1: //
   2: // Heccer : a compartmental solver that implements efficient Crank-Nicolson
   3: // integration for neuronal models.
   4: //
   5: 
   6: //////////////////////////////////////////////////////////////////////////////
   7: //'
   8: //' Heccer : testbed C implementation
   9: //'
  10: //' Copyright (C) 2006-2008 Hugo Cornelis
  11: //'
  12: //' functional ideas .. Hugo Cornelis, hugo.cornelis@gmail.com
  13: //'
  14: //' coding ............ Hugo Cornelis, hugo.cornelis@gmail.com
  15: //'
  16: //////////////////////////////////////////////////////////////////////////////
  17: 
  18: 
  19: #include "../../heccer/compartment.h"
  20: #include "../../heccer/heccer.h"
  21: 
  22: 
  23: #define HECCER_TEST_INTERVAL_DEFAULT_START                      (-0.1)
  24: #define HECCER_TEST_INTERVAL_DEFAULT_END                        (0.05)
  25: #define HECCER_TEST_INTERVAL_DEFAULT_ENTRIES                    50
  26: #define HECCER_TEST_STEPS 1
  27: 
  28: 
  29: struct Compartment compSoma =
  30: {
  31:     //m administrative overhead
  32: 
  33:     {
  34:         //m type of structure
  35: 
  36:         MATH_TYPE_Compartment,
  37:     },
  38: 
  39:     //m index of parent compartment, -1 for none
  40: 
  41:     -1,
  42: 
  43: /*     //m first mechanism */
  44: 
  45: /*     NULL, */
  46: 
  47: /*     //m number of mechanisms */
  48: 
  49: /*     0, */
  50: 
  51:     //m descriptive values, alphabetical order
  52: 
  53: /*     double dCm; */
  54: 
  55:     4.57537e-11, // unscaled 0.0164,
  56: 
  57: /*     double dEm; */
  58: 
  59:     -0.08,
  60: 
  61: /*     double dInitVm; */
  62: 
  63:     -0.068,
  64: 
  65: /*     double dInject;           */
  66: 
  67:     0,
  68: 
  69: /*     double dRa; */
  70: 
  71:     360502, // unscaled 2.5,
  72: 
  73: /*     double dRm; */
  74: 
  75:     3.58441e+08, // unscaled 1
  76: };
  77: 
  78: 
  79: //v a persistent sodium channel
  80: 
  81: struct ChannelAct caNaP =
  82: {
  83:     //m administrative overhead
  84: 
  85:     {
  86:         //m type of structure
  87: 
  88:         MATH_TYPE_ChannelAct,
  89:     },
  90: 
  91:     //m first set of descriptive values, alphabetical order
  92: 
  93:     //m initial reversal potential
  94: 
  95:     0.045,
  96: 
  97:     //m get reversal potential from this intermediary, -1 for none
  98: 
  99:     -1,
 100: 
 101:     //m maximal conductance when all channels are permissive
 102: 
 103:     2.789857767e-08,
 104: 
 105:     //m contributes to this concentration pool, -1 for none, boolean indicator only.
 106: 
 107:     -1,
 108: 
 109:     //m activation description
 110: 
 111:     {
 112:         //m power, for a standard heccer, something between 1 and 4 or so.
 113: 
 114:         3,
 115: 
 116:         //m gate definition
 117: 
 118:         {
 119:             //m initial value, commonly forward over backward steady states
 120: 
 121:             0.7612305421,
 122: 
 123:             //m corresponding index in tables, set to -1 for initialization.
 124: 
 125:             -1,
 126: 
 127:             {
 128:                 //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
 129: 
 130:                 {
 131:                     //m multiplier
 132: 
 133:                     200.0e3,
 134: 
 135:                     //m multiplier membrane dependence, 0.0 for no dependence
 136: 
 137:                     0.0,
 138: 
 139:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 140: 
 141:                     0.0,
 142: 
 143:                     //m choose between nominator or denominator, 1 means nominator, -1
 144:                     //m means denominator
 145: 
 146:                     -1.0,
 147: 
 148:                     //m nominator or denominator offset
 149: 
 150:                     1.0,
 151: 
 152:                     //m membrane offset
 153: 
 154:                     -0.018,
 155: 
 156:                     //m denormalized time constant
 157: 
 158:                     -16.0e-3,
 159:                 },
 160: 
 161:                 //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
 162: 
 163:                 {
 164:                     //m multiplier
 165: 
 166:                     25.0e3,
 167: 
 168:                     //m multiplier membrane dependence, 0.0 for no dependence
 169: 
 170:                     0.0,
 171: 
 172:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 173: 
 174:                     0.0,
 175: 
 176:                     //m choose between nominator or denominator, 1 means nominator, -1
 177:                     //m means denominator
 178: 
 179:                     -1.0,
 180: 
 181:                     //m nominator or denominator offset
 182: 
 183:                     1.0,
 184: 
 185:                     //m membrane offset
 186: 
 187:                     0.058,
 188: 
 189:                     //m denormalized time constant
 190: 
 191:                     8.0e-3,
 192:                 },
 193:             },
 194:         },
 195:     },
 196: 
 197: };
 198: 
 199: 
 200: int piC2m[] =
 201: {
 202:     1,
 203:     -1,
 204: };
 205: 
 206: 
 207: struct MathComponentArray mca =
 208: {
 209:     //m number of math components
 210: 
 211:     1,
 212: 
 213:     //m math component data
 214: 
 215:     &caNaP.mc,
 216: 
 217:     //m math component index, initialize to NULL
 218: 
 219:     NULL,
 220: 
 221: };
 222: 
 223: 
 224: struct Intermediary inter =
 225: {
 226:     //m compartment array
 227: 
 228:     1,
 229: 
 230:     &compSoma,
 231: 
 232:     //m all other mathematical components
 233: 
 234:     &mca,
 235: 
 236:     //m compartment 2 first mechanism number
 237: 
 238:     piC2m,
 239: };
 240: 
 241: 
 242: #include "main.c"
 243: 
 244: 
 245: