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 <stdlib.h>
  20: 
  21: #include "../../heccer/compartment.h"
  22: #include "../../heccer/heccer.h"
  23: #include "../../heccer/mathcomponent.h"
  24: 
  25: 
  26: #define HECCER_TEST_REPORTING_GRANULARITY 100000
  27: #define HECCER_TEST_STEPS 1000000
  28: #define HECCER_TEST_TESTED_THINGS ( HECCER_DUMP_VM_COMPARTMENT_MATRIX \
  29:                                     | HECCER_DUMP_VM_COMPARTMENT_DATA \
  30:                                     | HECCER_DUMP_VM_COMPARTMENT_OPERATIONS \
  31:                                     | HECCER_DUMP_VM_CHANNEL_POOL_FLUXES \
  32:                                     | HECCER_DUMP_VM_MECHANISM_DATA \
  33:                                     | HECCER_DUMP_VM_MECHANISM_OPERATIONS \
  34:                                     | HECCER_DUMP_VM_SUMMARY \
  35:         )
  36: #define HECCER_TEST_TIME_GRANULARITY (1e-14)
  37: #define HECCER_TEST_TIME_STEP (1e-11)
  38: 
  39: 
  40: struct Compartment comp =
  41: {
  42:     //m administrative overhead
  43: 
  44:     {
  45:         //m type of structure
  46: 
  47:         MATH_TYPE_Compartment,
  48:     },
  49: 
  50:     //m index of parent compartment, -1 for none
  51: 
  52:     -1,
  53: 
  54: /*      //m first mechanism */
  55: 
  56: /*      NULL, */
  57: 
  58: /*      //m number of mechanisms */
  59: 
  60: /*      0, */
  61: 
  62:     //m descriptive values, alphabetical order
  63: 
  64: /*     double dCm; */
  65: 
  66:     5.755329373e-12, // unscaled 0.0164,
  67: 
  68: /*     double dEm; */
  69: 
  70:     -0.08,
  71: 
  72: /*     double dInitVm; */
  73: 
  74:     -0.068,
  75: 
  76: /*     double dInject;           */
  77: 
  78:     1e-9,
  79: 
  80: /*     double dRa; */
  81: 
  82:     772813.4375, // unscaled 2.5,
  83: 
  84: /*     double dRm; */
  85: 
  86:     8.548598272e9, // unscaled 3
  87: };
  88: 
  89: 
  90: //v first calcium channel
  91: 
  92: struct ChannelActInact caiCaT =
  93: {
  94:     //m administrative overhead
  95: 
  96:     {
  97:         //m type of structure
  98: 
  99:         MATH_TYPE_ChannelActInact,
 100:     },
 101: 
 102:     //m first set of descriptive values, alphabetical order
 103: 
 104:     //m initial reversal potential
 105: 
 106:     0.1470214874,
 107: 
 108:     //m get reversal potential from this intermediary, -1 for none
 109: 
 110:     1,
 111: 
 112:     //m maximal conductance when all channels are permissive
 113: 
 114:     1.754672296e-09,
 115: 
 116:     //m contributes to this concentration pool, -1 for none, boolean indicator only.
 117: 
 118:     4,
 119: 
 120:     //m activation description
 121: 
 122:     {
 123:         //m power, for a standard heccer, something between 1 and 4 or so.
 124: 
 125:         1,
 126: 
 127:         //m gate definition
 128: 
 129:         {
 130:             //m initial value, commonly forward over backward steady states
 131: 
 132:             0.038918706451336625,
 133: 
 134:             //m corresponding index in tables, set to -1 for initialization.
 135: 
 136:             -1,
 137: 
 138:             {
 139:                 //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
 140: 
 141:                 {
 142:                     //m multiplier
 143: 
 144:                     2.6e3,
 145: 
 146:                     //m multiplier membrane dependence, 0.0 for no dependence
 147: 
 148:                     0.0,
 149: 
 150:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 151: 
 152:                     0.0,
 153: 
 154:                     //m choose between nominator or denominator, 1 means nominator, -1
 155:                     //m means denominator
 156: 
 157:                     -1.0,
 158: 
 159:                     //m nominator or denominator offset
 160: 
 161:                     1.0,
 162: 
 163:                     //m membrane offset
 164: 
 165:                     0.021,
 166: 
 167:                     //m denormalized time constant
 168: 
 169:                     -8e-3,
 170:                 },
 171: 
 172:                 //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
 173: 
 174:                 {
 175:                     //m multiplier
 176: 
 177:                     0.18e3,
 178: 
 179:                     //m multiplier membrane dependence, 0.0 for no dependence
 180: 
 181:                     0.0,
 182: 
 183:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 184: 
 185:                     0.0,
 186: 
 187:                     //m choose between nominator or denominator, 1 means nominator, -1
 188:                     //m means denominator
 189: 
 190:                     -1.0,
 191: 
 192:                     //m nominator or denominator offset
 193: 
 194:                     1.0,
 195: 
 196:                     //m membrane offset
 197: 
 198:                     0.04,
 199: 
 200:                     //m denormalized time constant
 201: 
 202:                     4e-3,
 203:                 },
 204:             },
 205:         },
 206:     },
 207: 
 208:     //m inactivation description
 209: 
 210:     {
 211:         //m power, for a standard heccer, something between 1 and 4 or so.
 212: 
 213:         1,
 214: 
 215:         //m gate definition
 216: 
 217:         {
 218:             //m initial value, commonly forward over backward steady states
 219: 
 220:             0.082602128127539254,
 221: 
 222:             //m corresponding index in tables, set to -1 for initialization.
 223: 
 224:             -1,
 225: 
 226:             {
 227:                 //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
 228: 
 229:                 {
 230:                     //m multiplier
 231: 
 232:                     0.0025e3,
 233: 
 234:                     //m multiplier membrane dependence, 0.0 for no dependence
 235: 
 236:                     0.0,
 237: 
 238:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 239: 
 240:                     0.0,
 241: 
 242:                     //m choose between nominator or denominator, 1 means nominator, -1
 243:                     //m means denominator
 244: 
 245:                     -1.0,
 246: 
 247:                     //m nominator or denominator offset
 248: 
 249:                     1.0,
 250: 
 251:                     //m membrane offset
 252: 
 253:                     0.04,
 254: 
 255:                     //m denormalized time constant
 256: 
 257:                     8e-3,
 258:                 },
 259: 
 260:                 //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
 261: 
 262:                 {
 263:                     //m multiplier
 264: 
 265:                     0.19e3,
 266: 
 267:                     //m multiplier membrane dependence, 0.0 for no dependence
 268: 
 269:                     0.0,
 270: 
 271:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 272: 
 273:                     0.0,
 274: 
 275:                     //m choose between nominator or denominator, 1 means nominator, -1
 276:                     //m means denominator
 277: 
 278:                     -1.0,
 279: 
 280:                     //m nominator or denominator offset
 281: 
 282:                     1.0,
 283: 
 284:                     //m membrane offset
 285: 
 286:                     0.05,
 287: 
 288:                     //m denormalized time constant
 289: 
 290:                     -10.0e-3,
 291:                 },
 292:             },
 293:         },
 294:     },
 295: };
 296: 
 297: 
 298: struct InternalNernst inCa1 =
 299: {
 300:     //m administrative overhead
 301: 
 302:     {
 303:         //m type of structure
 304: 
 305:         MATH_TYPE_InternalNernst,
 306:     },
 307: 
 308:     //m nernst constant
 309: 
 310:     0.013363,
 311: 
 312:     //m link to internal concentration
 313: 
 314:     4,
 315: 
 316:     //m constant external concentration
 317: 
 318:     2.4000,
 319: 
 320:     //m initial nernst potential
 321: 
 322:     0.1470214874,
 323: };
 324: 
 325: 
 326: struct ChannelActInact caiCaP =
 327: {
 328:     //m administrative overhead
 329: 
 330:     {
 331:         //m type of structure
 332: 
 333:         MATH_TYPE_ChannelActInact,
 334:     },
 335: 
 336:     //m first set of descriptive values, alphabetical order
 337: 
 338:     //m initial reversal potential
 339: 
 340:     0.1470214874,
 341: 
 342:     //m get reversal potential from this intermediary, -1 for none
 343: 
 344:     3,
 345: 
 346:     //m maximal conductance when all channels are permissive
 347: 
 348:     1.57921e-08,
 349: 
 350:     //m contributes to this concentration pool, -1 for none, boolean indicator only.
 351: 
 352:     4,
 353: 
 354:     //m activation description
 355: 
 356:     {
 357:         //m power, for a standard heccer, something between 1 and 4 or so.
 358: 
 359:         1,
 360: 
 361:         //m gate definition
 362: 
 363:         {
 364:             //m initial value, commonly forward over backward steady states
 365: 
 366:             0.001391094927,
 367: 
 368:             //m corresponding index in tables, set to -1 for initialization.
 369: 
 370:             -1,
 371: 
 372:             {
 373:                 //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
 374: 
 375:                 {
 376:                     //m multiplier
 377: 
 378:                     8.50e3,
 379: 
 380:                     //m multiplier membrane dependence, 0.0 for no dependence
 381: 
 382:                     0.0,
 383: 
 384:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 385: 
 386:                     0.0,
 387: 
 388:                     //m choose between nominator or denominator, 1 means nominator, -1
 389:                     //m means denominator
 390: 
 391:                     -1.0,
 392: 
 393:                     //m nominator or denominator offset
 394: 
 395:                     1.0,
 396: 
 397:                     //m membrane offset
 398: 
 399:                     -0.0080,
 400: 
 401:                     //m denormalized time constant
 402: 
 403:                     -12.5e-3,
 404:                 },
 405: 
 406:                 //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
 407: 
 408:                 {
 409:                     //m multiplier
 410: 
 411:                     35.0e3,
 412: 
 413:                     //m multiplier membrane dependence, 0.0 for no dependence
 414: 
 415:                     0.0,
 416: 
 417:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 418: 
 419:                     0.0,
 420: 
 421:                     //m choose between nominator or denominator, 1 means nominator, -1
 422:                     //m means denominator
 423: 
 424:                     -1.0,
 425: 
 426:                     //m nominator or denominator offset
 427: 
 428:                     1.0,
 429: 
 430:                     //m membrane offset
 431: 
 432:                     0.074,
 433: 
 434:                     //m denormalized time constant
 435: 
 436:                     14.5e-3,
 437:                 },
 438:             },
 439:         },
 440:     },
 441: 
 442:     //m inactivation description
 443: 
 444:     {
 445:         //m power, for a standard heccer, something between 1 and 4 or so.
 446: 
 447:         1,
 448: 
 449:         //m gate definition
 450: 
 451:         {
 452:             //m initial value, commonly forward over backward steady states
 453: 
 454:             0.9868968318,
 455: 
 456:             //m corresponding index in tables, set to -1 for initialization.
 457: 
 458:             -1,
 459: 
 460:             {
 461:                 //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
 462: 
 463:                 {
 464:                     //m multiplier
 465: 
 466:                     0.0015e3,
 467: 
 468:                     //m multiplier membrane dependence, 0.0 for no dependence
 469: 
 470:                     0.0,
 471: 
 472:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 473: 
 474:                     0.0,
 475: 
 476:                     //m choose between nominator or denominator, 1 means nominator, -1
 477:                     //m means denominator
 478: 
 479:                     -1.0,
 480: 
 481:                     //m nominator or denominator offset
 482: 
 483:                     1.0,
 484: 
 485:                     //m membrane offset
 486: 
 487:                     0.029,
 488: 
 489:                     //m denormalized time constant
 490: 
 491:                     8.0e-3,
 492:                 },
 493: 
 494:                 //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
 495: 
 496:                 {
 497:                     //m multiplier
 498: 
 499:                     0.0055e3,
 500: 
 501:                     //m multiplier membrane dependence, 0.0 for no dependence
 502: 
 503:                     0.0,
 504: 
 505:                     //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
 506: 
 507:                     0.0,
 508: 
 509:                     //m choose between nominator or denominator, 1 means nominator, -1
 510:                     //m means denominator
 511: 
 512:                     -1.0,
 513: 
 514:                     //m nominator or denominator offset
 515: 
 516:                     1.0,
 517: 
 518:                     //m membrane offset
 519: 
 520:                     0.023,
 521: 
 522:                     //m denormalized time constant
 523: 
 524:                     -8.0e-3,
 525:                 },
 526:             },
 527:         },
 528:     },
 529: };
 530: 
 531: 
 532: struct InternalNernst inCa2 =
 533: {
 534:     //m administrative overhead
 535: 
 536:     {
 537:         //m type of structure
 538: 
 539:         MATH_TYPE_InternalNernst,
 540:     },
 541: 
 542:     //m nernst constant
 543: 
 544:     0.013363,
 545: 
 546:     //m link to internal concentration
 547: 
 548:     4,
 549: 
 550:     //m constant external concentration
 551: 
 552:     2.4000,
 553: 
 554:     //m initial nernst potential
 555: 
 556:     0.1470214874,
 557: };
 558: 
 559: 
 560: struct ExponentialDecay exdecCa =
 561: {
 562:     //m administrative overhead
 563: 
 564:     {
 565:         //m type of structure
 566: 
 567:         MATH_TYPE_ExponentialDecay,
 568:     },
 569: 
 570:     //m initial value
 571: 
 572:     4e-5,
 573: 
 574:     //m beta
 575: 
 576:     7.579027046e+10,
 577: 
 578:     //m steady state
 579: 
 580:     4e-05,
 581: 
 582:     //m tau
 583: 
 584:     0.00010,
 585: 
 586:     //m external contribution delivered by these intermediaries
 587: 
 588:     {
 589:         0,
 590:         2,
 591:         -1,
 592:         -1,
 593:     },
 594: };
 595: 
 596: 
 597: int piC2m[] =
 598: {
 599:     5,
 600:     -1,
 601: };
 602: 
 603: 
 604: struct MathComponentArray mca =
 605: {
 606:     //m number of math components
 607: 
 608:     5,
 609: 
 610:     //m math component data
 611: 
 612:     NULL,
 613: 
 614:     //m math component index, initialize to NULL
 615: 
 616:     NULL,
 617: 
 618: };
 619: 
 620: 
 621: struct Intermediary inter =
 622: {
 623:     //m compartment array
 624: 
 625:     1,
 626: 
 627:     &comp,
 628: 
 629:     //m all other mathematical components
 630: 
 631:     &mca,
 632: 
 633:     //m compartment 2 first mechanism number
 634: 
 635:     piC2m,
 636: };
 637: 
 638: 
 639: int main(int argc, char *argv[])
 640: {
 641:     //- determine intermediary size, and allocate
 642: 
 643:     struct MathComponentInfo *pmciCaT = MathComponentInfoLookup(caiCaT.mc.iType);
 644: 
 645:     struct MathComponentInfo *pmciCaP = MathComponentInfoLookup(caiCaP.mc.iType);
 646: 
 647:     struct MathComponentInfo *pmciCa = MathComponentInfoLookup(exdecCa.mc.iType);
 648: 
 649:     struct MathComponentInfo *pmciNernst1 = MathComponentInfoLookup(inCa1.mc.iType);
 650: 
 651:     struct MathComponentInfo *pmciNernst2 = MathComponentInfoLookup(inCa2.mc.iType);
 652: 
 653:     int iChars = pmciCaT->iChars + pmciCaP->iChars + pmciCa->iChars + pmciNernst1->iChars + pmciNernst2->iChars;
 654: 
 655:     void *pmc = calloc(sizeof(char), iChars);
 656: 
 657:     //- prepare the mechanism intermediary
 658: 
 659:     struct ChannelActInact *pcaiCaT = (struct ChannelActInact *)pmc;
 660: 
 661:     *pcaiCaT = caiCaT;
 662: 
 663:     struct InternalNernst *pin1 = (struct InternalNernst *)&((char *)pcaiCaT)[pmciCaT->iChars];
 664: 
 665:     *pin1 = inCa1;
 666: 
 667:     struct ChannelActInact *pcaiCaP = (struct ChannelActInact *)&((char *)pin1)[pmciNernst1->iChars];
 668: 
 669:     *pcaiCaP = caiCaP;
 670: 
 671:     struct InternalNernst *pin2 = (struct InternalNernst *)&((char *)pcaiCaP)[pmciCaP->iChars];
 672: 
 673:     *pin2 = inCa2;
 674: 
 675:     struct ExponentialDecay *pexdec = (struct ExponentialDecay *)&((char *)pin2)[pmciNernst2->iChars];
 676: 
 677:     *pexdec = exdecCa;
 678: 
 679:     //- link the intermediary
 680: 
 681:     mca.pmc = pmc;
 682: 
 683:     //- do the simulation
 684: 
 685:     simulate(argc,argv);
 686: }
 687: 
 688: 
 689: #define main(argc,argv) simulate(argc,argv)
 690: 
 691: //t this prototype can give warning and perhaps errors.
 692: 
 693: int main(int argc, char *argv[]);
 694: 
 695: 
 696: #include "main.c"
 697: 
 698: 
 699: