001: //
002: // Heccer : a compartmental solver that implements efficient Crank-Nicolson
003: // integration for neuronal models.
004: //
005:
006: //////////////////////////////////////////////////////////////////////////////
007: //'
008: //' Heccer : testbed C implementation
009: //'
010: //' Copyright (C) 2006-2008 Hugo Cornelis
011: //'
012: //' functional ideas .. Hugo Cornelis, hugo.cornelis@gmail.com
013: //'
014: //' coding ............ Hugo Cornelis, hugo.cornelis@gmail.com
015: //'
016: //////////////////////////////////////////////////////////////////////////////
017:
018:
019: #include <stdlib.h>
020:
021: #include "../../heccer/addressing.h"
022: #include "../../heccer/compartment.h"
023: #include "../../heccer/heccer.h"
024:
025:
026: #define HECCER_TEST_OPTIONS (HECCER_OPTION_ENABLE_AGGREGATORS | HECCER_OPTION_ENABLE_INDIVIDUAL_CURRENTS)
027: #define HECCER_TEST_TESTED_THINGS ( HECCER_DUMP_VM_COMPARTMENT_MATRIX \
028: | HECCER_DUMP_VM_COMPARTMENT_MATRIX_DIAGONALS \
029: | HECCER_DUMP_VM_COMPARTMENT_OPERATIONS \
030: | HECCER_DUMP_VM_MECHANISM_DATA \
031: | HECCER_DUMP_VM_MECHANISM_OPERATIONS \
032: | HECCER_DUMP_VM_SUMMARY \
033: | HECCER_DUMP_VM_AGGREGATORS \
034: )
035: #define HECCER_TEST_TIME_STEP (6e-6)
036:
037:
038: struct Compartment pcomp[] =
039: {
040: {
041: //m administrative overhead
042:
043: {
044: //m type of structure
045:
046: MATH_TYPE_Compartment,
047:
048: #ifdef HECCER_SOURCE_NEUROSPACES
049:
050: //m identification
051:
052: ADDRESSING_NEUROSPACES_2_HECCER(1000),
053:
054: #endif
055:
056: #ifdef HECCER_SOURCE_TYPING
057:
058: //m model source type number
059:
060: //! source typing is used to compute aggregate currents ao
061: //! things.
062:
063: -1,
064:
065: #endif
066:
067: },
068:
069: //m index of parent compartment, -1 for none
070:
071: -1,
072:
073: /* //m first mechanism */
074:
075: /* NULL, */
076:
077: /* //m number of mechanisms */
078:
079: /* 0, */
080:
081: //m descriptive values, alphabetical order
082:
083: /* double dCm; */
084:
085: 4.57537e-11, // unscaled 0.0164,
086:
087: /* double dEm; */
088:
089: -0.08,
090:
091: /* double dInitVm; */
092:
093: -0.028,
094:
095: /* double dInject; */
096:
097: 0,
098:
099: /* double dRa; */
100:
101: 360502, // unscaled 2.5,
102:
103: /* double dRm; */
104:
105: 3.58441e+08, // unscaled 1
106: },
107:
108: {
109: //m administrative overhead
110:
111: {
112: //m type of structure
113:
114: MATH_TYPE_Compartment,
115:
116: #ifdef HECCER_SOURCE_NEUROSPACES
117:
118: //m identification
119:
120: ADDRESSING_NEUROSPACES_2_HECCER(2000),
121:
122: #endif
123:
124: #ifdef HECCER_SOURCE_TYPING
125:
126: //m model source type number
127:
128: //! source typing is used to compute aggregate currents ao
129: //! things.
130:
131: -1,
132:
133: #endif
134:
135: },
136:
137: //m index of parent compartment, -1 for none
138:
139: 0,
140:
141: /* //m first mechanism */
142:
143: /* NULL, */
144:
145: /* //m number of mechanisms */
146:
147: /* 0, */
148:
149: //m descriptive values, alphabetical order
150:
151: /* double dCm; */
152:
153: 5.755329373e-12, // unscaled 0.0164,
154:
155: /* double dEm; */
156:
157: -0.08,
158:
159: /* double dInitVm; */
160:
161: -0.068,
162:
163: /* double dInject; */
164:
165: 0,
166:
167: /* double dRa; */
168:
169: 772813.4375, // unscaled 2.5,
170:
171: /* double dRm; */
172:
173: 8.548598272e9, // unscaled 3
174: },
175: };
176:
177:
178: //v a simple fast sodium channel
179:
180: struct ChannelActInact pcaiCaT[] =
181: {
182: {
183: //m administrative overhead
184:
185: {
186: //m type of structure
187:
188: MATH_TYPE_ChannelActInact,
189:
190: #ifdef HECCER_SOURCE_NEUROSPACES
191:
192: //m identification
193:
194: ADDRESSING_NEUROSPACES_2_HECCER(3000),
195:
196: #endif
197:
198: #ifdef HECCER_SOURCE_TYPING
199:
200: //m model source type number
201:
202: //! source typing is used to compute aggregate currents ao
203: //! things.
204:
205: 0,
206:
207: #endif
208:
209: },
210:
211: //m first set of descriptive values, alphabetical order
212:
213: //m initial reversal potential
214:
215: 0.1375262439,
216:
217: //m get reversal potential from this intermediary, -1 for none
218:
219: -1,
220:
221: //m maximal conductance when all channels are permissive
222:
223: 1.394928884e-08,
224:
225: //m contributes to this concentration pool, -1 for none, boolean indicator only.
226:
227: 1,
228:
229: //m activation description
230:
231: {
232: //m power, for a standard heccer, something between 1 and 4 or so.
233:
234: 1,
235:
236: //m gate definition
237:
238: {
239: //m initial value, commonly forward over backward steady states
240:
241: 0.038918706451336625,
242:
243: //m corresponding index in tables, set to -1 for initialization.
244:
245: -1,
246:
247: {
248: //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
249:
250: {
251: //m multiplier
252:
253: 2.6e3,
254:
255: //m multiplier membrane dependence, 0.0 for no dependence
256:
257: 0.0,
258:
259: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
260:
261: 0.0,
262:
263: //m choose between nominator or denominator, 1 means nominator, -1
264: //m means denominator
265:
266: -1.0,
267:
268: //m nominator or denominator offset
269:
270: 1.0,
271:
272: //m membrane offset
273:
274: 0.021,
275:
276: //m denormalized time constant
277:
278: -8e-3,
279: },
280:
281: //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
282:
283: {
284: //m multiplier
285:
286: 0.18e3,
287:
288: //m multiplier membrane dependence, 0.0 for no dependence
289:
290: 0.0,
291:
292: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
293:
294: 0.0,
295:
296: //m choose between nominator or denominator, 1 means nominator, -1
297: //m means denominator
298:
299: -1.0,
300:
301: //m nominator or denominator offset
302:
303: 1.0,
304:
305: //m membrane offset
306:
307: 0.04,
308:
309: //m denormalized time constant
310:
311: 4e-3,
312: },
313: },
314: },
315: },
316:
317: //m inactivation description
318:
319: {
320: //m power, for a standard heccer, something between 1 and 4 or so.
321:
322: 1,
323:
324: //m gate definition
325:
326: {
327: //m initial value, commonly forward over backward steady states
328:
329: 0.082602128127539254,
330:
331: //m corresponding index in tables, set to -1 for initialization.
332:
333: -1,
334:
335: {
336: //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
337:
338: {
339: //m multiplier
340:
341: 0.0025e3,
342:
343: //m multiplier membrane dependence, 0.0 for no dependence
344:
345: 0.0,
346:
347: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
348:
349: 0.0,
350:
351: //m choose between nominator or denominator, 1 means nominator, -1
352: //m means denominator
353:
354: -1.0,
355:
356: //m nominator or denominator offset
357:
358: 1.0,
359:
360: //m membrane offset
361:
362: 0.04,
363:
364: //m denormalized time constant
365:
366: 8e-3,
367: },
368:
369: //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
370:
371: {
372: //m multiplier
373:
374: 0.19e3,
375:
376: //m multiplier membrane dependence, 0.0 for no dependence
377:
378: 0.0,
379:
380: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
381:
382: 0.0,
383:
384: //m choose between nominator or denominator, 1 means nominator, -1
385: //m means denominator
386:
387: -1.0,
388:
389: //m nominator or denominator offset
390:
391: 1.0,
392:
393: //m membrane offset
394:
395: 0.05,
396:
397: //m denormalized time constant
398:
399: -10.0e-3,
400: },
401: },
402: },
403: },
404: },
405:
406: {
407: //m administrative overhead
408:
409: {
410: //m type of structure
411:
412: MATH_TYPE_ChannelActInact,
413:
414: #ifdef HECCER_SOURCE_NEUROSPACES
415:
416: //m identification
417:
418: ADDRESSING_NEUROSPACES_2_HECCER(4000),
419:
420: #endif
421:
422: #ifdef HECCER_SOURCE_TYPING
423:
424: //m model source type number
425:
426: //! source typing is used to compute aggregate currents ao
427: //! things.
428:
429: 0,
430:
431: #endif
432:
433: },
434:
435: //m first set of descriptive values, alphabetical order
436:
437: //m initial reversal potential
438:
439: 0.1470214874,
440:
441: //m get reversal potential from this intermediary, -1 for none
442:
443: -1,
444:
445: //m maximal conductance when all channels are permissive
446:
447: 1.754672296e-09,
448:
449: //m contributes to this concentration pool, -1 for none, boolean indicator only.
450:
451: 3,
452:
453: //m activation description
454:
455: {
456: //m power, for a standard heccer, something between 1 and 4 or so.
457:
458: 1,
459:
460: //m gate definition
461:
462: {
463: //m initial value, commonly forward over backward steady states
464:
465: 0.038918706451336625,
466:
467: //m corresponding index in tables, set to -1 for initialization.
468:
469: -1,
470:
471: {
472: //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
473:
474: {
475: //m multiplier
476:
477: 2.6e3,
478:
479: //m multiplier membrane dependence, 0.0 for no dependence
480:
481: 0.0,
482:
483: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
484:
485: 0.0,
486:
487: //m choose between nominator or denominator, 1 means nominator, -1
488: //m means denominator
489:
490: -1.0,
491:
492: //m nominator or denominator offset
493:
494: 1.0,
495:
496: //m membrane offset
497:
498: 0.021,
499:
500: //m denormalized time constant
501:
502: -8e-3,
503: },
504:
505: //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
506:
507: {
508: //m multiplier
509:
510: 0.18e3,
511:
512: //m multiplier membrane dependence, 0.0 for no dependence
513:
514: 0.0,
515:
516: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
517:
518: 0.0,
519:
520: //m choose between nominator or denominator, 1 means nominator, -1
521: //m means denominator
522:
523: -1.0,
524:
525: //m nominator or denominator offset
526:
527: 1.0,
528:
529: //m membrane offset
530:
531: 0.04,
532:
533: //m denormalized time constant
534:
535: 4e-3,
536: },
537: },
538: },
539: },
540:
541: //m inactivation description
542:
543: {
544: //m power, for a standard heccer, something between 1 and 4 or so.
545:
546: 1,
547:
548: //m gate definition
549:
550: {
551: //m initial value, commonly forward over backward steady states
552:
553: 0.082602128127539254,
554:
555: //m corresponding index in tables, set to -1 for initialization.
556:
557: -1,
558:
559: {
560: //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
561:
562: {
563: //m multiplier
564:
565: 0.0025e3,
566:
567: //m multiplier membrane dependence, 0.0 for no dependence
568:
569: 0.0,
570:
571: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
572:
573: 0.0,
574:
575: //m choose between nominator or denominator, 1 means nominator, -1
576: //m means denominator
577:
578: -1.0,
579:
580: //m nominator or denominator offset
581:
582: 1.0,
583:
584: //m membrane offset
585:
586: 0.04,
587:
588: //m denormalized time constant
589:
590: 8e-3,
591: },
592:
593: //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
594:
595: {
596: //m multiplier
597:
598: 0.19e3,
599:
600: //m multiplier membrane dependence, 0.0 for no dependence
601:
602: 0.0,
603:
604: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
605:
606: 0.0,
607:
608: //m choose between nominator or denominator, 1 means nominator, -1
609: //m means denominator
610:
611: -1.0,
612:
613: //m nominator or denominator offset
614:
615: 1.0,
616:
617: //m membrane offset
618:
619: 0.05,
620:
621: //m denormalized time constant
622:
623: -10.0e-3,
624: },
625: },
626: },
627: },
628: },
629: };
630:
631:
632: struct ExponentialDecay pexdecCa[] =
633: {
634: {
635: //m administrative overhead
636:
637: {
638: //m type of structure
639:
640: MATH_TYPE_ExponentialDecay,
641:
642: #ifdef HECCER_SOURCE_NEUROSPACES
643:
644: //m identification
645:
646: ADDRESSING_NEUROSPACES_2_HECCER(5000),
647:
648: #endif
649:
650: #ifdef HECCER_SOURCE_TYPING
651:
652: //m model source type number
653:
654: //! source typing is used to compute aggregate currents ao
655: //! things.
656:
657: 1,
658:
659: #endif
660:
661: },
662:
663: //m initial value
664:
665: 4e-5,
666:
667: //m beta
668:
669: 7.579027046e+10,
670:
671: //m steady state
672:
673: 4e-05,
674:
675: //m tau
676:
677: 0.00010,
678:
679: //m external contribution delivered by these intermediaries
680:
681: {
682: 0,
683: -1,
684: -1,
685: -1,
686: },
687: },
688:
689: {
690: //m administrative overhead
691:
692: {
693: //m type of structure
694:
695: MATH_TYPE_ExponentialDecay,
696:
697: #ifdef HECCER_SOURCE_NEUROSPACES
698:
699: //m identification
700:
701: ADDRESSING_NEUROSPACES_2_HECCER(6000),
702:
703: #endif
704:
705: #ifdef HECCER_SOURCE_TYPING
706:
707: //m model source type number
708:
709: //! source typing is used to compute aggregate currents ao
710: //! things.
711:
712: 1,
713:
714: #endif
715:
716: },
717:
718: //m initial value
719:
720: 4e-5,
721:
722: //m beta
723:
724: 9412391936.0,
725:
726: //m steady state
727:
728: 4e-05,
729:
730: //m tau
731:
732: 0.00020,
733:
734: //m external contribution delivered by these intermediaries
735:
736: {
737: 2,
738: -1,
739: -1,
740: -1,
741: },
742: }
743: };
744:
745:
746: int piC2m[] =
747: {
748: 2,
749: 4,
750: -1,
751: };
752:
753:
754: struct MathComponentArray mca =
755: {
756: //m number of math components
757:
758: 4,
759:
760: //m math component data
761:
762: NULL,
763:
764: //m math component index, initialize to NULL
765:
766: NULL,
767:
768: };
769:
770:
771: struct Intermediary inter =
772: {
773: //m compartment array
774:
775: 2,
776:
777: pcomp,
778:
779: //m all other mathematical components
780:
781: &mca,
782:
783: //m compartment 2 first mechanism number
784:
785: piC2m,
786: };
787:
788:
789: int main(int argc, char *argv[])
790: {
791: //- determine intermediary size, and allocate
792:
793: struct MathComponentInfo *pmciCa = MathComponentInfoLookup(pexdecCa[0].mc.iType);
794:
795: struct MathComponentInfo *pmciCaT = MathComponentInfoLookup(pcaiCaT[0].mc.iType);
796:
797: int iChars = 2 * pmciCaT->iChars + 2 * pmciCa->iChars;
798:
799: void *pmc = calloc(sizeof(char), iChars);
800:
801: //- prepare the mechanism intermediary
802:
803: struct ChannelActInact *pcai0 = (struct ChannelActInact *)pmc;
804:
805: *pcai0 = pcaiCaT[0];
806:
807: struct ExponentialDecay *pexdec0 = (struct ExponentialDecay *)&((char *)pcai0)[pmciCaT->iChars];
808:
809: *pexdec0 = pexdecCa[0];
810:
811: struct ChannelActInact *pcai1 = (struct ChannelActInact *)&((char *)pexdec0)[pmciCa->iChars];
812:
813: *pcai1 = pcaiCaT[1];
814:
815: struct ExponentialDecay *pexdec1 = (struct ExponentialDecay *)&((char *)pcai1)[pmciCaT->iChars];
816:
817: *pexdec1 = pexdecCa[1];
818:
819: //- link the intermediary
820:
821: mca.pmc = pmc;
822:
823: //- do the simulation
824:
825: simulate(argc,argv);
826: }
827:
828:
829: #define main(argc,argv) simulate(argc,argv)
830:
831: //t this prototype can give warning and perhaps errors.
832:
833: int main(int argc, char *argv[]);
834:
835:
836: #include "main.c"
837:
838: