file:/local_home/local_home/hugo/neurospaces_project/heccer/source/c/snapshots/0/tests/code/pool2.c (Mon Jun 16 00:03:44 2008
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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:
24:
25: #define HECCER_TEST_REPORTING_GRANULARITY 100
26: #define HECCER_TEST_STEPS 1000
27: #define HECCER_TEST_TESTED_THINGS ( HECCER_DUMP_VM_COMPARTMENT_MATRIX \
28: | HECCER_DUMP_VM_COMPARTMENT_DATA \
29: | HECCER_DUMP_VM_COMPARTMENT_OPERATIONS \
30: | HECCER_DUMP_VM_CHANNEL_POOL_FLUXES \
31: | HECCER_DUMP_VM_MECHANISM_DATA \
32: | HECCER_DUMP_VM_MECHANISM_OPERATIONS \
33: | HECCER_DUMP_VM_SUMMARY \
34: )
35: #define HECCER_TEST_TIME_STEP (1e-6)
36:
37:
38: struct Compartment pcomp[] =
39: {
40: {
41: //m administrative overhead
42:
43: {
44: //m type of structure
45:
46: MATH_TYPE_Compartment,
47: },
48:
49: //m index of parent compartment, -1 for none
50:
51: -1,
52:
53: /* //m first mechanism */
54:
55: /* NULL, */
56:
57: /* //m number of mechanisms */
58:
59: /* 0, */
60:
61: //m descriptive values, alphabetical order
62:
63: /* double dCm; */
64:
65: 4.57537e-11, // unscaled 0.0164,
66:
67: /* double dEm; */
68:
69: -0.08,
70:
71: /* double dInitVm; */
72:
73: -0.028,
74:
75: /* double dInject; */
76:
77: 0,
78:
79: /* double dRa; */
80:
81: 360502, // unscaled 2.5,
82:
83: /* double dRm; */
84:
85: 3.58441e+08, // unscaled 1
86: },
87:
88: {
89: //m administrative overhead
90:
91: {
92: //m type of structure
93:
94: MATH_TYPE_Compartment,
95: },
96:
97: //m index of parent compartment, -1 for none
98:
99: 0,
100:
101: /* //m first mechanism */
102:
103: /* NULL, */
104:
105: /* //m number of mechanisms */
106:
107: /* 0, */
108:
109: //m descriptive values, alphabetical order
110:
111: /* double dCm; */
112:
113: 5.755329373e-12, // unscaled 0.0164,
114:
115: /* double dEm; */
116:
117: -0.08,
118:
119: /* double dInitVm; */
120:
121: -0.068,
122:
123: /* double dInject; */
124:
125: 0,
126:
127: /* double dRa; */
128:
129: 772813.4375, // unscaled 2.5,
130:
131: /* double dRm; */
132:
133: 8.548598272e9, // unscaled 3
134: },
135: };
136:
137:
138: //v a simple fast sodium channel
139:
140: struct ChannelActInact pcaiCaT[] =
141: {
142: {
143: //m administrative overhead
144:
145: {
146: //m type of structure
147:
148: MATH_TYPE_ChannelActInact,
149: },
150:
151: //m first set of descriptive values, alphabetical order
152:
153: //m initial reversal potential
154:
155: 0.1375262439,
156:
157: //m get reversal potential from this intermediary, -1 for none
158:
159: -1,
160:
161: //m maximal conductance when all channels are permissive
162:
163: 1.394928884e-08,
164:
165: //m contributes to this concentration pool, -1 for none, boolean indicator only.
166:
167: 1,
168:
169: //m activation description
170:
171: {
172: //m power, for a standard heccer, something between 1 and 4 or so.
173:
174: 1,
175:
176: //m gate definition
177:
178: {
179: //m initial value, commonly forward over backward steady states
180:
181: 0.038918706451336625,
182:
183: //m corresponding index in tables, set to -1 for initialization.
184:
185: -1,
186:
187: {
188: //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
189:
190: {
191: //m multiplier
192:
193: 2.6e3,
194:
195: //m multiplier membrane dependence, 0.0 for no dependence
196:
197: 0.0,
198:
199: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
200:
201: 0.0,
202:
203: //m choose between nominator or denominator, 1 means nominator, -1
204: //m means denominator
205:
206: -1.0,
207:
208: //m nominator or denominator offset
209:
210: 1.0,
211:
212: //m membrane offset
213:
214: 0.021,
215:
216: //m denormalized time constant
217:
218: -8e-3,
219: },
220:
221: //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
222:
223: {
224: //m multiplier
225:
226: 0.18e3,
227:
228: //m multiplier membrane dependence, 0.0 for no dependence
229:
230: 0.0,
231:
232: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
233:
234: 0.0,
235:
236: //m choose between nominator or denominator, 1 means nominator, -1
237: //m means denominator
238:
239: -1.0,
240:
241: //m nominator or denominator offset
242:
243: 1.0,
244:
245: //m membrane offset
246:
247: 0.04,
248:
249: //m denormalized time constant
250:
251: 4e-3,
252: },
253: },
254: },
255: },
256:
257: //m inactivation description
258:
259: {
260: //m power, for a standard heccer, something between 1 and 4 or so.
261:
262: 1,
263:
264: //m gate definition
265:
266: {
267: //m initial value, commonly forward over backward steady states
268:
269: 0.082602128127539254,
270:
271: //m corresponding index in tables, set to -1 for initialization.
272:
273: -1,
274:
275: {
276: //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
277:
278: {
279: //m multiplier
280:
281: 0.0025e3,
282:
283: //m multiplier membrane dependence, 0.0 for no dependence
284:
285: 0.0,
286:
287: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
288:
289: 0.0,
290:
291: //m choose between nominator or denominator, 1 means nominator, -1
292: //m means denominator
293:
294: -1.0,
295:
296: //m nominator or denominator offset
297:
298: 1.0,
299:
300: //m membrane offset
301:
302: 0.04,
303:
304: //m denormalized time constant
305:
306: 8e-3,
307: },
308:
309: //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
310:
311: {
312: //m multiplier
313:
314: 0.19e3,
315:
316: //m multiplier membrane dependence, 0.0 for no dependence
317:
318: 0.0,
319:
320: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
321:
322: 0.0,
323:
324: //m choose between nominator or denominator, 1 means nominator, -1
325: //m means denominator
326:
327: -1.0,
328:
329: //m nominator or denominator offset
330:
331: 1.0,
332:
333: //m membrane offset
334:
335: 0.05,
336:
337: //m denormalized time constant
338:
339: -10.0e-3,
340: },
341: },
342: },
343: },
344: },
345:
346: {
347: //m administrative overhead
348:
349: {
350: //m type of structure
351:
352: MATH_TYPE_ChannelActInact,
353: },
354:
355: //m first set of descriptive values, alphabetical order
356:
357: //m initial reversal potential
358:
359: 0.1470214874,
360:
361: //m get reversal potential from this intermediary, -1 for none
362:
363: -1,
364:
365: //m maximal conductance when all channels are permissive
366:
367: 1.754672296e-09,
368:
369: //m contributes to this concentration pool, -1 for none, boolean indicator only.
370:
371: 3,
372:
373: //m activation description
374:
375: {
376: //m power, for a standard heccer, something between 1 and 4 or so.
377:
378: 1,
379:
380: //m gate definition
381:
382: {
383: //m initial value, commonly forward over backward steady states
384:
385: 0.038918706451336625,
386:
387: //m corresponding index in tables, set to -1 for initialization.
388:
389: -1,
390:
391: {
392: //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
393:
394: {
395: //m multiplier
396:
397: 2.6e3,
398:
399: //m multiplier membrane dependence, 0.0 for no dependence
400:
401: 0.0,
402:
403: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
404:
405: 0.0,
406:
407: //m choose between nominator or denominator, 1 means nominator, -1
408: //m means denominator
409:
410: -1.0,
411:
412: //m nominator or denominator offset
413:
414: 1.0,
415:
416: //m membrane offset
417:
418: 0.021,
419:
420: //m denormalized time constant
421:
422: -8e-3,
423: },
424:
425: //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
426:
427: {
428: //m multiplier
429:
430: 0.18e3,
431:
432: //m multiplier membrane dependence, 0.0 for no dependence
433:
434: 0.0,
435:
436: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
437:
438: 0.0,
439:
440: //m choose between nominator or denominator, 1 means nominator, -1
441: //m means denominator
442:
443: -1.0,
444:
445: //m nominator or denominator offset
446:
447: 1.0,
448:
449: //m membrane offset
450:
451: 0.04,
452:
453: //m denormalized time constant
454:
455: 4e-3,
456: },
457: },
458: },
459: },
460:
461: //m inactivation description
462:
463: {
464: //m power, for a standard heccer, something between 1 and 4 or so.
465:
466: 1,
467:
468: //m gate definition
469:
470: {
471: //m initial value, commonly forward over backward steady states
472:
473: 0.082602128127539254,
474:
475: //m corresponding index in tables, set to -1 for initialization.
476:
477: -1,
478:
479: {
480: //m forward kinetiks, commonly denoted with alpha or non-perm to perm rate
481:
482: {
483: //m multiplier
484:
485: 0.0025e3,
486:
487: //m multiplier membrane dependence, 0.0 for no dependence
488:
489: 0.0,
490:
491: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
492:
493: 0.0,
494:
495: //m choose between nominator or denominator, 1 means nominator, -1
496: //m means denominator
497:
498: -1.0,
499:
500: //m nominator or denominator offset
501:
502: 1.0,
503:
504: //m membrane offset
505:
506: 0.04,
507:
508: //m denormalized time constant
509:
510: 8e-3,
511: },
512:
513: //m backward kinetiks, commonly denoted with beta or perm to non-perm rate
514:
515: {
516: //m multiplier
517:
518: 0.19e3,
519:
520: //m multiplier membrane dependence, 0.0 for no dependence
521:
522: 0.0,
523:
524: //m 2b: multiplier membrane dependence offset, 0.0 for no dependence
525:
526: 0.0,
527:
528: //m choose between nominator or denominator, 1 means nominator, -1
529: //m means denominator
530:
531: -1.0,
532:
533: //m nominator or denominator offset
534:
535: 1.0,
536:
537: //m membrane offset
538:
539: 0.05,
540:
541: //m denormalized time constant
542:
543: -10.0e-3,
544: },
545: },
546: },
547: },
548: },
549: };
550:
551:
552: struct ExponentialDecay pexdecCa[] =
553: {
554: {
555: //m administrative overhead
556:
557: {
558: //m type of structure
559:
560: MATH_TYPE_ExponentialDecay,
561: },
562:
563: //m initial value
564:
565: 4e-5,
566:
567: //m beta
568:
569: 7.579027046e+10,
570:
571: //m steady state
572:
573: 4e-05,
574:
575: //m tau
576:
577: 0.00010,
578:
579: //m external contribution delivered by these intermediaries
580:
581: {
582: 0,
583: -1,
584: -1,
585: -1,
586: },
587: },
588:
589: {
590: //m administrative overhead
591:
592: {
593: //m type of structure
594:
595: MATH_TYPE_ExponentialDecay,
596: },
597:
598: //m initial value
599:
600: 4e-5,
601:
602: //m beta
603:
604: 9412391936.0,
605:
606: //m steady state
607:
608: 4e-05,
609:
610: //m tau
611:
612: 0.00020,
613:
614: //m external contribution delivered by these intermediaries
615:
616: {
617: 2,
618: -1,
619: -1,
620: -1,
621: },
622: }
623: };
624:
625:
626: int piC2m[] =
627: {
628: 2,
629: 4,
630: -1,
631: };
632:
633:
634: struct MathComponentArray mca =
635: {
636: //m number of math components
637:
638: 4,
639:
640: //m math component data
641:
642: NULL,
643:
644: //m math component index, initialize to NULL
645:
646: NULL,
647:
648: };
649:
650:
651: struct Intermediary inter =
652: {
653: //m compartment array
654:
655: 2,
656:
657: pcomp,
658:
659: //m all other mathematical components
660:
661: &mca,
662:
663: //m compartment 2 first mechanism number
664:
665: piC2m,
666: };
667:
668:
669: int main(int argc, char *argv[])
670: {
671: //- determine intermediary size, and allocate
672:
673: struct MathComponentInfo *pmciCa = MathComponentInfoLookup(pexdecCa[0].mc.iType);
674:
675: struct MathComponentInfo *pmciCaT = MathComponentInfoLookup(pcaiCaT[0].mc.iType);
676:
677: int iChars = 2 * pmciCaT->iChars + 2 * pmciCa->iChars;
678:
679: void *pmc = calloc(sizeof(char), iChars);
680:
681: //- prepare the mechanism intermediary
682:
683: struct ChannelActInact *pcai0 = (struct ChannelActInact *)pmc;
684:
685: *pcai0 = pcaiCaT[0];
686:
687: struct ExponentialDecay *pexdec0 = (struct ExponentialDecay *)&((char *)pcai0)[pmciCaT->iChars];
688:
689: *pexdec0 = pexdecCa[0];
690:
691: struct ChannelActInact *pcai1 = (struct ChannelActInact *)&((char *)pexdec0)[pmciCa->iChars];
692:
693: *pcai1 = pcaiCaT[1];
694:
695: struct ExponentialDecay *pexdec1 = (struct ExponentialDecay *)&((char *)pcai1)[pmciCaT->iChars];
696:
697: *pexdec1 = pexdecCa[1];
698:
699: //- link the intermediary
700:
701: mca.pmc = pmc;
702:
703: //- do the simulation
704:
705: simulate(argc,argv);
706: }
707:
708:
709: #define main(argc,argv) simulate(argc,argv)
710:
711: //t this prototype can give warning and perhaps errors.
712:
713: int main(int argc, char *argv[]);
714:
715:
716: #include "main.c"
717:
718:
719:
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