Nektar++
Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Private Types | Private Attributes | Static Private Attributes | List of all members
Nektar::FentonKarma Class Reference

#include <FentonKarma.h>

Inheritance diagram for Nektar::FentonKarma:
[legend]

Public Member Functions

 FentonKarma (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
 Constructor. More...
 
 ~FentonKarma () override
 Destructor. More...
 
- Public Member Functions inherited from Nektar::CellModel
 CellModel (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
 
virtual ~CellModel ()
 
void Initialise ()
 Initialise the cell model storage and set initial conditions. More...
 
void TimeIntegrate (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
 Time integrate the cell model by one PDE timestep. More...
 
void Update (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
 Compute the derivatives of cell model variables. More...
 
void GenerateSummary (SummaryList &s)
 Print a summary of the cell model. More...
 
size_t GetNumCellVariables ()
 
std::string GetCellVarName (size_t idx)
 
Array< OneD, NekDouble > GetCellSolutionCoeffs (size_t idx)
 
Array< OneD, NekDouble > GetCellSolution (size_t idx)
 

Static Public Member Functions

static CellModelSharedPtr create (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
 Creates an instance of this class. More...
 

Static Public Attributes

static std::string className
 Name of class. More...
 

Protected Member Functions

void v_Update (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time) override
 Computes the reaction terms $f(u,v)$ and $g(u,v)$. More...
 
void v_GenerateSummary (SummaryList &s) override
 Prints a summary of the model parameters. More...
 
void v_SetInitialConditions () override
 
std::string v_GetCellVarName (size_t idx) override
 
- Protected Member Functions inherited from Nektar::CellModel
virtual void v_Update (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)=0
 
virtual void v_GenerateSummary (SummaryList &s)=0
 
virtual std::string v_GetCellVarName (size_t idx)
 
virtual void v_SetInitialConditions ()=0
 
void LoadCellModel ()
 

Private Types

enum  Variants {
  eBR , eMBR , eMLR1 , eGP ,
  eCF1 , eCF2a , eCF2b , eCF2c ,
  eCF3a , eCF3b , eFC2002Set1a , eFC2002Set1b ,
  eFC2002Set1c , eFC2002Set1d , eFC2002Set1e , eFC2002Set2 ,
  eFC2002Set4a , eFC2002Set4b , eFC2002Set4c , eFC2002Set4d ,
  eFC2002Set5 , eFC2002Set6 , eFC2002Set7 , eFC2002Set8 ,
  eFC2002Set9 , eLawson , eCAF
}
 

Private Attributes

NekDouble C_m
 
NekDouble V_0
 
NekDouble V_fi
 
NekDouble u_fi
 
NekDouble u_c
 
NekDouble u_v
 
NekDouble u_r
 
NekDouble g_fi_max
 
NekDouble tau_d
 
NekDouble tau_v1_minus
 
NekDouble tau_v2_minus
 
NekDouble tau_v_plus
 
NekDouble tau_0
 
NekDouble tau_r
 
NekDouble tau_si
 
NekDouble tau_y_plus
 
NekDouble tau_y_minus
 
NekDouble u_csi
 
NekDouble k1
 
NekDouble k2
 
NekDouble tau_w_minus
 
NekDouble tau_w_plus
 
bool isCF3
 
enum Variants model_variant
 

Static Private Attributes

static std::string lookupIds []
 
static std::string def
 

Additional Inherited Members

- Protected Attributes inherited from Nektar::CellModel
LibUtilities::SessionReaderSharedPtr m_session
 Session. More...
 
MultiRegions::ExpListSharedPtr m_field
 Transmembrane potential field from PDE system. More...
 
size_t m_nq
 Number of physical points. More...
 
size_t m_nvar
 Number of variables in cell model (inc. transmembrane voltage) More...
 
NekDouble m_lastTime
 Timestep for pde model. More...
 
size_t m_substeps
 Number of substeps to take. More...
 
Array< OneD, Array< OneD, NekDouble > > m_cellSol
 Cell model solution variables. More...
 
Array< OneD, Array< OneD, NekDouble > > m_wsp
 Cell model integration workspace. More...
 
bool m_useNodal
 Flag indicating whether nodal projection in use. More...
 
StdRegions::StdNodalTriExpSharedPtr m_nodalTri
 StdNodalTri for cell model calculations. More...
 
StdRegions::StdNodalTetExpSharedPtr m_nodalTet
 
Array< OneD, Array< OneD, NekDouble > > m_nodalTmp
 Temporary array for nodal projection. More...
 
std::vector< int > m_concentrations
 Indices of cell model variables which are concentrations. More...
 
std::vector< int > m_gates
 Indices of cell model variables which are gates. More...
 
Array< OneD, Array< OneD, NekDouble > > m_gates_tau
 Storage for gate tau values. More...
 

Detailed Description

Definition at line 42 of file FentonKarma.h.

Member Enumeration Documentation

◆ Variants

enum Nektar::FentonKarma::Variants
private
Enumerator
eBR 
eMBR 
eMLR1 
eGP 
eCF1 
eCF2a 
eCF2b 
eCF2c 
eCF3a 
eCF3b 
eFC2002Set1a 
eFC2002Set1b 
eFC2002Set1c 
eFC2002Set1d 
eFC2002Set1e 
eFC2002Set2 
eFC2002Set4a 
eFC2002Set4b 
eFC2002Set4c 
eFC2002Set4d 
eFC2002Set5 
eFC2002Set6 
eFC2002Set7 
eFC2002Set8 
eFC2002Set9 
eLawson 
eCAF 

Definition at line 102 of file FentonKarma.h.

103 {
104 eBR,
105 eMBR,
106 eMLR1,
107 eGP,
108 eCF1,
109 eCF2a,
110 eCF2b,
111 eCF2c,
112 eCF3a,
113 eCF3b,
114 eFC2002Set1a,
115 eFC2002Set1b,
116 eFC2002Set1c,
117 eFC2002Set1d,
118 eFC2002Set1e,
119 eFC2002Set2,
120 eFC2002Set4a,
121 eFC2002Set4b,
122 eFC2002Set4c,
123 eFC2002Set4d,
124 eFC2002Set5,
125 eFC2002Set6,
126 eFC2002Set7,
127 eFC2002Set8,
128 eFC2002Set9,
129 eLawson,
130 eCAF
131 };

Constructor & Destructor Documentation

◆ FentonKarma()

Nektar::FentonKarma::FentonKarma ( const LibUtilities::SessionReaderSharedPtr &  pSession,
const MultiRegions::ExpListSharedPtr &  pField 
)

Constructor.

Initialise Fenton-Karma model parameters. k1 is k in the original model. k2 is an additional parameter introduced in Cherry&Fenton 2004. u_r and u_fi are introduced by Cherry&Fenton 2004 and is the same as u_c in the original model.

Definition at line 122 of file FentonKarma.cpp.

124 : CellModel(pSession, pField)
125{
126 model_variant = pSession->GetSolverInfoAsEnum<FentonKarma::Variants>(
127 "CellModelVariant");
128
129 C_m = 1; // picoF
130 V_0 = -85;
131 V_fi = 15;
132
133 switch (model_variant)
134 {
135 case eBR: // (Fenton, Karma, Chaos 8(1), 1998)
136 g_fi_max = 4;
137 tau_r = 33.33;
138 tau_si = 29;
139 tau_0 = 12.5;
140 tau_v_plus = 3.33;
141 tau_v1_minus = 1250;
142 tau_v2_minus = 19.6;
143 tau_w_plus = 870;
144 tau_w_minus = 41;
145 u_c = 0.13;
146 u_v = 0.04;
147 u_r = 0.13;
148 u_fi = 0.13;
149 u_csi = 0.85;
150 k1 = 10;
151 k2 = 0.0;
152 break;
153 case eMBR: // (Fenton, Karma, Chaos 8(1), 1998)
154 g_fi_max = 4;
155 tau_r = 50;
156 tau_si = 44.84;
157 tau_0 = 8.3;
158 tau_v_plus = 3.33;
159 tau_v1_minus = 1000;
160 tau_v2_minus = 19.2;
161 tau_w_plus = 667;
162 tau_w_minus = 11;
163 u_c = 0.13;
164 u_v = 0.04;
165 u_r = 0.13;
166 u_fi = 0.13;
167 u_csi = 0.85;
168 k1 = 10;
169 k2 = 0.0;
170 break;
171 case eMLR1: // (Fenton, Karma, Chaos 8(1), 1998)
172 g_fi_max = 5.8;
173 tau_r = 130;
174 tau_si = 127;
175 tau_0 = 12.5;
176 tau_v_plus = 10;
177 tau_v1_minus = 18.2;
178 tau_v2_minus = 18.2;
179 tau_w_plus = 1020;
180 tau_w_minus = 80;
181 u_c = 0.13;
182 u_v = 0.0;
183 u_r = 0.13;
184 u_fi = 0.13;
185 u_csi = 0.85;
186 k1 = 10;
187 k2 = 0.0;
188 break;
189 case eGP: // (Fenton, Karma, Chaos 8(1), 1998)
190 g_fi_max = 8.7;
191 tau_r = 25;
192 tau_si = 22.22;
193 tau_0 = 12.5;
194 tau_v_plus = 10;
195 tau_v1_minus = 333;
196 tau_v2_minus = 40;
197 tau_w_plus = 1000;
198 tau_w_minus = 65;
199 u_c = 0.13;
200 u_v = 0.025;
201 u_r = 0.13;
202 u_fi = 0.13;
203 u_csi = 0.85;
204 k1 = 10;
205 k2 = 0.0;
206 break;
207 case eCF1: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
208 g_fi_max = 6.6666;
209 tau_r = 12.5;
210 tau_si = 10;
211 tau_0 = 1.5;
212 tau_v_plus = 10;
213 tau_v1_minus = 350;
214 tau_v2_minus = 80;
215 tau_w_plus = 562;
216 tau_w_minus = 48.5;
217 u_c = 0.25;
218 u_v = 0.001;
219 u_r = 0.25;
220 u_fi = 0.15;
221 u_csi = 0.2;
222 k1 = 15;
223 k2 = 0;
224 break;
225 case eCF2a: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
226 g_fi_max = 6.6666;
227 tau_r = 31;
228 tau_si = 26.5;
229 tau_0 = 1.5;
230 tau_v_plus = 10;
231 tau_v1_minus = 20;
232 tau_v2_minus = 20;
233 tau_w_plus = 800;
234 tau_w_minus = 45;
235 u_c = 0.25;
236 u_v = 0.05;
237 u_r = 0.6;
238 u_fi = 0.11;
239 u_csi = 0.7;
240 k1 = 10;
241 k2 = 1;
242 break;
243 case eCF2b: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
244 g_fi_max = 6.6666;
245 tau_r = 31;
246 tau_si = 26.5;
247 tau_0 = 1.5;
248 tau_v_plus = 10;
249 tau_v1_minus = 100;
250 tau_v2_minus = 20;
251 tau_w_plus = 800;
252 tau_w_minus = 45;
253 u_c = 0.25;
254 u_v = 0.05;
255 u_r = 0.6;
256 u_fi = 0.11;
257 u_csi = 0.7;
258 k1 = 10;
259 k2 = 1;
260 break;
261 case eCF2c: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
262 g_fi_max = 6.6666;
263 tau_r = 31;
264 tau_si = 26.5;
265 tau_0 = 1.5;
266 tau_v_plus = 10;
267 tau_v1_minus = 150;
268 tau_v2_minus = 20;
269 tau_w_plus = 800;
270 tau_w_minus = 45;
271 u_c = 0.25;
272 u_v = 0.05;
273 u_r = 0.6;
274 u_fi = 0.11;
275 u_csi = 0.7;
276 k1 = 10;
277 k2 = 1;
278 break;
279 case eCF3a: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
280 g_fi_max = 13.3333;
281 tau_r = 38;
282 tau_si = 127;
283 tau_0 = 8.3;
284 tau_v_plus = 3.33;
285 tau_v1_minus = 45;
286 tau_v2_minus = 300;
287 tau_w_plus = 600;
288 tau_w_minus = 40;
289 tau_y_plus = 1000;
290 tau_y_minus = 230;
291 u_c = 0.25;
292 u_v = 0.5;
293 u_r = 0.25;
294 u_fi = 0.25;
295 u_csi = 0.7;
296 k1 = 60;
297 k2 = 0;
298 break;
299 case eCF3b: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
300 g_fi_max = 13.3333;
301 tau_r = 38;
302 tau_si = 127;
303 tau_0 = 8.3;
304 tau_v_plus = 3.33;
305 tau_v1_minus = 20;
306 tau_v2_minus = 300;
307 tau_w_plus = 600;
308 tau_w_minus = 40;
309 tau_y_plus = 1000;
310 tau_y_minus = 230;
311 u_c = 0.25;
312 u_v = 0.5;
313 u_r = 0.25;
314 u_fi = 0.25;
315 u_csi = 0.7;
316 k1 = 60;
317 k2 = 0;
318 break;
319 case eFC2002Set1a: // (Fenton, Cherry, Chaos 12(852), 2002)
320 g_fi_max = 1 / 0.41; // 2.44 - Fig 1A
321 tau_r = 50;
322 tau_si = 45;
323 tau_0 = 1 / 0.12; // 8.33
324 tau_v_plus = 3.33;
325 tau_v1_minus = 1000;
326 tau_v2_minus = 19.6;
327 tau_w_plus = 667;
328 tau_w_minus = 11;
329 u_c = 0.13;
330 u_v = 0.055;
331 u_r = u_c;
332 u_fi = u_c;
333 u_csi = 0.85;
334 k1 = 10;
335 k2 = 0;
336 break;
337 case eFC2002Set1b: // (Fenton, Cherry, Chaos 12(852), 2002)
338 g_fi_max = 1 / 0.392; // 2.55 - Fig 1B
339 tau_r = 50;
340 tau_si = 45;
341 tau_0 = 1 / 0.12; // 8.33
342 tau_v_plus = 3.33;
343 tau_v1_minus = 1000;
344 tau_v2_minus = 19.6;
345 tau_w_plus = 667;
346 tau_w_minus = 11;
347 u_c = 0.13;
348 u_v = 0.055;
349 u_r = u_c;
350 u_fi = u_c;
351 u_csi = 0.85;
352 k1 = 10;
353 k2 = 0;
354 break;
355 case eFC2002Set1c: // (Fenton, Cherry, Chaos 12(852), 2002)
356 g_fi_max = 1 / 0.381; // 2.62 - Fig 1C
357 tau_r = 50;
358 tau_si = 45;
359 tau_0 = 1 / 0.12; // 8.33
360 tau_v_plus = 3.33;
361 tau_v1_minus = 1000;
362 tau_v2_minus = 19.6;
363 tau_w_plus = 667;
364 tau_w_minus = 11;
365 u_c = 0.13;
366 u_v = 0.055;
367 u_r = u_c;
368 u_fi = u_c;
369 u_csi = 0.85;
370 k1 = 10;
371 k2 = 0;
372 break;
373 case eFC2002Set1d: // (Fenton, Cherry, Chaos 12(852), 2002)
374 g_fi_max = 1 / 0.36; // 2.77 - Fig 1D
375 tau_r = 50;
376 tau_si = 45;
377 tau_0 = 1 / 0.12; // 8.33
378 tau_v_plus = 3.33;
379 tau_v1_minus = 1000;
380 tau_v2_minus = 19.6;
381 tau_w_plus = 667;
382 tau_w_minus = 11;
383 u_c = 0.13;
384 u_v = 0.055;
385 u_r = u_c;
386 u_fi = u_c;
387 u_csi = 0.85;
388 k1 = 10;
389 k2 = 0;
390 break;
391 case eFC2002Set1e: // (Fenton, Cherry, Chaos 12(852), 2002)
392 g_fi_max = 1 / 0.25; // 4 - Fig 1E
393 tau_r = 50;
394 tau_si = 45;
395 tau_0 = 1 / 0.12; // 8.33
396 tau_v_plus = 3.33;
397 tau_v1_minus = 1000;
398 tau_v2_minus = 19.6;
399 tau_w_plus = 667;
400 tau_w_minus = 11;
401 u_c = 0.13;
402 u_v = 0.055;
403 u_r = u_c;
404 u_fi = u_c;
405 u_csi = 0.85;
406 k1 = 10;
407 k2 = 0;
408 break;
409 case eFC2002Set2: // (Fenton, Cherry, Chaos 12(852), 2002)
410 g_fi_max = 4;
411 tau_r = 190;
412 tau_si = 100000;
413 tau_0 = 10;
414 tau_v_plus = 10;
415 tau_v1_minus = 10;
416 tau_v2_minus = 10;
417 tau_w_plus = 100000;
418 tau_w_minus = 100000;
419 u_c = 0.13;
420 u_v = 100;
421 u_r = u_c;
422 u_fi = u_c;
423 u_csi = 100;
424 k1 = 10;
425 k2 = 0;
426 break;
427 case eFC2002Set4a: // (Fenton, Cherry, Chaos 12(852), 2002)
428 g_fi_max = 1.0 / 0.407;
429 tau_r = 34;
430 tau_si = 26.5;
431 tau_0 = 9;
432 tau_v_plus = 3.33;
433 tau_v1_minus = 5; // Opposite convention
434 tau_v2_minus = 15.6; // to the paper
435 tau_w_plus = 350;
436 tau_w_minus = 80;
437 u_c = 0.15;
438 u_v = 0.04;
439 u_r = u_c;
440 u_fi = u_c;
441 u_csi = 0.45;
442 k1 = 15;
443 k2 = 0;
444 break;
445 case eFC2002Set4b: // (Fenton, Cherry, Chaos 12(852), 2002)
446 g_fi_max = 1.0 / 0.41;
447 tau_r = 34;
448 tau_si = 26.5;
449 tau_0 = 9;
450 tau_v_plus = 3.33;
451 tau_v1_minus = 5; // Opposite convention
452 tau_v2_minus = 15.6; // to the paper
453 tau_w_plus = 350;
454 tau_w_minus = 80;
455 u_c = 0.15;
456 u_v = 0.04;
457 u_r = u_c;
458 u_fi = u_c;
459 u_csi = 0.45;
460 k1 = 15;
461 k2 = 0;
462 break;
463 case eFC2002Set4c: // (Fenton, Cherry, Chaos 12(852), 2002)
464 g_fi_max = 1.0 / 0.405;
465 tau_r = 34;
466 tau_si = 26.5;
467 tau_0 = 9;
468 tau_v_plus = 3.33;
469 tau_v1_minus = 5; // Opposite convention
470 tau_v2_minus = 15.6; // to the paper
471 tau_w_plus = 350;
472 tau_w_minus = 80;
473 u_c = 0.15;
474 u_v = 0.04;
475 u_r = u_c;
476 u_fi = u_c;
477 u_csi = 0.45;
478 k1 = 15;
479 k2 = 0;
480 break;
481 case eFC2002Set4d: // (Fenton, Cherry, Chaos 12(852), 2002)
482 g_fi_max = 1.0 / 0.4;
483 tau_r = 34;
484 tau_si = 26.5;
485 tau_0 = 9;
486 tau_v_plus = 3.33;
487 tau_v1_minus = 5; // Opposite convention
488 tau_v2_minus = 15.6; // to the paper
489 tau_w_plus = 350;
490 tau_w_minus = 80;
491 u_c = 0.15;
492 u_v = 0.04;
493 u_r = u_c;
494 u_fi = u_c;
495 u_csi = 0.45;
496 k1 = 15;
497 k2 = 0;
498 break;
499 case eFC2002Set5: // (Fenton, Cherry, Chaos 12(852), 2002)
500 g_fi_max = 2.76;
501 tau_r = 33.33;
502 tau_si = 29;
503 tau_0 = 5;
504 tau_v_plus = 3.33;
505 tau_v1_minus = 2; // Opposite convention
506 tau_v2_minus = 12; // to the paper
507 tau_w_plus = 1000;
508 tau_w_minus = 100;
509 u_c = 0.13;
510 u_v = 0.14;
511 u_r = u_c;
512 u_fi = u_c;
513 u_csi = 0.70;
514 k1 = 15;
515 k2 = 0;
516 break;
517 case eFC2002Set6: // (Fenton, Cherry, Chaos 12(852), 2002)
518 g_fi_max = 2.53;
519 tau_r = 33.33;
520 tau_si = 29;
521 tau_0 = 9;
522 tau_v_plus = 3.33;
523 tau_v1_minus = 8; // Opposite convention
524 tau_v2_minus = 9; // to the paper
525 tau_w_plus = 250;
526 tau_w_minus = 60;
527 u_c = 0.13;
528 u_v = 0.04;
529 u_r = u_c;
530 u_fi = u_c;
531 u_csi = 0.50;
532 k1 = 15;
533 k2 = 0;
534 break;
535 case eFC2002Set7: // (Fenton, Cherry, Chaos 12(852), 2002)
536 g_fi_max = 4;
537 tau_r = 100;
538 tau_si = 100000;
539 tau_0 = 12;
540 tau_v_plus = 10;
541 tau_v1_minus = 7; // Opposite convention
542 tau_v2_minus = 7; // to the paper
543 tau_w_plus = 100000;
544 tau_w_minus = 100000;
545 u_c = 0.13;
546 u_v = 100;
547 u_r = u_c;
548 u_fi = u_c;
549 u_csi = 100;
550 k1 = 10;
551 k2 = 0;
552 break;
553 case eFC2002Set8: // (Fenton, Cherry, Chaos 12(852), 2002)
554 g_fi_max = 2.2;
555 tau_r = 33.25;
556 tau_si = 29;
557 tau_0 = 12.5;
558 tau_v_plus = 13.03;
559 tau_v1_minus = 1250; // Opposite convention
560 tau_v2_minus = 19.6; // to the paper
561 tau_w_plus = 800;
562 tau_w_minus = 40;
563 u_c = 0.13;
564 u_v = 0.04;
565 u_r = u_c;
566 u_fi = u_c;
567 u_csi = 0.85;
568 k1 = 10;
569 k2 = 0;
570 break;
571 case eFC2002Set9: // (Fenton, Cherry, Chaos 12(852), 2002)
572 g_fi_max = 4;
573 tau_r = 28;
574 tau_si = 29;
575 tau_0 = 12.5;
576 tau_v_plus = 3.33;
577 tau_v1_minus = 2; // Opposite convention
578 tau_v2_minus = 15; // to the paper
579 tau_w_plus = 670;
580 tau_w_minus = 61;
581 u_c = 0.13;
582 u_v = 0.05;
583 u_r = u_c;
584 u_fi = u_c;
585 u_csi = 0.45;
586 k1 = 10;
587 k2 = 0;
588 break;
589 case eLawson: // (Lawson, Front. Physiol, 2018)
590 g_fi_max = 3;
591 tau_r = 1 / 0.02;
592 tau_si = 1 / 0.0223;
593 tau_0 = 1 / 0.12;
594 tau_v_plus = 3.33;
595 tau_v1_minus = 1000;
596 tau_v2_minus = 19.6;
597 tau_w_plus = 667;
598 tau_w_minus = 11;
599 u_c = 0.13;
600 u_v = 0.055;
601 u_r = u_c;
602 u_fi = u_c;
603 u_csi = 0.85;
604 k1 = 10;
605 k2 = 0;
606 break;
607 case eCAF:
608 g_fi_max = 8;
609 tau_r = 70;
610 tau_si = 114;
611 tau_0 = 32.5; // 8.33
612 tau_v_plus = 5.75;
613 tau_v1_minus = 60;
614 tau_v2_minus = 82.5;
615 tau_w_plus = 300;
616 tau_w_minus = 400;
617 u_c = 0.16;
618 u_v = 0.04;
619 u_r = u_c;
620 u_fi = u_c;
621 u_csi = 0.85;
622 k1 = 10;
623 k2 = 0;
624 break;
625 }
626
627 tau_d = C_m / g_fi_max;
628
629 isCF3 = (model_variant == eCF3a || model_variant == eCF3b);
630
631 // List gates and concentrations
632 m_gates.push_back(1);
633 m_gates.push_back(2);
634 m_nvar = 3;
635
636 // Cherry-Fenton 2004 Model 3 has extra gating variable
637 if (isCF3)
638 {
639 m_gates.push_back(3);
640 m_nvar = 4;
641 }
642
643 ASSERTL0(!isCF3, "Cherry-Fenton model 3 not implemented yet.");
644}
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:208
Nektar::CellModel::m_gates
std::vector< int > m_gates
Indices of cell model variables which are gates.
Definition: CellModel.h:141
Nektar::CellModel::m_nvar
size_t m_nvar
Number of variables in cell model (inc. transmembrane voltage)
Definition: CellModel.h:119
Nektar::CellModel::CellModel
CellModel(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Definition: CellModel.cpp:66
Nektar::FentonKarma::tau_v1_minus
NekDouble tau_v1_minus
Definition: FentonKarma.h:86
Nektar::FentonKarma::tau_w_plus
NekDouble tau_w_plus
Definition: FentonKarma.h:98
Nektar::FentonKarma::tau_y_plus
NekDouble tau_y_plus
Definition: FentonKarma.h:92
Nektar::FentonKarma::model_variant
enum Variants model_variant
Definition: FentonKarma.h:132
Nektar::FentonKarma::tau_v2_minus
NekDouble tau_v2_minus
Definition: FentonKarma.h:87
Nektar::FentonKarma::g_fi_max
NekDouble g_fi_max
Definition: FentonKarma.h:84
Nektar::FentonKarma::tau_v_plus
NekDouble tau_v_plus
Definition: FentonKarma.h:88
Nektar::FentonKarma::tau_w_minus
NekDouble tau_w_minus
Definition: FentonKarma.h:97
Nektar::FentonKarma::tau_y_minus
NekDouble tau_y_minus
Definition: FentonKarma.h:93

References ASSERTL0, C_m, eBR, eCAF, eCF1, eCF2a, eCF2b, eCF2c, eCF3a, eCF3b, eFC2002Set1a, eFC2002Set1b, eFC2002Set1c, eFC2002Set1d, eFC2002Set1e, eFC2002Set2, eFC2002Set4a, eFC2002Set4b, eFC2002Set4c, eFC2002Set4d, eFC2002Set5, eFC2002Set6, eFC2002Set7, eFC2002Set8, eFC2002Set9, eGP, eLawson, eMBR, eMLR1, g_fi_max, isCF3, k1, k2, Nektar::CellModel::m_gates, Nektar::CellModel::m_nvar, model_variant, tau_0, tau_d, tau_r, tau_si, tau_v1_minus, tau_v2_minus, tau_v_plus, tau_w_minus, tau_w_plus, tau_y_minus, tau_y_plus, u_c, u_csi, u_fi, u_r, u_v, V_0, and V_fi.

◆ ~FentonKarma()

Nektar::FentonKarma::~FentonKarma ( )
override

Destructor.

Definition at line 649 of file FentonKarma.cpp.

650{
651}

Member Function Documentation

◆ create()

static CellModelSharedPtr Nektar::FentonKarma::create ( const LibUtilities::SessionReaderSharedPtr &  pSession,
const MultiRegions::ExpListSharedPtr &  pField 
)
inlinestatic

Creates an instance of this class.

Definition at line 46 of file FentonKarma.h.

49 {
50 return MemoryManager<FentonKarma>::AllocateSharedPtr(pSession, pField);
51 }
Nektar::MemoryManager::AllocateSharedPtr
static std::shared_ptr< DataType > AllocateSharedPtr(const Args &...args)
Allocate a shared pointer from the memory pool.
Definition: NekMemoryManager.hpp:166

References Nektar::MemoryManager< DataType >::AllocateSharedPtr().

◆ v_GenerateSummary()

void Nektar::FentonKarma::v_GenerateSummary ( SummaryList &  s)
overrideprotectedvirtual

Prints a summary of the model parameters.

Implements Nektar::CellModel.

Definition at line 732 of file FentonKarma.cpp.

733{
734 SolverUtils::AddSummaryItem(s, "Cell model", "Fenton Karma");
735 SolverUtils::AddSummaryItem(s, "Cell model var.", lookupIds[model_variant]);
736}
Nektar::FentonKarma::lookupIds
static std::string lookupIds[]
Definition: FentonKarma.h:134
Nektar::SolverUtils::AddSummaryItem
void AddSummaryItem(SummaryList &l, const std::string &name, const std::string &value)
Adds a summary item to the summary info list.
Definition: Misc.cpp:47

References Nektar::SolverUtils::AddSummaryItem(), lookupIds, and model_variant.

◆ v_GetCellVarName()

std::string Nektar::FentonKarma::v_GetCellVarName ( size_t  idx)
overrideprotectedvirtual

Reimplemented from Nektar::CellModel.

Definition at line 749 of file FentonKarma.cpp.

750{
751 switch (idx)
752 {
753 case 0:
754 return "u";
755 case 1:
756 return "v";
757 case 2:
758 return "w";
759 case 3:
760 return "y";
761 default:
762 return "unknown";
763 }
764}

◆ v_SetInitialConditions()

void Nektar::FentonKarma::v_SetInitialConditions ( )
overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 738 of file FentonKarma.cpp.

739{
740 Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
741 Vmath::Fill(m_nq, 1.0, m_cellSol[1], 1);
742 Vmath::Fill(m_nq, 1.0, m_cellSol[2], 1);
743 if (isCF3)
744 {
745 Vmath::Fill(m_nq, 0.1, m_cellSol[2], 1);
746 }
747}
Nektar::CellModel::m_cellSol
Array< OneD, Array< OneD, NekDouble > > m_cellSol
Cell model solution variables.
Definition: CellModel.h:126
Nektar::CellModel::m_nq
size_t m_nq
Number of physical points.
Definition: CellModel.h:117
Vmath::Fill
void Fill(int n, const T alpha, T *x, const int incx)
Fill a vector with a constant value.
Definition: Vmath.hpp:54

References Vmath::Fill(), isCF3, Nektar::CellModel::m_cellSol, and Nektar::CellModel::m_nq.

◆ v_Update()

void Nektar::FentonKarma::v_Update ( const Array< OneD, const Array< OneD, NekDouble > > &  inarray,
Array< OneD, Array< OneD, NekDouble > > &  outarray,
const NekDouble  time 
)
overrideprotectedvirtual

Computes the reaction terms $f(u,v)$ and $g(u,v)$.

Implements Nektar::CellModel.

Definition at line 653 of file FentonKarma.cpp.

657{
658 ASSERTL0(inarray.get() != outarray.get(),
659 "Must have different arrays for input and output.");
660
661 // Variables
662 // 0 u membrane potential
663 // 1 v v gate
664 // 2 w w gate
665
666 // Declare pointers
667 const NekDouble *u = &inarray[0][0];
668 const NekDouble *v = &inarray[1][0];
669 const NekDouble *w = &inarray[2][0];
670 const NekDouble *y = isCF3 ? &inarray[3][0] : nullptr;
671 NekDouble *u_new = &outarray[0][0];
672 NekDouble *v_new = &outarray[1][0];
673 NekDouble *w_new = &outarray[2][0];
674 // NekDouble *y_new = isCF3 ? &outarray[3][0] : 0;
675 NekDouble *v_tau = &m_gates_tau[0][0];
676 NekDouble *w_tau = &m_gates_tau[1][0];
677 // NekDouble *y_tau = isCF3 ? &m_gates_tau[2][0] : 0;
678
679 // Temporary variables
680 NekDouble J_fi, J_so, J_si, h1, h2, h3, alpha, beta;
681
682 double V;
683 // Compute rates for each point in domain
684 for (size_t i = 0; i < m_nq; ++i)
685 {
686 // *u is dimensional
687 // V is non-dimensional for what follows
688 V = (*u - V_0) / (V_fi - V_0);
689
690 // Heavyside functions
691 h1 = (V < u_c) ? 0.0 : 1.0;
692 h2 = (V < u_v) ? 0.0 : 1.0;
693 h3 = (V < u_r) ? 0.0 : 1.0;
694
695 // w-gate
696 alpha = (1 - h1) / tau_w_minus;
697 beta = h1 / tau_w_plus;
698 *w_tau = 1.0 / (alpha + beta);
699 *w_new = alpha * (*w_tau);
700
701 // v-gate
702 alpha = (1 - h1) / (h2 * tau_v1_minus + (1 - h2) * tau_v2_minus);
703 beta = h1 / tau_v_plus;
704 *v_tau = 1.0 / (alpha + beta);
705 *v_new = alpha * (*v_tau);
706
707 // y-gate
708 if (isCF3)
709 {
710 // TODO: implementation for y_tau and y_new
711 }
712
713 // J_fi
714 J_fi = -(*v) * h1 * (1 - V) * (V - u_c) / tau_d;
715
716 // J_so
717 // added extra (1-k2*v) term from Cherry&Fenton 2004
718 J_so = V * (1 - h3) * (1 - k2 * (*v)) / tau_0 +
719 (isCF3 ? h3 * V * (*y) / tau_r : h3 / tau_r);
720
721 // J_si
722 J_si = -(*w) * (1 + tanh(k1 * (V - u_csi))) / (2.0 * tau_si);
723
724 // u
725 *u_new = -J_fi - J_so - J_si;
726 *u_new *= C_m * (V_fi - V_0);
727
728 ++u, ++v, ++w, ++u_new, ++v_new, ++w_new, ++v_tau, ++w_tau;
729 }
730}
Nektar::CellModel::m_gates_tau
Array< OneD, Array< OneD, NekDouble > > m_gates_tau
Storage for gate tau values.
Definition: CellModel.h:143
Nektar::LibUtilities::beta
@ beta
Gauss Radau pinned at x=-1,.
Definition: PointsType.h:59
Nektar::UnitTests::w
std::vector< double > w(NPUPPER)
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:43

References ASSERTL0, Nektar::LibUtilities::beta, C_m, isCF3, k1, k2, Nektar::CellModel::m_gates_tau, Nektar::CellModel::m_nq, tau_0, tau_d, tau_r, tau_si, tau_v1_minus, tau_v2_minus, tau_v_plus, tau_w_minus, tau_w_plus, u_c, u_csi, u_r, u_v, V_0, V_fi, and Nektar::UnitTests::w().

Member Data Documentation

◆ C_m

NekDouble Nektar::FentonKarma::C_m
private

Definition at line 77 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ className

std::string Nektar::FentonKarma::className
static
Initial value:
=
GetCellModelFactory().RegisterCreatorFunction(
"FentonKarma", FentonKarma::create, "Phenomenological Model.")
Nektar::FentonKarma::create
static CellModelSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Creates an instance of this class.
Definition: FentonKarma.h:46
Nektar::LibUtilities::NekFactory::RegisterCreatorFunction
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, std::string pDesc="")
Register a class with the factory.
Definition: NekFactory.hpp:197
Nektar::GetCellModelFactory
CellModelFactory & GetCellModelFactory()
Definition: CellModel.cpp:46

Name of class.

Definition at line 54 of file FentonKarma.h.

◆ def

std::string Nektar::FentonKarma::def
staticprivate
Initial value:
=
LibUtilities::SessionReader::RegisterDefaultSolverInfo("CellModelVariant",
"BR")
Nektar::LibUtilities::SessionReader::RegisterDefaultSolverInfo
static std::string RegisterDefaultSolverInfo(const std::string &pName, const std::string &pValue)
Registers the default string value of a solver info property.
Definition: SessionReader.h:593

Definition at line 135 of file FentonKarma.h.

◆ g_fi_max

NekDouble Nektar::FentonKarma::g_fi_max
private

Definition at line 84 of file FentonKarma.h.

Referenced by FentonKarma().

◆ isCF3

bool Nektar::FentonKarma::isCF3
private

Definition at line 100 of file FentonKarma.h.

Referenced by FentonKarma(), v_SetInitialConditions(), and v_Update().

◆ k1

NekDouble Nektar::FentonKarma::k1
private

Definition at line 95 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ k2

NekDouble Nektar::FentonKarma::k2
private

Definition at line 96 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ lookupIds

std::string Nektar::FentonKarma::lookupIds
staticprivate

Definition at line 134 of file FentonKarma.h.

Referenced by v_GenerateSummary().

◆ model_variant

enum Variants Nektar::FentonKarma::model_variant
private

Definition at line 132 of file FentonKarma.h.

Referenced by FentonKarma(), and v_GenerateSummary().

◆ tau_0

NekDouble Nektar::FentonKarma::tau_0
private

Definition at line 89 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_d

NekDouble Nektar::FentonKarma::tau_d
private

Definition at line 85 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_r

NekDouble Nektar::FentonKarma::tau_r
private

Definition at line 90 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_si

NekDouble Nektar::FentonKarma::tau_si
private

Definition at line 91 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v1_minus

NekDouble Nektar::FentonKarma::tau_v1_minus
private

Definition at line 86 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v2_minus

NekDouble Nektar::FentonKarma::tau_v2_minus
private

Definition at line 87 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v_plus

NekDouble Nektar::FentonKarma::tau_v_plus
private

Definition at line 88 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_w_minus

NekDouble Nektar::FentonKarma::tau_w_minus
private

Definition at line 97 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_w_plus

NekDouble Nektar::FentonKarma::tau_w_plus
private

Definition at line 98 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_y_minus

NekDouble Nektar::FentonKarma::tau_y_minus
private

Definition at line 93 of file FentonKarma.h.

Referenced by FentonKarma().

◆ tau_y_plus

NekDouble Nektar::FentonKarma::tau_y_plus
private

Definition at line 92 of file FentonKarma.h.

Referenced by FentonKarma().

◆ u_c

NekDouble Nektar::FentonKarma::u_c
private

Definition at line 81 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_csi

NekDouble Nektar::FentonKarma::u_csi
private

Definition at line 94 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_fi

NekDouble Nektar::FentonKarma::u_fi
private

Definition at line 80 of file FentonKarma.h.

Referenced by FentonKarma().

◆ u_r

NekDouble Nektar::FentonKarma::u_r
private

Definition at line 83 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_v

NekDouble Nektar::FentonKarma::u_v
private

Definition at line 82 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ V_0

NekDouble Nektar::FentonKarma::V_0
private

Definition at line 78 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ V_fi

NekDouble Nektar::FentonKarma::V_fi
private

Definition at line 79 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

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