wormsim 0.0.1__py3-none-any.whl

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Files changed (796) hide show
  1. wormsim/__init__.py +0 -0
  2. wormsim/abstract_circuit.py +172 -0
  3. wormsim/circuit.pkl +0 -0
  4. wormsim/components/__init__.py +0 -0
  5. wormsim/components/mechanism/__init__.py +0 -0
  6. wormsim/components/mechanism/modfile/__init__.py +0 -0
  7. wormsim/components/mechanism/modfile/cainternm.mod +75 -0
  8. wormsim/components/mechanism/modfile/cca1.mod +87 -0
  9. wormsim/components/mechanism/modfile/egl19.mod +100 -0
  10. wormsim/components/mechanism/modfile/egl2.mod +76 -0
  11. wormsim/components/mechanism/modfile/egl36.mod +92 -0
  12. wormsim/components/mechanism/modfile/exc_syn_advance.mod +91 -0
  13. wormsim/components/mechanism/modfile/gapjunction.mod +41 -0
  14. wormsim/components/mechanism/modfile/gapjunction_advance.mod +40 -0
  15. wormsim/components/mechanism/modfile/inh_syn_advance.mod +91 -0
  16. wormsim/components/mechanism/modfile/irk.mod +76 -0
  17. wormsim/components/mechanism/modfile/kcnl.mod +76 -0
  18. wormsim/components/mechanism/modfile/kqt3.mod +110 -0
  19. wormsim/components/mechanism/modfile/kvs1.mod +87 -0
  20. wormsim/components/mechanism/modfile/nca.mod +41 -0
  21. wormsim/components/mechanism/modfile/neuron_to_neuron_exc_syn.mod +92 -0
  22. wormsim/components/mechanism/modfile/neuron_to_neuron_inh_syn.mod +92 -0
  23. wormsim/components/mechanism/modfile/shk1.mod +86 -0
  24. wormsim/components/mechanism/modfile/shl1.mod +101 -0
  25. wormsim/components/mechanism/modfile/slo1_egl19.mod +148 -0
  26. wormsim/components/mechanism/modfile/slo1_unc2.mod +139 -0
  27. wormsim/components/mechanism/modfile/slo2_egl19.mod +148 -0
  28. wormsim/components/mechanism/modfile/slo2_unc2.mod +138 -0
  29. wormsim/components/mechanism/modfile/unc2.mod +90 -0
  30. wormsim/components/mechanism/x86_64/__init__.py +0 -0
  31. wormsim/components/mechanism/x86_64/cainternm.c +594 -0
  32. wormsim/components/mechanism/x86_64/cainternm.o +0 -0
  33. wormsim/components/mechanism/x86_64/cca1.c +621 -0
  34. wormsim/components/mechanism/x86_64/cca1.o +0 -0
  35. wormsim/components/mechanism/x86_64/egl19.c +681 -0
  36. wormsim/components/mechanism/x86_64/egl19.o +0 -0
  37. wormsim/components/mechanism/x86_64/egl2.c +569 -0
  38. wormsim/components/mechanism/x86_64/egl2.o +0 -0
  39. wormsim/components/mechanism/x86_64/egl36.c +615 -0
  40. wormsim/components/mechanism/x86_64/egl36.o +0 -0
  41. wormsim/components/mechanism/x86_64/exc_syn_advance.c +587 -0
  42. wormsim/components/mechanism/x86_64/exc_syn_advance.o +0 -0
  43. wormsim/components/mechanism/x86_64/gapjunction.c +364 -0
  44. wormsim/components/mechanism/x86_64/gapjunction.o +0 -0
  45. wormsim/components/mechanism/x86_64/gapjunction_advance.c +378 -0
  46. wormsim/components/mechanism/x86_64/gapjunction_advance.o +0 -0
  47. wormsim/components/mechanism/x86_64/inh_syn_advance.c +587 -0
  48. wormsim/components/mechanism/x86_64/inh_syn_advance.o +0 -0
  49. wormsim/components/mechanism/x86_64/irk.c +577 -0
  50. wormsim/components/mechanism/x86_64/irk.o +0 -0
  51. wormsim/components/mechanism/x86_64/kcnl.c +565 -0
  52. wormsim/components/mechanism/x86_64/kcnl.o +0 -0
  53. wormsim/components/mechanism/x86_64/kqt3.c +723 -0
  54. wormsim/components/mechanism/x86_64/kqt3.o +0 -0
  55. wormsim/components/mechanism/x86_64/kvs1.c +621 -0
  56. wormsim/components/mechanism/x86_64/kvs1.o +0 -0
  57. wormsim/components/mechanism/x86_64/makemod2c_inc +185 -0
  58. wormsim/components/mechanism/x86_64/mod_func.c +82 -0
  59. wormsim/components/mechanism/x86_64/mod_func.o +0 -0
  60. wormsim/components/mechanism/x86_64/nca.c +366 -0
  61. wormsim/components/mechanism/x86_64/nca.o +0 -0
  62. wormsim/components/mechanism/x86_64/neuron_to_neuron_exc_syn.c +572 -0
  63. wormsim/components/mechanism/x86_64/neuron_to_neuron_exc_syn.o +0 -0
  64. wormsim/components/mechanism/x86_64/neuron_to_neuron_inh_syn.c +572 -0
  65. wormsim/components/mechanism/x86_64/neuron_to_neuron_inh_syn.o +0 -0
  66. wormsim/components/mechanism/x86_64/shk1.c +616 -0
  67. wormsim/components/mechanism/x86_64/shk1.o +0 -0
  68. wormsim/components/mechanism/x86_64/shl1.c +676 -0
  69. wormsim/components/mechanism/x86_64/shl1.o +0 -0
  70. wormsim/components/mechanism/x86_64/slo1_egl19.c +820 -0
  71. wormsim/components/mechanism/x86_64/slo1_egl19.o +0 -0
  72. wormsim/components/mechanism/x86_64/slo1_unc2.c +777 -0
  73. wormsim/components/mechanism/x86_64/slo1_unc2.o +0 -0
  74. wormsim/components/mechanism/x86_64/slo2_egl19.c +820 -0
  75. wormsim/components/mechanism/x86_64/slo2_egl19.o +0 -0
  76. wormsim/components/mechanism/x86_64/slo2_unc2.c +775 -0
  77. wormsim/components/mechanism/x86_64/slo2_unc2.o +0 -0
  78. wormsim/components/mechanism/x86_64/special +17 -0
  79. wormsim/components/mechanism/x86_64/unc2.c +636 -0
  80. wormsim/components/mechanism/x86_64/unc2.o +0 -0
  81. wormsim/components/model/ADAL.hoc +135 -0
  82. wormsim/components/model/ADAR.hoc +135 -0
  83. wormsim/components/model/ADEL.hoc +183 -0
  84. wormsim/components/model/ADER.hoc +183 -0
  85. wormsim/components/model/ADFL.hoc +164 -0
  86. wormsim/components/model/ADFR.hoc +164 -0
  87. wormsim/components/model/ADLL.hoc +185 -0
  88. wormsim/components/model/ADLR.hoc +185 -0
  89. wormsim/components/model/AFDL.hoc +164 -0
  90. wormsim/components/model/AFDR.hoc +164 -0
  91. wormsim/components/model/AIAL.hoc +129 -0
  92. wormsim/components/model/AIAR.hoc +129 -0
  93. wormsim/components/model/AIBL.hoc +147 -0
  94. wormsim/components/model/AIBR.hoc +147 -0
  95. wormsim/components/model/AIML.hoc +130 -0
  96. wormsim/components/model/AIMR.hoc +130 -0
  97. wormsim/components/model/AINL.hoc +157 -0
  98. wormsim/components/model/AINR.hoc +157 -0
  99. wormsim/components/model/AIYL.hoc +129 -0
  100. wormsim/components/model/AIYR.hoc +129 -0
  101. wormsim/components/model/AIZL.hoc +137 -0
  102. wormsim/components/model/AIZR.hoc +137 -0
  103. wormsim/components/model/ALA.hoc +148 -0
  104. wormsim/components/model/ALML.hoc +203 -0
  105. wormsim/components/model/ALMR.hoc +203 -0
  106. wormsim/components/model/ALNL.hoc +175 -0
  107. wormsim/components/model/ALNR.hoc +175 -0
  108. wormsim/components/model/AQR.hoc +187 -0
  109. wormsim/components/model/AS01.hoc +151 -0
  110. wormsim/components/model/AS02.hoc +152 -0
  111. wormsim/components/model/AS03.hoc +151 -0
  112. wormsim/components/model/AS04.hoc +154 -0
  113. wormsim/components/model/AS05.hoc +155 -0
  114. wormsim/components/model/AS06.hoc +153 -0
  115. wormsim/components/model/AS07.hoc +156 -0
  116. wormsim/components/model/AS08.hoc +158 -0
  117. wormsim/components/model/AS09.hoc +154 -0
  118. wormsim/components/model/AS10.hoc +153 -0
  119. wormsim/components/model/AS11.hoc +154 -0
  120. wormsim/components/model/ASEL.hoc +173 -0
  121. wormsim/components/model/ASER.hoc +173 -0
  122. wormsim/components/model/ASGL.hoc +160 -0
  123. wormsim/components/model/ASGR.hoc +160 -0
  124. wormsim/components/model/ASHL.hoc +165 -0
  125. wormsim/components/model/ASHR.hoc +165 -0
  126. wormsim/components/model/ASIL.hoc +168 -0
  127. wormsim/components/model/ASIR.hoc +168 -0
  128. wormsim/components/model/ASJL.hoc +167 -0
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  130. wormsim/components/model/ASKL.hoc +165 -0
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  132. wormsim/components/model/AUAL.hoc +164 -0
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  134. wormsim/components/model/AVAL.hoc +197 -0
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  146. wormsim/components/model/AVHR.hoc +172 -0
  147. wormsim/components/model/AVJL.hoc +173 -0
  148. wormsim/components/model/AVJR.hoc +172 -0
  149. wormsim/components/model/AVKL.hoc +204 -0
  150. wormsim/components/model/AVKR.hoc +204 -0
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  152. wormsim/components/model/AVM.hoc +203 -0
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  157. wormsim/components/model/AWCL.hoc +168 -0
  158. wormsim/components/model/AWCR.hoc +168 -0
  159. wormsim/components/model/BAGL.hoc +160 -0
  160. wormsim/components/model/BAGR.hoc +160 -0
  161. wormsim/components/model/BDUL.hoc +136 -0
  162. wormsim/components/model/BDUR.hoc +136 -0
  163. wormsim/components/model/CANL.hoc +165 -0
  164. wormsim/components/model/CANR.hoc +165 -0
  165. wormsim/components/model/CEPDL.hoc +182 -0
  166. wormsim/components/model/CEPDR.hoc +182 -0
  167. wormsim/components/model/CEPVL.hoc +179 -0
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  169. wormsim/components/model/DA01.hoc +177 -0
  170. wormsim/components/model/DA02.hoc +180 -0
  171. wormsim/components/model/DA03.hoc +160 -0
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  173. wormsim/components/model/DA05.hoc +176 -0
  174. wormsim/components/model/DA06.hoc +187 -0
  175. wormsim/components/model/DA07.hoc +175 -0
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  178. wormsim/components/model/DB01.hoc +193 -0
  179. wormsim/components/model/DB02.hoc +184 -0
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  185. wormsim/components/model/DD01.hoc +180 -0
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  194. wormsim/components/model/FLPL.hoc +261 -0
  195. wormsim/components/model/FLPR.hoc +261 -0
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  728. wormsim/components/param/cell/SMDVL.json +30 -0
  729. wormsim/components/param/cell/SMDVR.json +30 -0
  730. wormsim/components/param/cell/URADL.json +30 -0
  731. wormsim/components/param/cell/URADR.json +30 -0
  732. wormsim/components/param/cell/URAVL.json +30 -0
  733. wormsim/components/param/cell/URAVR.json +30 -0
  734. wormsim/components/param/cell/URBL.json +30 -0
  735. wormsim/components/param/cell/URBR.json +30 -0
  736. wormsim/components/param/cell/URXL.json +30 -0
  737. wormsim/components/param/cell/URXR.json +30 -0
  738. wormsim/components/param/cell/URYDL.json +30 -0
  739. wormsim/components/param/cell/URYDR.json +30 -0
  740. wormsim/components/param/cell/URYVL.json +30 -0
  741. wormsim/components/param/cell/URYVR.json +30 -0
  742. wormsim/components/param/cell/VA01.json +30 -0
  743. wormsim/components/param/cell/VA02.json +30 -0
  744. wormsim/components/param/cell/VA03.json +30 -0
  745. wormsim/components/param/cell/VA04.json +30 -0
  746. wormsim/components/param/cell/VA05.json +30 -0
  747. wormsim/components/param/cell/VA06.json +30 -0
  748. wormsim/components/param/cell/VA07.json +30 -0
  749. wormsim/components/param/cell/VA08.json +30 -0
  750. wormsim/components/param/cell/VA09.json +30 -0
  751. wormsim/components/param/cell/VA10.json +30 -0
  752. wormsim/components/param/cell/VA11.json +30 -0
  753. wormsim/components/param/cell/VA12.json +30 -0
  754. wormsim/components/param/cell/VB01.json +30 -0
  755. wormsim/components/param/cell/VB02.json +30 -0
  756. wormsim/components/param/cell/VB03.json +30 -0
  757. wormsim/components/param/cell/VB04.json +30 -0
  758. wormsim/components/param/cell/VB05.json +30 -0
  759. wormsim/components/param/cell/VB06.json +30 -0
  760. wormsim/components/param/cell/VB07.json +30 -0
  761. wormsim/components/param/cell/VB08.json +30 -0
  762. wormsim/components/param/cell/VB09.json +30 -0
  763. wormsim/components/param/cell/VB10.json +30 -0
  764. wormsim/components/param/cell/VB11.json +30 -0
  765. wormsim/components/param/cell/VC01.json +30 -0
  766. wormsim/components/param/cell/VC02.json +30 -0
  767. wormsim/components/param/cell/VC03.json +30 -0
  768. wormsim/components/param/cell/VC04.json +30 -0
  769. wormsim/components/param/cell/VC05.json +30 -0
  770. wormsim/components/param/cell/VC06.json +30 -0
  771. wormsim/components/param/cell/VD01.json +30 -0
  772. wormsim/components/param/cell/VD02.json +30 -0
  773. wormsim/components/param/cell/VD03.json +30 -0
  774. wormsim/components/param/cell/VD04.json +30 -0
  775. wormsim/components/param/cell/VD05.json +30 -0
  776. wormsim/components/param/cell/VD06.json +30 -0
  777. wormsim/components/param/cell/VD07.json +30 -0
  778. wormsim/components/param/cell/VD08.json +30 -0
  779. wormsim/components/param/cell/VD09.json +30 -0
  780. wormsim/components/param/cell/VD10.json +30 -0
  781. wormsim/components/param/cell/VD11.json +30 -0
  782. wormsim/components/param/cell/VD12.json +30 -0
  783. wormsim/components/param/cell/VD13.json +30 -0
  784. wormsim/components/param/cell/__init__.py +0 -0
  785. wormsim/components/param/cell/template.json +30 -0
  786. wormsim/components/param/connection/SI5-302-RIA.xlsx +0 -0
  787. wormsim/components/param/connection/SI5-302.xlsx +0 -0
  788. wormsim/components/param/connection/__init__.py +0 -0
  789. wormsim/components/param/connection/muscle_neuron.xlsx +0 -0
  790. wormsim/components/param/connection/neuron_muscle.xlsx +0 -0
  791. wormsim/config.json +682 -0
  792. wormsim/simulate.py +660 -0
  793. wormsim-0.0.1.dist-info/METADATA +7 -0
  794. wormsim-0.0.1.dist-info/RECORD +796 -0
  795. wormsim-0.0.1.dist-info/WHEEL +5 -0
  796. wormsim-0.0.1.dist-info/top_level.txt +1 -0
@@ -0,0 +1,681 @@
1
+ /* Created by Language version: 7.7.0 */
2
+ /* VECTORIZED */
3
+ #define NRN_VECTORIZED 1
4
+ #include <stdio.h>
5
+ #include <stdlib.h>
6
+ #include <math.h>
7
+ #include "scoplib_ansi.h"
8
+ #undef PI
9
+ #define nil 0
10
+ #include "md1redef.h"
11
+ #include "section.h"
12
+ #include "nrniv_mf.h"
13
+ #include "md2redef.h"
14
+
15
+ #if METHOD3
16
+ extern int _method3;
17
+ #endif
18
+
19
+ #if !NRNGPU
20
+ #undef exp
21
+ #define exp hoc_Exp
22
+ extern double hoc_Exp(double);
23
+ #endif
24
+
25
+ #define nrn_init _nrn_init__egl19
26
+ #define _nrn_initial _nrn_initial__egl19
27
+ #define nrn_cur _nrn_cur__egl19
28
+ #define _nrn_current _nrn_current__egl19
29
+ #define nrn_jacob _nrn_jacob__egl19
30
+ #define nrn_state _nrn_state__egl19
31
+ #define _net_receive _net_receive__egl19
32
+ #define setparames setparames__egl19
33
+ #define states states__egl19
34
+
35
+ #define _threadargscomma_ _p, _ppvar, _thread, _nt,
36
+ #define _threadargsprotocomma_ double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt,
37
+ #define _threadargs_ _p, _ppvar, _thread, _nt
38
+ #define _threadargsproto_ double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt
39
+ /*SUPPRESS 761*/
40
+ /*SUPPRESS 762*/
41
+ /*SUPPRESS 763*/
42
+ /*SUPPRESS 765*/
43
+ extern double *getarg();
44
+ /* Thread safe. No static _p or _ppvar. */
45
+
46
+ #define t _nt->_t
47
+ #define dt _nt->_dt
48
+ #define gbegl19 _p[0]
49
+ #define minf _p[1]
50
+ #define hinf _p[2]
51
+ #define tm _p[3]
52
+ #define th _p[4]
53
+ #define m _p[5]
54
+ #define h _p[6]
55
+ #define eca _p[7]
56
+ #define ica _p[8]
57
+ #define Dm _p[9]
58
+ #define Dh _p[10]
59
+ #define v _p[11]
60
+ #define _g _p[12]
61
+ #define _ion_eca *_ppvar[0]._pval
62
+ #define _ion_ica *_ppvar[1]._pval
63
+ #define _ion_dicadv *_ppvar[2]._pval
64
+
65
+ #if MAC
66
+ #if !defined(v)
67
+ #define v _mlhv
68
+ #endif
69
+ #if !defined(h)
70
+ #define h _mlhh
71
+ #endif
72
+ #endif
73
+
74
+ #if defined(__cplusplus)
75
+ extern "C" {
76
+ #endif
77
+ static int hoc_nrnpointerindex = -1;
78
+ static Datum* _extcall_thread;
79
+ static Prop* _extcall_prop;
80
+ /* external NEURON variables */
81
+ /* declaration of user functions */
82
+ static void _hoc_setparames(void);
83
+ static int _mechtype;
84
+ extern void _nrn_cacheloop_reg(int, int);
85
+ extern void hoc_register_prop_size(int, int, int);
86
+ extern void hoc_register_limits(int, HocParmLimits*);
87
+ extern void hoc_register_units(int, HocParmUnits*);
88
+ extern void nrn_promote(Prop*, int, int);
89
+ extern Memb_func* memb_func;
90
+
91
+ #define NMODL_TEXT 1
92
+ #if NMODL_TEXT
93
+ static const char* nmodl_file_text;
94
+ static const char* nmodl_filename;
95
+ extern void hoc_reg_nmodl_text(int, const char*);
96
+ extern void hoc_reg_nmodl_filename(int, const char*);
97
+ #endif
98
+
99
+ extern void _nrn_setdata_reg(int, void(*)(Prop*));
100
+ static void _setdata(Prop* _prop) {
101
+ _extcall_prop = _prop;
102
+ }
103
+ static void _hoc_setdata() {
104
+ Prop *_prop, *hoc_getdata_range(int);
105
+ _prop = hoc_getdata_range(_mechtype);
106
+ _setdata(_prop);
107
+ hoc_retpushx(1.);
108
+ }
109
+ /* connect user functions to hoc names */
110
+ static VoidFunc hoc_intfunc[] = {
111
+ "setdata_egl19", _hoc_setdata,
112
+ "setparames_egl19", _hoc_setparames,
113
+ 0, 0
114
+ };
115
+ /* declare global and static user variables */
116
+ #define ath ath_egl19
117
+ double ath = 0.4;
118
+ #define atm atm_egl19
119
+ double atm = 2.9;
120
+ #define ahinf ahinf_egl19
121
+ double ahinf = 1.43;
122
+ #define bth bth_egl19
123
+ double bth = 44.6;
124
+ #define btm btm_egl19
125
+ double btm = 5.2;
126
+ #define bhinf bhinf_egl19
127
+ double bhinf = 0.14;
128
+ #define cth cth_egl19
129
+ double cth = -23;
130
+ #define ctm ctm_egl19
131
+ double ctm = 6;
132
+ #define chinf chinf_egl19
133
+ double chinf = 5.96;
134
+ #define dth dth_egl19
135
+ double dth = 5;
136
+ #define dtm dtm_egl19
137
+ double dtm = 1.9;
138
+ #define dhinf dhinf_egl19
139
+ double dhinf = 0.6;
140
+ #define eth eth_egl19
141
+ double eth = 36.4;
142
+ #define etm etm_egl19
143
+ double etm = 1.4;
144
+ #define fth fth_egl19
145
+ double fth = 28.7;
146
+ #define ftm ftm_egl19
147
+ double ftm = 30;
148
+ #define gth gth_egl19
149
+ double gth = 3.7;
150
+ #define gtm gtm_egl19
151
+ double gtm = 2.3;
152
+ #define hth hth_egl19
153
+ double hth = 43.1;
154
+ #define kib kib_egl19
155
+ double kib = 8.1;
156
+ #define ki ki_egl19
157
+ double ki = 12;
158
+ #define ka ka_egl19
159
+ double ka = 7.5;
160
+ #define vhhb vhhb_egl19
161
+ double vhhb = -20.5;
162
+ #define vhh vhh_egl19
163
+ double vhh = 24.9;
164
+ #define vhm vhm_egl19
165
+ double vhm = 5.6;
166
+ /* some parameters have upper and lower limits */
167
+ static HocParmLimits _hoc_parm_limits[] = {
168
+ 0,0,0
169
+ };
170
+ static HocParmUnits _hoc_parm_units[] = {
171
+ "vhm_egl19", "mV",
172
+ "ka_egl19", "mV",
173
+ "vhh_egl19", "mV",
174
+ "ki_egl19", "mV",
175
+ "vhhb_egl19", "mV",
176
+ "kib_egl19", "mV",
177
+ "atm_egl19", "ms",
178
+ "btm_egl19", "mV",
179
+ "ctm_egl19", "mV",
180
+ "dtm_egl19", "ms",
181
+ "etm_egl19", "mV",
182
+ "ftm_egl19", "mV",
183
+ "gtm_egl19", "ms",
184
+ "bth_egl19", "ms",
185
+ "cth_egl19", "mV",
186
+ "dth_egl19", "mV",
187
+ "eth_egl19", "ms",
188
+ "fth_egl19", "mV",
189
+ "gth_egl19", "mV",
190
+ "hth_egl19", "ms",
191
+ "gbegl19_egl19", "nS/um2",
192
+ "tm_egl19", "ms",
193
+ "th_egl19", "ms",
194
+ 0,0
195
+ };
196
+ static double delta_t = 0.01;
197
+ static double h0 = 0;
198
+ static double m0 = 0;
199
+ /* connect global user variables to hoc */
200
+ static DoubScal hoc_scdoub[] = {
201
+ "vhm_egl19", &vhm_egl19,
202
+ "ka_egl19", &ka_egl19,
203
+ "vhh_egl19", &vhh_egl19,
204
+ "ki_egl19", &ki_egl19,
205
+ "vhhb_egl19", &vhhb_egl19,
206
+ "kib_egl19", &kib_egl19,
207
+ "ahinf_egl19", &ahinf_egl19,
208
+ "bhinf_egl19", &bhinf_egl19,
209
+ "chinf_egl19", &chinf_egl19,
210
+ "dhinf_egl19", &dhinf_egl19,
211
+ "atm_egl19", &atm_egl19,
212
+ "btm_egl19", &btm_egl19,
213
+ "ctm_egl19", &ctm_egl19,
214
+ "dtm_egl19", &dtm_egl19,
215
+ "etm_egl19", &etm_egl19,
216
+ "ftm_egl19", &ftm_egl19,
217
+ "gtm_egl19", &gtm_egl19,
218
+ "ath_egl19", &ath_egl19,
219
+ "bth_egl19", &bth_egl19,
220
+ "cth_egl19", &cth_egl19,
221
+ "dth_egl19", &dth_egl19,
222
+ "eth_egl19", &eth_egl19,
223
+ "fth_egl19", &fth_egl19,
224
+ "gth_egl19", &gth_egl19,
225
+ "hth_egl19", &hth_egl19,
226
+ 0,0
227
+ };
228
+ static DoubVec hoc_vdoub[] = {
229
+ 0,0,0
230
+ };
231
+ static double _sav_indep;
232
+ static void nrn_alloc(Prop*);
233
+ static void nrn_init(_NrnThread*, _Memb_list*, int);
234
+ static void nrn_state(_NrnThread*, _Memb_list*, int);
235
+ static void nrn_cur(_NrnThread*, _Memb_list*, int);
236
+ static void nrn_jacob(_NrnThread*, _Memb_list*, int);
237
+
238
+ static int _ode_count(int);
239
+ static void _ode_map(int, double**, double**, double*, Datum*, double*, int);
240
+ static void _ode_spec(_NrnThread*, _Memb_list*, int);
241
+ static void _ode_matsol(_NrnThread*, _Memb_list*, int);
242
+
243
+ #define _cvode_ieq _ppvar[3]._i
244
+ static void _ode_matsol_instance1(_threadargsproto_);
245
+ /* connect range variables in _p that hoc is supposed to know about */
246
+ static const char *_mechanism[] = {
247
+ "7.7.0",
248
+ "egl19",
249
+ "gbegl19_egl19",
250
+ 0,
251
+ "minf_egl19",
252
+ "hinf_egl19",
253
+ "tm_egl19",
254
+ "th_egl19",
255
+ 0,
256
+ "m_egl19",
257
+ "h_egl19",
258
+ 0,
259
+ 0};
260
+ static Symbol* _ca_sym;
261
+
262
+ extern Prop* need_memb(Symbol*);
263
+
264
+ static void nrn_alloc(Prop* _prop) {
265
+ Prop *prop_ion;
266
+ double *_p; Datum *_ppvar;
267
+ _p = nrn_prop_data_alloc(_mechtype, 13, _prop);
268
+ /*initialize range parameters*/
269
+ gbegl19 = 1;
270
+ _prop->param = _p;
271
+ _prop->param_size = 13;
272
+ _ppvar = nrn_prop_datum_alloc(_mechtype, 4, _prop);
273
+ _prop->dparam = _ppvar;
274
+ /*connect ionic variables to this model*/
275
+ prop_ion = need_memb(_ca_sym);
276
+ nrn_promote(prop_ion, 0, 1);
277
+ _ppvar[0]._pval = &prop_ion->param[0]; /* eca */
278
+ _ppvar[1]._pval = &prop_ion->param[3]; /* ica */
279
+ _ppvar[2]._pval = &prop_ion->param[4]; /* _ion_dicadv */
280
+
281
+ }
282
+ static void _initlists();
283
+ /* some states have an absolute tolerance */
284
+ static Symbol** _atollist;
285
+ static HocStateTolerance _hoc_state_tol[] = {
286
+ 0,0
287
+ };
288
+ static void _update_ion_pointer(Datum*);
289
+ extern Symbol* hoc_lookup(const char*);
290
+ extern void _nrn_thread_reg(int, int, void(*)(Datum*));
291
+ extern void _nrn_thread_table_reg(int, void(*)(double*, Datum*, Datum*, _NrnThread*, int));
292
+ extern void hoc_register_tolerance(int, HocStateTolerance*, Symbol***);
293
+ extern void _cvode_abstol( Symbol**, double*, int);
294
+
295
+ void _egl19_reg() {
296
+ int _vectorized = 1;
297
+ _initlists();
298
+ ion_reg("ca", -10000.);
299
+ _ca_sym = hoc_lookup("ca_ion");
300
+ register_mech(_mechanism, nrn_alloc,nrn_cur, nrn_jacob, nrn_state, nrn_init, hoc_nrnpointerindex, 1);
301
+ _mechtype = nrn_get_mechtype(_mechanism[1]);
302
+ _nrn_setdata_reg(_mechtype, _setdata);
303
+ _nrn_thread_reg(_mechtype, 2, _update_ion_pointer);
304
+ #if NMODL_TEXT
305
+ hoc_reg_nmodl_text(_mechtype, nmodl_file_text);
306
+ hoc_reg_nmodl_filename(_mechtype, nmodl_filename);
307
+ #endif
308
+ hoc_register_prop_size(_mechtype, 13, 4);
309
+ hoc_register_dparam_semantics(_mechtype, 0, "ca_ion");
310
+ hoc_register_dparam_semantics(_mechtype, 1, "ca_ion");
311
+ hoc_register_dparam_semantics(_mechtype, 2, "ca_ion");
312
+ hoc_register_dparam_semantics(_mechtype, 3, "cvodeieq");
313
+ hoc_register_cvode(_mechtype, _ode_count, _ode_map, _ode_spec, _ode_matsol);
314
+ hoc_register_tolerance(_mechtype, _hoc_state_tol, &_atollist);
315
+ hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
316
+ ivoc_help("help ?1 egl19 /home/zjj/8TB/robot_arm/project/BAAIWorm_v1/eworm/components/mechanism/modfile/egl19.mod\n");
317
+ hoc_register_limits(_mechtype, _hoc_parm_limits);
318
+ hoc_register_units(_mechtype, _hoc_parm_units);
319
+ }
320
+ static int _reset;
321
+ static char *modelname = "egl19 current for C. elegans neuron model";
322
+
323
+ static int error;
324
+ static int _ninits = 0;
325
+ static int _match_recurse=1;
326
+ static void _modl_cleanup(){ _match_recurse=1;}
327
+ static int setparames(_threadargsprotocomma_ double);
328
+
329
+ static int _ode_spec1(_threadargsproto_);
330
+ /*static int _ode_matsol1(_threadargsproto_);*/
331
+ static int _slist1[2], _dlist1[2];
332
+ static int states(_threadargsproto_);
333
+
334
+ /*CVODE*/
335
+ static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {int _reset = 0; {
336
+ setparames ( _threadargscomma_ v ) ;
337
+ Dm = ( minf - m ) / tm ;
338
+ Dh = ( hinf - h ) / th ;
339
+ }
340
+ return _reset;
341
+ }
342
+ static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
343
+ setparames ( _threadargscomma_ v ) ;
344
+ Dm = Dm / (1. - dt*( ( ( ( - 1.0 ) ) ) / tm )) ;
345
+ Dh = Dh / (1. - dt*( ( ( ( - 1.0 ) ) ) / th )) ;
346
+ return 0;
347
+ }
348
+ /*END CVODE*/
349
+ static int states (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) { {
350
+ setparames ( _threadargscomma_ v ) ;
351
+ m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / tm)))*(- ( ( ( minf ) ) / tm ) / ( ( ( ( - 1.0 ) ) ) / tm ) - m) ;
352
+ h = h + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / th)))*(- ( ( ( hinf ) ) / th ) / ( ( ( ( - 1.0 ) ) ) / th ) - h) ;
353
+ }
354
+ return 0;
355
+ }
356
+
357
+ static int setparames ( _threadargsprotocomma_ double _lv ) {
358
+ minf = 1.0 / ( 1.0 + exp ( - ( _lv - vhm ) / ka ) ) ;
359
+ hinf = ( ahinf / ( 1.0 + exp ( - ( _lv - vhh ) / ki ) ) + bhinf ) * ( chinf / ( 1.0 + exp ( ( _lv - vhhb ) / kib ) ) + dhinf ) ;
360
+ tm = atm * exp ( - pow( ( ( _lv - btm ) / ctm ) , 2.0 ) ) + dtm * exp ( - pow( ( ( _lv - etm ) / ftm ) , 2.0 ) ) + gtm ;
361
+ th = ath * ( ( bth / ( 1.0 + exp ( ( _lv - cth ) / dth ) ) ) + ( eth / ( 1.0 + exp ( ( _lv - fth ) / gth ) ) ) + hth ) ;
362
+ return 0; }
363
+
364
+ static void _hoc_setparames(void) {
365
+ double _r;
366
+ double* _p; Datum* _ppvar; Datum* _thread; _NrnThread* _nt;
367
+ if (_extcall_prop) {_p = _extcall_prop->param; _ppvar = _extcall_prop->dparam;}else{ _p = (double*)0; _ppvar = (Datum*)0; }
368
+ _thread = _extcall_thread;
369
+ _nt = nrn_threads;
370
+ _r = 1.;
371
+ setparames ( _p, _ppvar, _thread, _nt, *getarg(1) );
372
+ hoc_retpushx(_r);
373
+ }
374
+
375
+ static int _ode_count(int _type){ return 2;}
376
+
377
+ static void _ode_spec(_NrnThread* _nt, _Memb_list* _ml, int _type) {
378
+ double* _p; Datum* _ppvar; Datum* _thread;
379
+ Node* _nd; double _v; int _iml, _cntml;
380
+ _cntml = _ml->_nodecount;
381
+ _thread = _ml->_thread;
382
+ for (_iml = 0; _iml < _cntml; ++_iml) {
383
+ _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
384
+ _nd = _ml->_nodelist[_iml];
385
+ v = NODEV(_nd);
386
+ eca = _ion_eca;
387
+ _ode_spec1 (_p, _ppvar, _thread, _nt);
388
+ }}
389
+
390
+ static void _ode_map(int _ieq, double** _pv, double** _pvdot, double* _pp, Datum* _ppd, double* _atol, int _type) {
391
+ double* _p; Datum* _ppvar;
392
+ int _i; _p = _pp; _ppvar = _ppd;
393
+ _cvode_ieq = _ieq;
394
+ for (_i=0; _i < 2; ++_i) {
395
+ _pv[_i] = _pp + _slist1[_i]; _pvdot[_i] = _pp + _dlist1[_i];
396
+ _cvode_abstol(_atollist, _atol, _i);
397
+ }
398
+ }
399
+
400
+ static void _ode_matsol_instance1(_threadargsproto_) {
401
+ _ode_matsol1 (_p, _ppvar, _thread, _nt);
402
+ }
403
+
404
+ static void _ode_matsol(_NrnThread* _nt, _Memb_list* _ml, int _type) {
405
+ double* _p; Datum* _ppvar; Datum* _thread;
406
+ Node* _nd; double _v; int _iml, _cntml;
407
+ _cntml = _ml->_nodecount;
408
+ _thread = _ml->_thread;
409
+ for (_iml = 0; _iml < _cntml; ++_iml) {
410
+ _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
411
+ _nd = _ml->_nodelist[_iml];
412
+ v = NODEV(_nd);
413
+ eca = _ion_eca;
414
+ _ode_matsol_instance1(_threadargs_);
415
+ }}
416
+ extern void nrn_update_ion_pointer(Symbol*, Datum*, int, int);
417
+ static void _update_ion_pointer(Datum* _ppvar) {
418
+ nrn_update_ion_pointer(_ca_sym, _ppvar, 0, 0);
419
+ nrn_update_ion_pointer(_ca_sym, _ppvar, 1, 3);
420
+ nrn_update_ion_pointer(_ca_sym, _ppvar, 2, 4);
421
+ }
422
+
423
+ static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
424
+ int _i; double _save;{
425
+ h = h0;
426
+ m = m0;
427
+ {
428
+ setparames ( _threadargscomma_ v ) ;
429
+ m = minf ;
430
+ h = hinf ;
431
+ }
432
+
433
+ }
434
+ }
435
+
436
+ static void nrn_init(_NrnThread* _nt, _Memb_list* _ml, int _type){
437
+ double* _p; Datum* _ppvar; Datum* _thread;
438
+ Node *_nd; double _v; int* _ni; int _iml, _cntml;
439
+ #if CACHEVEC
440
+ _ni = _ml->_nodeindices;
441
+ #endif
442
+ _cntml = _ml->_nodecount;
443
+ _thread = _ml->_thread;
444
+ for (_iml = 0; _iml < _cntml; ++_iml) {
445
+ _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
446
+ #if CACHEVEC
447
+ if (use_cachevec) {
448
+ _v = VEC_V(_ni[_iml]);
449
+ }else
450
+ #endif
451
+ {
452
+ _nd = _ml->_nodelist[_iml];
453
+ _v = NODEV(_nd);
454
+ }
455
+ v = _v;
456
+ eca = _ion_eca;
457
+ initmodel(_p, _ppvar, _thread, _nt);
458
+ }
459
+ }
460
+
461
+ static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
462
+ ica = gbegl19 * m * h * ( v - 60.0 ) ;
463
+ }
464
+ _current += ica;
465
+
466
+ } return _current;
467
+ }
468
+
469
+ static void nrn_cur(_NrnThread* _nt, _Memb_list* _ml, int _type) {
470
+ double* _p; Datum* _ppvar; Datum* _thread;
471
+ Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
472
+ #if CACHEVEC
473
+ _ni = _ml->_nodeindices;
474
+ #endif
475
+ _cntml = _ml->_nodecount;
476
+ _thread = _ml->_thread;
477
+ for (_iml = 0; _iml < _cntml; ++_iml) {
478
+ _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
479
+ #if CACHEVEC
480
+ if (use_cachevec) {
481
+ _v = VEC_V(_ni[_iml]);
482
+ }else
483
+ #endif
484
+ {
485
+ _nd = _ml->_nodelist[_iml];
486
+ _v = NODEV(_nd);
487
+ }
488
+ eca = _ion_eca;
489
+ _g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
490
+ { double _dica;
491
+ _dica = ica;
492
+ _rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
493
+ _ion_dicadv += (_dica - ica)/.001 ;
494
+ }
495
+ _g = (_g - _rhs)/.001;
496
+ _ion_ica += ica ;
497
+ #if CACHEVEC
498
+ if (use_cachevec) {
499
+ VEC_RHS(_ni[_iml]) -= _rhs;
500
+ }else
501
+ #endif
502
+ {
503
+ NODERHS(_nd) -= _rhs;
504
+ }
505
+
506
+ }
507
+
508
+ }
509
+
510
+ static void nrn_jacob(_NrnThread* _nt, _Memb_list* _ml, int _type) {
511
+ double* _p; Datum* _ppvar; Datum* _thread;
512
+ Node *_nd; int* _ni; int _iml, _cntml;
513
+ #if CACHEVEC
514
+ _ni = _ml->_nodeindices;
515
+ #endif
516
+ _cntml = _ml->_nodecount;
517
+ _thread = _ml->_thread;
518
+ for (_iml = 0; _iml < _cntml; ++_iml) {
519
+ _p = _ml->_data[_iml];
520
+ #if CACHEVEC
521
+ if (use_cachevec) {
522
+ VEC_D(_ni[_iml]) += _g;
523
+ }else
524
+ #endif
525
+ {
526
+ _nd = _ml->_nodelist[_iml];
527
+ NODED(_nd) += _g;
528
+ }
529
+
530
+ }
531
+
532
+ }
533
+
534
+ static void nrn_state(_NrnThread* _nt, _Memb_list* _ml, int _type) {
535
+ double* _p; Datum* _ppvar; Datum* _thread;
536
+ Node *_nd; double _v = 0.0; int* _ni; int _iml, _cntml;
537
+ #if CACHEVEC
538
+ _ni = _ml->_nodeindices;
539
+ #endif
540
+ _cntml = _ml->_nodecount;
541
+ _thread = _ml->_thread;
542
+ for (_iml = 0; _iml < _cntml; ++_iml) {
543
+ _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
544
+ _nd = _ml->_nodelist[_iml];
545
+ #if CACHEVEC
546
+ if (use_cachevec) {
547
+ _v = VEC_V(_ni[_iml]);
548
+ }else
549
+ #endif
550
+ {
551
+ _nd = _ml->_nodelist[_iml];
552
+ _v = NODEV(_nd);
553
+ }
554
+ v=_v;
555
+ {
556
+ eca = _ion_eca;
557
+ { states(_p, _ppvar, _thread, _nt);
558
+ } }}
559
+
560
+ }
561
+
562
+ static void terminal(){}
563
+
564
+ static void _initlists(){
565
+ double _x; double* _p = &_x;
566
+ int _i; static int _first = 1;
567
+ if (!_first) return;
568
+ _slist1[0] = &(m) - _p; _dlist1[0] = &(Dm) - _p;
569
+ _slist1[1] = &(h) - _p; _dlist1[1] = &(Dh) - _p;
570
+ _first = 0;
571
+ }
572
+
573
+ #if defined(__cplusplus)
574
+ } /* extern "C" */
575
+ #endif
576
+
577
+ #if NMODL_TEXT
578
+ static const char* nmodl_filename = "/home/zjj/8TB/robot_arm/project/BAAIWorm_v1/eworm/components/mechanism/modfile/egl19.mod";
579
+ static const char* nmodl_file_text =
580
+ "TITLE egl19 current for C. elegans neuron model\n"
581
+ "\n"
582
+ "\n"
583
+ "COMMENT\n"
584
+ "voltage-gated calcium channel\n"
585
+ "\n"
586
+ "model and parameters from:\n"
587
+ "Nicoletti, M., et al. (2019). \"Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD.\" PLoS One 14(7): e0218738.\n"
588
+ "ENDCOMMENT\n"
589
+ "\n"
590
+ "\n"
591
+ "UNITS {\n"
592
+ " (nS) = (nanosiemens)\n"
593
+ " (mV) = (millivolt)\n"
594
+ " (pA) = (picoamp)\n"
595
+ " (um) = (micron)\n"
596
+ "}\n"
597
+ "\n"
598
+ "\n"
599
+ "NEURON {\n"
600
+ " SUFFIX egl19\n"
601
+ " USEION ca READ eca WRITE ica\n"
602
+ " RANGE gbegl19, minf, hinf, tm, th, m, h\n"
603
+ "}\n"
604
+ "\n"
605
+ "\n"
606
+ "PARAMETER {\n"
607
+ " gbegl19 = 1 (nS/um2)\n"
608
+ " vhm = 5.6 (mV)\n"
609
+ " ka = 7.5 (mV)\n"
610
+ " vhh = 24.9 (mV)\n"
611
+ " ki = 12.0 (mV)\n"
612
+ " vhhb = -20.5 (mV)\n"
613
+ " kib = 8.1 (mV)\n"
614
+ " ahinf = 1.43\n"
615
+ " bhinf = 0.14\n"
616
+ " chinf = 5.96\n"
617
+ " dhinf = 0.60\n"
618
+ " atm = 2.9 (ms)\n"
619
+ " btm = 5.2 (mV)\n"
620
+ " ctm = 6.0 (mV)\n"
621
+ " dtm = 1.9 (ms)\n"
622
+ " etm = 1.4 (mV)\n"
623
+ " ftm = 30.0 (mV)\n"
624
+ " gtm = 2.3 (ms)\n"
625
+ " ath = 0.4\n"
626
+ " bth = 44.6 (ms)\n"
627
+ " cth = -23.0 (mV)\n"
628
+ " dth = 5.0 (mV)\n"
629
+ " eth = 36.4 (ms)\n"
630
+ " fth = 28.7 (mV)\n"
631
+ " gth = 3.7 (mV)\n"
632
+ " hth = 43.1 (ms)\n"
633
+ "}\n"
634
+ "\n"
635
+ "\n"
636
+ "ASSIGNED {\n"
637
+ " v (mV)\n"
638
+ " eca (mV)\n"
639
+ " ica (pA/um2)\n"
640
+ " minf\n"
641
+ " hinf\n"
642
+ " tm (ms)\n"
643
+ " th (ms)\n"
644
+ "}\n"
645
+ "\n"
646
+ "\n"
647
+ "STATE {\n"
648
+ " m\n"
649
+ " h\n"
650
+ "}\n"
651
+ "\n"
652
+ "\n"
653
+ "BREAKPOINT {\n"
654
+ " SOLVE states METHOD cnexp\n"
655
+ " :ica = gbegl19 * m * h * (v - eca)\n"
656
+ " ica = gbegl19 * m * h * (v - 60) : eca=60 mV\n"
657
+ "}\n"
658
+ "\n"
659
+ "\n"
660
+ "INITIAL {\n"
661
+ " setparames(v)\n"
662
+ " m = minf\n"
663
+ " h = hinf\n"
664
+ "}\n"
665
+ "\n"
666
+ "\n"
667
+ "DERIVATIVE states {\n"
668
+ " setparames(v)\n"
669
+ " m' = (minf - m) / tm\n"
670
+ " h' = (hinf - h) / th\n"
671
+ "}\n"
672
+ "\n"
673
+ "\n"
674
+ "PROCEDURE setparames(v (mV)) {\n"
675
+ " minf = 1 / (1 + exp(-(v - vhm) / ka))\n"
676
+ " hinf = (ahinf / (1 + exp(-(v - vhh) / ki)) + bhinf) * (chinf / (1 + exp((v - vhhb) / kib)) + dhinf)\n"
677
+ " tm = atm * exp(-((v - btm) / ctm) ^ 2) + dtm * exp(-((v - etm) / ftm) ^ 2) + gtm\n"
678
+ " th = ath * ((bth / (1 + exp((v - cth) / dth))) + (eth / (1 + exp((v - fth) / gth))) + hth)\n"
679
+ "}\n"
680
+ ;
681
+ #endif