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...
 
virtual ~FentonKarma ()
 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...
 
unsigned int GetNumCellVariables ()
 
std::string GetCellVarName (unsigned int idx)
 
Array< OneD, NekDouble > GetCellSolutionCoeffs (unsigned int idx)
 
Array< OneD, NekDouble > GetCellSolution (unsigned int 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

virtual void v_Update (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
 Computes the reaction terms $f(u,v)$ and $g(u,v)$. More...
 
virtual void v_GenerateSummary (SummaryList &s)
 Prints a summary of the model parameters. More...
 
virtual void v_SetInitialConditions ()
 
virtual std::string v_GetCellVarName (unsigned int idx)
 
- Protected Member Functions inherited from Nektar::CellModel
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...
 
int m_nq
 Number of physical points. More...
 
int m_nvar
 Number of variables in cell model (inc. transmembrane voltage) More...
 
NekDouble m_lastTime
 Timestep for pde model. More...
 
int 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 105 of file FentonKarma.h.

105  {
106  eBR,
107  eMBR,
108  eMLR1,
109  eGP,
110  eCF1,
111  eCF2a,
112  eCF2b,
113  eCF2c,
114  eCF3a,
115  eCF3b,
116  eFC2002Set1a,
117  eFC2002Set1b,
118  eFC2002Set1c,
119  eFC2002Set1d,
120  eFC2002Set1e,
121  eFC2002Set2,
122  eFC2002Set4a,
123  eFC2002Set4b,
124  eFC2002Set4c,
125  eFC2002Set4d,
126  eFC2002Set5,
127  eFC2002Set6,
128  eFC2002Set7,
129  eFC2002Set8,
130  eFC2002Set9,
131  eLawson,
132  eCAF
133  };

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 125 of file FentonKarma.cpp.

128  : CellModel(pSession, pField)
129  {
130  model_variant = pSession->GetSolverInfoAsEnum<FentonKarma::Variants>(
131  "CellModelVariant");
132 
133  C_m = 1; // picoF
134  V_0 = -85;
135  V_fi = 15;
136 
137  switch (model_variant) {
138  case eBR: // (Fenton, Karma, Chaos 8(1), 1998)
139  g_fi_max = 4;
140  tau_r = 33.33;
141  tau_si = 29;
142  tau_0 = 12.5;
143  tau_v_plus = 3.33;
144  tau_v1_minus = 1250;
145  tau_v2_minus = 19.6;
146  tau_w_plus = 870;
147  tau_w_minus = 41;
148  u_c = 0.13;
149  u_v = 0.04;
150  u_r = 0.13;
151  u_fi = 0.13;
152  u_csi = 0.85;
153  k1 = 10;
154  k2 = 0.0;
155  break;
156  case eMBR: // (Fenton, Karma, Chaos 8(1), 1998)
157  g_fi_max = 4;
158  tau_r = 50;
159  tau_si = 44.84;
160  tau_0 = 8.3;
161  tau_v_plus = 3.33;
162  tau_v1_minus = 1000;
163  tau_v2_minus = 19.2;
164  tau_w_plus = 667;
165  tau_w_minus = 11;
166  u_c = 0.13;
167  u_v = 0.04;
168  u_r = 0.13;
169  u_fi = 0.13;
170  u_csi = 0.85;
171  k1 = 10;
172  k2 = 0.0;
173  break;
174  case eMLR1: // (Fenton, Karma, Chaos 8(1), 1998)
175  g_fi_max = 5.8;
176  tau_r = 130;
177  tau_si = 127;
178  tau_0 = 12.5;
179  tau_v_plus = 10;
180  tau_v1_minus = 18.2;
181  tau_v2_minus = 18.2;
182  tau_w_plus = 1020;
183  tau_w_minus = 80;
184  u_c = 0.13;
185  u_v = 0.0;
186  u_r = 0.13;
187  u_fi = 0.13;
188  u_csi = 0.85;
189  k1 = 10;
190  k2 = 0.0;
191  break;
192  case eGP: // (Fenton, Karma, Chaos 8(1), 1998)
193  g_fi_max = 8.7;
194  tau_r = 25;
195  tau_si = 22.22;
196  tau_0 = 12.5;
197  tau_v_plus = 10;
198  tau_v1_minus = 333;
199  tau_v2_minus = 40;
200  tau_w_plus = 1000;
201  tau_w_minus = 65;
202  u_c = 0.13;
203  u_v = 0.025;
204  u_r = 0.13;
205  u_fi = 0.13;
206  u_csi = 0.85;
207  k1 = 10;
208  k2 = 0.0;
209  break;
210  case eCF1: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
211  g_fi_max = 6.6666;
212  tau_r = 12.5;
213  tau_si = 10;
214  tau_0 = 1.5;
215  tau_v_plus = 10;
216  tau_v1_minus = 350;
217  tau_v2_minus = 80;
218  tau_w_plus = 562;
219  tau_w_minus = 48.5;
220  u_c = 0.25;
221  u_v = 0.001;
222  u_r = 0.25;
223  u_fi = 0.15;
224  u_csi = 0.2;
225  k1 = 15;
226  k2 = 0;
227  break;
228  case eCF2a: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
229  g_fi_max = 6.6666;
230  tau_r = 31;
231  tau_si = 26.5;
232  tau_0 = 1.5;
233  tau_v_plus = 10;
234  tau_v1_minus = 20;
235  tau_v2_minus = 20;
236  tau_w_plus = 800;
237  tau_w_minus = 45;
238  u_c = 0.25;
239  u_v = 0.05;
240  u_r = 0.6;
241  u_fi = 0.11;
242  u_csi = 0.7;
243  k1 = 10;
244  k2 = 1;
245  break;
246  case eCF2b: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
247  g_fi_max = 6.6666;
248  tau_r = 31;
249  tau_si = 26.5;
250  tau_0 = 1.5;
251  tau_v_plus = 10;
252  tau_v1_minus = 100;
253  tau_v2_minus = 20;
254  tau_w_plus = 800;
255  tau_w_minus = 45;
256  u_c = 0.25;
257  u_v = 0.05;
258  u_r = 0.6;
259  u_fi = 0.11;
260  u_csi = 0.7;
261  k1 = 10;
262  k2 = 1;
263  break;
264  case eCF2c: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
265  g_fi_max = 6.6666;
266  tau_r = 31;
267  tau_si = 26.5;
268  tau_0 = 1.5;
269  tau_v_plus = 10;
270  tau_v1_minus = 150;
271  tau_v2_minus = 20;
272  tau_w_plus = 800;
273  tau_w_minus = 45;
274  u_c = 0.25;
275  u_v = 0.05;
276  u_r = 0.6;
277  u_fi = 0.11;
278  u_csi = 0.7;
279  k1 = 10;
280  k2 = 1;
281  break;
282  case eCF3a: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
283  g_fi_max = 13.3333;
284  tau_r = 38;
285  tau_si = 127;
286  tau_0 = 8.3;
287  tau_v_plus = 3.33;
288  tau_v1_minus = 45;
289  tau_v2_minus = 300;
290  tau_w_plus = 600;
291  tau_w_minus = 40;
292  tau_y_plus = 1000;
293  tau_y_minus = 230;
294  u_c = 0.25;
295  u_v = 0.5;
296  u_r = 0.25;
297  u_fi = 0.25;
298  u_csi = 0.7;
299  k1 = 60;
300  k2 = 0;
301  break;
302  case eCF3b: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
303  g_fi_max = 13.3333;
304  tau_r = 38;
305  tau_si = 127;
306  tau_0 = 8.3;
307  tau_v_plus = 3.33;
308  tau_v1_minus = 20;
309  tau_v2_minus = 300;
310  tau_w_plus = 600;
311  tau_w_minus = 40;
312  tau_y_plus = 1000;
313  tau_y_minus = 230;
314  u_c = 0.25;
315  u_v = 0.5;
316  u_r = 0.25;
317  u_fi = 0.25;
318  u_csi = 0.7;
319  k1 = 60;
320  k2 = 0;
321  break;
322  case eFC2002Set1a: // (Fenton, Cherry, Chaos 12(852), 2002)
323  g_fi_max = 1/0.41; //2.44 - Fig 1A
324  tau_r = 50;
325  tau_si = 45;
326  tau_0 = 1/0.12; //8.33
327  tau_v_plus = 3.33;
328  tau_v1_minus = 1000;
329  tau_v2_minus = 19.6;
330  tau_w_plus = 667;
331  tau_w_minus = 11;
332  u_c = 0.13;
333  u_v = 0.055;
334  u_r = u_c;
335  u_fi = u_c;
336  u_csi = 0.85;
337  k1 = 10;
338  k2 = 0;
339  break;
340  case eFC2002Set1b: // (Fenton, Cherry, Chaos 12(852), 2002)
341  g_fi_max = 1/0.392; //2.55 - Fig 1B
342  tau_r = 50;
343  tau_si = 45;
344  tau_0 = 1/0.12; //8.33
345  tau_v_plus = 3.33;
346  tau_v1_minus = 1000;
347  tau_v2_minus = 19.6;
348  tau_w_plus = 667;
349  tau_w_minus = 11;
350  u_c = 0.13;
351  u_v = 0.055;
352  u_r = u_c;
353  u_fi = u_c;
354  u_csi = 0.85;
355  k1 = 10;
356  k2 = 0;
357  break;
358  case eFC2002Set1c: // (Fenton, Cherry, Chaos 12(852), 2002)
359  g_fi_max = 1/0.381; //2.62 - Fig 1C
360  tau_r = 50;
361  tau_si = 45;
362  tau_0 = 1/0.12; //8.33
363  tau_v_plus = 3.33;
364  tau_v1_minus = 1000;
365  tau_v2_minus = 19.6;
366  tau_w_plus = 667;
367  tau_w_minus = 11;
368  u_c = 0.13;
369  u_v = 0.055;
370  u_r = u_c;
371  u_fi = u_c;
372  u_csi = 0.85;
373  k1 = 10;
374  k2 = 0;
375  break;
376  case eFC2002Set1d: // (Fenton, Cherry, Chaos 12(852), 2002)
377  g_fi_max = 1/0.36; //2.77 - Fig 1D
378  tau_r = 50;
379  tau_si = 45;
380  tau_0 = 1/0.12; //8.33
381  tau_v_plus = 3.33;
382  tau_v1_minus = 1000;
383  tau_v2_minus = 19.6;
384  tau_w_plus = 667;
385  tau_w_minus = 11;
386  u_c = 0.13;
387  u_v = 0.055;
388  u_r = u_c;
389  u_fi = u_c;
390  u_csi = 0.85;
391  k1 = 10;
392  k2 = 0;
393  break;
394  case eFC2002Set1e: // (Fenton, Cherry, Chaos 12(852), 2002)
395  g_fi_max = 1/0.25; // 4 - Fig 1E
396  tau_r = 50;
397  tau_si = 45;
398  tau_0 = 1/0.12; //8.33
399  tau_v_plus = 3.33;
400  tau_v1_minus = 1000;
401  tau_v2_minus = 19.6;
402  tau_w_plus = 667;
403  tau_w_minus = 11;
404  u_c = 0.13;
405  u_v = 0.055;
406  u_r = u_c;
407  u_fi = u_c;
408  u_csi = 0.85;
409  k1 = 10;
410  k2 = 0;
411  break;
412  case eFC2002Set2: // (Fenton, Cherry, Chaos 12(852), 2002)
413  g_fi_max = 4;
414  tau_r = 190;
415  tau_si = 100000;
416  tau_0 = 10;
417  tau_v_plus = 10;
418  tau_v1_minus = 10;
419  tau_v2_minus = 10;
420  tau_w_plus = 100000;
421  tau_w_minus = 100000;
422  u_c = 0.13;
423  u_v = 100;
424  u_r = u_c;
425  u_fi = u_c;
426  u_csi = 100;
427  k1 = 10;
428  k2 = 0;
429  break;
430  case eFC2002Set4a: // (Fenton, Cherry, Chaos 12(852), 2002)
431  g_fi_max = 1.0/0.407;
432  tau_r = 34;
433  tau_si = 26.5;
434  tau_0 = 9;
435  tau_v_plus = 3.33;
436  tau_v1_minus = 5; // Opposite convention
437  tau_v2_minus = 15.6; // to the paper
438  tau_w_plus = 350;
439  tau_w_minus = 80;
440  u_c = 0.15;
441  u_v = 0.04;
442  u_r = u_c;
443  u_fi = u_c;
444  u_csi = 0.45;
445  k1 = 15;
446  k2 = 0;
447  break;
448  case eFC2002Set4b: // (Fenton, Cherry, Chaos 12(852), 2002)
449  g_fi_max = 1.0/0.41;
450  tau_r = 34;
451  tau_si = 26.5;
452  tau_0 = 9;
453  tau_v_plus = 3.33;
454  tau_v1_minus = 5; // Opposite convention
455  tau_v2_minus = 15.6; // to the paper
456  tau_w_plus = 350;
457  tau_w_minus = 80;
458  u_c = 0.15;
459  u_v = 0.04;
460  u_r = u_c;
461  u_fi = u_c;
462  u_csi = 0.45;
463  k1 = 15;
464  k2 = 0;
465  break;
466  case eFC2002Set4c: // (Fenton, Cherry, Chaos 12(852), 2002)
467  g_fi_max = 1.0/0.405;
468  tau_r = 34;
469  tau_si = 26.5;
470  tau_0 = 9;
471  tau_v_plus = 3.33;
472  tau_v1_minus = 5; // Opposite convention
473  tau_v2_minus = 15.6; // to the paper
474  tau_w_plus = 350;
475  tau_w_minus = 80;
476  u_c = 0.15;
477  u_v = 0.04;
478  u_r = u_c;
479  u_fi = u_c;
480  u_csi = 0.45;
481  k1 = 15;
482  k2 = 0;
483  break;
484  case eFC2002Set4d: // (Fenton, Cherry, Chaos 12(852), 2002)
485  g_fi_max = 1.0/0.4;
486  tau_r = 34;
487  tau_si = 26.5;
488  tau_0 = 9;
489  tau_v_plus = 3.33;
490  tau_v1_minus = 5; // Opposite convention
491  tau_v2_minus = 15.6; // to the paper
492  tau_w_plus = 350;
493  tau_w_minus = 80;
494  u_c = 0.15;
495  u_v = 0.04;
496  u_r = u_c;
497  u_fi = u_c;
498  u_csi = 0.45;
499  k1 = 15;
500  k2 = 0;
501  break;
502  case eFC2002Set5: // (Fenton, Cherry, Chaos 12(852), 2002)
503  g_fi_max = 2.76;
504  tau_r = 33.33;
505  tau_si = 29;
506  tau_0 = 5;
507  tau_v_plus = 3.33;
508  tau_v1_minus = 2; // Opposite convention
509  tau_v2_minus = 12; // to the paper
510  tau_w_plus = 1000;
511  tau_w_minus = 100;
512  u_c = 0.13;
513  u_v = 0.14;
514  u_r = u_c;
515  u_fi = u_c;
516  u_csi = 0.70;
517  k1 = 15;
518  k2 = 0;
519  break;
520  case eFC2002Set6: // (Fenton, Cherry, Chaos 12(852), 2002)
521  g_fi_max = 2.53;
522  tau_r = 33.33;
523  tau_si = 29;
524  tau_0 = 9;
525  tau_v_plus = 3.33;
526  tau_v1_minus = 8; // Opposite convention
527  tau_v2_minus = 9; // to the paper
528  tau_w_plus = 250;
529  tau_w_minus = 60;
530  u_c = 0.13;
531  u_v = 0.04;
532  u_r = u_c;
533  u_fi = u_c;
534  u_csi = 0.50;
535  k1 = 15;
536  k2 = 0;
537  break;
538  case eFC2002Set7: // (Fenton, Cherry, Chaos 12(852), 2002)
539  g_fi_max = 4;
540  tau_r = 100;
541  tau_si = 100000;
542  tau_0 = 12;
543  tau_v_plus = 10;
544  tau_v1_minus = 7; // Opposite convention
545  tau_v2_minus = 7; // to the paper
546  tau_w_plus = 100000;
547  tau_w_minus = 100000;
548  u_c = 0.13;
549  u_v = 100;
550  u_r = u_c;
551  u_fi = u_c;
552  u_csi = 100;
553  k1 = 10;
554  k2 = 0;
555  break;
556  case eFC2002Set8: // (Fenton, Cherry, Chaos 12(852), 2002)
557  g_fi_max = 2.2;
558  tau_r = 33.25;
559  tau_si = 29;
560  tau_0 = 12.5;
561  tau_v_plus = 13.03;
562  tau_v1_minus = 1250; // Opposite convention
563  tau_v2_minus = 19.6; // to the paper
564  tau_w_plus = 800;
565  tau_w_minus = 40;
566  u_c = 0.13;
567  u_v = 0.04;
568  u_r = u_c;
569  u_fi = u_c;
570  u_csi = 0.85;
571  k1 = 10;
572  k2 = 0;
573  break;
574  case eFC2002Set9: // (Fenton, Cherry, Chaos 12(852), 2002)
575  g_fi_max = 4;
576  tau_r = 28;
577  tau_si = 29;
578  tau_0 = 12.5;
579  tau_v_plus = 3.33;
580  tau_v1_minus = 2; // Opposite convention
581  tau_v2_minus = 15; // to the paper
582  tau_w_plus = 670;
583  tau_w_minus = 61;
584  u_c = 0.13;
585  u_v = 0.05;
586  u_r = u_c;
587  u_fi = u_c;
588  u_csi = 0.45;
589  k1 = 10;
590  k2 = 0;
591  break;
592  case eLawson: // (Lawson, Front. Physiol, 2018)
593  g_fi_max = 3;
594  tau_r = 1/0.02;
595  tau_si = 1/0.0223;
596  tau_0 = 1/0.12;
597  tau_v_plus = 3.33;
598  tau_v1_minus = 1000;
599  tau_v2_minus = 19.6;
600  tau_w_plus = 667;
601  tau_w_minus = 11;
602  u_c = 0.13;
603  u_v = 0.055;
604  u_r = u_c;
605  u_fi = u_c;
606  u_csi = 0.85;
607  k1 = 10;
608  k2 = 0;
609  break;
610  case eCAF:
611  g_fi_max = 8;
612  tau_r = 70;
613  tau_si = 114;
614  tau_0 = 32.5; //8.33
615  tau_v_plus = 5.75;
616  tau_v1_minus = 60;
617  tau_v2_minus = 82.5;
618  tau_w_plus = 300;
619  tau_w_minus = 400;
620  u_c = 0.16;
621  u_v = 0.04;
622  u_r = u_c;
623  u_fi = u_c;
624  u_csi = 0.85;
625  k1 = 10;
626  k2 = 0;
627  break;
628  }
629 
630  tau_d = C_m/g_fi_max;
631 
632  isCF3 = (model_variant == eCF3a || model_variant == eCF3b);
633 
634  // List gates and concentrations
635  m_gates.push_back(1);
636  m_gates.push_back(2);
637  m_nvar = 3;
638 
639  // Cherry-Fenton 2004 Model 3 has extra gating variable
640  if (isCF3)
641  {
642  m_gates.push_back(3);
643  m_nvar = 4;
644  }
645 
646  ASSERTL0(!isCF3, "Cherry-Fenton model 3 not implemented yet.");
647  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:216
Nektar::CellModel::m_gates
std::vector< int > m_gates
Indices of cell model variables which are gates.
Definition: CellModel.h:140
Nektar::CellModel::CellModel
CellModel(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Definition: CellModel.cpp:66
Nektar::CellModel::m_nvar
int m_nvar
Number of variables in cell model (inc. transmembrane voltage)
Definition: CellModel.h:118
Nektar::FentonKarma::tau_v1_minus
NekDouble tau_v1_minus
Definition: FentonKarma.h:89
Nektar::FentonKarma::tau_w_plus
NekDouble tau_w_plus
Definition: FentonKarma.h:101
Nektar::FentonKarma::tau_y_plus
NekDouble tau_y_plus
Definition: FentonKarma.h:95
Nektar::FentonKarma::model_variant
enum Variants model_variant
Definition: FentonKarma.h:134
Nektar::FentonKarma::tau_v2_minus
NekDouble tau_v2_minus
Definition: FentonKarma.h:90
Nektar::FentonKarma::g_fi_max
NekDouble g_fi_max
Definition: FentonKarma.h:87
Nektar::FentonKarma::tau_v_plus
NekDouble tau_v_plus
Definition: FentonKarma.h:91
Nektar::FentonKarma::tau_w_minus
NekDouble tau_w_minus
Definition: FentonKarma.h:100
Nektar::FentonKarma::tau_y_minus
NekDouble tau_y_minus
Definition: FentonKarma.h:96

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 ( )
virtual

Destructor.

Definition at line 654 of file FentonKarma.cpp.

655  {
656 
657  }

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>
51  ::AllocateSharedPtr(pSession, pField);
52  }
Nektar::MemoryManager::AllocateSharedPtr
static std::shared_ptr< DataType > AllocateSharedPtr(const Args &...args)
Allocate a shared pointer from the memory pool.
Definition: NekMemoryManager.hpp:171

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

◆ v_GenerateSummary()

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

Prints a summary of the model parameters.

Implements Nektar::CellModel.

Definition at line 742 of file FentonKarma.cpp.

743  {
744  SolverUtils::AddSummaryItem(s, "Cell model", "Fenton Karma");
745  SolverUtils::AddSummaryItem(s, "Cell model var.", lookupIds[model_variant]);
746  }
Nektar::FentonKarma::lookupIds
static std::string lookupIds[]
Definition: FentonKarma.h:136
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 ( unsigned int  idx)
protectedvirtual

Reimplemented from Nektar::CellModel.

Definition at line 761 of file FentonKarma.cpp.

762  {
763  switch (idx)
764  {
765  case 0: return "u";
766  case 1: return "v";
767  case 2: return "w";
768  case 3: return "y";
769  default: return "unknown";
770  }
771  }

◆ v_SetInitialConditions()

void Nektar::FentonKarma::v_SetInitialConditions ( )
protectedvirtual

Implements Nektar::CellModel.

Definition at line 749 of file FentonKarma.cpp.

750  {
751  Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
752  Vmath::Fill(m_nq, 1.0, m_cellSol[1], 1);
753  Vmath::Fill(m_nq, 1.0, m_cellSol[2], 1);
754  if (isCF3)
755  {
756  Vmath::Fill(m_nq, 0.1, m_cellSol[2], 1);
757  }
758 
759  }
Nektar::CellModel::m_cellSol
Array< OneD, Array< OneD, NekDouble > > m_cellSol
Cell model solution variables.
Definition: CellModel.h:125
Nektar::CellModel::m_nq
int m_nq
Number of physical points.
Definition: CellModel.h:116
Vmath::Fill
void Fill(int n, const T alpha, T *x, const int incx)
Fill a vector with a constant value.
Definition: Vmath.cpp:45

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 
)
protectedvirtual

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

Implements Nektar::CellModel.

Definition at line 661 of file FentonKarma.cpp.

665  {
666  ASSERTL0(inarray.get() != outarray.get(),
667  "Must have different arrays for input and output.");
668 
669  // Variables
670  // 0 u membrane potential
671  // 1 v v gate
672  // 2 w w gate
673  int n = m_nq;
674  int i = 0;
675 
676  // Declare pointers
677  const NekDouble *u = &inarray[0][0];
678  const NekDouble *v = &inarray[1][0];
679  const NekDouble *w = &inarray[2][0];
680  const NekDouble *y = isCF3 ? &inarray[3][0] : 0;
681  NekDouble *u_new = &outarray[0][0];
682  NekDouble *v_new = &outarray[1][0];
683  NekDouble *w_new = &outarray[2][0];
684  //NekDouble *y_new = isCF3 ? &outarray[3][0] : 0;
685  NekDouble *v_tau = &m_gates_tau[0][0];
686  NekDouble *w_tau = &m_gates_tau[1][0];
687  //NekDouble *y_tau = isCF3 ? &m_gates_tau[2][0] : 0;
688 
689  // Temporary variables
690  NekDouble J_fi, J_so, J_si, h1, h2, h3, alpha, beta;
691 
692  double V;
693  // Compute rates for each point in domain
694  for (i = 0; i < n; ++i)
695  {
696  // *u is dimensional
697  // V is non-dimensional for what follows
698  V = (*u - V_0)/(V_fi - V_0);
699 
700  // Heavyside functions
701  h1 = (V < u_c) ? 0.0 : 1.0;
702  h2 = (V < u_v) ? 0.0 : 1.0;
703  h3 = (V < u_r) ? 0.0 : 1.0;
704 
705  // w-gate
706  alpha = (1-h1)/tau_w_minus;
707  beta = h1/tau_w_plus;
708  *w_tau = 1.0 / (alpha + beta);
709  *w_new = alpha * (*w_tau);
710 
711  // v-gate
712  alpha = (1-h1)/(h2*tau_v1_minus + (1-h2)*tau_v2_minus);
713  beta = h1/tau_v_plus;
714  *v_tau = 1.0 / (alpha + beta);
715  *v_new = alpha * (*v_tau);
716 
717  // y-gate
718  if (isCF3)
719  {
720  // TODO: implementation for y_tau and y_new
721  }
722 
723  // J_fi
724  J_fi = -(*v)*h1*(1 - V)*(V - u_c)/tau_d;
725 
726  // J_so
727  // added extra (1-k2*v) term from Cherry&Fenton 2004
728  J_so = V*(1-h3)*(1-k2*(*v))/tau_0 +
729  (isCF3 ? h3*V*(*y)/tau_r : h3/tau_r);
730 
731  // J_si
732  J_si = -(*w)*(1 + tanh(k1*(V - u_csi)))/(2.0*tau_si);
733 
734  // u
735  *u_new = -J_fi - J_so - J_si;
736  *u_new *= C_m*(V_fi - V_0);
737 
738  ++u, ++v, ++w, ++u_new, ++v_new, ++w_new, ++v_tau, ++w_tau;
739  }
740  }
Nektar::CellModel::m_gates_tau
Array< OneD, Array< OneD, NekDouble > > m_gates_tau
Storage for gate tau values.
Definition: CellModel.h:142
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:43

References ASSERTL0, 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, and V_fi.

Member Data Documentation

◆ C_m

NekDouble Nektar::FentonKarma::C_m
private

Definition at line 80 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:200
Nektar::GetCellModelFactory
CellModelFactory & GetCellModelFactory()
Definition: CellModel.cpp:46

Name of class.

Definition at line 55 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:659

Definition at line 137 of file FentonKarma.h.

◆ g_fi_max

NekDouble Nektar::FentonKarma::g_fi_max
private

Definition at line 87 of file FentonKarma.h.

Referenced by FentonKarma().

◆ isCF3

bool Nektar::FentonKarma::isCF3
private

Definition at line 103 of file FentonKarma.h.

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

◆ k1

NekDouble Nektar::FentonKarma::k1
private

Definition at line 98 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ k2

NekDouble Nektar::FentonKarma::k2
private

Definition at line 99 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ lookupIds

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

Definition at line 136 of file FentonKarma.h.

Referenced by v_GenerateSummary().

◆ model_variant

enum Variants Nektar::FentonKarma::model_variant
private

Definition at line 103 of file FentonKarma.h.

Referenced by FentonKarma(), and v_GenerateSummary().

◆ tau_0

NekDouble Nektar::FentonKarma::tau_0
private

Definition at line 92 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_d

NekDouble Nektar::FentonKarma::tau_d
private

Definition at line 88 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_r

NekDouble Nektar::FentonKarma::tau_r
private

Definition at line 93 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_si

NekDouble Nektar::FentonKarma::tau_si
private

Definition at line 94 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v1_minus

NekDouble Nektar::FentonKarma::tau_v1_minus
private

Definition at line 89 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v2_minus

NekDouble Nektar::FentonKarma::tau_v2_minus
private

Definition at line 90 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_v_plus

NekDouble Nektar::FentonKarma::tau_v_plus
private

Definition at line 91 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_w_minus

NekDouble Nektar::FentonKarma::tau_w_minus
private

Definition at line 100 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_w_plus

NekDouble Nektar::FentonKarma::tau_w_plus
private

Definition at line 101 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ tau_y_minus

NekDouble Nektar::FentonKarma::tau_y_minus
private

Definition at line 96 of file FentonKarma.h.

Referenced by FentonKarma().

◆ tau_y_plus

NekDouble Nektar::FentonKarma::tau_y_plus
private

Definition at line 95 of file FentonKarma.h.

Referenced by FentonKarma().

◆ u_c

NekDouble Nektar::FentonKarma::u_c
private

Definition at line 84 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_csi

NekDouble Nektar::FentonKarma::u_csi
private

Definition at line 97 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_fi

NekDouble Nektar::FentonKarma::u_fi
private

Definition at line 83 of file FentonKarma.h.

Referenced by FentonKarma().

◆ u_r

NekDouble Nektar::FentonKarma::u_r
private

Definition at line 86 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ u_v

NekDouble Nektar::FentonKarma::u_v
private

Definition at line 85 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ V_0

NekDouble Nektar::FentonKarma::V_0
private

Definition at line 81 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

◆ V_fi

NekDouble Nektar::FentonKarma::V_fi
private

Definition at line 82 of file FentonKarma.h.

Referenced by FentonKarma(), and v_Update().

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