_Et2.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Comment : mtau deduced from text (said to be 6 times faster than for NaTa)\n"
|
||||
":Comment : so I used the equations from NaT and multiplied by 6\n"
|
||||
":Reference : Modeled according to kinetics derived from Magistretti & Alonso 1999\n"
|
||||
":Comment: corrected rates using q10 = 2.3, target temperature 35, orginal 21\n"
|
||||
": **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX Nap_Et2\n"
|
||||
" USEION na READ ena WRITE ina\n"
|
||||
" RANGE gNap_Et2bar, gNap_Et2, ina, celsius\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gNap_Et2bar = 0.000671 (S/cm2)\n"
|
||||
" celsius = 35\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ena (mV)\n"
|
||||
" ina (mA/cm2)\n"
|
||||
" gNap_Et2 (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
" mAlpha\n"
|
||||
" mBeta\n"
|
||||
" hInf\n"
|
||||
" hTau\n"
|
||||
" hAlpha\n"
|
||||
" hBeta\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE {\n"
|
||||
" m\n"
|
||||
" h\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gNap_Et2 = gNap_Et2bar*m*m*m*h\n"
|
||||
" ina = gNap_Et2*(v-ena)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
" h' = (hInf-h)/hTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
" h = hInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" LOCAL qt\n"
|
||||
" qt = 2.3^((celsius-21)/10)\n"
|
||||
" UNITSOFF\n"
|
||||
" mInf = 1.0/(1+exp((v- -52.6)/-4.6))\n"
|
||||
" if(v == -38){\n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
" mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6)))\n"
|
||||
" mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6)))\n"
|
||||
" mTau = 6*(1/(mAlpha + mBeta))/qt\n"
|
||||
"\n"
|
||||
" if(v == -17){\n"
|
||||
" v = v + 0.0001\n"
|
||||
" }\n"
|
||||
" if(v == -64.4){\n"
|
||||
" v = v+0.0001\n"
|
||||
" }\n"
|
||||
"\n"
|
||||
" hInf = 1.0/(1+exp((v- -48.8)/10))\n"
|
||||
" hAlpha = -2.88e-6 * (v + 17) / (1 - exp((v + 17)/4.63))\n"
|
||||
" hBeta = 6.94e-6 * (v + 64.4) / (1 - exp(-(v + 64.4)/2.63))\n"
|
||||
" hTau = (1/(hAlpha + hBeta))/qt\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/Nap_Et2.o
Normal file
BIN
x86_64/Nap_Et2.o
Normal file
Binary file not shown.
559
x86_64/SK_E2.c
Normal file
559
x86_64/SK_E2.c
Normal file
@ -0,0 +1,559 @@
|
||||
/* 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
|
||||
#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__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_ _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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gSK_E2bar _p[0]
|
||||
#define gSK_E2bar_columnindex 0
|
||||
#define ik _p[1]
|
||||
#define ik_columnindex 1
|
||||
#define gSK_E2 _p[2]
|
||||
#define gSK_E2_columnindex 2
|
||||
#define z _p[3]
|
||||
#define z_columnindex 3
|
||||
#define ek _p[4]
|
||||
#define ek_columnindex 4
|
||||
#define cai _p[5]
|
||||
#define cai_columnindex 5
|
||||
#define zInf _p[6]
|
||||
#define zInf_columnindex 6
|
||||
#define Dz _p[7]
|
||||
#define Dz_columnindex 7
|
||||
#define v _p[8]
|
||||
#define v_columnindex 8
|
||||
#define _g _p[9]
|
||||
#define _g_columnindex 9
|
||||
#define _ion_ek *_ppvar[0]._pval
|
||||
#define _ion_ik *_ppvar[1]._pval
|
||||
#define _ion_dikdv *_ppvar[2]._pval
|
||||
#define _ion_cai *_ppvar[3]._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_rates(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_SK_E2", _hoc_setdata,
|
||||
"rates_SK_E2", _hoc_rates,
|
||||
0, 0
|
||||
};
|
||||
/* declare global and static user variables */
|
||||
#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;
|
||||
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[4]._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",
|
||||
"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;
|
||||
|
||||
extern Prop* need_memb(Symbol*);
|
||||
|
||||
static void nrn_alloc(Prop* _prop) {
|
||||
Prop *prop_ion;
|
||||
double *_p; Datum *_ppvar;
|
||||
_p = nrn_prop_data_alloc(_mechtype, 10, _prop);
|
||||
/*initialize range parameters*/
|
||||
gSK_E2bar = 0.098377;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 10;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 5, _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 */
|
||||
prop_ion = need_memb(_ca_sym);
|
||||
nrn_promote(prop_ion, 1, 0);
|
||||
_ppvar[3]._pval = &prop_ion->param[1]; /* cai */
|
||||
|
||||
}
|
||||
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 _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]);
|
||||
_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, 10, 5);
|
||||
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, "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 /mnt/c/neuron/neurenv/mech/SK_E2.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
static int error;
|
||||
static int _ninits = 0;
|
||||
static int _match_recurse=1;
|
||||
static void _modl_cleanup(){ _match_recurse=1;}
|
||||
static int rates(_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; {
|
||||
rates ( _threadargscomma_ cai ) ;
|
||||
Dz = ( zInf - z ) / zTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargscomma_ cai ) ;
|
||||
Dz = Dz / (1. - dt*( ( ( ( - 1.0 ) ) ) / zTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargscomma_ cai ) ;
|
||||
z = z + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / zTau)))*(- ( ( ( zInf ) ) / zTau ) / ( ( ( ( - 1.0 ) ) ) / zTau ) - z) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsprotocomma_ 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;
|
||||
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.;
|
||||
rates ( _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;
|
||||
cai = _ion_cai;
|
||||
_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;
|
||||
cai = _ion_cai;
|
||||
_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);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 3, 1);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
z = z0;
|
||||
{
|
||||
rates ( _threadargscomma_ cai ) ;
|
||||
z = zInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
cai = _ion_cai;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, 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(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;
|
||||
cai = _ion_cai;
|
||||
_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;
|
||||
cai = _ion_cai;
|
||||
{ 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] = z_columnindex; _dlist1[0] = Dz_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/SK_E2.mod";
|
||||
static 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"
|
||||
"}\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"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/SK_E2.o
Normal file
BIN
x86_64/SK_E2.o
Normal file
Binary file not shown.
559
x86_64/SK_E2_soma.c
Normal file
559
x86_64/SK_E2_soma.c
Normal file
@ -0,0 +1,559 @@
|
||||
/* 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
|
||||
#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__SK_E2_soma
|
||||
#define _nrn_initial _nrn_initial__SK_E2_soma
|
||||
#define nrn_cur _nrn_cur__SK_E2_soma
|
||||
#define _nrn_current _nrn_current__SK_E2_soma
|
||||
#define nrn_jacob _nrn_jacob__SK_E2_soma
|
||||
#define nrn_state _nrn_state__SK_E2_soma
|
||||
#define _net_receive _net_receive__SK_E2_soma
|
||||
#define rates rates__SK_E2_soma
|
||||
#define states states__SK_E2_soma
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gSK_E2bar _p[0]
|
||||
#define gSK_E2bar_columnindex 0
|
||||
#define ik _p[1]
|
||||
#define ik_columnindex 1
|
||||
#define gSK_E2 _p[2]
|
||||
#define gSK_E2_columnindex 2
|
||||
#define z _p[3]
|
||||
#define z_columnindex 3
|
||||
#define ek _p[4]
|
||||
#define ek_columnindex 4
|
||||
#define cai _p[5]
|
||||
#define cai_columnindex 5
|
||||
#define zInf _p[6]
|
||||
#define zInf_columnindex 6
|
||||
#define Dz _p[7]
|
||||
#define Dz_columnindex 7
|
||||
#define v _p[8]
|
||||
#define v_columnindex 8
|
||||
#define _g _p[9]
|
||||
#define _g_columnindex 9
|
||||
#define _ion_ek *_ppvar[0]._pval
|
||||
#define _ion_ik *_ppvar[1]._pval
|
||||
#define _ion_dikdv *_ppvar[2]._pval
|
||||
#define _ion_cai *_ppvar[3]._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_rates(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_SK_E2_soma", _hoc_setdata,
|
||||
"rates_SK_E2_soma", _hoc_rates,
|
||||
0, 0
|
||||
};
|
||||
/* declare global and static user variables */
|
||||
#define zTau zTau_SK_E2_soma
|
||||
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_soma", "ms",
|
||||
"gSK_E2bar_SK_E2_soma", "mho/cm2",
|
||||
"ik_SK_E2_soma", "mA/cm2",
|
||||
"gSK_E2_SK_E2_soma", "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_soma", &zTau_SK_E2_soma,
|
||||
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[4]._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",
|
||||
"SK_E2_soma",
|
||||
"gSK_E2bar_SK_E2_soma",
|
||||
0,
|
||||
"ik_SK_E2_soma",
|
||||
"gSK_E2_SK_E2_soma",
|
||||
0,
|
||||
"z_SK_E2_soma",
|
||||
0,
|
||||
0};
|
||||
static Symbol* _k_sym;
|
||||
static Symbol* _ca_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, 10, _prop);
|
||||
/*initialize range parameters*/
|
||||
gSK_E2bar = 0.003869;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 10;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 5, _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 */
|
||||
prop_ion = need_memb(_ca_sym);
|
||||
nrn_promote(prop_ion, 1, 0);
|
||||
_ppvar[3]._pval = &prop_ion->param[1]; /* cai */
|
||||
|
||||
}
|
||||
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 _SK_E2_soma_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]);
|
||||
_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, 10, 5);
|
||||
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, "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_soma /mnt/c/neuron/neurenv/mech/SK_E2_soma.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
static int error;
|
||||
static int _ninits = 0;
|
||||
static int _match_recurse=1;
|
||||
static void _modl_cleanup(){ _match_recurse=1;}
|
||||
static int rates(_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; {
|
||||
rates ( _threadargscomma_ cai ) ;
|
||||
Dz = ( zInf - z ) / zTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargscomma_ cai ) ;
|
||||
Dz = Dz / (1. - dt*( ( ( ( - 1.0 ) ) ) / zTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargscomma_ cai ) ;
|
||||
z = z + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / zTau)))*(- ( ( ( zInf ) ) / zTau ) / ( ( ( ( - 1.0 ) ) ) / zTau ) - z) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsprotocomma_ 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;
|
||||
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.;
|
||||
rates ( _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;
|
||||
cai = _ion_cai;
|
||||
_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;
|
||||
cai = _ion_cai;
|
||||
_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);
|
||||
nrn_update_ion_pointer(_ca_sym, _ppvar, 3, 1);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
z = z0;
|
||||
{
|
||||
rates ( _threadargscomma_ cai ) ;
|
||||
z = zInf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
cai = _ion_cai;
|
||||
initmodel(_p, _ppvar, _thread, _nt);
|
||||
}
|
||||
}
|
||||
|
||||
static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt, 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(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;
|
||||
cai = _ion_cai;
|
||||
_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;
|
||||
cai = _ion_cai;
|
||||
{ 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] = z_columnindex; _dlist1[0] = Dz_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/SK_E2_soma.mod";
|
||||
static 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_soma\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 = 0.003869 (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"
|
||||
"}\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"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/SK_E2_soma.o
Normal file
BIN
x86_64/SK_E2_soma.o
Normal file
Binary file not shown.
537
x86_64/SKv3_1.c
Normal file
537
x86_64/SKv3_1.c
Normal file
@ -0,0 +1,537 @@
|
||||
/* 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
|
||||
#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__SKv3_1
|
||||
#define _nrn_initial _nrn_initial__SKv3_1
|
||||
#define nrn_cur _nrn_cur__SKv3_1
|
||||
#define _nrn_current _nrn_current__SKv3_1
|
||||
#define nrn_jacob _nrn_jacob__SKv3_1
|
||||
#define nrn_state _nrn_state__SKv3_1
|
||||
#define _net_receive _net_receive__SKv3_1
|
||||
#define rates rates__SKv3_1
|
||||
#define states states__SKv3_1
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gSKv3_1bar _p[0]
|
||||
#define gSKv3_1bar_columnindex 0
|
||||
#define ik _p[1]
|
||||
#define ik_columnindex 1
|
||||
#define gSKv3_1 _p[2]
|
||||
#define gSKv3_1_columnindex 2
|
||||
#define m _p[3]
|
||||
#define m_columnindex 3
|
||||
#define ek _p[4]
|
||||
#define ek_columnindex 4
|
||||
#define mInf _p[5]
|
||||
#define mInf_columnindex 5
|
||||
#define mTau _p[6]
|
||||
#define mTau_columnindex 6
|
||||
#define Dm _p[7]
|
||||
#define Dm_columnindex 7
|
||||
#define v _p[8]
|
||||
#define v_columnindex 8
|
||||
#define _g _p[9]
|
||||
#define _g_columnindex 9
|
||||
#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_rates(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_SKv3_1", _hoc_setdata,
|
||||
"rates_SKv3_1", _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[] = {
|
||||
"gSKv3_1bar_SKv3_1", "S/cm2",
|
||||
"ik_SKv3_1", "mA/cm2",
|
||||
"gSKv3_1_SKv3_1", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double m0 = 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 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",
|
||||
"SKv3_1",
|
||||
"gSKv3_1bar_SKv3_1",
|
||||
0,
|
||||
"ik_SKv3_1",
|
||||
"gSKv3_1_SKv3_1",
|
||||
0,
|
||||
"m_SKv3_1",
|
||||
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, 10, _prop);
|
||||
/*initialize range parameters*/
|
||||
gSKv3_1bar = 1.93618;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 10;
|
||||
_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 _SKv3_1_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, 10, 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 SKv3_1 /mnt/c/neuron/neurenv/mech/SKv3_1.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / mTau)))*(- ( ( ( mInf ) ) / mTau ) / ( ( ( ( - 1.0 ) ) ) / mTau ) - m) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
mInf = 1.0 / ( 1.0 + exp ( ( ( v - ( 18.700 ) ) / ( - 9.700 ) ) ) ) ;
|
||||
mTau = 0.2 * 20.000 / ( 1.0 + exp ( ( ( v - ( - 46.560 ) ) / ( - 44.140 ) ) ) ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
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;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
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;{ {
|
||||
gSKv3_1 = gSKv3_1bar * m ;
|
||||
ik = gSKv3_1 * ( v - ek ) ;
|
||||
}
|
||||
_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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/SKv3_1.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992)\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX SKv3_1\n"
|
||||
" USEION k READ ek WRITE ik\n"
|
||||
" RANGE gSKv3_1bar, gSKv3_1, ik \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gSKv3_1bar = 1.936176 (S/cm2) \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ek (mV)\n"
|
||||
" ik (mA/cm2)\n"
|
||||
" gSKv3_1 (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE { \n"
|
||||
" m\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gSKv3_1 = gSKv3_1bar*m\n"
|
||||
" ik = gSKv3_1*(v-ek)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" UNITSOFF\n"
|
||||
" mInf = 1/(1+exp(((v -(18.700))/(-9.700))))\n"
|
||||
" mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140))))\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/SKv3_1.o
Normal file
BIN
x86_64/SKv3_1.o
Normal file
Binary file not shown.
537
x86_64/SKv3_1_apic.c
Normal file
537
x86_64/SKv3_1_apic.c
Normal file
@ -0,0 +1,537 @@
|
||||
/* 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
|
||||
#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__SKv3_1_apic
|
||||
#define _nrn_initial _nrn_initial__SKv3_1_apic
|
||||
#define nrn_cur _nrn_cur__SKv3_1_apic
|
||||
#define _nrn_current _nrn_current__SKv3_1_apic
|
||||
#define nrn_jacob _nrn_jacob__SKv3_1_apic
|
||||
#define nrn_state _nrn_state__SKv3_1_apic
|
||||
#define _net_receive _net_receive__SKv3_1_apic
|
||||
#define rates rates__SKv3_1_apic
|
||||
#define states states__SKv3_1_apic
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gSKv3_1bar _p[0]
|
||||
#define gSKv3_1bar_columnindex 0
|
||||
#define ik _p[1]
|
||||
#define ik_columnindex 1
|
||||
#define gSKv3_1 _p[2]
|
||||
#define gSKv3_1_columnindex 2
|
||||
#define m _p[3]
|
||||
#define m_columnindex 3
|
||||
#define ek _p[4]
|
||||
#define ek_columnindex 4
|
||||
#define mInf _p[5]
|
||||
#define mInf_columnindex 5
|
||||
#define mTau _p[6]
|
||||
#define mTau_columnindex 6
|
||||
#define Dm _p[7]
|
||||
#define Dm_columnindex 7
|
||||
#define v _p[8]
|
||||
#define v_columnindex 8
|
||||
#define _g _p[9]
|
||||
#define _g_columnindex 9
|
||||
#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_rates(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_SKv3_1_apic", _hoc_setdata,
|
||||
"rates_SKv3_1_apic", _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[] = {
|
||||
"gSKv3_1bar_SKv3_1_apic", "S/cm2",
|
||||
"ik_SKv3_1_apic", "mA/cm2",
|
||||
"gSKv3_1_SKv3_1_apic", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double m0 = 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 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",
|
||||
"SKv3_1_apic",
|
||||
"gSKv3_1bar_SKv3_1_apic",
|
||||
0,
|
||||
"ik_SKv3_1_apic",
|
||||
"gSKv3_1_SKv3_1_apic",
|
||||
0,
|
||||
"m_SKv3_1_apic",
|
||||
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, 10, _prop);
|
||||
/*initialize range parameters*/
|
||||
gSKv3_1bar = 0.039763;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 10;
|
||||
_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 _SKv3_1_apic_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, 10, 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 SKv3_1_apic /mnt/c/neuron/neurenv/mech/SKv3_1_apic.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / mTau)))*(- ( ( ( mInf ) ) / mTau ) / ( ( ( ( - 1.0 ) ) ) / mTau ) - m) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
mInf = 1.0 / ( 1.0 + exp ( ( ( v - ( 18.700 ) ) / ( - 9.700 ) ) ) ) ;
|
||||
mTau = 0.2 * 20.000 / ( 1.0 + exp ( ( ( v - ( - 46.560 ) ) / ( - 44.140 ) ) ) ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
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;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
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;{ {
|
||||
gSKv3_1 = gSKv3_1bar * m ;
|
||||
ik = gSKv3_1 * ( v - ek ) ;
|
||||
}
|
||||
_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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/SKv3_1_apic.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992)\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX SKv3_1_apic\n"
|
||||
" USEION k READ ek WRITE ik\n"
|
||||
" RANGE gSKv3_1bar, gSKv3_1, ik \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gSKv3_1bar = 0.039763 (S/cm2) \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ek (mV)\n"
|
||||
" ik (mA/cm2)\n"
|
||||
" gSKv3_1 (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE { \n"
|
||||
" m\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gSKv3_1 = gSKv3_1bar*m\n"
|
||||
" ik = gSKv3_1*(v-ek)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" UNITSOFF\n"
|
||||
" mInf = 1/(1+exp(((v -(18.700))/(-9.700))))\n"
|
||||
" mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140))))\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/SKv3_1_apic.o
Normal file
BIN
x86_64/SKv3_1_apic.o
Normal file
Binary file not shown.
537
x86_64/SKv3_1_soma.c
Normal file
537
x86_64/SKv3_1_soma.c
Normal file
@ -0,0 +1,537 @@
|
||||
/* 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
|
||||
#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__SKv3_1_soma
|
||||
#define _nrn_initial _nrn_initial__SKv3_1_soma
|
||||
#define nrn_cur _nrn_cur__SKv3_1_soma
|
||||
#define _nrn_current _nrn_current__SKv3_1_soma
|
||||
#define nrn_jacob _nrn_jacob__SKv3_1_soma
|
||||
#define nrn_state _nrn_state__SKv3_1_soma
|
||||
#define _net_receive _net_receive__SKv3_1_soma
|
||||
#define rates rates__SKv3_1_soma
|
||||
#define states states__SKv3_1_soma
|
||||
|
||||
#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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gSKv3_1bar _p[0]
|
||||
#define gSKv3_1bar_columnindex 0
|
||||
#define ik _p[1]
|
||||
#define ik_columnindex 1
|
||||
#define gSKv3_1 _p[2]
|
||||
#define gSKv3_1_columnindex 2
|
||||
#define m _p[3]
|
||||
#define m_columnindex 3
|
||||
#define ek _p[4]
|
||||
#define ek_columnindex 4
|
||||
#define mInf _p[5]
|
||||
#define mInf_columnindex 5
|
||||
#define mTau _p[6]
|
||||
#define mTau_columnindex 6
|
||||
#define Dm _p[7]
|
||||
#define Dm_columnindex 7
|
||||
#define v _p[8]
|
||||
#define v_columnindex 8
|
||||
#define _g _p[9]
|
||||
#define _g_columnindex 9
|
||||
#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_rates(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_SKv3_1_soma", _hoc_setdata,
|
||||
"rates_SKv3_1_soma", _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[] = {
|
||||
"gSKv3_1bar_SKv3_1_soma", "S/cm2",
|
||||
"ik_SKv3_1_soma", "mA/cm2",
|
||||
"gSKv3_1_SKv3_1_soma", "S/cm2",
|
||||
0,0
|
||||
};
|
||||
static double delta_t = 0.01;
|
||||
static double m0 = 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 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",
|
||||
"SKv3_1_soma",
|
||||
"gSKv3_1bar_SKv3_1_soma",
|
||||
0,
|
||||
"ik_SKv3_1_soma",
|
||||
"gSKv3_1_SKv3_1_soma",
|
||||
0,
|
||||
"m_SKv3_1_soma",
|
||||
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, 10, _prop);
|
||||
/*initialize range parameters*/
|
||||
gSKv3_1bar = 0.072929;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 10;
|
||||
_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 _SKv3_1_soma_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, 10, 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 SKv3_1_soma /mnt/c/neuron/neurenv/mech/SKv3_1_soma.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
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_ ) ;
|
||||
Dm = ( mInf - m ) / mTau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
rates ( _threadargs_ ) ;
|
||||
Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / mTau )) ;
|
||||
return 0;
|
||||
}
|
||||
/*END CVODE*/
|
||||
static int states (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
rates ( _threadargs_ ) ;
|
||||
m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / mTau)))*(- ( ( ( mInf ) ) / mTau ) / ( ( ( ( - 1.0 ) ) ) / mTau ) - m) ;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
static int rates ( _threadargsproto_ ) {
|
||||
mInf = 1.0 / ( 1.0 + exp ( ( ( v - ( 18.700 ) ) / ( - 9.700 ) ) ) ) ;
|
||||
mTau = 0.2 * 20.000 / ( 1.0 + exp ( ( ( v - ( - 46.560 ) ) / ( - 44.140 ) ) ) ) ;
|
||||
return 0; }
|
||||
|
||||
static void _hoc_rates(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.;
|
||||
rates ( _p, _ppvar, _thread, _nt );
|
||||
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;
|
||||
{
|
||||
rates ( _threadargs_ ) ;
|
||||
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;{ {
|
||||
gSKv3_1 = gSKv3_1bar * m ;
|
||||
ik = gSKv3_1 * ( v - ek ) ;
|
||||
}
|
||||
_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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/SKv3_1_soma.mod";
|
||||
static const char* nmodl_file_text =
|
||||
":Comment : L6\n"
|
||||
":Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992)\n"
|
||||
"\n"
|
||||
"NEURON {\n"
|
||||
" SUFFIX SKv3_1_soma\n"
|
||||
" USEION k READ ek WRITE ik\n"
|
||||
" RANGE gSKv3_1bar, gSKv3_1, ik \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"UNITS {\n"
|
||||
" (S) = (siemens)\n"
|
||||
" (mV) = (millivolt)\n"
|
||||
" (mA) = (milliamp)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PARAMETER {\n"
|
||||
" gSKv3_1bar = 0.072929 (S/cm2) \n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"ASSIGNED {\n"
|
||||
" v (mV)\n"
|
||||
" ek (mV)\n"
|
||||
" ik (mA/cm2)\n"
|
||||
" gSKv3_1 (S/cm2)\n"
|
||||
" mInf\n"
|
||||
" mTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"STATE { \n"
|
||||
" m\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"BREAKPOINT {\n"
|
||||
" SOLVE states METHOD cnexp\n"
|
||||
" gSKv3_1 = gSKv3_1bar*m\n"
|
||||
" ik = gSKv3_1*(v-ek)\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"DERIVATIVE states {\n"
|
||||
" rates()\n"
|
||||
" m' = (mInf-m)/mTau\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"INITIAL{\n"
|
||||
" rates()\n"
|
||||
" m = mInf\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
"PROCEDURE rates(){\n"
|
||||
" UNITSOFF\n"
|
||||
" mInf = 1/(1+exp(((v -(18.700))/(-9.700))))\n"
|
||||
" mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140))))\n"
|
||||
" UNITSON\n"
|
||||
"}\n"
|
||||
"\n"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/SKv3_1_soma.o
Normal file
BIN
x86_64/SKv3_1_soma.o
Normal file
Binary file not shown.
733
x86_64/hhqt.c
Normal file
733
x86_64/hhqt.c
Normal file
@ -0,0 +1,733 @@
|
||||
/* 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
|
||||
#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__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_ _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(int);
|
||||
/* Thread safe. No static _p or _ppvar. */
|
||||
|
||||
#define t _nt->_t
|
||||
#define dt _nt->_dt
|
||||
#define gnabar _p[0]
|
||||
#define gnabar_columnindex 0
|
||||
#define gkbar _p[1]
|
||||
#define gkbar_columnindex 1
|
||||
#define gl _p[2]
|
||||
#define gl_columnindex 2
|
||||
#define el _p[3]
|
||||
#define el_columnindex 3
|
||||
#define celsius _p[4]
|
||||
#define celsius_columnindex 4
|
||||
#define gna _p[5]
|
||||
#define gna_columnindex 5
|
||||
#define gk _p[6]
|
||||
#define gk_columnindex 6
|
||||
#define il _p[7]
|
||||
#define il_columnindex 7
|
||||
#define m _p[8]
|
||||
#define m_columnindex 8
|
||||
#define h _p[9]
|
||||
#define h_columnindex 9
|
||||
#define n _p[10]
|
||||
#define n_columnindex 10
|
||||
#define ena _p[11]
|
||||
#define ena_columnindex 11
|
||||
#define ek _p[12]
|
||||
#define ek_columnindex 12
|
||||
#define ina _p[13]
|
||||
#define ina_columnindex 13
|
||||
#define ik _p[14]
|
||||
#define ik_columnindex 14
|
||||
#define minf _p[15]
|
||||
#define minf_columnindex 15
|
||||
#define hinf _p[16]
|
||||
#define hinf_columnindex 16
|
||||
#define ninf _p[17]
|
||||
#define ninf_columnindex 17
|
||||
#define mtau _p[18]
|
||||
#define mtau_columnindex 18
|
||||
#define htau _p[19]
|
||||
#define htau_columnindex 19
|
||||
#define ntau _p[20]
|
||||
#define ntau_columnindex 20
|
||||
#define Dm _p[21]
|
||||
#define Dm_columnindex 21
|
||||
#define Dh _p[22]
|
||||
#define Dh_columnindex 22
|
||||
#define Dn _p[23]
|
||||
#define Dn_columnindex 23
|
||||
#define v _p[24]
|
||||
#define v_columnindex 24
|
||||
#define _g _p[25]
|
||||
#define _g_columnindex 25
|
||||
#define _ion_ena *_ppvar[0]._pval
|
||||
#define _ion_ina *_ppvar[1]._pval
|
||||
#define _ion_dinadv *_ppvar[2]._pval
|
||||
#define _ion_ek *_ppvar[3]._pval
|
||||
#define _ion_ik *_ppvar[4]._pval
|
||||
#define _ion_dikdv *_ppvar[5]._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 */
|
||||
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_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_hhqt", _hoc_setdata,
|
||||
"rates_hhqt", _hoc_rates,
|
||||
"vtrap_hhqt", _hoc_vtrap,
|
||||
0, 0
|
||||
};
|
||||
#define vtrap vtrap_hhqt
|
||||
extern double vtrap( _threadargsprotocomma_ double , double );
|
||||
/* declare global and static user variables */
|
||||
/* 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",
|
||||
"celsius_hhqt", "degC",
|
||||
"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;
|
||||
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[6]._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",
|
||||
"hhqt",
|
||||
"gnabar_hhqt",
|
||||
"gkbar_hhqt",
|
||||
"gl_hhqt",
|
||||
"el_hhqt",
|
||||
"celsius_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;
|
||||
|
||||
extern Prop* need_memb(Symbol*);
|
||||
|
||||
static void nrn_alloc(Prop* _prop) {
|
||||
Prop *prop_ion;
|
||||
double *_p; Datum *_ppvar;
|
||||
_p = nrn_prop_data_alloc(_mechtype, 26, _prop);
|
||||
/*initialize range parameters*/
|
||||
gnabar = 0.12;
|
||||
gkbar = 0.036;
|
||||
gl = 0.0003;
|
||||
el = -54.3;
|
||||
celsius = 29;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 26;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 7, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
prop_ion = need_memb(_na_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[0]._pval = &prop_ion->param[0]; /* ena */
|
||||
_ppvar[1]._pval = &prop_ion->param[3]; /* ina */
|
||||
_ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dinadv */
|
||||
prop_ion = need_memb(_k_sym);
|
||||
nrn_promote(prop_ion, 0, 1);
|
||||
_ppvar[3]._pval = &prop_ion->param[0]; /* ek */
|
||||
_ppvar[4]._pval = &prop_ion->param[3]; /* ik */
|
||||
_ppvar[5]._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 _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]);
|
||||
_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, 26, 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 /mnt/c/neuron/neurenv/mech/hhqt.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static char *modelname = "";
|
||||
|
||||
static int error;
|
||||
static int _ninits = 0;
|
||||
static int _match_recurse=1;
|
||||
static void _modl_cleanup(){ _match_recurse=1;}
|
||||
static int rates(_threadargsprotocomma_ double);
|
||||
|
||||
static int _ode_spec1(_threadargsproto_);
|
||||
/*static int _ode_matsol1(_threadargsproto_);*/
|
||||
static int _slist1[3], _dlist1[3];
|
||||
static int states(_threadargsproto_);
|
||||
|
||||
/*CVODE*/
|
||||
static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {int _reset = 0; {
|
||||
rates ( _threadargscomma_ v ) ;
|
||||
Dm = ( minf - m ) / mtau ;
|
||||
Dh = ( hinf - h ) / htau ;
|
||||
Dn = ( ninf - n ) / ntau ;
|
||||
}
|
||||
return _reset;
|
||||
}
|
||||
static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
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 (double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) { {
|
||||
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 ( _threadargsprotocomma_ 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;
|
||||
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.;
|
||||
rates ( _p, _ppvar, _thread, _nt, *getarg(1) );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
double vtrap ( _threadargsprotocomma_ 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;
|
||||
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 = vtrap ( _p, _ppvar, _thread, _nt, *getarg(1) , *getarg(2) );
|
||||
hoc_retpushx(_r);
|
||||
}
|
||||
|
||||
static int _ode_count(int _type){ return 3;}
|
||||
|
||||
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);
|
||||
ena = _ion_ena;
|
||||
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 < 3; ++_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);
|
||||
ena = _ion_ena;
|
||||
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(_na_sym, _ppvar, 0, 0);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 1, 3);
|
||||
nrn_update_ion_pointer(_na_sym, _ppvar, 2, 4);
|
||||
nrn_update_ion_pointer(_k_sym, _ppvar, 3, 0);
|
||||
nrn_update_ion_pointer(_k_sym, _ppvar, 4, 3);
|
||||
nrn_update_ion_pointer(_k_sym, _ppvar, 5, 4);
|
||||
}
|
||||
|
||||
static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, NrnThread* _nt) {
|
||||
int _i; double _save;{
|
||||
h = h0;
|
||||
m = m0;
|
||||
n = n0;
|
||||
{
|
||||
rates ( _threadargscomma_ v ) ;
|
||||
m = minf ;
|
||||
h = hinf ;
|
||||
n = ninf ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
ena = _ion_ena;
|
||||
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;{ {
|
||||
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(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);
|
||||
}
|
||||
ena = _ion_ena;
|
||||
ek = _ion_ek;
|
||||
_g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
|
||||
{ double _dik;
|
||||
double _dina;
|
||||
_dina = ina;
|
||||
_dik = ik;
|
||||
_rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
|
||||
_ion_dinadv += (_dina - ina)/.001 ;
|
||||
_ion_dikdv += (_dik - ik)/.001 ;
|
||||
}
|
||||
_g = (_g - _rhs)/.001;
|
||||
_ion_ina += ina ;
|
||||
_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;
|
||||
{
|
||||
ena = _ion_ena;
|
||||
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_columnindex; _dlist1[0] = Dm_columnindex;
|
||||
_slist1[1] = h_columnindex; _dlist1[1] = Dh_columnindex;
|
||||
_slist1[2] = n_columnindex; _dlist1[2] = Dn_columnindex;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
} /* extern "C" */
|
||||
#endif
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/hhqt.mod";
|
||||
static 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, celsius\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"
|
||||
" celsius = 29 (degC)\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"
|
||||
"}\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"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/hhqt.o
Normal file
BIN
x86_64/hhqt.o
Normal file
Binary file not shown.
BIN
x86_64/libnrnmech.so
Normal file
BIN
x86_64/libnrnmech.so
Normal file
Binary file not shown.
200
x86_64/makemod2c_inc
Normal file
200
x86_64/makemod2c_inc
Normal file
@ -0,0 +1,200 @@
|
||||
./CaDynamics_E2.c: /mnt/c/neuron/neurenv/mech/CaDynamics_E2.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "CaDynamics_E2.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./CaDynamics_E2.o: ./CaDynamics_E2.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./CaDynamics_E2_soma.c: /mnt/c/neuron/neurenv/mech/CaDynamics_E2_soma.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "CaDynamics_E2_soma.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./CaDynamics_E2_soma.o: ./CaDynamics_E2_soma.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./Ca_HVA.c: /mnt/c/neuron/neurenv/mech/Ca_HVA.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "Ca_HVA.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./Ca_HVA.o: ./Ca_HVA.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./Ca_HVA_soma.c: /mnt/c/neuron/neurenv/mech/Ca_HVA_soma.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "Ca_HVA_soma.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./Ca_HVA_soma.o: ./Ca_HVA_soma.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./Ca_LVAst.c: /mnt/c/neuron/neurenv/mech/Ca_LVAst.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "Ca_LVAst.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./Ca_LVAst.o: ./Ca_LVAst.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./Ca_LVAst_soma.c: /mnt/c/neuron/neurenv/mech/Ca_LVAst_soma.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "Ca_LVAst_soma.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./Ca_LVAst_soma.o: ./Ca_LVAst_soma.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./Ca.c: /mnt/c/neuron/neurenv/mech/Ca.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "Ca.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./Ca.o: ./Ca.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./hhqt.c: /mnt/c/neuron/neurenv/mech/hhqt.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "hhqt.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./hhqt.o: ./hhqt.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./Ih.c: /mnt/c/neuron/neurenv/mech/Ih.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "Ih.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./Ih.o: ./Ih.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./Im.c: /mnt/c/neuron/neurenv/mech/Im.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "Im.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./Im.o: ./Im.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./K_Pst.c: /mnt/c/neuron/neurenv/mech/K_Pst.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "K_Pst.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./K_Pst.o: ./K_Pst.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./K_Tst.c: /mnt/c/neuron/neurenv/mech/K_Tst.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "K_Tst.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./K_Tst.o: ./K_Tst.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./Nap_Et2.c: /mnt/c/neuron/neurenv/mech/Nap_Et2.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "Nap_Et2.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./Nap_Et2.o: ./Nap_Et2.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./NaTa_t.c: /mnt/c/neuron/neurenv/mech/NaTa_t.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "NaTa_t.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./NaTa_t.o: ./NaTa_t.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./NaTa_t_myel.c: /mnt/c/neuron/neurenv/mech/NaTa_t_myel.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "NaTa_t_myel.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./NaTa_t_myel.o: ./NaTa_t_myel.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./NaTa_t_nor.c: /mnt/c/neuron/neurenv/mech/NaTa_t_nor.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "NaTa_t_nor.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./NaTa_t_nor.o: ./NaTa_t_nor.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./NaTs2_t_apic.c: /mnt/c/neuron/neurenv/mech/NaTs2_t_apic.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "NaTs2_t_apic.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./NaTs2_t_apic.o: ./NaTs2_t_apic.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./NaTs2_t.c: /mnt/c/neuron/neurenv/mech/NaTs2_t.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "NaTs2_t.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./NaTs2_t.o: ./NaTs2_t.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./NaTs2_t_soma.c: /mnt/c/neuron/neurenv/mech/NaTs2_t_soma.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "NaTs2_t_soma.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./NaTs2_t_soma.o: ./NaTs2_t_soma.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./SK_E2.c: /mnt/c/neuron/neurenv/mech/SK_E2.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "SK_E2.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./SK_E2.o: ./SK_E2.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./SK_E2_soma.c: /mnt/c/neuron/neurenv/mech/SK_E2_soma.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "SK_E2_soma.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./SK_E2_soma.o: ./SK_E2_soma.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./SKv3_1_apic.c: /mnt/c/neuron/neurenv/mech/SKv3_1_apic.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "SKv3_1_apic.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./SKv3_1_apic.o: ./SKv3_1_apic.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./SKv3_1.c: /mnt/c/neuron/neurenv/mech/SKv3_1.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "SKv3_1.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./SKv3_1.o: ./SKv3_1.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./SKv3_1_soma.c: /mnt/c/neuron/neurenv/mech/SKv3_1_soma.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "SKv3_1_soma.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./SKv3_1_soma.o: ./SKv3_1_soma.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
./xtra.c: /mnt/c/neuron/neurenv/mech/xtra.mod
|
||||
@printf " -> $(C_GREEN)NMODL$(C_RESET) $<\\n"
|
||||
(cd "/mnt/c/neuron/neurenv/mech"; MODLUNIT=$(NRNUNITS) $(NOCMODL) "xtra.mod" -o "/mnt/c/neuron/neurenv/x86_64")
|
||||
|
||||
./xtra.o: ./xtra.c
|
||||
@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\\n"
|
||||
$(COMPILE) -I"/mnt/c/neuron/neurenv/mech" $(INCLUDES) -fPIC -c $< -o $@
|
||||
|
||||
94
x86_64/mod_func.cpp
Normal file
94
x86_64/mod_func.cpp
Normal file
@ -0,0 +1,94 @@
|
||||
#include <stdio.h>
|
||||
#include "hocdec.h"
|
||||
extern int nrnmpi_myid;
|
||||
extern int nrn_nobanner_;
|
||||
#if defined(__cplusplus)
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
extern void _CaDynamics_E2_reg(void);
|
||||
extern void _CaDynamics_E2_soma_reg(void);
|
||||
extern void _Ca_HVA_reg(void);
|
||||
extern void _Ca_HVA_soma_reg(void);
|
||||
extern void _Ca_LVAst_reg(void);
|
||||
extern void _Ca_LVAst_soma_reg(void);
|
||||
extern void _Ca_reg(void);
|
||||
extern void _hhqt_reg(void);
|
||||
extern void _Ih_reg(void);
|
||||
extern void _Im_reg(void);
|
||||
extern void _K_Pst_reg(void);
|
||||
extern void _K_Tst_reg(void);
|
||||
extern void _Nap_Et2_reg(void);
|
||||
extern void _NaTa_t_reg(void);
|
||||
extern void _NaTa_t_myel_reg(void);
|
||||
extern void _NaTa_t_nor_reg(void);
|
||||
extern void _NaTs2_t_apic_reg(void);
|
||||
extern void _NaTs2_t_reg(void);
|
||||
extern void _NaTs2_t_soma_reg(void);
|
||||
extern void _SK_E2_reg(void);
|
||||
extern void _SK_E2_soma_reg(void);
|
||||
extern void _SKv3_1_apic_reg(void);
|
||||
extern void _SKv3_1_reg(void);
|
||||
extern void _SKv3_1_soma_reg(void);
|
||||
extern void _xtra_reg(void);
|
||||
|
||||
void modl_reg() {
|
||||
if (!nrn_nobanner_) if (nrnmpi_myid < 1) {
|
||||
fprintf(stderr, "Additional mechanisms from files\n");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/CaDynamics_E2.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/CaDynamics_E2_soma.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/Ca_HVA.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/Ca_HVA_soma.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/Ca_LVAst.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/Ca_LVAst_soma.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/Ca.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/hhqt.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/Ih.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/Im.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/K_Pst.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/K_Tst.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/Nap_Et2.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/NaTa_t.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/NaTa_t_myel.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/NaTa_t_nor.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/NaTs2_t_apic.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/NaTs2_t.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/NaTs2_t_soma.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/SK_E2.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/SK_E2_soma.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/SKv3_1_apic.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/SKv3_1.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/SKv3_1_soma.mod\"");
|
||||
fprintf(stderr, " \"/mnt/c/neuron/neurenv/mech/xtra.mod\"");
|
||||
fprintf(stderr, "\n");
|
||||
}
|
||||
_CaDynamics_E2_reg();
|
||||
_CaDynamics_E2_soma_reg();
|
||||
_Ca_HVA_reg();
|
||||
_Ca_HVA_soma_reg();
|
||||
_Ca_LVAst_reg();
|
||||
_Ca_LVAst_soma_reg();
|
||||
_Ca_reg();
|
||||
_hhqt_reg();
|
||||
_Ih_reg();
|
||||
_Im_reg();
|
||||
_K_Pst_reg();
|
||||
_K_Tst_reg();
|
||||
_Nap_Et2_reg();
|
||||
_NaTa_t_reg();
|
||||
_NaTa_t_myel_reg();
|
||||
_NaTa_t_nor_reg();
|
||||
_NaTs2_t_apic_reg();
|
||||
_NaTs2_t_reg();
|
||||
_NaTs2_t_soma_reg();
|
||||
_SK_E2_reg();
|
||||
_SK_E2_soma_reg();
|
||||
_SKv3_1_apic_reg();
|
||||
_SKv3_1_reg();
|
||||
_SKv3_1_soma_reg();
|
||||
_xtra_reg();
|
||||
}
|
||||
|
||||
#if defined(__cplusplus)
|
||||
}
|
||||
#endif
|
||||
BIN
x86_64/mod_func.o
Normal file
BIN
x86_64/mod_func.o
Normal file
Binary file not shown.
BIN
x86_64/special
Normal file
BIN
x86_64/special
Normal file
Binary file not shown.
325
x86_64/xtra.c
Normal file
325
x86_64/xtra.c
Normal file
@ -0,0 +1,325 @@
|
||||
/* 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
|
||||
#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__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 _threadargs_ /**/
|
||||
#define _threadargsproto_ /**/
|
||||
/*SUPPRESS 761*/
|
||||
/*SUPPRESS 762*/
|
||||
/*SUPPRESS 763*/
|
||||
/*SUPPRESS 765*/
|
||||
extern double *getarg(int);
|
||||
static double *_p; static Datum *_ppvar;
|
||||
|
||||
#define t nrn_threads->_t
|
||||
#define dt nrn_threads->_dt
|
||||
#define es _p[0]
|
||||
#define es_columnindex 0
|
||||
#define x _p[1]
|
||||
#define x_columnindex 1
|
||||
#define y _p[2]
|
||||
#define y_columnindex 2
|
||||
#define z _p[3]
|
||||
#define z_columnindex 3
|
||||
#define type _p[4]
|
||||
#define type_columnindex 4
|
||||
#define order _p[5]
|
||||
#define order_columnindex 5
|
||||
#define ex *_ppvar[0]._pval
|
||||
#define _p_ex _ppvar[0]._pval
|
||||
#define area *_ppvar[1]._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 = 0;
|
||||
/* external NEURON variables */
|
||||
/* declaration of user functions */
|
||||
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) {
|
||||
_p = _prop->param; _ppvar = _prop->dparam;
|
||||
}
|
||||
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_xtra", _hoc_setdata,
|
||||
0, 0
|
||||
};
|
||||
/* declare global and static user variables */
|
||||
#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, double* _pp, Datum* _ppd, Datum* _thread, NrnThread* _nt) ;
|
||||
static void nrn_alloc(Prop*);
|
||||
static void nrn_init(NrnThread*, _Memb_list*, int);
|
||||
static void nrn_state(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_;
|
||||
|
||||
extern Prop* need_memb(Symbol*);
|
||||
|
||||
static void nrn_alloc(Prop* _prop) {
|
||||
Prop *prop_ion;
|
||||
double *_p; Datum *_ppvar;
|
||||
_p = nrn_prop_data_alloc(_mechtype, 6, _prop);
|
||||
/*initialize range parameters*/
|
||||
es = 0;
|
||||
x = 0;
|
||||
y = 0;
|
||||
z = 0;
|
||||
type = 0;
|
||||
order = 0;
|
||||
_prop->param = _p;
|
||||
_prop->param_size = 6;
|
||||
_ppvar = nrn_prop_datum_alloc(_mechtype, 2, _prop);
|
||||
_prop->dparam = _ppvar;
|
||||
/*connect ionic variables to this model*/
|
||||
_ppvar[1]._pval = &nrn_alloc_node_->_area; /* diam */
|
||||
|
||||
}
|
||||
static void _initlists();
|
||||
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 _xtra_reg() {
|
||||
int _vectorized = 0;
|
||||
_initlists();
|
||||
register_mech(_mechanism, nrn_alloc,(void*)0, (void*)0, (void*)0, nrn_init, hoc_nrnpointerindex, 0);
|
||||
_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, 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 /mnt/c/neuron/neurenv/mech/xtra.mod\n");
|
||||
hoc_register_limits(_mechtype, _hoc_parm_limits);
|
||||
hoc_register_units(_mechtype, _hoc_parm_units);
|
||||
}
|
||||
static int _reset;
|
||||
static 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, double* _pp, Datum* _ppd, Datum* _thread, NrnThread* _nt) {
|
||||
_p = _pp; _ppvar = _ppd;
|
||||
v = NODEV(_nd);
|
||||
ex = stim * es ;
|
||||
}
|
||||
|
||||
static void initmodel() {
|
||||
int _i; double _save;_ninits++;
|
||||
{
|
||||
{
|
||||
ex = stim * es ;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
static void nrn_init(NrnThread* _nt, _Memb_list* _ml, int _type){
|
||||
Node *_nd; double _v; int* _ni; int _iml, _cntml;
|
||||
#if CACHEVEC
|
||||
_ni = _ml->_nodeindices;
|
||||
#endif
|
||||
_cntml = _ml->_nodecount;
|
||||
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();
|
||||
}}
|
||||
|
||||
static double _nrn_current(double _v){double _current=0.;v=_v;{
|
||||
} return _current;
|
||||
}
|
||||
|
||||
static void nrn_state(NrnThread* _nt, _Memb_list* _ml, int _type){
|
||||
Node *_nd; double _v = 0.0; int* _ni; int _iml, _cntml;
|
||||
#if CACHEVEC
|
||||
_ni = _ml->_nodeindices;
|
||||
#endif
|
||||
_cntml = _ml->_nodecount;
|
||||
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;
|
||||
{
|
||||
}}
|
||||
|
||||
}
|
||||
|
||||
static void terminal(){}
|
||||
|
||||
static void _initlists() {
|
||||
int _i; static int _first = 1;
|
||||
if (!_first) return;
|
||||
_first = 0;
|
||||
}
|
||||
|
||||
#if NMODL_TEXT
|
||||
static const char* nmodl_filename = "/mnt/c/neuron/neurenv/mech/xtra.mod";
|
||||
static 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"
|
||||
;
|
||||
#endif
|
||||
BIN
x86_64/xtra.o
Normal file
BIN
x86_64/xtra.o
Normal file
Binary file not shown.
Loading…
x
Reference in New Issue
Block a user