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Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Private Attributes | List of all members
Nektar::Fox02 Class Reference

#include <Fox02.h>

Inheritance diagram for Nektar::Fox02:
[legend]

Public Member Functions

 Fox02 (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
 Constructor. More...
 
virtual ~Fox02 ()
 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 ()
 
- Protected Member Functions inherited from Nektar::CellModel
virtual std::string v_GetCellVarName (unsigned int idx)
 
void LoadCellModel ()
 

Private Attributes

NekDouble m_chi
 
NekDouble m_sigmai
 

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 41 of file Fox02.h.

Constructor & Destructor Documentation

◆ Fox02()

Nektar::Fox02::Fox02 ( const LibUtilities::SessionReaderSharedPtr &  pSession,
const MultiRegions::ExpListSharedPtr &  pField 
)

Constructor.

Definition at line 48 of file Fox02.cpp.

50  : CellModel(pSession, pField)
51 {
52  pSession->LoadParameter("chi", m_chi);
53  pSession->LoadParameter("sigmai", m_sigmai);
54 
55  m_nvar = 13;
56 
57  m_gates.push_back(1);
58  m_gates.push_back(2);
59  m_gates.push_back(3);
60  m_gates.push_back(4);
61  m_gates.push_back(5);
62  m_gates.push_back(6);
63  m_gates.push_back(7);
64  m_gates.push_back(8);
65  m_gates.push_back(9);
66  m_gates.push_back(10);
67  m_concentrations.push_back(11);
68  m_concentrations.push_back(12);
69 }
Nektar::CellModel::m_concentrations
std::vector< int > m_concentrations
Indices of cell model variables which are concentrations.
Definition: CellModel.h:139
Nektar::CellModel::m_gates
std::vector< int > m_gates
Indices of cell model variables which are gates.
Definition: CellModel.h:141
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:119
Nektar::Fox02::m_chi
NekDouble m_chi
Definition: Fox02.h:79
Nektar::Fox02::m_sigmai
NekDouble m_sigmai
Definition: Fox02.h:80

References m_chi, Nektar::CellModel::m_concentrations, Nektar::CellModel::m_gates, Nektar::CellModel::m_nvar, and m_sigmai.

◆ ~Fox02()

virtual Nektar::Fox02::~Fox02 ( )
inlinevirtual

Destructor.

Definition at line 61 of file Fox02.h.

62  {
63  }

Member Function Documentation

◆ create()

static CellModelSharedPtr Nektar::Fox02::create ( const LibUtilities::SessionReaderSharedPtr &  pSession,
const MultiRegions::ExpListSharedPtr &  pField 
)
inlinestatic

Creates an instance of this class.

Definition at line 46 of file Fox02.h.

49  {
50  return MemoryManager<Fox02>::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:168

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

◆ v_GenerateSummary()

void Nektar::Fox02::v_GenerateSummary ( SummaryList &  s)
protectedvirtual

Prints a summary of the model parameters.

Implements Nektar::CellModel.

Definition at line 975 of file Fox02.cpp.

976 {
977  SolverUtils::AddSummaryItem(s, "Cell model", "Fox02");
978 }
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

References Nektar::SolverUtils::AddSummaryItem().

◆ v_SetInitialConditions()

void Nektar::Fox02::v_SetInitialConditions ( )
protectedvirtual

Implements Nektar::CellModel.

Definition at line 983 of file Fox02.cpp.

984 {
985  Vmath::Fill(m_nq, -94.7, m_cellSol[0], 1);
986  Vmath::Fill(m_nq, 0.00024676, m_cellSol[1], 1);
987  Vmath::Fill(m_nq, 0.99869, m_cellSol[2], 1);
988  Vmath::Fill(m_nq, 0.99887, m_cellSol[3], 1);
989  Vmath::Fill(m_nq, 0.229, m_cellSol[4], 1);
990  Vmath::Fill(m_nq, 0.0001, m_cellSol[5], 1);
991  Vmath::Fill(m_nq, 0.00003742, m_cellSol[6], 1);
992  Vmath::Fill(m_nq, 1.0, m_cellSol[7], 1);
993  Vmath::Fill(m_nq, 0.0472, m_cellSol[8], 1);
994  Vmath::Fill(m_nq, 0.983, m_cellSol[9], 1);
995  Vmath::Fill(m_nq, 0.0001, m_cellSol[10], 1);
996  Vmath::Fill(m_nq, 0.942, m_cellSol[11], 1);
997  Vmath::Fill(m_nq, 320.0, m_cellSol[12], 1);
998 }
Nektar::CellModel::m_cellSol
Array< OneD, Array< OneD, NekDouble > > m_cellSol
Cell model solution variables.
Definition: CellModel.h:126
Nektar::CellModel::m_nq
int 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.cpp:45

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

◆ v_Update()

void Nektar::Fox02::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 71 of file Fox02.cpp.

74 {
75  for (unsigned int i = 0; i < m_nq; ++i)
76  {
77 
78  // Inputs:
79  // Time units: millisecond
80  NekDouble var_chaste_interface__membrane__V = inarray[0][i];
81  // Units: millivolt; Initial value: -94.7
82  NekDouble var_chaste_interface__fast_sodium_current_m_gate__m =
83  inarray[1][i];
84  // Units: dimensionless; Initial value: 0.00024676
85  NekDouble var_chaste_interface__fast_sodium_current_h_gate__h =
86  inarray[2][i];
87  // Units: dimensionless; Initial value: 0.99869
88  NekDouble var_chaste_interface__fast_sodium_current_j_gate__j =
89  inarray[3][i];
90  // Units: dimensionless; Initial value: 0.99887
91  NekDouble
92  var_chaste_interface__rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__X_kr =
93  inarray[4][i];
94  // Units: dimensionless; Initial value: 0.229
95  NekDouble
96  var_chaste_interface__slow_activating_delayed_rectifiyer_K_current_X_ks_gate__X_ks =
97  inarray[5][i];
98  // Units: dimensionless; Initial value: 0.0001
99  NekDouble
100  var_chaste_interface__transient_outward_potassium_current_X_to_gate__X_to =
101  inarray[6][i];
102  // Units: dimensionless; Initial value: 0.00003742
103  NekDouble
104  var_chaste_interface__transient_outward_potassium_current_Y_to_gate__Y_to =
105  inarray[7][i];
106  // Units: dimensionless; Initial value: 1
107  NekDouble var_chaste_interface__L_type_Ca_current_f_gate__f =
108  inarray[8][i];
109  // Units: dimensionless; Initial value: 0.983
110  NekDouble var_chaste_interface__L_type_Ca_current_d_gate__d =
111  inarray[9][i];
112  // Units: dimensionless; Initial value: 0.0001
113  NekDouble var_chaste_interface__L_type_Ca_current_f_Ca_gate__f_Ca =
114  inarray[10][i];
115  // Units: dimensionless; Initial value: 0.942
116  NekDouble var_chaste_interface__calcium_dynamics__Ca_i = inarray[11][i];
117  // Units: micromolar; Initial value: 0.0472
118  NekDouble var_chaste_interface__calcium_dynamics__Ca_SR =
119  inarray[12][i];
120  // Units: micromolar; Initial value: 320
121 
122  // Mathematics
123  NekDouble d_dt_chaste_interface__membrane__V;
124  const NekDouble var_membrane__R = 8.314; // joule_per_mole_kelvin
125  const NekDouble var_membrane__T = 310.0; // kelvin
126  const NekDouble var_membrane__F = 96.5; // coulomb_per_millimole
127  const NekDouble var_fast_sodium_current__j =
128  var_chaste_interface__fast_sodium_current_j_gate__j; // dimensionless
129  const NekDouble var_fast_sodium_current__h =
130  var_chaste_interface__fast_sodium_current_h_gate__h; // dimensionless
131  const NekDouble var_fast_sodium_current__m =
132  var_chaste_interface__fast_sodium_current_m_gate__m; // dimensionless
133  const NekDouble var_fast_sodium_current__V =
134  var_chaste_interface__membrane__V; // millivolt
135  const NekDouble var_standard_ionic_concentrations__Na_o =
136  138.0; // millimolar
137  const NekDouble var_standard_ionic_concentrations__Na_i =
138  10.0; // millimolar
139  const NekDouble var_L_type_Ca_current__f =
140  var_chaste_interface__L_type_Ca_current_f_gate__f; // dimensionless
141  const NekDouble var_L_type_Ca_current__f_Ca =
142  var_chaste_interface__L_type_Ca_current_f_Ca_gate__f_Ca; // dimensionless
143  const NekDouble var_L_type_Ca_current__F =
144  var_membrane__F; // coulomb_per_millimole
145  const NekDouble var_L_type_Ca_current__P_Ca =
146  1.26e-05; // cm_per_millisecond
147  const NekDouble var_L_type_Ca_current__V =
148  var_chaste_interface__membrane__V; // millivolt
149  const NekDouble var_L_type_Ca_current__C_sc = 1.0; // microF_per_cm2
150  const NekDouble var_L_type_Ca_current__T = var_membrane__T; // kelvin
151  const NekDouble var_standard_ionic_concentrations__Ca_o =
152  2000.0; // micromolar
153  const NekDouble var_L_type_Ca_current__Ca_o =
154  var_standard_ionic_concentrations__Ca_o; // micromolar
155  const NekDouble var_L_type_Ca_current__R =
156  var_membrane__R; // joule_per_mole_kelvin
157  const NekDouble var_L_type_Ca_current__Ca_i =
158  var_chaste_interface__calcium_dynamics__Ca_i; // micromolar
159  const NekDouble var_L_type_Ca_current__i_Ca_max =
160  ((((var_L_type_Ca_current__P_Ca / var_L_type_Ca_current__C_sc) *
161  4.0 * var_L_type_Ca_current__V *
162  pow(var_L_type_Ca_current__F, 2.0)) /
163  (var_L_type_Ca_current__R * var_L_type_Ca_current__T)) *
164  ((var_L_type_Ca_current__Ca_i *
165  exp((2.0 * var_L_type_Ca_current__V * var_L_type_Ca_current__F) /
166  (var_L_type_Ca_current__R * var_L_type_Ca_current__T))) -
167  (0.341 * var_L_type_Ca_current__Ca_o))) /
168  (exp((2.0 * var_L_type_Ca_current__V * var_L_type_Ca_current__F) /
169  (var_L_type_Ca_current__R * var_L_type_Ca_current__T)) -
170  1.0); // microA_per_microF
171  const NekDouble var_L_type_Ca_current__d =
172  var_chaste_interface__L_type_Ca_current_d_gate__d; // dimensionless
173  const NekDouble var_L_type_Ca_current__i_Ca =
174  var_L_type_Ca_current__i_Ca_max * var_L_type_Ca_current__f *
175  var_L_type_Ca_current__d *
176  var_L_type_Ca_current__f_Ca; // microA_per_microF
177  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__V =
178  var_chaste_interface__membrane__V; // millivolt
179  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__X_kr =
180  var_chaste_interface__rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__X_kr; // dimensionless
181  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__V =
182  var_chaste_interface__membrane__V; // millivolt
183  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__X_ks =
184  var_chaste_interface__slow_activating_delayed_rectifiyer_K_current_X_ks_gate__X_ks; // dimensionless
185  const NekDouble var_transient_outward_potassium_current__Y_to =
186  var_chaste_interface__transient_outward_potassium_current_Y_to_gate__Y_to; // dimensionless
187  const NekDouble var_transient_outward_potassium_current__X_to =
188  var_chaste_interface__transient_outward_potassium_current_X_to_gate__X_to; // dimensionless
189  const NekDouble var_transient_outward_potassium_current__V =
190  var_chaste_interface__membrane__V; // millivolt
191  const NekDouble var_Na_Ca_exchanger__Na_o =
192  var_standard_ionic_concentrations__Na_o; // millimolar
193  const NekDouble var_Na_Ca_exchanger__K_sat = 0.2; // dimensionless
194  const NekDouble var_Na_Ca_exchanger__Ca_i =
195  var_chaste_interface__calcium_dynamics__Ca_i; // micromolar
196  const NekDouble var_Na_Ca_exchanger__K_mNa = 87.5; // millimolar
197  const NekDouble var_Na_Ca_exchanger__Ca_o =
198  var_standard_ionic_concentrations__Ca_o; // micromolar
199  const NekDouble var_Na_Ca_exchanger__K_NaCa =
200  1500.0; // microA_per_microF
201  const NekDouble var_Na_Ca_exchanger__T = var_membrane__T; // kelvin
202  const NekDouble var_Na_Ca_exchanger__V =
203  var_chaste_interface__membrane__V; // millivolt
204  const NekDouble var_Na_Ca_exchanger__Na_i =
205  var_standard_ionic_concentrations__Na_i; // millimolar
206  const NekDouble var_Na_Ca_exchanger__eta = 0.35; // dimensionless
207  const NekDouble var_Na_Ca_exchanger__K_mCa = 1380.0; // micromolar
208  const NekDouble var_Na_Ca_exchanger__F =
209  var_membrane__F; // coulomb_per_millimole
210  const NekDouble var_Na_Ca_exchanger__R =
211  var_membrane__R; // joule_per_mole_kelvin
212  const NekDouble var_Na_Ca_exchanger__i_NaCa =
213  (var_Na_Ca_exchanger__K_NaCa /
214  ((pow(var_Na_Ca_exchanger__K_mNa, 3.0) +
215  pow(var_Na_Ca_exchanger__Na_o, 3.0)) *
216  (var_Na_Ca_exchanger__K_mCa + var_Na_Ca_exchanger__Ca_o) *
217  (1.0 +
218  (var_Na_Ca_exchanger__K_sat *
219  exp(((var_Na_Ca_exchanger__eta - 1.0) * var_Na_Ca_exchanger__V *
220  var_Na_Ca_exchanger__F) /
221  (var_Na_Ca_exchanger__R * var_Na_Ca_exchanger__T)))))) *
222  ((exp((var_Na_Ca_exchanger__eta * var_Na_Ca_exchanger__V *
223  var_Na_Ca_exchanger__F) /
224  (var_Na_Ca_exchanger__R * var_Na_Ca_exchanger__T)) *
225  pow(var_Na_Ca_exchanger__Na_i, 3.0) * var_Na_Ca_exchanger__Ca_o) -
226  (exp(((var_Na_Ca_exchanger__eta - 1.0) * var_Na_Ca_exchanger__V *
227  var_Na_Ca_exchanger__F) /
228  (var_Na_Ca_exchanger__R * var_Na_Ca_exchanger__T)) *
229  pow(var_Na_Ca_exchanger__Na_o, 3.0) *
230  var_Na_Ca_exchanger__Ca_i)); // microA_per_microF
231  const NekDouble var_sarcolemmal_calcium_pump__Ca_i =
232  var_chaste_interface__calcium_dynamics__Ca_i; // micromolar
233  const NekDouble var_sarcolemmal_calcium_pump__i_pCa_max =
234  0.05; // microA_per_microF
235  const NekDouble var_sarcolemmal_calcium_pump__K_mpCa =
236  0.05; // micromolar
237  const NekDouble var_sarcolemmal_calcium_pump__i_p_Ca =
238  (var_sarcolemmal_calcium_pump__i_pCa_max *
239  var_sarcolemmal_calcium_pump__Ca_i) /
240  (var_sarcolemmal_calcium_pump__K_mpCa +
241  var_sarcolemmal_calcium_pump__Ca_i); // microA_per_microF
242  const NekDouble var_calcium_background_current__R =
243  var_membrane__R; // joule_per_mole_kelvin
244  const NekDouble var_calcium_background_current__Ca_i =
245  var_chaste_interface__calcium_dynamics__Ca_i; // micromolar
246  const NekDouble var_calcium_background_current__F =
247  var_membrane__F; // coulomb_per_millimole
248  const NekDouble var_calcium_background_current__T =
249  var_membrane__T; // kelvin
250  const NekDouble var_calcium_background_current__Ca_o =
251  var_standard_ionic_concentrations__Ca_o; // micromolar
252  const NekDouble var_calcium_background_current__E_Ca =
253  ((var_calcium_background_current__R *
254  var_calcium_background_current__T) /
255  (2.0 * var_calcium_background_current__F)) *
256  log(var_calcium_background_current__Ca_o /
257  var_calcium_background_current__Ca_i); // millivolt
258  const NekDouble var_calcium_background_current__g_Cab =
259  0.0003842; // milliS_per_microF
260  const NekDouble var_calcium_background_current__V =
261  var_chaste_interface__membrane__V; // millivolt
262  const NekDouble var_calcium_background_current__i_Ca_b =
263  var_calcium_background_current__g_Cab *
264  (var_calcium_background_current__V -
265  var_calcium_background_current__E_Ca); // microA_per_microF
266  const NekDouble var_fast_sodium_current_m_gate__m =
267  var_fast_sodium_current__m; // dimensionless
268  const NekDouble var_fast_sodium_current_m_gate__V =
269  var_fast_sodium_current__V; // millivolt
270  const NekDouble var_fast_sodium_current_m_gate__E0_m =
271  var_fast_sodium_current_m_gate__V + 47.13; // millivolt
272  const NekDouble var_fast_sodium_current_m_gate__alpha_m =
273  (0.32 * var_fast_sodium_current_m_gate__E0_m) /
274  (1.0 -
275  exp((-0.1) *
276  var_fast_sodium_current_m_gate__E0_m)); // per_millisecond
277  const NekDouble var_fast_sodium_current_m_gate__beta_m =
278  0.08 *
279  exp((-var_fast_sodium_current_m_gate__V) / 11.0); // per_millisecond
280  const NekDouble
281  var_fast_sodium_current_m_gate__d_m_d_environment__time =
282  (var_fast_sodium_current_m_gate__alpha_m *
283  (1.0 - var_fast_sodium_current_m_gate__m)) -
284  (var_fast_sodium_current_m_gate__beta_m *
285  var_fast_sodium_current_m_gate__m); // per_millisecond
286  const NekDouble
287  var_fast_sodium_current__fast_sodium_current_m_gate__d_m_d_environment__time =
288  var_fast_sodium_current_m_gate__d_m_d_environment__time; // per_millisecond
289  const NekDouble var_fast_sodium_current_h_gate__V =
290  var_fast_sodium_current__V; // millivolt
291  const NekDouble var_fast_sodium_current_h_gate__beta_h =
292  7.5 / (1.0 + exp((-0.1) * (var_fast_sodium_current_h_gate__V +
293  11.0))); // per_millisecond
294  const NekDouble var_fast_sodium_current_h_gate__alpha_h =
295  0.135 * exp((var_fast_sodium_current_h_gate__V + 80.0) /
296  (-6.8)); // per_millisecond
297  const NekDouble var_fast_sodium_current_h_gate__h =
298  var_fast_sodium_current__h; // dimensionless
299  const NekDouble
300  var_fast_sodium_current_h_gate__d_h_d_environment__time =
301  (var_fast_sodium_current_h_gate__alpha_h *
302  (1.0 - var_fast_sodium_current_h_gate__h)) -
303  (var_fast_sodium_current_h_gate__beta_h *
304  var_fast_sodium_current_h_gate__h); // per_millisecond
305  const NekDouble
306  var_fast_sodium_current__fast_sodium_current_h_gate__d_h_d_environment__time =
307  var_fast_sodium_current_h_gate__d_h_d_environment__time; // per_millisecond
308  const NekDouble var_fast_sodium_current_j_gate__V =
309  var_fast_sodium_current__V; // millivolt
310  const NekDouble var_fast_sodium_current_j_gate__alpha_j =
311  (0.175 *
312  exp((var_fast_sodium_current_j_gate__V + 100.0) / (-23.0))) /
313  (1.0 + exp(0.15 * (var_fast_sodium_current_j_gate__V +
314  79.0))); // per_millisecond
315  const NekDouble var_fast_sodium_current_j_gate__beta_j =
316  0.3 / (1.0 + exp((-0.1) * (var_fast_sodium_current_j_gate__V +
317  32.0))); // per_millisecond
318  const NekDouble var_fast_sodium_current_j_gate__j =
319  var_fast_sodium_current__j; // dimensionless
320  const NekDouble
321  var_fast_sodium_current_j_gate__d_j_d_environment__time =
322  (var_fast_sodium_current_j_gate__alpha_j *
323  (1.0 - var_fast_sodium_current_j_gate__j)) -
324  (var_fast_sodium_current_j_gate__beta_j *
325  var_fast_sodium_current_j_gate__j); // per_millisecond
326  const NekDouble
327  var_fast_sodium_current__fast_sodium_current_j_gate__d_j_d_environment__time =
328  var_fast_sodium_current_j_gate__d_j_d_environment__time; // per_millisecond
329  const NekDouble
330  var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__V =
331  var_rapid_activating_delayed_rectifiyer_K_current__V; // millivolt
332  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__tau_X_kr =
333  43.0 +
334  (1.0 /
335  (exp((-5.495) +
336  (0.1691 *
337  var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__V)) +
338  exp((-7.677) -
339  (0.0128 *
340  var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__V)))); // millisecond
341  const NekDouble
342  var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__X_kr =
343  var_rapid_activating_delayed_rectifiyer_K_current__X_kr; // dimensionless
344  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__X_kr_inf =
345  1.0 /
346  (1.0 +
347  exp((-2.182) -
348  (0.1819 *
349  var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__V))); // dimensionless
350  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__d_X_kr_d_environment__time =
351  (var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__X_kr_inf -
352  var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__X_kr) /
353  var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__tau_X_kr; // per_millisecond
354  const NekDouble
355  var_rapid_activating_delayed_rectifiyer_K_current__rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__d_X_kr_d_environment__time =
356  var_rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__d_X_kr_d_environment__time; // per_millisecond
357  const NekDouble
358  var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__V =
359  var_slow_activating_delayed_rectifiyer_K_current__V; // millivolt
360  const NekDouble var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__tau_X_ks =
361  1.0 /
362  (((7.19e-05 *
363  (var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__V -
364  10.0)) /
365  (1.0 -
366  exp((-0.148) *
367  (var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__V -
368  10.0)))) +
369  ((0.000131 *
370  (var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__V -
371  10.0)) /
372  (exp(0.0687 *
373  (var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__V -
374  10.0)) -
375  1.0))); // millisecond
376  const NekDouble
377  var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__X_ks_infinity =
378  1.0 /
379  (1.0 +
380  exp((var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__V -
381  16.0) /
382  (-13.6))); // dimensionless
383  const NekDouble
384  var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__X_ks =
385  var_slow_activating_delayed_rectifiyer_K_current__X_ks; // dimensionless
386  const NekDouble var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__d_X_ks_d_environment__time =
387  (var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__X_ks_infinity -
388  var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__X_ks) /
389  var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__tau_X_ks; // per_millisecond
390  const NekDouble
391  var_slow_activating_delayed_rectifiyer_K_current__slow_activating_delayed_rectifiyer_K_current_X_ks_gate__d_X_ks_d_environment__time =
392  var_slow_activating_delayed_rectifiyer_K_current_X_ks_gate__d_X_ks_d_environment__time; // per_millisecond
393  const NekDouble var_transient_outward_potassium_current_X_to_gate__V =
394  var_transient_outward_potassium_current__V; // millivolt
395  const NekDouble
396  var_transient_outward_potassium_current_X_to_gate__alpha_X_to =
397  0.04516 *
398  exp(0.03577 *
399  var_transient_outward_potassium_current_X_to_gate__V); // per_millisecond
400  const NekDouble
401  var_transient_outward_potassium_current_X_to_gate__X_to =
402  var_transient_outward_potassium_current__X_to; // dimensionless
403  const NekDouble
404  var_transient_outward_potassium_current_X_to_gate__beta_X_to =
405  0.0989 *
406  exp((-0.06237) *
407  var_transient_outward_potassium_current_X_to_gate__V); // per_millisecond
408  const NekDouble
409  var_transient_outward_potassium_current_X_to_gate__d_X_to_d_environment__time =
410  (var_transient_outward_potassium_current_X_to_gate__alpha_X_to *
411  (1.0 -
412  var_transient_outward_potassium_current_X_to_gate__X_to)) -
413  (var_transient_outward_potassium_current_X_to_gate__beta_X_to *
414  var_transient_outward_potassium_current_X_to_gate__X_to); // per_millisecond
415  const NekDouble
416  var_transient_outward_potassium_current__transient_outward_potassium_current_X_to_gate__d_X_to_d_environment__time =
417  var_transient_outward_potassium_current_X_to_gate__d_X_to_d_environment__time; // per_millisecond
418  const NekDouble var_transient_outward_potassium_current_Y_to_gate__V =
419  var_transient_outward_potassium_current__V; // millivolt
420  const NekDouble
421  var_transient_outward_potassium_current_Y_to_gate__beta_Y_to =
422  (0.005415 *
423  exp((var_transient_outward_potassium_current_Y_to_gate__V +
424  33.5) /
425  5.0)) /
426  (1.0 +
427  (0.051335 *
428  exp((var_transient_outward_potassium_current_Y_to_gate__V +
429  33.5) /
430  5.0))); // per_millisecond
431  const NekDouble
432  var_transient_outward_potassium_current_Y_to_gate__alpha_Y_to =
433  (0.005415 *
434  exp((var_transient_outward_potassium_current_Y_to_gate__V +
435  33.5) /
436  (-5.0))) /
437  (1.0 +
438  (0.051335 *
439  exp((var_transient_outward_potassium_current_Y_to_gate__V +
440  33.5) /
441  (-5.0)))); // per_millisecond
442  const NekDouble
443  var_transient_outward_potassium_current_Y_to_gate__Y_to =
444  var_transient_outward_potassium_current__Y_to; // dimensionless
445  const NekDouble
446  var_transient_outward_potassium_current_Y_to_gate__d_Y_to_d_environment__time =
447  (var_transient_outward_potassium_current_Y_to_gate__alpha_Y_to *
448  (1.0 -
449  var_transient_outward_potassium_current_Y_to_gate__Y_to)) -
450  (var_transient_outward_potassium_current_Y_to_gate__beta_Y_to *
451  var_transient_outward_potassium_current_Y_to_gate__Y_to); // per_millisecond
452  const NekDouble
453  var_transient_outward_potassium_current__transient_outward_potassium_current_Y_to_gate__d_Y_to_d_environment__time =
454  var_transient_outward_potassium_current_Y_to_gate__d_Y_to_d_environment__time; // per_millisecond
455  const NekDouble var_L_type_Ca_current_f_gate__V =
456  var_L_type_Ca_current__V; // millivolt
457  const NekDouble var_L_type_Ca_current_f_gate__tau_f =
458  30.0 +
459  (200.0 / (1.0 + exp((var_L_type_Ca_current_f_gate__V + 20.0) /
460  9.5))); // millisecond
461  const NekDouble var_L_type_Ca_current_f_gate__f =
462  var_L_type_Ca_current__f; // dimensionless
463  const NekDouble var_L_type_Ca_current_f_gate__f_infinity =
464  1.0 / (1.0 + exp((var_L_type_Ca_current_f_gate__V + 12.5) /
465  5.0)); // dimensionless
466  const NekDouble var_L_type_Ca_current_f_gate__d_f_d_environment__time =
467  (var_L_type_Ca_current_f_gate__f_infinity -
468  var_L_type_Ca_current_f_gate__f) /
469  var_L_type_Ca_current_f_gate__tau_f; // per_millisecond
470  const NekDouble
471  var_L_type_Ca_current__L_type_Ca_current_f_gate__d_f_d_environment__time =
472  var_L_type_Ca_current_f_gate__d_f_d_environment__time; // per_millisecond
473  const NekDouble var_L_type_Ca_current_d_gate__V =
474  var_L_type_Ca_current__V; // millivolt
475  const NekDouble var_L_type_Ca_current_d_gate__E0_m =
476  var_L_type_Ca_current_d_gate__V + 40.0; // millivolt
477  const NekDouble var_L_type_Ca_current_d_gate__tau_d =
478  1.0 /
479  (((0.25 * exp((-0.01) * var_L_type_Ca_current_d_gate__V)) /
480  (1.0 + exp((-0.07) * var_L_type_Ca_current_d_gate__V))) +
481  ((0.07 * exp((-0.05) * var_L_type_Ca_current_d_gate__E0_m)) /
482  (1.0 +
483  exp(0.05 * var_L_type_Ca_current_d_gate__E0_m)))); // millisecond
484  const NekDouble var_L_type_Ca_current_d_gate__d =
485  var_L_type_Ca_current__d; // dimensionless
486  const NekDouble var_L_type_Ca_current_d_gate__d_infinity =
487  1.0 / (1.0 + exp((var_L_type_Ca_current_d_gate__V + 10.0) /
488  (-6.24))); // dimensionless
489  const NekDouble var_L_type_Ca_current_d_gate__d_d_d_environment__time =
490  (var_L_type_Ca_current_d_gate__d_infinity -
491  var_L_type_Ca_current_d_gate__d) /
492  var_L_type_Ca_current_d_gate__tau_d; // per_millisecond
493  const NekDouble
494  var_L_type_Ca_current__L_type_Ca_current_d_gate__d_d_d_environment__time =
495  var_L_type_Ca_current_d_gate__d_d_d_environment__time; // per_millisecond
496  const NekDouble var_L_type_Ca_current_f_Ca_gate__f_Ca =
497  var_L_type_Ca_current__f_Ca; // dimensionless
498  const NekDouble var_L_type_Ca_current_f_Ca_gate__K_mfCa =
499  0.18; // micromolar
500  const NekDouble var_L_type_Ca_current_f_Ca_gate__Ca_i =
501  var_L_type_Ca_current__Ca_i; // micromolar
502  const NekDouble var_L_type_Ca_current_f_Ca_gate__f_Ca_infinity =
503  1.0 / (1.0 + pow(var_L_type_Ca_current_f_Ca_gate__Ca_i /
504  var_L_type_Ca_current_f_Ca_gate__K_mfCa,
505  3.0)); // dimensionless
506  const NekDouble var_L_type_Ca_current_f_Ca_gate__tau_f_Ca =
507  30.0; // millisecond
508  const NekDouble
509  var_L_type_Ca_current_f_Ca_gate__d_f_Ca_d_environment__time =
510  (var_L_type_Ca_current_f_Ca_gate__f_Ca_infinity -
511  var_L_type_Ca_current_f_Ca_gate__f_Ca) /
512  var_L_type_Ca_current_f_Ca_gate__tau_f_Ca; // per_millisecond
513  const NekDouble
514  var_L_type_Ca_current__L_type_Ca_current_f_Ca_gate__d_f_Ca_d_environment__time =
515  var_L_type_Ca_current_f_Ca_gate__d_f_Ca_d_environment__time; // per_millisecond
516  const NekDouble var_calcium_dynamics__Ca_i =
517  var_chaste_interface__calcium_dynamics__Ca_i; // micromolar
518  const NekDouble var_calcium_dynamics__CMDN_tot = 10.0; // micromolar
519  const NekDouble var_calcium_dynamics__K_mCMDN = 2.0; // micromolar
520  const NekDouble var_calcium_dynamics__beta_i =
521  1.0 /
522  (1.0 +
523  ((var_calcium_dynamics__CMDN_tot * var_calcium_dynamics__K_mCMDN) /
524  pow(var_calcium_dynamics__K_mCMDN + var_calcium_dynamics__Ca_i,
525  2.0))); // dimensionless
526  const NekDouble var_calcium_dynamics__V_myo = 2.584e-05; // microlitre
527  const NekDouble var_calcium_dynamics__F =
528  var_membrane__F; // coulomb_per_millimole
529  const NekDouble var_calcium_dynamics__C_sc =
530  var_L_type_Ca_current__C_sc; // microF_per_cm2
531  const NekDouble var_calcium_dynamics__A_Cap = 0.0001534; // cm2
532  const NekDouble var_calcium_dynamics__Ca_SR =
533  var_chaste_interface__calcium_dynamics__Ca_SR; // micromolar
534  const NekDouble var_calcium_dynamics__P_rel = 6.0; // per_millisecond
535  const NekDouble var_calcium_dynamics__V =
536  var_chaste_interface__membrane__V; // millivolt
537  const NekDouble var_calcium_dynamics__f_Ca =
538  var_chaste_interface__L_type_Ca_current_f_Ca_gate__f_Ca; // dimensionless
539  const NekDouble var_calcium_dynamics__gamma =
540  1.0 / (1.0 + pow(2000.0 / var_calcium_dynamics__Ca_SR,
541  3.0)); // dimensionless
542  const NekDouble var_calcium_dynamics__d =
543  var_chaste_interface__L_type_Ca_current_d_gate__d; // dimensionless
544  const NekDouble var_calcium_dynamics__f =
545  var_chaste_interface__L_type_Ca_current_f_gate__f; // dimensionless
546  const NekDouble var_calcium_dynamics__J_rel =
547  (var_calcium_dynamics__P_rel * var_calcium_dynamics__f *
548  var_calcium_dynamics__d * var_calcium_dynamics__f_Ca *
549  ((var_calcium_dynamics__gamma * var_calcium_dynamics__Ca_SR) -
550  var_calcium_dynamics__Ca_i)) /
551  (1.0 + (1.65 * exp(var_calcium_dynamics__V /
552  20.0))); // micromolar_per_millisecond
553  const NekDouble var_calcium_dynamics__P_leak = 1e-06; // per_millisecond
554  const NekDouble var_calcium_dynamics__J_leak =
555  var_calcium_dynamics__P_leak *
556  (var_calcium_dynamics__Ca_SR -
557  var_calcium_dynamics__Ca_i); // micromolar_per_millisecond
558  const NekDouble var_calcium_dynamics__K_mup = 0.32; // micromolar
559  const NekDouble var_calcium_dynamics__V_up =
560  0.1; // micromolar_per_millisecond
561  const NekDouble var_calcium_dynamics__J_up =
562  var_calcium_dynamics__V_up /
563  (1.0 + pow(var_calcium_dynamics__K_mup / var_calcium_dynamics__Ca_i,
564  2.0)); // micromolar_per_millisecond
565  const NekDouble var_calcium_dynamics__i_Ca =
566  var_L_type_Ca_current__i_Ca; // microA_per_microF
567  const NekDouble var_calcium_dynamics__i_Ca_b =
568  var_calcium_background_current__i_Ca_b; // microA_per_microF
569  const NekDouble var_calcium_dynamics__i_p_Ca =
570  var_sarcolemmal_calcium_pump__i_p_Ca; // microA_per_microF
571  const NekDouble var_calcium_dynamics__i_NaCa =
572  var_Na_Ca_exchanger__i_NaCa; // microA_per_microF
573  const NekDouble var_calcium_dynamics__K_mCSQN = 600.0; // micromolar
574  const NekDouble var_calcium_dynamics__CSQN_tot = 10000.0; // micromolar
575  const NekDouble var_calcium_dynamics__V_SR = 2e-06; // microlitre
576  const NekDouble var_calcium_dynamics__beta_SR =
577  1.0 /
578  (1.0 +
579  ((var_calcium_dynamics__CSQN_tot * var_calcium_dynamics__K_mCSQN) /
580  pow(var_calcium_dynamics__K_mCSQN + var_calcium_dynamics__Ca_SR,
581  2.0))); // dimensionless
582  const NekDouble var_calcium_dynamics__d_Ca_i_d_environment__time =
583  var_calcium_dynamics__beta_i *
584  (((var_calcium_dynamics__J_rel + var_calcium_dynamics__J_leak) -
585  var_calcium_dynamics__J_up) -
586  (((var_calcium_dynamics__A_Cap * var_calcium_dynamics__C_sc) /
587  (2.0 * var_calcium_dynamics__F * var_calcium_dynamics__V_myo)) *
588  ((var_calcium_dynamics__i_Ca + var_calcium_dynamics__i_Ca_b +
589  var_calcium_dynamics__i_p_Ca) -
590  (2.0 * var_calcium_dynamics__i_NaCa)))); // 'micromole per litre
591  // per millisecond'
592  const NekDouble var_calcium_dynamics__d_Ca_SR_d_environment__time =
593  (var_calcium_dynamics__beta_SR *
594  ((var_calcium_dynamics__J_up - var_calcium_dynamics__J_leak) -
595  var_calcium_dynamics__J_rel) *
596  var_calcium_dynamics__V_myo) /
597  var_calcium_dynamics__V_SR; // 'micromole per litre per millisecond'
598  const NekDouble
599  var_chaste_interface__fast_sodium_current_m_gate__d_m_d_environment__time =
600  var_fast_sodium_current__fast_sodium_current_m_gate__d_m_d_environment__time; // per_millisecond
601  const NekDouble
602  var_chaste_interface__fast_sodium_current_h_gate__d_h_d_environment__time =
603  var_fast_sodium_current__fast_sodium_current_h_gate__d_h_d_environment__time; // per_millisecond
604  const NekDouble
605  var_chaste_interface__fast_sodium_current_j_gate__d_j_d_environment__time =
606  var_fast_sodium_current__fast_sodium_current_j_gate__d_j_d_environment__time; // per_millisecond
607  const NekDouble
608  var_chaste_interface__rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__d_X_kr_d_environment__time =
609  var_rapid_activating_delayed_rectifiyer_K_current__rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__d_X_kr_d_environment__time; // per_millisecond
610  const NekDouble
611  var_chaste_interface__slow_activating_delayed_rectifiyer_K_current_X_ks_gate__d_X_ks_d_environment__time =
612  var_slow_activating_delayed_rectifiyer_K_current__slow_activating_delayed_rectifiyer_K_current_X_ks_gate__d_X_ks_d_environment__time; // per_millisecond
613  const NekDouble
614  var_chaste_interface__transient_outward_potassium_current_X_to_gate__d_X_to_d_environment__time =
615  var_transient_outward_potassium_current__transient_outward_potassium_current_X_to_gate__d_X_to_d_environment__time; // per_millisecond
616  const NekDouble
617  var_chaste_interface__transient_outward_potassium_current_Y_to_gate__d_Y_to_d_environment__time =
618  var_transient_outward_potassium_current__transient_outward_potassium_current_Y_to_gate__d_Y_to_d_environment__time; // per_millisecond
619  const NekDouble
620  var_chaste_interface__L_type_Ca_current_f_gate__d_f_d_environment__time =
621  var_L_type_Ca_current__L_type_Ca_current_f_gate__d_f_d_environment__time; // per_millisecond
622  const NekDouble
623  var_chaste_interface__L_type_Ca_current_d_gate__d_d_d_environment__time =
624  var_L_type_Ca_current__L_type_Ca_current_d_gate__d_d_d_environment__time; // per_millisecond
625  const NekDouble
626  var_chaste_interface__L_type_Ca_current_f_Ca_gate__d_f_Ca_d_environment__time =
627  var_L_type_Ca_current__L_type_Ca_current_f_Ca_gate__d_f_Ca_d_environment__time; // per_millisecond
628  const NekDouble
629  var_chaste_interface__calcium_dynamics__d_Ca_i_d_environment__time =
630  var_calcium_dynamics__d_Ca_i_d_environment__time; // micromolar_per_millisecond
631  const NekDouble
632  var_chaste_interface__calcium_dynamics__d_Ca_SR_d_environment__time =
633  var_calcium_dynamics__d_Ca_SR_d_environment__time; // micromolar_per_millisecond
634  const NekDouble d_dt_chaste_interface__fast_sodium_current_m_gate__m =
635  var_chaste_interface__fast_sodium_current_m_gate__d_m_d_environment__time; // per_millisecond
636  const NekDouble d_dt_chaste_interface__fast_sodium_current_h_gate__h =
637  var_chaste_interface__fast_sodium_current_h_gate__d_h_d_environment__time; // per_millisecond
638  const NekDouble d_dt_chaste_interface__fast_sodium_current_j_gate__j =
639  var_chaste_interface__fast_sodium_current_j_gate__d_j_d_environment__time; // per_millisecond
640  const NekDouble
641  d_dt_chaste_interface__rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__X_kr =
642  var_chaste_interface__rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__d_X_kr_d_environment__time; // per_millisecond
643  const NekDouble
644  d_dt_chaste_interface__slow_activating_delayed_rectifiyer_K_current_X_ks_gate__X_ks =
645  var_chaste_interface__slow_activating_delayed_rectifiyer_K_current_X_ks_gate__d_X_ks_d_environment__time; // per_millisecond
646  const NekDouble
647  d_dt_chaste_interface__transient_outward_potassium_current_X_to_gate__X_to =
648  var_chaste_interface__transient_outward_potassium_current_X_to_gate__d_X_to_d_environment__time; // per_millisecond
649  const NekDouble
650  d_dt_chaste_interface__transient_outward_potassium_current_Y_to_gate__Y_to =
651  var_chaste_interface__transient_outward_potassium_current_Y_to_gate__d_Y_to_d_environment__time; // per_millisecond
652  const NekDouble d_dt_chaste_interface__L_type_Ca_current_f_gate__f =
653  var_chaste_interface__L_type_Ca_current_f_gate__d_f_d_environment__time; // per_millisecond
654  const NekDouble d_dt_chaste_interface__L_type_Ca_current_d_gate__d =
655  var_chaste_interface__L_type_Ca_current_d_gate__d_d_d_environment__time; // per_millisecond
656  const NekDouble d_dt_chaste_interface__L_type_Ca_current_f_Ca_gate__f_Ca =
657  var_chaste_interface__L_type_Ca_current_f_Ca_gate__d_f_Ca_d_environment__time; // per_millisecond
658  const NekDouble d_dt_chaste_interface__calcium_dynamics__Ca_i =
659  var_chaste_interface__calcium_dynamics__d_Ca_i_d_environment__time; // 'micromole per litre per millisecond'
660  const NekDouble d_dt_chaste_interface__calcium_dynamics__Ca_SR =
661  var_chaste_interface__calcium_dynamics__d_Ca_SR_d_environment__time; // 'micromole per litre per millisecond'
662 
663  const NekDouble var_fast_sodium_current__g_Na =
664  12.8; // milliS_per_microF
665  const NekDouble var_fast_sodium_current__R =
666  var_membrane__R; // joule_per_mole_kelvin
667  const NekDouble var_fast_sodium_current__Na_o =
668  var_standard_ionic_concentrations__Na_o; // millimolar
669  const NekDouble var_fast_sodium_current__F =
670  var_membrane__F; // coulomb_per_millimole
671  const NekDouble var_fast_sodium_current__T = var_membrane__T; // kelvin
672  const NekDouble var_fast_sodium_current__Na_i =
673  var_standard_ionic_concentrations__Na_i; // millimolar
674  const NekDouble var_fast_sodium_current__E_Na =
675  ((var_fast_sodium_current__R * var_fast_sodium_current__T) /
676  var_fast_sodium_current__F) *
677  log(var_fast_sodium_current__Na_o /
678  var_fast_sodium_current__Na_i); // millivolt
679  const NekDouble var_fast_sodium_current__i_Na =
680  var_fast_sodium_current__g_Na *
681  pow(var_fast_sodium_current__m, 3.0) * var_fast_sodium_current__h *
682  var_fast_sodium_current__j *
683  (var_fast_sodium_current__V -
684  var_fast_sodium_current__E_Na); // microA_per_microF
685  const NekDouble var_membrane__i_Na =
686  var_fast_sodium_current__i_Na; // microA_per_microF
687  const NekDouble var_membrane__i_Ca =
688  var_L_type_Ca_current__i_Ca; // microA_per_microF
689  const NekDouble var_L_type_Ca_current__P_CaK =
690  5.79e-07; // cm_per_millisecond
691  const NekDouble var_standard_ionic_concentrations__K_o =
692  4.0; // millimolar
693  const NekDouble var_L_type_Ca_current__K_o =
694  var_standard_ionic_concentrations__K_o; // millimolar
695  const NekDouble var_L_type_Ca_current__i_Ca_half =
696  -0.265; // microA_per_microF
697  const NekDouble var_standard_ionic_concentrations__K_i =
698  149.4; // millimolar
699  const NekDouble var_L_type_Ca_current__K_i =
700  var_standard_ionic_concentrations__K_i; // millimolar
701  const NekDouble var_L_type_Ca_current__i_CaK =
702  ((((((var_L_type_Ca_current__P_CaK / var_L_type_Ca_current__C_sc) *
703  var_L_type_Ca_current__f * var_L_type_Ca_current__d *
704  var_L_type_Ca_current__f_Ca) /
705  (1.0 + (var_L_type_Ca_current__i_Ca_max /
706  var_L_type_Ca_current__i_Ca_half))) *
707  1000.0 * var_L_type_Ca_current__V *
708  pow(var_L_type_Ca_current__F, 2.0)) /
709  (var_L_type_Ca_current__R * var_L_type_Ca_current__T)) *
710  ((var_L_type_Ca_current__K_i *
711  exp((var_L_type_Ca_current__V * var_L_type_Ca_current__F) /
712  (var_L_type_Ca_current__R * var_L_type_Ca_current__T))) -
713  var_L_type_Ca_current__K_o)) /
714  (exp((var_L_type_Ca_current__V * var_L_type_Ca_current__F) /
715  (var_L_type_Ca_current__R * var_L_type_Ca_current__T)) -
716  1.0); // microA_per_microF
717  const NekDouble var_membrane__i_CaK =
718  var_L_type_Ca_current__i_CaK; // microA_per_microF
719  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__K_o =
720  var_standard_ionic_concentrations__K_o; // millimolar
721  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__R =
722  var_membrane__R; // joule_per_mole_kelvin
723  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__F =
724  var_membrane__F; // coulomb_per_millimole
725  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__K_i =
726  var_standard_ionic_concentrations__K_i; // millimolar
727  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__T =
728  var_membrane__T; // kelvin
729  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__E_K =
730  ((var_rapid_activating_delayed_rectifiyer_K_current__R *
731  var_rapid_activating_delayed_rectifiyer_K_current__T) /
732  var_rapid_activating_delayed_rectifiyer_K_current__F) *
733  log(var_rapid_activating_delayed_rectifiyer_K_current__K_o /
734  var_rapid_activating_delayed_rectifiyer_K_current__K_i); // millivolt
735  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__R_V =
736  1.0 /
737  (1.0 +
738  (2.5 *
739  exp(0.1 * (var_rapid_activating_delayed_rectifiyer_K_current__V +
740  28.0)))); // dimensionless
741  const NekDouble
742  var_rapid_activating_delayed_rectifiyer_K_current__g_Kr =
743  0.0136; // milliS_per_microF
744  const NekDouble var_rapid_activating_delayed_rectifiyer_K_current__i_Kr =
745  var_rapid_activating_delayed_rectifiyer_K_current__g_Kr *
746  var_rapid_activating_delayed_rectifiyer_K_current__R_V *
747  var_rapid_activating_delayed_rectifiyer_K_current__X_kr *
748  sqrt(var_rapid_activating_delayed_rectifiyer_K_current__K_o / 4.0) *
749  (var_rapid_activating_delayed_rectifiyer_K_current__V -
750  var_rapid_activating_delayed_rectifiyer_K_current__E_K); // microA_per_microF
751  const NekDouble var_membrane__i_Kr =
752  var_rapid_activating_delayed_rectifiyer_K_current__i_Kr; // microA_per_microF
753  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__g_Ks =
754  0.0245; // milliS_per_microF
755  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__T =
756  var_membrane__T; // kelvin
757  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__K_o =
758  var_standard_ionic_concentrations__K_o; // millimolar
759  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__R =
760  var_membrane__R; // joule_per_mole_kelvin
761  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__Na_o =
762  var_standard_ionic_concentrations__Na_o; // millimolar
763  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__Na_i =
764  var_standard_ionic_concentrations__Na_i; // millimolar
765  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__K_i =
766  var_standard_ionic_concentrations__K_i; // millimolar
767  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__F =
768  var_membrane__F; // coulomb_per_millimole
769  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__E_Ks =
770  ((var_slow_activating_delayed_rectifiyer_K_current__R *
771  var_slow_activating_delayed_rectifiyer_K_current__T) /
772  var_slow_activating_delayed_rectifiyer_K_current__F) *
773  log((var_slow_activating_delayed_rectifiyer_K_current__K_o +
774  (0.01833 *
775  var_slow_activating_delayed_rectifiyer_K_current__Na_o)) /
776  (var_slow_activating_delayed_rectifiyer_K_current__K_i +
777  (0.01833 *
778  var_slow_activating_delayed_rectifiyer_K_current__Na_i))); // millivolt
779  const NekDouble var_slow_activating_delayed_rectifiyer_K_current__i_Ks =
780  var_slow_activating_delayed_rectifiyer_K_current__g_Ks *
781  pow(var_slow_activating_delayed_rectifiyer_K_current__X_ks, 2.0) *
782  (var_slow_activating_delayed_rectifiyer_K_current__V -
783  var_slow_activating_delayed_rectifiyer_K_current__E_Ks); // microA_per_microF
784  const NekDouble var_membrane__i_Ks =
785  var_slow_activating_delayed_rectifiyer_K_current__i_Ks; // microA_per_microF
786  const NekDouble var_transient_outward_potassium_current__g_to =
787  0.23815; // milliS_per_microF
788  const NekDouble var_transient_outward_potassium_current__E_K =
789  var_rapid_activating_delayed_rectifiyer_K_current__E_K; // millivolt
790  const NekDouble var_transient_outward_potassium_current__i_to =
791  var_transient_outward_potassium_current__g_to *
792  var_transient_outward_potassium_current__X_to *
793  var_transient_outward_potassium_current__Y_to *
794  (var_transient_outward_potassium_current__V -
795  var_transient_outward_potassium_current__E_K); // microA_per_microF
796  const NekDouble var_membrane__i_to =
797  var_transient_outward_potassium_current__i_to; // microA_per_microF
798  const NekDouble var_time_independent_potassium_current__E_K =
799  var_rapid_activating_delayed_rectifiyer_K_current__E_K; // millivolt
800  const NekDouble var_time_independent_potassium_current__K_o =
801  var_standard_ionic_concentrations__K_o; // millimolar
802  const NekDouble var_time_independent_potassium_current__g_K1 =
803  2.8; // milliS_per_microF
804  const NekDouble var_time_independent_potassium_current__F =
805  var_membrane__F; // coulomb_per_millimole
806  const NekDouble var_time_independent_potassium_current_K1_gate__F =
807  var_time_independent_potassium_current__F; // coulomb_per_millimole
808  const NekDouble var_time_independent_potassium_current__V =
809  var_chaste_interface__membrane__V; // millivolt
810  const NekDouble var_time_independent_potassium_current_K1_gate__V =
811  var_time_independent_potassium_current__V; // millivolt
812  const NekDouble var_time_independent_potassium_current__T =
813  var_membrane__T; // kelvin
814  const NekDouble var_time_independent_potassium_current_K1_gate__T =
815  var_time_independent_potassium_current__T; // kelvin
816  const NekDouble var_time_independent_potassium_current_K1_gate__E_K =
817  var_time_independent_potassium_current__E_K; // millivolt
818  const NekDouble var_time_independent_potassium_current__R =
819  var_membrane__R; // joule_per_mole_kelvin
820  const NekDouble var_time_independent_potassium_current_K1_gate__R =
821  var_time_independent_potassium_current__R; // joule_per_mole_kelvin
822  const NekDouble
823  var_time_independent_potassium_current_K1_gate__K1_infinity =
824  1.0 /
825  (2.0 +
826  exp(((1.62 *
827  var_time_independent_potassium_current_K1_gate__F) /
828  (var_time_independent_potassium_current_K1_gate__R *
829  var_time_independent_potassium_current_K1_gate__T)) *
830  (var_time_independent_potassium_current_K1_gate__V -
831  var_time_independent_potassium_current_K1_gate__E_K))); // dimensionless
832  const NekDouble var_time_independent_potassium_current__K1_infinity =
833  var_time_independent_potassium_current_K1_gate__K1_infinity; // dimensionless
834  const NekDouble var_time_independent_potassium_current__K_mK1 =
835  13.0; // millimolar
836  const NekDouble var_time_independent_potassium_current__i_K1 =
837  ((var_time_independent_potassium_current__g_K1 *
838  var_time_independent_potassium_current__K1_infinity *
839  var_time_independent_potassium_current__K_o) /
840  (var_time_independent_potassium_current__K_o +
841  var_time_independent_potassium_current__K_mK1)) *
842  (var_time_independent_potassium_current__V -
843  var_time_independent_potassium_current__E_K); // microA_per_microF
844  const NekDouble var_membrane__i_K1 =
845  var_time_independent_potassium_current__i_K1; // microA_per_microF
846  const NekDouble var_plateau_potassium_current__g_Kp =
847  0.002216; // milliS_per_microF
848  const NekDouble var_plateau_potassium_current__V =
849  var_chaste_interface__membrane__V; // millivolt
850  const NekDouble var_plateau_potassium_current_Kp_gate__V =
851  var_plateau_potassium_current__V; // millivolt
852  const NekDouble var_plateau_potassium_current_Kp_gate__Kp_V =
853  1.0 /
854  (1.0 + exp((7.488 - var_plateau_potassium_current_Kp_gate__V) /
855  5.98)); // dimensionless
856  const NekDouble var_plateau_potassium_current__Kp_V =
857  var_plateau_potassium_current_Kp_gate__Kp_V; // dimensionless
858  const NekDouble var_plateau_potassium_current__E_K =
859  var_rapid_activating_delayed_rectifiyer_K_current__E_K; // millivolt
860  const NekDouble var_plateau_potassium_current__i_Kp =
861  var_plateau_potassium_current__g_Kp *
862  var_plateau_potassium_current__Kp_V *
863  (var_plateau_potassium_current__V -
864  var_plateau_potassium_current__E_K); // microA_per_microF
865  const NekDouble var_membrane__i_Kp =
866  var_plateau_potassium_current__i_Kp; // microA_per_microF
867  const NekDouble var_membrane__i_NaCa =
868  var_Na_Ca_exchanger__i_NaCa; // microA_per_microF
869  const NekDouble var_sodium_potassium_pump__K_mNai = 10.0; // millimolar
870  const NekDouble var_sodium_potassium_pump__V =
871  var_chaste_interface__membrane__V; // millivolt
872  const NekDouble var_sodium_potassium_pump__F =
873  var_membrane__F; // coulomb_per_millimole
874  const NekDouble var_sodium_potassium_pump__T =
875  var_membrane__T; // kelvin
876  const NekDouble var_sodium_potassium_pump__Na_o =
877  var_standard_ionic_concentrations__Na_o; // millimolar
878  const NekDouble var_sodium_potassium_pump__sigma =
879  (1.0 / 7.0) * (exp(var_sodium_potassium_pump__Na_o / 67.3) -
880  1.0); // dimensionless
881  const NekDouble var_sodium_potassium_pump__R =
882  var_membrane__R; // joule_per_mole_kelvin
883  const NekDouble var_sodium_potassium_pump__f_NaK =
884  1.0 / (1.0 +
885  (0.1245 * exp(((-0.1) * var_sodium_potassium_pump__V *
886  var_sodium_potassium_pump__F) /
887  (var_sodium_potassium_pump__R *
888  var_sodium_potassium_pump__T))) +
889  (0.0365 * var_sodium_potassium_pump__sigma *
890  exp(((-var_sodium_potassium_pump__V) *
891  var_sodium_potassium_pump__F) /
892  (var_sodium_potassium_pump__R *
893  var_sodium_potassium_pump__T)))); // dimensionless
894  const NekDouble var_sodium_potassium_pump__i_NaK_max =
895  0.693; // microA_per_microF
896  const NekDouble var_sodium_potassium_pump__K_o =
897  var_standard_ionic_concentrations__K_o; // millimolar
898  const NekDouble var_sodium_potassium_pump__Na_i =
899  var_standard_ionic_concentrations__Na_i; // millimolar
900  const NekDouble var_sodium_potassium_pump__K_mKo = 1.5; // millimolar
901  const NekDouble var_sodium_potassium_pump__i_NaK =
902  (((var_sodium_potassium_pump__i_NaK_max *
903  var_sodium_potassium_pump__f_NaK) /
904  (1.0 + pow(var_sodium_potassium_pump__K_mNai /
905  var_sodium_potassium_pump__Na_i,
906  1.5))) *
907  var_sodium_potassium_pump__K_o) /
908  (var_sodium_potassium_pump__K_o +
909  var_sodium_potassium_pump__K_mKo); // microA_per_microF
910  const NekDouble var_membrane__i_NaK =
911  var_sodium_potassium_pump__i_NaK; // microA_per_microF
912  const NekDouble var_membrane__i_p_Ca =
913  var_sarcolemmal_calcium_pump__i_p_Ca; // microA_per_microF
914  const NekDouble var_membrane__i_Ca_b =
915  var_calcium_background_current__i_Ca_b; // microA_per_microF
916  const NekDouble var_sodium_background_current__g_Nab =
917  0.0031; // milliS_per_microF
918  const NekDouble var_sodium_background_current__V =
919  var_chaste_interface__membrane__V; // millivolt
920  const NekDouble var_sodium_background_current__E_Na =
921  var_fast_sodium_current__E_Na; // millivolt
922  const NekDouble var_sodium_background_current__i_Na_b =
923  var_sodium_background_current__g_Nab *
924  (var_sodium_background_current__V -
925  var_sodium_background_current__E_Na); // microA_per_microF
926  const NekDouble var_membrane__i_Na_b =
927  var_sodium_background_current__i_Na_b; // microA_per_microF
928  const NekDouble var_chaste_interface__membrane__i_Stim = 0.0;
929  const NekDouble var_membrane__i_Stim_converter =
930  var_chaste_interface__membrane__i_Stim; // uA_per_cm2
931  const NekDouble
932  var_membrane__chaste_interface__chaste_membrane_capacitance =
933  1.0; // uF_per_cm2
934  const NekDouble var_membrane__i_Stim =
935  var_membrane__i_Stim_converter /
936  var_membrane__chaste_interface__chaste_membrane_capacitance; // microA_per_microF
937  const NekDouble var_membrane__d_V_d_environment__time =
938  -(var_membrane__i_Na + var_membrane__i_Ca + var_membrane__i_CaK +
939  var_membrane__i_Kr + var_membrane__i_Ks + var_membrane__i_to +
940  var_membrane__i_K1 + var_membrane__i_Kp + var_membrane__i_NaCa +
941  var_membrane__i_NaK + var_membrane__i_p_Ca +
942  var_membrane__i_Na_b + var_membrane__i_Ca_b +
943  var_membrane__i_Stim); // 'millivolt per millisecond'
944  const NekDouble
945  var_chaste_interface__membrane__d_V_d_environment__time =
946  var_membrane__d_V_d_environment__time; // ___units_1
947  d_dt_chaste_interface__membrane__V =
948  var_chaste_interface__membrane__d_V_d_environment__time; // 'millivolt
949  // per
950  // millisecond'
951  outarray[0][i] = d_dt_chaste_interface__membrane__V;
952  outarray[1][i] = d_dt_chaste_interface__fast_sodium_current_m_gate__m;
953  outarray[2][i] = d_dt_chaste_interface__fast_sodium_current_h_gate__h;
954  outarray[3][i] = d_dt_chaste_interface__fast_sodium_current_j_gate__j;
955  outarray[4][i] =
956  d_dt_chaste_interface__rapid_activating_delayed_rectifiyer_K_current_X_kr_gate__X_kr;
957  outarray[5][i] =
958  d_dt_chaste_interface__slow_activating_delayed_rectifiyer_K_current_X_ks_gate__X_ks;
959  outarray[6][i] =
960  d_dt_chaste_interface__transient_outward_potassium_current_X_to_gate__X_to;
961  outarray[7][i] =
962  d_dt_chaste_interface__transient_outward_potassium_current_Y_to_gate__Y_to;
963  outarray[8][i] = d_dt_chaste_interface__L_type_Ca_current_f_gate__f;
964  outarray[9][i] = d_dt_chaste_interface__L_type_Ca_current_d_gate__d;
965  outarray[10][i] =
966  d_dt_chaste_interface__L_type_Ca_current_f_Ca_gate__f_Ca;
967  outarray[11][i] = d_dt_chaste_interface__calcium_dynamics__Ca_i;
968  outarray[12][i] = d_dt_chaste_interface__calcium_dynamics__Ca_SR;
969  }
970 }
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:43
tinysimd::log
scalarT< T > log(scalarT< T > in)
Definition: scalar.hpp:300
tinysimd::sqrt
scalarT< T > sqrt(scalarT< T > in)
Definition: scalar.hpp:291

References tinysimd::log(), Nektar::CellModel::m_nq, and tinysimd::sqrt().

Member Data Documentation

◆ className

std::string Nektar::Fox02::className
static
Initial value:
= GetCellModelFactory().RegisterCreatorFunction(
"Fox02", Fox02::create, "Fox 2002 cell model.")
Nektar::Fox02::create
static CellModelSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Creates an instance of this class.
Definition: Fox02.h:46
Nektar::LibUtilities::NekFactory::RegisterCreatorFunction
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, std::string pDesc="")
Register a class with the factory.
Definition: NekFactory.hpp:198
Nektar::GetCellModelFactory
CellModelFactory & GetCellModelFactory()
Definition: CellModel.cpp:46

Name of class.

Definition at line 54 of file Fox02.h.

◆ m_chi

NekDouble Nektar::Fox02::m_chi
private

Definition at line 79 of file Fox02.h.

Referenced by Fox02().

◆ m_sigmai

NekDouble Nektar::Fox02::m_sigmai
private

Definition at line 80 of file Fox02.h.

Referenced by Fox02().

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