file:/local_home/local_home/hugo/neurospaces_project/heccer/source/c/snapshots/0/tests/code/perfectclamp-passive10-2.c (Mon Jun 16 00:04:08 2008
) HOME
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/addressing.h"
22: #include "../../heccer/heccer.h"
23: #include "../../heccer/perfectclamp.h"
24:
25:
26: #include "main.h"
27:
28:
29: #define HECCER_TEST_REPORTING_GRANULARITY 100
30: #define HECCER_TEST_STEPS 1000
31: #define HECCER_TEST_TESTED_THINGS ( HECCER_DUMP_VM_COMPARTMENT_MATRIX \
32: | HECCER_DUMP_VM_MECHANISM_OPERATIONS \
33: )
34: #define HECCER_TEST_TIME_STEP (3e-6)
35:
36:
37: struct Compartment comp[] =
38: {
39: {
40: //m administrative overhead
41:
42: {
43: //m type of structure
44:
45: MATH_TYPE_Compartment,
46: },
47:
48: //m index of parent compartment, -1 for none
49:
50: -1,
51:
52: /* //m first mechanism */
53:
54: /* NULL, */
55:
56: /* //m number of mechanisms */
57:
58: /* 0, */
59:
60: //m descriptive values, alphabetical order
61:
62: /* double dCm; */
63:
64: 4.575370291e-11, // unscaled 0.0164,
65:
66: /* double dEm; */
67:
68: -0.08,
69:
70: /* double dInitVm; */
71:
72: -0.068,
73:
74: /* double dInject; */
75:
76: 1e-8,
77:
78: /* double dRa; */
79:
80: 36050196.88, // unscaled 2.5,
81:
82: /* double dRm; */
83:
84: 3584409.28, // unscaled 3
85: },
86: /* [ /Purkinje/soma ] */
87: /* activation = 0 */
88: /* Vm = -0.0680000037 */
89: /* previous_state = 0 */
90: /* Im = 0.00378972129 */
91: /* Em = -0.07999999821 */
92: /* Rm = 358440928 */
93: /* Cm = 4.575370291e-11 */
94: /* Ra = 360501.9688 */
95: /* inject = 0 */
96: /* dia = 2.979999954e-05 */
97: /* len = 0 */
98: /* initVm = -0.0680000037 */
99: /* somatopetal = none */
100: /* somatopetaltag = 1 */
101: /* somatofugal = /Purkinje/main */
102: /* somatofugaltag = 0 */
103:
104: {
105: //m administrative overhead
106:
107: {
108: //m type of structure
109:
110: MATH_TYPE_Compartment,
111: },
112:
113: //m index of parent compartment, -1 for none
114:
115: 0,
116:
117: /* //m first mechanism */
118:
119: /* NULL, */
120:
121: /* //m number of mechanisms */
122:
123: /* 0, */
124:
125: //m descriptive values, alphabetical order
126:
127: /* double dCm; */
128:
129: 5.755329373e-12, // unscaled 0.0164,
130:
131: /* double dEm; */
132:
133: -0.08,
134:
135: /* double dInitVm; */
136:
137: -0.068,
138:
139: /* double dInject; */
140:
141: 0,
142:
143: /* double dRa; */
144:
145: 77281343.75, // unscaled 2.5,
146:
147: /* double dRm; */
148:
149: 85485982.720, // unscaled 3
150: },
151: /* [ /Purkinje/main ] */
152: /* activation = 0 */
153: /* Vm = -0.0680000037 */
154: /* previous_state = 0 */
155: /* Im = 0.03594784066 */
156: /* Em = -0.07999999821 */
157: /* Rm = 8548598272 */
158: /* Cm = 5.755329373e-12 */
159: /* Ra = 772813.4375 */
160: /* inject = 0 */
161: /* dia = 7.720000212e-06 */
162: /* len = 1.446968781e-05 */
163: /* initVm = -0.0680000037 */
164: /* somatopetal = /Purkinje/soma */
165: /* somatopetaltag = 0 */
166: /* somatofugal = /Purkinje/main[1] */
167: /* somatofugaltag = 0 */
168:
169: {
170: //m administrative overhead
171:
172: {
173: //m type of structure
174:
175: MATH_TYPE_Compartment,
176: },
177:
178: //m index of parent compartment, -1 for none
179:
180: 1,
181:
182: /* //m first mechanism */
183:
184: /* NULL, */
185:
186: /* //m number of mechanisms */
187:
188: /* 0, */
189:
190: //m descriptive values, alphabetical order
191:
192: /* double dCm; */
193:
194: 9.952665428e-12, // unscaled 0.0164,
195:
196: /* double dEm; */
197:
198: -0.08,
199:
200: /* double dInitVm; */
201:
202: -0.068,
203:
204: /* double dInject; */
205:
206: 0,
207:
208: /* double dRa; */
209:
210: 110708325, // unscaled 2.5,
211:
212: /* double dRm; */
213:
214: 49433994.240, // unscaled 3
215: },
216: /* [ /Purkinje/main[1] ] */
217: /* activation = 0 */
218: /* Vm = -0.0680000037 */
219: /* previous_state = 0 */
220: /* Im = 0.03594784066 */
221: /* Em = -0.07999999821 */
222: /* Rm = 4943399424 */
223: /* Cm = 9.952665428e-12 */
224: /* Ra = 1107083.25 */
225: /* inject = 0 */
226: /* dia = 8.220000382e-06 */
227: /* len = 2.350032264e-05 */
228: /* initVm = -0.0680000037 */
229: /* somatopetal = /Purkinje/main */
230: /* somatopetaltag = 0 */
231: /* somatofugal = /Purkinje/main[2] /Purkinje/b0s01 */
232: /* somatofugaltag = 0 */
233:
234: {
235: //m administrative overhead
236:
237: {
238: //m type of structure
239:
240: MATH_TYPE_Compartment,
241: },
242:
243: //m index of parent compartment, -1 for none
244:
245: 2,
246:
247: /* //m first mechanism */
248:
249: /* NULL, */
250:
251: /* //m number of mechanisms */
252:
253: /* 0, */
254:
255: //m descriptive values, alphabetical order
256:
257: /* double dCm; */
258:
259: 3.048169139e-12, // unscaled 0.0164,
260:
261: /* double dEm; */
262:
263: -0.08,
264:
265: /* double dInitVm; */
266:
267: -0.068,
268:
269: /* double dInject; */
270:
271: 0,
272:
273: /* double dRa; */
274:
275: 30664696.88, // unscaled 2.5,
276:
277: /* double dRm; */
278:
279: 1.614083584e+8, // unscaled 3
280: },
281: /* [ /Purkinje/main[2] ] */
282: /* activation = 0 */
283: /* Vm = -0.0680000037 */
284: /* previous_state = 0 */
285: /* Im = 0.03594784439 */
286: /* Em = -0.07999999821 */
287: /* Rm = 1.614083584e+10 */
288: /* Cm = 3.048169139e-12 */
289: /* Ra = 306646.9688 */
290: /* inject = 0 */
291: /* dia = 8.500000149e-06 */
292: /* len = 6.960275186e-06 */
293: /* initVm = -0.0680000037 */
294: /* somatopetal = /Purkinje/main[1] */
295: /* somatopetaltag = 0 */
296: /* somatofugal = /Purkinje/main[3] /Purkinje/b0s02 */
297: /* somatofugaltag = 0 */
298:
299: {
300: //m administrative overhead
301:
302: {
303: //m type of structure
304:
305: MATH_TYPE_Compartment,
306: },
307:
308: //m index of parent compartment, -1 for none
309:
310: 3,
311:
312: /* //m first mechanism */
313:
314: /* NULL, */
315:
316: /* //m number of mechanisms */
317:
318: /* 0, */
319:
320: //m descriptive values, alphabetical order
321:
322: /* double dCm; */
323:
324: 1.866796431e-12, // unscaled 0.0164,
325:
326: /* double dEm; */
327:
328: -0.08,
329:
330: /* double dInitVm; */
331:
332: -0.068,
333:
334: /* double dInject; */
335:
336: 0,
337:
338: /* double dRa; */
339:
340: 14715007.81, // unscaled 2.5,
341:
342: /* double dRm; */
343:
344: 2.635531059e+8, // unscaled 3
345: },
346: /* [ /Purkinje/main[3] ] */
347: /* activation = 0 */
348: /* Vm = -0.0680000037 */
349: /* previous_state = 0 */
350: /* Im = 0.03594784439 */
351: /* Em = -0.07999999821 */
352: /* Rm = 2.635531059e+10 */
353: /* Cm = 1.866796431e-12 */
354: /* Ra = 147150.0781 */
355: /* inject = 0 */
356: /* dia = 9.22000072e-06 */
357: /* len = 3.929816558e-06 */
358: /* initVm = -0.0680000037 */
359: /* somatopetal = /Purkinje/main[2] */
360: /* somatopetaltag = 0 */
361: /* somatofugal = /Purkinje/main[4] */
362: /* somatofugaltag = 0 */
363:
364: {
365: //m administrative overhead
366:
367: {
368: //m type of structure
369:
370: MATH_TYPE_Compartment,
371: },
372:
373: //m index of parent compartment, -1 for none
374:
375: 4,
376:
377: /* //m first mechanism */
378:
379: /* NULL, */
380:
381: /* //m number of mechanisms */
382:
383: /* 0, */
384:
385: //m descriptive values, alphabetical order
386:
387: /* double dCm; */
388:
389: 3.81543408e-12, // unscaled 0.0164,
390:
391: /* double dEm; */
392:
393: -0.08,
394:
395: /* double dInitVm; */
396:
397: -0.068,
398:
399: /* double dInject; */
400:
401: 0,
402:
403: /* double dRa; */
404:
405: 33550193.75, // unscaled 2.5,
406:
407: /* double dRm; */
408:
409: 1.289499341e+8, // unscaled 3
410: },
411: /* [ /Purkinje/main[4] ] */
412: /* activation = 0 */
413: /* Vm = -0.0680000037 */
414: /* previous_state = 0 */
415: /* Im = 0.03594784439 */
416: /* Em = -0.07999999821 */
417: /* Rm = 1.289499341e+10 */
418: /* Cm = 3.81543408e-12 */
419: /* Ra = 335501.9375 */
420: /* inject = 0 */
421: /* dia = 8.890000572e-06 */
422: /* len = 8.330066521e-06 */
423: /* initVm = -0.0680000037 */
424: /* somatopetal = /Purkinje/main[3] */
425: /* somatopetaltag = 0 */
426: /* somatofugal = /Purkinje/main[5] */
427: /* somatofugaltag = 0 */
428:
429: {
430: //m administrative overhead
431:
432: {
433: //m type of structure
434:
435: MATH_TYPE_Compartment,
436: },
437:
438: //m index of parent compartment, -1 for none
439:
440: 5,
441:
442: /* //m first mechanism */
443:
444: /* NULL, */
445:
446: /* //m number of mechanisms */
447:
448: /* 0, */
449:
450: //m descriptive values, alphabetical order
451:
452: /* double dCm; */
453:
454: 2.239454065e-12, // unscaled 0.0164,
455:
456: /* double dEm; */
457:
458: -0.08,
459:
460: /* double dInitVm; */
461:
462: -0.068,
463:
464: /* double dInject; */
465:
466: 0,
467:
468: /* double dRa; */
469:
470: 23012895.31, // unscaled 2.5,
471:
472: /* double dRm; */
473:
474: 2.196964147e+8, // unscaled 3
475: },
476: /* [ /Purkinje/main[5] ] */
477: /* activation = 0 */
478: /* Vm = -0.0680000037 */
479: /* previous_state = 0 */
480: /* Im = 0.03594784439 */
481: /* Em = -0.07999999821 */
482: /* Rm = 2.196964147e+10 */
483: /* Cm = 2.239454065e-12 */
484: /* Ra = 230128.9531 */
485: /* inject = 0 */
486: /* dia = 8.439999874e-06 */
487: /* len = 5.149985554e-06 */
488: /* initVm = -0.0680000037 */
489: /* somatopetal = /Purkinje/main[4] */
490: /* somatopetaltag = 0 */
491: /* somatofugal = /Purkinje/main[6] /Purkinje/b0s03 */
492: /* somatofugaltag = 0 */
493:
494: {
495: //m administrative overhead
496:
497: {
498: //m type of structure
499:
500: MATH_TYPE_Compartment,
501: },
502:
503: //m index of parent compartment, -1 for none
504:
505: 6,
506:
507: /* //m first mechanism */
508:
509: /* NULL, */
510:
511: /* //m number of mechanisms */
512:
513: /* 0, */
514:
515: //m descriptive values, alphabetical order
516:
517: /* double dCm; */
518:
519: 1.754059463e-12, // unscaled 0.0164,
520:
521: /* double dEm; */
522:
523: -0.08,
524:
525: /* double dInitVm; */
526:
527: -0.068,
528:
529: /* double dInject; */
530:
531: 0,
532:
533: /* double dRa; */
534:
535: 16978185.94, // unscaled 2.5,
536:
537: /* double dRm; */
538:
539: 2.804921958e+8, // unscaled 3
540: },
541: /* [ /Purkinje/main[6] ] */
542: /* activation = 0 */
543: /* Vm = -0.0680000037 */
544: /* previous_state = 0 */
545: /* Im = 0.03594784439 */
546: /* Em = -0.07999999821 */
547: /* Rm = 2.804921958e+10 */
548: /* Cm = 1.754059463e-12 */
549: /* Ra = 169781.8594 */
550: /* inject = 0 */
551: /* dia = 8.609999895e-06 */
552: /* len = 3.954098247e-06 */
553: /* initVm = -0.0680000037 */
554: /* somatopetal = /Purkinje/main[5] */
555: /* somatopetaltag = 0 */
556: /* somatofugal = /Purkinje/main[7] /Purkinje/b0s04 */
557: /* somatofugaltag = 0 */
558:
559: {
560: //m administrative overhead
561:
562: {
563: //m type of structure
564:
565: MATH_TYPE_Compartment,
566: },
567:
568: //m index of parent compartment, -1 for none
569:
570: 7,
571:
572: /* //m first mechanism */
573:
574: /* NULL, */
575:
576: /* //m number of mechanisms */
577:
578: /* 0, */
579:
580: //m descriptive values, alphabetical order
581:
582: /* double dCm; */
583:
584: 3.37096605e-12, // unscaled 0.0164,
585:
586: /* double dEm; */
587:
588: -0.08,
589:
590: /* double dInitVm; */
591:
592: -0.068,
593:
594: /* double dInject; */
595:
596: 0,
597:
598: /* double dRa; */
599:
600: 44225412.5, // unscaled 2.5,
601:
602: /* double dRm; */
603:
604: 1.459522355e+8, // unscaled 3
605: },
606: /* [ /Purkinje/main[7] ] */
607: /* activation = 0 */
608: /* Vm = -0.0680000037 */
609: /* previous_state = 0 */
610: /* Im = 0.03594784811 */
611: /* Em = -0.07999999821 */
612: /* Rm = 1.459522355e+10 */
613: /* Cm = 3.37096605e-12 */
614: /* Ra = 442254.125 */
615: /* inject = 0 */
616: /* dia = 7.780000487e-06 */
617: /* len = 8.409710063e-06 */
618: /* initVm = -0.0680000037 */
619: /* somatopetal = /Purkinje/main[6] */
620: /* somatopetaltag = 0 */
621: /* somatofugal = /Purkinje/main[8] */
622: /* somatofugaltag = 0 */
623:
624: {
625: //m administrative overhead
626:
627: {
628: //m type of structure
629:
630: MATH_TYPE_Compartment,
631: },
632:
633: //m index of parent compartment, -1 for none
634:
635: 8,
636:
637: /* //m first mechanism */
638:
639: /* NULL, */
640:
641: /* //m number of mechanisms */
642:
643: /* 0, */
644:
645: //m descriptive values, alphabetical order
646:
647: /* double dCm; */
648:
649: 5.048512389e-12, // unscaled 0.0164,
650:
651: /* double dEm; */
652:
653: -0.08,
654:
655: /* double dInitVm; */
656:
657: -0.068,
658:
659: /* double dInject; */
660:
661: 0,
662:
663: /* double dRa; */
664:
665: 51879109.38, // unscaled 2.5,
666:
667: /* double dRm; */
668:
669: 97454448.640, // unscaled 3
670: },
671: /* [ /Purkinje/main[8] ] */
672: /* activation = 0 */
673: /* Vm = -0.0680000037 */
674: /* previous_state = 0 */
675: /* Im = 0.03594784066 */
676: /* Em = -0.07999999821 */
677: /* Rm = 9745444864 */
678: /* Cm = 5.048512389e-12 */
679: /* Ra = 518791.0938 */
680: /* inject = 0 */
681: /* dia = 8.439999874e-06 */
682: /* len = 1.160986722e-05 */
683: /* initVm = -0.0680000037 */
684: /* somatopetal = /Purkinje/main[7] */
685: /* somatopetaltag = 0 */
686: /* somatofugal = /Purkinje/br1 /Purkinje/br2 */
687: /* somatofugaltag = 0 */
688:
689: };
690:
691:
692: int piC2m[] =
693: {
694: 0,
695: 0,
696: 0,
697: 0,
698: 0,
699: 0,
700: 0,
701: 0,
702: 0,
703: 0,
704: -1,
705: };
706:
707:
708: struct Intermediary inter =
709: {
710: //m compartment array
711:
712: 10,
713:
714: comp,
715:
716: //m all other mathematical components
717:
718: NULL,
719:
720: //m compartment 2 first mechanism number
721:
722: piC2m,
723: };
724:
725:
726: int main(int argc, char *argv[])
727: {
728: //- allocate a voltage clamp object
729:
730: ppc = PerfectClampNew("pc object");
731:
732: //- set fields
733:
734: double dCommand = 0.1;
735:
736: PerfectClampSetFields(ppc, dCommand, NULL);
737:
738: //d connect the voltage clamp object with the compartment of interest
739:
740: #define HECCER_TEST_INITIATE \
741: double *pdVm = HeccerAddressCompartmentVariable(pheccer, 0, "Vm"); \
742: PerfectClampAddVariable(ppc, pdVm)
743:
744: //d schedule the voltage clamper
745:
746: #define HECCER_TEST_SCHEDULE PerfectClampSingleStep(ppc, dSimulationTime)
747:
748: //- do the simulation
749:
750: simulate(argc, argv);
751: }
752:
753:
754: #define main(argc,argv) simulate(argc,argv)
755:
756: //t this prototype can give warning and perhaps errors.
757:
758: int main(int argc, char *argv[]);
759:
760:
761: #include "main.c"
762:
763:
764:
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