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,
  eFC2002Set4, 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 
eFC2002Set4 
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  eFC2002Set4,
123  eFC2002Set5,
124  eFC2002Set6,
125  eFC2002Set7,
126  eFC2002Set8,
127  eFC2002Set9,
128  eLawson,
129  eCAF
130  };

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 115 of file FentonKarma.cpp.

References ASSERTL0, C_m, eBR, eCAF, eCF1, eCF2a, eCF2b, eCF2c, eCF3a, eCF3b, eFC2002Set1a, eFC2002Set1b, eFC2002Set1c, eFC2002Set1d, eFC2002Set1e, eFC2002Set2, eFC2002Set4, 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.

118  : CellModel(pSession, pField)
119  {
120  model_variant = pSession->GetSolverInfoAsEnum<FentonKarma::Variants>(
121  "CellModelVariant");
122 
123  C_m = 1; // picoF
124  V_0 = -85;
125  V_fi = 15;
126 
127  switch (model_variant) {
128  case eBR: // (Fenton, Karma, Chaos 8(1), 1998)
129  g_fi_max = 4;
130  tau_r = 33.33;
131  tau_si = 29;
132  tau_0 = 12.5;
133  tau_v_plus = 3.33;
134  tau_v1_minus = 1250;
135  tau_v2_minus = 19.6;
136  tau_w_plus = 870;
137  tau_w_minus = 41;
138  u_c = 0.13;
139  u_v = 0.04;
140  u_r = 0.13;
141  u_fi = 0.13;
142  u_csi = 0.85;
143  k1 = 10;
144  k2 = 0.0;
145  break;
146  case eMBR: // (Fenton, Karma, Chaos 8(1), 1998)
147  g_fi_max = 4;
148  tau_r = 50;
149  tau_si = 44.84;
150  tau_0 = 8.3;
151  tau_v_plus = 3.33;
152  tau_v1_minus = 1000;
153  tau_v2_minus = 19.2;
154  tau_w_plus = 667;
155  tau_w_minus = 11;
156  u_c = 0.13;
157  u_v = 0.04;
158  u_r = 0.13;
159  u_fi = 0.13;
160  u_csi = 0.85;
161  k1 = 10;
162  k2 = 0.0;
163  break;
164  case eMLR1: // (Fenton, Karma, Chaos 8(1), 1998)
165  g_fi_max = 5.8;
166  tau_r = 130;
167  tau_si = 127;
168  tau_0 = 12.5;
169  tau_v_plus = 10;
170  tau_v1_minus = 18.2;
171  tau_v2_minus = 18.2;
172  tau_w_plus = 1020;
173  tau_w_minus = 80;
174  u_c = 0.13;
175  u_v = 0.0;
176  u_r = 0.13;
177  u_fi = 0.13;
178  u_csi = 0.85;
179  k1 = 10;
180  k2 = 0.0;
181  break;
182  case eGP: // (Fenton, Karma, Chaos 8(1), 1998)
183  g_fi_max = 8.7;
184  tau_r = 25;
185  tau_si = 22.22;
186  tau_0 = 12.5;
187  tau_v_plus = 10;
188  tau_v1_minus = 333;
189  tau_v2_minus = 40;
190  tau_w_plus = 1000;
191  tau_w_minus = 65;
192  u_c = 0.13;
193  u_v = 0.025;
194  u_r = 0.13;
195  u_fi = 0.13;
196  u_csi = 0.85;
197  k1 = 10;
198  k2 = 0.0;
199  break;
200  case eCF1: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
201  g_fi_max = 6.6666;
202  tau_r = 12.5;
203  tau_si = 10;
204  tau_0 = 1.5;
205  tau_v_plus = 10;
206  tau_v1_minus = 350;
207  tau_v2_minus = 80;
208  tau_w_plus = 562;
209  tau_w_minus = 48.5;
210  u_c = 0.25;
211  u_v = 0.001;
212  u_r = 0.25;
213  u_fi = 0.15;
214  u_csi = 0.2;
215  k1 = 15;
216  k2 = 0;
217  break;
218  case eCF2a: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
219  g_fi_max = 6.6666;
220  tau_r = 31;
221  tau_si = 26.5;
222  tau_0 = 1.5;
223  tau_v_plus = 10;
224  tau_v1_minus = 20;
225  tau_v2_minus = 20;
226  tau_w_plus = 800;
227  tau_w_minus = 45;
228  u_c = 0.25;
229  u_v = 0.05;
230  u_r = 0.6;
231  u_fi = 0.11;
232  u_csi = 0.7;
233  k1 = 10;
234  k2 = 1;
235  break;
236  case eCF2b: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
237  g_fi_max = 6.6666;
238  tau_r = 31;
239  tau_si = 26.5;
240  tau_0 = 1.5;
241  tau_v_plus = 10;
242  tau_v1_minus = 100;
243  tau_v2_minus = 20;
244  tau_w_plus = 800;
245  tau_w_minus = 45;
246  u_c = 0.25;
247  u_v = 0.05;
248  u_r = 0.6;
249  u_fi = 0.11;
250  u_csi = 0.7;
251  k1 = 10;
252  k2 = 1;
253  break;
254  case eCF2c: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
255  g_fi_max = 6.6666;
256  tau_r = 31;
257  tau_si = 26.5;
258  tau_0 = 1.5;
259  tau_v_plus = 10;
260  tau_v1_minus = 150;
261  tau_v2_minus = 20;
262  tau_w_plus = 800;
263  tau_w_minus = 45;
264  u_c = 0.25;
265  u_v = 0.05;
266  u_r = 0.6;
267  u_fi = 0.11;
268  u_csi = 0.7;
269  k1 = 10;
270  k2 = 1;
271  break;
272  case eCF3a: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
273  g_fi_max = 13.3333;
274  tau_r = 38;
275  tau_si = 127;
276  tau_0 = 8.3;
277  tau_v_plus = 3.33;
278  tau_v1_minus = 45;
279  tau_v2_minus = 300;
280  tau_w_plus = 600;
281  tau_w_minus = 40;
282  tau_y_plus = 1000;
283  tau_y_minus = 230;
284  u_c = 0.25;
285  u_v = 0.5;
286  u_r = 0.25;
287  u_fi = 0.25;
288  u_csi = 0.7;
289  k1 = 60;
290  k2 = 0;
291  break;
292  case eCF3b: // (Cherry, Fenton, Am J Physiol Heart 286, 2004)
293  g_fi_max = 13.3333;
294  tau_r = 38;
295  tau_si = 127;
296  tau_0 = 8.3;
297  tau_v_plus = 3.33;
298  tau_v1_minus = 20;
299  tau_v2_minus = 300;
300  tau_w_plus = 600;
301  tau_w_minus = 40;
302  tau_y_plus = 1000;
303  tau_y_minus = 230;
304  u_c = 0.25;
305  u_v = 0.5;
306  u_r = 0.25;
307  u_fi = 0.25;
308  u_csi = 0.7;
309  k1 = 60;
310  k2 = 0;
311  break;
312  case eFC2002Set1a: // (Fenton, Cherry, Chaos 12(852), 2002)
313  g_fi_max = 1/0.41; //2.44 - Fig 1A
314  tau_r = 50;
315  tau_si = 45;
316  tau_0 = 1/0.12; //8.33
317  tau_v_plus = 3.33;
318  tau_v1_minus = 1000;
319  tau_v2_minus = 19.6;
320  tau_w_plus = 667;
321  tau_w_minus = 11;
322  u_c = 0.13;
323  u_v = 0.055;
324  u_r = u_c;
325  u_fi = u_c;
326  u_csi = 0.85;
327  k1 = 10;
328  k2 = 0;
329  break;
330  case eFC2002Set1b: // (Fenton, Cherry, Chaos 12(852), 2002)
331  g_fi_max = 1/0.392; //2.55 - Fig 1B
332  tau_r = 50;
333  tau_si = 45;
334  tau_0 = 1/0.12; //8.33
335  tau_v_plus = 3.33;
336  tau_v1_minus = 1000;
337  tau_v2_minus = 19.6;
338  tau_w_plus = 667;
339  tau_w_minus = 11;
340  u_c = 0.13;
341  u_v = 0.055;
342  u_r = u_c;
343  u_fi = u_c;
344  u_csi = 0.85;
345  k1 = 10;
346  k2 = 0;
347  break;
348  case eFC2002Set1c: // (Fenton, Cherry, Chaos 12(852), 2002)
349  g_fi_max = 1/0.381; //2.62 - Fig 1C
350  tau_r = 50;
351  tau_si = 45;
352  tau_0 = 1/0.12; //8.33
353  tau_v_plus = 3.33;
354  tau_v1_minus = 1000;
355  tau_v2_minus = 19.6;
356  tau_w_plus = 667;
357  tau_w_minus = 11;
358  u_c = 0.13;
359  u_v = 0.055;
360  u_r = u_c;
361  u_fi = u_c;
362  u_csi = 0.85;
363  k1 = 10;
364  k2 = 0;
365  break;
366  case eFC2002Set1d: // (Fenton, Cherry, Chaos 12(852), 2002)
367  g_fi_max = 1/0.36; //2.77 - Fig 1D
368  tau_r = 50;
369  tau_si = 45;
370  tau_0 = 1/0.12; //8.33
371  tau_v_plus = 3.33;
372  tau_v1_minus = 1000;
373  tau_v2_minus = 19.6;
374  tau_w_plus = 667;
375  tau_w_minus = 11;
376  u_c = 0.13;
377  u_v = 0.055;
378  u_r = u_c;
379  u_fi = u_c;
380  u_csi = 0.85;
381  k1 = 10;
382  k2 = 0;
383  break;
384  case eFC2002Set1e: // (Fenton, Cherry, Chaos 12(852), 2002)
385  g_fi_max = 1/0.25; // 4 - Fig 1E
386  tau_r = 50;
387  tau_si = 45;
388  tau_0 = 1/0.12; //8.33
389  tau_v_plus = 3.33;
390  tau_v1_minus = 1000;
391  tau_v2_minus = 19.6;
392  tau_w_plus = 667;
393  tau_w_minus = 11;
394  u_c = 0.13;
395  u_v = 0.055;
396  u_r = u_c;
397  u_fi = u_c;
398  u_csi = 0.85;
399  k1 = 10;
400  k2 = 0;
401  break;
402  case eFC2002Set2: // (Fenton, Cherry, Chaos 12(852), 2002)
403  g_fi_max = 4;
404  tau_r = 190;
405  tau_si = 100000;
406  tau_0 = 10;
407  tau_v_plus = 10;
408  tau_v1_minus = 10;
409  tau_v2_minus = 10;
410  tau_w_plus = 100000;
411  tau_w_minus = 100000;
412  u_c = 0.13;
413  u_v = 100;
414  u_r = u_c;
415  u_fi = u_c;
416  u_csi = 100;
417  k1 = 10;
418  k2 = 0;
419  break;
420  case eFC2002Set4: // (Fenton, Cherry, Chaos 12(852), 2002)
421  g_fi_max = 2.46;
422  tau_r = 34;
423  tau_si = 26.5;
424  tau_0 = 9;
425  tau_v_plus = 3.33;
426  tau_v1_minus = 5; // Opposite convention
427  tau_v2_minus = 15.6; // to the paper
428  tau_w_plus = 350;
429  tau_w_minus = 80;
430  u_c = 0.15;
431  u_v = 0.04;
432  u_r = u_c;
433  u_fi = u_c;
434  u_csi = 0.45;
435  k1 = 15;
436  k2 = 0;
437  break;
438  case eFC2002Set5: // (Fenton, Cherry, Chaos 12(852), 2002)
439  g_fi_max = 2.76;
440  tau_r = 33.33;
441  tau_si = 29;
442  tau_0 = 5;
443  tau_v_plus = 3.33;
444  tau_v1_minus = 2; // Opposite convention
445  tau_v2_minus = 12; // to the paper
446  tau_w_plus = 1000;
447  tau_w_minus = 100;
448  u_c = 0.13;
449  u_v = 0.14;
450  u_r = u_c;
451  u_fi = u_c;
452  u_csi = 0.70;
453  k1 = 15;
454  k2 = 0;
455  break;
456  case eFC2002Set6: // (Fenton, Cherry, Chaos 12(852), 2002)
457  g_fi_max = 2.53;
458  tau_r = 33.33;
459  tau_si = 29;
460  tau_0 = 9;
461  tau_v_plus = 3.33;
462  tau_v1_minus = 8; // Opposite convention
463  tau_v2_minus = 9; // to the paper
464  tau_w_plus = 250;
465  tau_w_minus = 60;
466  u_c = 0.13;
467  u_v = 0.04;
468  u_r = u_c;
469  u_fi = u_c;
470  u_csi = 0.50;
471  k1 = 15;
472  k2 = 0;
473  break;
474  case eFC2002Set7: // (Fenton, Cherry, Chaos 12(852), 2002)
475  g_fi_max = 4;
476  tau_r = 100;
477  tau_si = 100000;
478  tau_0 = 12;
479  tau_v_plus = 10;
480  tau_v1_minus = 7; // Opposite convention
481  tau_v2_minus = 7; // to the paper
482  tau_w_plus = 100000;
483  tau_w_minus = 100000;
484  u_c = 0.13;
485  u_v = 100;
486  u_r = u_c;
487  u_fi = u_c;
488  u_csi = 100;
489  k1 = 10;
490  k2 = 0;
491  break;
492  case eFC2002Set8: // (Fenton, Cherry, Chaos 12(852), 2002)
493  g_fi_max = 2.2;
494  tau_r = 33.25;
495  tau_si = 29;
496  tau_0 = 12.5;
497  tau_v_plus = 13.03;
498  tau_v1_minus = 1250; // Opposite convention
499  tau_v2_minus = 19.6; // to the paper
500  tau_w_plus = 800;
501  tau_w_minus = 40;
502  u_c = 0.13;
503  u_v = 0.04;
504  u_r = u_c;
505  u_fi = u_c;
506  u_csi = 0.85;
507  k1 = 10;
508  k2 = 0;
509  break;
510  case eFC2002Set9: // (Fenton, Cherry, Chaos 12(852), 2002)
511  g_fi_max = 4;
512  tau_r = 28;
513  tau_si = 29;
514  tau_0 = 12.5;
515  tau_v_plus = 3.33;
516  tau_v1_minus = 2; // Opposite convention
517  tau_v2_minus = 15; // to the paper
518  tau_w_plus = 670;
519  tau_w_minus = 61;
520  u_c = 0.13;
521  u_v = 0.05;
522  u_r = u_c;
523  u_fi = u_c;
524  u_csi = 0.45;
525  k1 = 10;
526  k2 = 0;
527  break;
528  case eLawson: // (Lawson, Front. Physiol, 2018)
529  g_fi_max = 3;
530  tau_r = 1/0.02;
531  tau_si = 1/0.0223;
532  tau_0 = 1/0.12;
533  tau_v_plus = 3.33;
534  tau_v1_minus = 1000;
535  tau_v2_minus = 19.6;
536  tau_w_plus = 667;
537  tau_w_minus = 11;
538  u_c = 0.13;
539  u_v = 0.055;
540  u_r = u_c;
541  u_fi = u_c;
542  u_csi = 0.85;
543  k1 = 10;
544  k2 = 0;
545  break;
546  case eCAF:
547  g_fi_max = 8;
548  tau_r = 70;
549  tau_si = 114;
550  tau_0 = 32.5; //8.33
551  tau_v_plus = 5.75;
552  tau_v1_minus = 60;
553  tau_v2_minus = 82.5;
554  tau_w_plus = 300;
555  tau_w_minus = 400;
556  u_c = 0.16;
557  u_v = 0.04;
558  u_r = u_c;
559  u_fi = u_c;
560  u_csi = 0.85;
561  k1 = 10;
562  k2 = 0;
563  break;
564  }
565 
566  tau_d = C_m/g_fi_max;
567 
568  isCF3 = (model_variant == eCF3a || model_variant == eCF3b);
569 
570  // List gates and concentrations
571  m_gates.push_back(1);
572  m_gates.push_back(2);
573  m_nvar = 3;
574 
575  // Cherry-Fenton 2004 Model 3 has extra gating variable
576  if (isCF3)
577  {
578  m_gates.push_back(3);
579  m_nvar = 4;
580  }
581 
582  ASSERTL0(!isCF3, "Cherry-Fenton model 3 not implemented yet.");
583  }
Nektar::FentonKarma::tau_y_minus
NekDouble tau_y_minus
Definition: FentonKarma.h:96
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:216
Nektar::FentonKarma::tau_y_plus
NekDouble tau_y_plus
Definition: FentonKarma.h:95
Nektar::FentonKarma::tau_v1_minus
NekDouble tau_v1_minus
Definition: FentonKarma.h:89
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::CellModel::m_gates
std::vector< int > m_gates
Indices of cell model variables which are gates.
Definition: CellModel.h:140
Nektar::FentonKarma::tau_w_plus
NekDouble tau_w_plus
Definition: FentonKarma.h:101
Nektar::FentonKarma::tau_v2_minus
NekDouble tau_v2_minus
Definition: FentonKarma.h:90
Nektar::FentonKarma::model_variant
enum Variants model_variant
Definition: FentonKarma.h:131
Nektar::FentonKarma::g_fi_max
NekDouble g_fi_max
Definition: FentonKarma.h:87
Nektar::FentonKarma::tau_w_minus
NekDouble tau_w_minus
Definition: FentonKarma.h:100
Nektar::FentonKarma::tau_v_plus
NekDouble tau_v_plus
Definition: FentonKarma.h:91

◆ ~FentonKarma()

Nektar::FentonKarma::~FentonKarma ( )
virtual

Destructor.

Definition at line 590 of file FentonKarma.cpp.

591  {
592 
593  }

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.

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

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:161

◆ v_GenerateSummary()

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

Prints a summary of the model parameters.

Implements Nektar::CellModel.

Definition at line 678 of file FentonKarma.cpp.

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

679  {
680  SolverUtils::AddSummaryItem(s, "Cell model", "Fenton Karma");
681  SolverUtils::AddSummaryItem(s, "Cell model var.", lookupIds[model_variant]);
682  }
Nektar::FentonKarma::lookupIds
static std::string lookupIds[]
Definition: FentonKarma.h:133
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:49
Nektar::FentonKarma::model_variant
enum Variants model_variant
Definition: FentonKarma.h:131

◆ v_GetCellVarName()

std::string Nektar::FentonKarma::v_GetCellVarName ( unsigned int  idx)
protectedvirtual

Reimplemented from Nektar::CellModel.

Definition at line 697 of file FentonKarma.cpp.

698  {
699  switch (idx)
700  {
701  case 0: return "u";
702  case 1: return "v";
703  case 2: return "w";
704  case 3: return "y";
705  default: return "unknown";
706  }
707  }

◆ v_SetInitialConditions()

void Nektar::FentonKarma::v_SetInitialConditions ( )
protectedvirtual

Implements Nektar::CellModel.

Definition at line 685 of file FentonKarma.cpp.

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

686  {
687  Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
688  Vmath::Fill(m_nq, 1.0, m_cellSol[1], 1);
689  Vmath::Fill(m_nq, 1.0, m_cellSol[2], 1);
690  if (isCF3)
691  {
692  Vmath::Fill(m_nq, 0.1, m_cellSol[2], 1);
693  }
694 
695  }
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
Nektar::CellModel::m_cellSol
Array< OneD, Array< OneD, NekDouble > > m_cellSol
Cell model solution variables.
Definition: CellModel.h:125

◆ 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 597 of file FentonKarma.cpp.

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.

601  {
602  ASSERTL0(inarray.get() != outarray.get(),
603  "Must have different arrays for input and output.");
604 
605  // Variables
606  // 0 u membrane potential
607  // 1 v v gate
608  // 2 w w gate
609  int n = m_nq;
610  int i = 0;
611 
612  // Declare pointers
613  const NekDouble *u = &inarray[0][0];
614  const NekDouble *v = &inarray[1][0];
615  const NekDouble *w = &inarray[2][0];
616  const NekDouble *y = isCF3 ? &inarray[3][0] : 0;
617  NekDouble *u_new = &outarray[0][0];
618  NekDouble *v_new = &outarray[1][0];
619  NekDouble *w_new = &outarray[2][0];
620  //NekDouble *y_new = isCF3 ? &outarray[3][0] : 0;
621  NekDouble *v_tau = &m_gates_tau[0][0];
622  NekDouble *w_tau = &m_gates_tau[1][0];
623  //NekDouble *y_tau = isCF3 ? &m_gates_tau[2][0] : 0;
624 
625  // Temporary variables
626  NekDouble J_fi, J_so, J_si, h1, h2, h3, alpha, beta;
627 
628  double V;
629  // Compute rates for each point in domain
630  for (i = 0; i < n; ++i)
631  {
632  // *u is dimensional
633  // V is non-dimensional for what follows
634  V = (*u - V_0)/(V_fi - V_0);
635 
636  // Heavyside functions
637  h1 = (V < u_c) ? 0.0 : 1.0;
638  h2 = (V < u_v) ? 0.0 : 1.0;
639  h3 = (V < u_r) ? 0.0 : 1.0;
640 
641  // w-gate
642  alpha = (1-h1)/tau_w_minus;
643  beta = h1/tau_w_plus;
644  *w_tau = 1.0 / (alpha + beta);
645  *w_new = alpha * (*w_tau);
646 
647  // v-gate
648  alpha = (1-h1)/(h2*tau_v1_minus + (1-h2)*tau_v2_minus);
649  beta = h1/tau_v_plus;
650  *v_tau = 1.0 / (alpha + beta);
651  *v_new = alpha * (*v_tau);
652 
653  // y-gate
654  if (isCF3)
655  {
656  // TODO: implementation for y_tau and y_new
657  }
658 
659  // J_fi
660  J_fi = -(*v)*h1*(1 - V)*(V - u_c)/tau_d;
661 
662  // J_so
663  // added extra (1-k2*v) term from Cherry&Fenton 2004
664  J_so = V*(1-h3)*(1-k2*(*v))/tau_0 +
665  (isCF3 ? h3*V*(*y)/tau_r : h3/tau_r);
666 
667  // J_si
668  J_si = -(*w)*(1 + tanh(k1*(V - u_csi)))/(2.0*tau_si);
669 
670  // u
671  *u_new = -J_fi - J_so - J_si;
672  *u_new *= C_m*(V_fi - V_0);
673 
674  ++u, ++v, ++w, ++u_new, ++v_new, ++w_new, ++v_tau, ++w_tau;
675  }
676  }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:216
Nektar::CellModel::m_nq
int m_nq
Number of physical points.
Definition: CellModel.h:116
Nektar::FentonKarma::tau_v1_minus
NekDouble tau_v1_minus
Definition: FentonKarma.h:89
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
Nektar::FentonKarma::tau_w_plus
NekDouble tau_w_plus
Definition: FentonKarma.h:101
Nektar::FentonKarma::tau_v2_minus
NekDouble tau_v2_minus
Definition: FentonKarma.h:90
Nektar::FentonKarma::tau_w_minus
NekDouble tau_w_minus
Definition: FentonKarma.h:100
Nektar::FentonKarma::tau_v_plus
NekDouble tau_v_plus
Definition: FentonKarma.h:91

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.")

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")

Definition at line 134 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 133 of file FentonKarma.h.

Referenced by v_GenerateSummary().

◆ model_variant

enum Variants Nektar::FentonKarma::model_variant
private

Definition at line 131 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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