Nektar++
CourtemancheRamirezNattel98.cpp
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1///////////////////////////////////////////////////////////////////////////////
2//
3// File: CourtemancheRamirezNattel98.cpp
4//
5// For more information, please see: http://www.nektar.info
6//
7// The MIT License
8//
9// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
10// Department of Aeronautics, Imperial College London (UK), and Scientific
11// Computing and Imaging Institute, University of Utah (USA).
12//
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30//
31// Description: Courtemanche-Ramirez-Nattel ionic atrial cell model.
32//
33///////////////////////////////////////////////////////////////////////////////
34
35#include <iostream>
36#include <string>
37
38#include <CardiacEPSolver/CellModels/CourtemancheRamirezNattel98.h>
39#include <LibUtilities/BasicUtils/VmathArray.hpp>
40
41using namespace std;
42
43namespace Nektar
44{
45std::string CourtemancheRamirezNattel98::className =
46 GetCellModelFactory().RegisterCreatorFunction(
47 "CourtemancheRamirezNattel98", CourtemancheRamirezNattel98::create,
48 "Ionic model of human atrial cell electrophysiology.");
49
50// Register cell model variants
51std::string CourtemancheRamirezNattel98::lookupIds[2] = {
52 LibUtilities::SessionReader::RegisterEnumValue(
53 "CellModelVariant", "Original", CourtemancheRamirezNattel98::eOriginal),
54 LibUtilities::SessionReader::RegisterEnumValue(
55 "CellModelVariant", "AF", CourtemancheRamirezNattel98::eAF)};
56
57// Register default variant
58std::string CourtemancheRamirezNattel98::def =
59 LibUtilities::SessionReader::RegisterDefaultSolverInfo("CellModelVariant",
60 "Original");
61
62/**
63 *
64 */
65CourtemancheRamirezNattel98::CourtemancheRamirezNattel98(
66 const LibUtilities::SessionReaderSharedPtr &pSession,
67 const MultiRegions::ExpListSharedPtr &pField)
68 : CellModel(pSession, pField)
69{
70 model_variant =
71 pSession->GetSolverInfoAsEnum<CourtemancheRamirezNattel98::Variants>(
72 "CellModelVariant");
73
74 C_m = 100; // picoF
75 g_Na = 7.8; // nanoS_per_picoF
76 g_K1 = 0.09; // nanoS_per_picoF
77 g_Kr = 0.029411765;
78 g_Ks = 0.12941176;
79 g_b_Na = 0.0006744375;
80 g_b_Ca = 0.001131;
81 R = 8.3143;
82 T = 310.0;
83 F = 96.4867;
84 Na_o = 140.0; // millimolar
85 K_o = 5.4; // millimolar
86 sigma = 1.0 / 7.0 * (exp(Na_o / 67.3) - 1);
87 K_i = 1.5;
88 K_m_Na_i = 10.0;
89 I_Na_K_max = 0.59933874;
90 I_NaCa_max = 1600.0;
91 gamma = 0.35;
92 Ca_o = 1.8;
93 K_m_Na = 87.5;
94 K_m_Ca = 1.38;
95 K_sat = 0.1;
96 I_p_Ca_max = 0.275;
97 Trpn_max = 0.07;
98 Km_Trpn = 0.0005;
99 Cmdn_max = 0.05;
100 Csqn_max = 10.0;
101 Km_Cmdn = 0.00238;
102 Km_Csqn = 0.8;
103 NSR_I_up_max = 0.005;
104 NSR_I_Ca_max = 15.0;
105 NSR_K_up = 0.00092;
106 JSR_K_rel = 30.0;
107 JSR_V_cell = 20100.0;
108 JSR_V_rel = 0.0048 * JSR_V_cell;
109 JSR_V_up = 0.0552 * JSR_V_cell;
110 tau_tr = 180.0;
111 K_Q10 = 3.0;
112 V_i = 0.68 * JSR_V_cell;
113
114 switch (model_variant)
115 {
116 case eOriginal:
117 g_to = 0.1652; // nanoS_per_picoF
118 g_Kur_scaling = 1.0;
119 g_Ca_L = 0.12375;
120 break;
121 case eAF:
122 g_to = 0.0826; // nanoS_per_picoF
123 g_Kur_scaling = 0.5;
124 g_Ca_L = 0.037125;
125 break;
126 }
127
128 m_nvar = 21;
129
130 // List gates and concentrations
131 m_gates.push_back(1);
132 m_gates.push_back(2);
133 m_gates.push_back(3);
134 m_gates.push_back(4);
135 m_gates.push_back(5);
136 m_gates.push_back(6);
137 m_gates.push_back(7);
138 m_gates.push_back(8);
139 m_gates.push_back(9);
140 m_gates.push_back(10);
141 m_gates.push_back(11);
142 m_gates.push_back(12);
143 m_gates.push_back(13);
144 m_gates.push_back(14);
145 m_gates.push_back(15);
146 m_concentrations.push_back(16);
147 m_concentrations.push_back(17);
148 m_concentrations.push_back(18);
149 m_concentrations.push_back(19);
150 m_concentrations.push_back(20);
151}
152
153/**
154 *
155 */
156CourtemancheRamirezNattel98::~CourtemancheRamirezNattel98()
157{
158}
159
160void CourtemancheRamirezNattel98::v_Update(
161 const Array<OneD, const Array<OneD, NekDouble>> &inarray,
162 Array<OneD, Array<OneD, NekDouble>> &outarray,
163 [[maybe_unused]] const NekDouble time)
164{
165 ASSERTL0(inarray.get() != outarray.get(),
166 "Must have different arrays for input and output.");
167
168 // Variables
169 // 0 V membrane potential
170 // 2 m fast sodium current m gate
171 // 3 h fast sodium current h gate
172 // 4 j fast sodium current j gate
173 // 5 o_a transient outward potassium o_a gate
174 // 6 o_i transient outward potassium o_i gate
175 // 7 u_a ultra-rapid delayed rectifier K current gate
176 // 8 u_i ultra-rapid delayed rectifier K current gate
177 // 9 x_r rapid delayed rectifier K current gate
178 // 10 x_s slow delayed rectifier K current gate
179 // 11 d L_type calcium gate
180 // 12 f L-type calcium gate
181 // 13 f_Ca L-type calcium gate
182 // 14 u Ca release u gate
183 // 15 v Ca release v gate
184 // 16 w Ca release w gate
185 // 17 Na_i Sodium
186 // 18 Ca_i Calcium
187 // 19 K_i Potassium
188 // 20 Ca_rel Calcium Rel
189 // 21 Ca_up Calcium up
190 size_t n = m_nq;
191 size_t i = 0;
192 NekDouble alpha, beta;
193 Vmath::Zero(n, outarray[0], 1);
194
195 Array<OneD, NekDouble> &tmp = outarray[11];
196 Array<OneD, NekDouble> &tmp2 = outarray[12];
197
198 // E_Na
199 Array<OneD, NekDouble> &tmp_E_na = outarray[14];
200 Vmath::Sdiv(n, Na_o, inarray[16], 1, tmp_E_na, 1);
201 Vmath::Vlog(n, tmp_E_na, 1, tmp_E_na, 1);
202 Vmath::Smul(n, R * T / F, tmp_E_na, 1, tmp_E_na, 1);
203
204 // Sodium I_Na
205 Array<OneD, NekDouble> &tmp_I_Na = outarray[15];
206 Vmath::Vsub(n, inarray[0], 1, tmp_E_na, 1, tmp_I_Na, 1);
207 Vmath::Vmul(n, inarray[1], 1, tmp_I_Na, 1, tmp_I_Na, 1);
208 Vmath::Vmul(n, inarray[1], 1, tmp_I_Na, 1, tmp_I_Na, 1);
209 Vmath::Vmul(n, inarray[1], 1, tmp_I_Na, 1, tmp_I_Na, 1);
210 Vmath::Vmul(n, inarray[2], 1, tmp_I_Na, 1, tmp_I_Na, 1);
211 Vmath::Vmul(n, inarray[3], 1, tmp_I_Na, 1, tmp_I_Na, 1);
212 Vmath::Smul(n, C_m * g_Na, tmp_I_Na, 1, tmp_I_Na, 1);
213 Vmath::Vsub(n, outarray[0], 1, tmp_I_Na, 1, outarray[0], 1);
214 Vmath::Smul(n, -1.0, tmp_I_Na, 1, outarray[16], 1);
215
216 // Background current, sodium
217 Array<OneD, NekDouble> &tmp_I_b_Na = outarray[15];
218 Vmath::Vsub(n, inarray[0], 1, tmp_E_na, 1, tmp_I_b_Na, 1);
219 Vmath::Smul(n, C_m * g_b_Na, tmp_I_b_Na, 1, tmp_I_b_Na, 1);
220 Vmath::Vsub(n, outarray[0], 1, tmp_I_b_Na, 1, outarray[0], 1);
221 Vmath::Vsub(n, outarray[16], 1, tmp_I_b_Na, 1, outarray[16], 1);
222
223 // V - E_K
224 Array<OneD, NekDouble> &tmp_V_E_k = outarray[14];
225 Vmath::Sdiv(n, K_o, inarray[18], 1, tmp_V_E_k, 1);
226 Vmath::Vlog(n, tmp_V_E_k, 1, tmp_V_E_k, 1);
227 Vmath::Smul(n, R * T / F, tmp_V_E_k, 1, tmp_V_E_k, 1);
228 Vmath::Vsub(n, inarray[0], 1, tmp_V_E_k, 1, tmp_V_E_k, 1);
229
230 // Potassium I_K1
231 Array<OneD, NekDouble> &tmp_I_K1 = outarray[15];
232 Vmath::Sadd(n, 80.0, inarray[0], 1, tmp_I_K1, 1);
233 Vmath::Smul(n, 0.07, tmp_I_K1, 1, tmp_I_K1, 1);
234 Vmath::Vexp(n, tmp_I_K1, 1, tmp_I_K1, 1);
235 Vmath::Sadd(n, 1.0, tmp_I_K1, 1, tmp_I_K1, 1);
236 Vmath::Vdiv(n, tmp_V_E_k, 1, tmp_I_K1, 1, tmp_I_K1, 1);
237 Vmath::Smul(n, C_m * g_K1, tmp_I_K1, 1, tmp_I_K1, 1);
238 Vmath::Vsub(n, outarray[0], 1, tmp_I_K1, 1, outarray[0], 1);
239 Vmath::Smul(n, -1.0, tmp_I_K1, 1, outarray[18], 1);
240
241 // Transient Outward K+ current
242 Array<OneD, NekDouble> &tmp_I_to = outarray[15];
243 Vmath::Vmul(n, inarray[5], 1, tmp_V_E_k, 1, tmp_I_to, 1);
244 Vmath::Vmul(n, inarray[4], 1, tmp_I_to, 1, tmp_I_to, 1);
245 Vmath::Vmul(n, inarray[4], 1, tmp_I_to, 1, tmp_I_to, 1);
246 Vmath::Vmul(n, inarray[4], 1, tmp_I_to, 1, tmp_I_to, 1);
247 Vmath::Smul(n, C_m * g_to, tmp_I_to, 1, tmp_I_to, 1);
248 Vmath::Vsub(n, outarray[0], 1, tmp_I_to, 1, outarray[0], 1);
249 Vmath::Vsub(n, outarray[18], 1, tmp_I_to, 1, outarray[18], 1);
250
251 // Ultrarapid Delayed rectifier K+ current
252 Array<OneD, NekDouble> &tmp_I_kur = outarray[15];
253 Vmath::Sadd(n, -15.0, inarray[0], 1, tmp_I_kur, 1);
254 Vmath::Smul(n, -1.0 / 13.0, tmp_I_kur, 1, tmp_I_kur, 1);
255 Vmath::Vexp(n, tmp_I_kur, 1, tmp_I_kur, 1);
256 Vmath::Sadd(n, 1.0, tmp_I_kur, 1, tmp_I_kur, 1);
257 Vmath::Sdiv(n, 0.05, tmp_I_kur, 1, tmp_I_kur, 1);
258 Vmath::Sadd(n, 0.005, tmp_I_kur, 1, tmp_I_kur, 1);
259 Vmath::Vmul(n, tmp_V_E_k, 1, tmp_I_kur, 1, tmp_I_kur, 1);
260 Vmath::Vmul(n, inarray[6], 1, tmp_I_kur, 1, tmp_I_kur, 1);
261 Vmath::Vmul(n, inarray[6], 1, tmp_I_kur, 1, tmp_I_kur, 1);
262 Vmath::Vmul(n, inarray[6], 1, tmp_I_kur, 1, tmp_I_kur, 1);
263 Vmath::Vmul(n, inarray[7], 1, tmp_I_kur, 1, tmp_I_kur, 1);
264 Vmath::Smul(n, C_m * g_Kur_scaling, tmp_I_kur, 1, tmp_I_kur, 1);
265 Vmath::Vsub(n, outarray[0], 1, tmp_I_kur, 1, outarray[0], 1);
266 Vmath::Vsub(n, outarray[18], 1, tmp_I_kur, 1, outarray[18], 1);
267
268 // Rapid delayed outward rectifier K+ current
269 Array<OneD, NekDouble> &tmp_I_Kr = outarray[15];
270 Vmath::Sadd(n, 15.0, inarray[0], 1, tmp_I_Kr, 1);
271 Vmath::Smul(n, 1.0 / 22.4, tmp_I_Kr, 1, tmp_I_Kr, 1);
272 Vmath::Vexp(n, tmp_I_Kr, 1, tmp_I_Kr, 1);
273 Vmath::Sadd(n, 1.0, tmp_I_Kr, 1, tmp_I_Kr, 1);
274 Vmath::Vdiv(n, tmp_V_E_k, 1, tmp_I_Kr, 1, tmp_I_Kr, 1);
275 Vmath::Vmul(n, inarray[8], 1, tmp_I_Kr, 1, tmp_I_Kr, 1);
276 Vmath::Smul(n, C_m * g_Kr, tmp_I_Kr, 1, tmp_I_Kr, 1);
277 Vmath::Vsub(n, outarray[0], 1, tmp_I_Kr, 1, outarray[0], 1);
278 Vmath::Vsub(n, outarray[18], 1, tmp_I_Kr, 1, outarray[18], 1);
279
280 // Slow delayed outward rectifier K+ Current
281 Array<OneD, NekDouble> &tmp_I_Ks = outarray[15];
282 Vmath::Vmul(n, inarray[9], 1, tmp_V_E_k, 1, tmp_I_Ks, 1);
283 Vmath::Vmul(n, inarray[9], 1, tmp_I_Ks, 1, tmp_I_Ks, 1);
284 Vmath::Smul(n, C_m * g_Ks, tmp_I_Ks, 1, tmp_I_Ks, 1);
285 Vmath::Vsub(n, outarray[0], 1, tmp_I_Ks, 1, outarray[0], 1);
286 Vmath::Vsub(n, outarray[18], 1, tmp_I_Ks, 1, outarray[18], 1);
287
288 // Background current, calcium
289 Array<OneD, NekDouble> &tmp_I_b_Ca = outarray[1];
290 Vmath::Sdiv(n, Ca_o, inarray[17], 1, tmp_I_b_Ca, 1);
291 Vmath::Vlog(n, tmp_I_b_Ca, 1, tmp_I_b_Ca, 1);
292 Vmath::Smul(n, 0.5 * R * T / F, tmp_I_b_Ca, 1, tmp_I_b_Ca, 1);
293 Vmath::Vsub(n, inarray[0], 1, tmp_I_b_Ca, 1, tmp_I_b_Ca, 1);
294 Vmath::Smul(n, C_m * g_b_Ca, tmp_I_b_Ca, 1, tmp_I_b_Ca, 1);
295 Vmath::Vsub(n, outarray[0], 1, tmp_I_b_Ca, 1, outarray[0], 1);
296
297 // L-Type Ca2+ current
298 Array<OneD, NekDouble> &tmp_I_Ca_L = outarray[2];
299 Vmath::Sadd(n, -65.0, inarray[0], 1, tmp_I_Ca_L, 1);
300 Vmath::Vmul(n, inarray[10], 1, tmp_I_Ca_L, 1, tmp_I_Ca_L, 1);
301 Vmath::Vmul(n, inarray[11], 1, tmp_I_Ca_L, 1, tmp_I_Ca_L, 1);
302 Vmath::Vmul(n, inarray[12], 1, tmp_I_Ca_L, 1, tmp_I_Ca_L, 1);
303 Vmath::Smul(n, C_m * g_Ca_L, tmp_I_Ca_L, 1, tmp_I_Ca_L, 1);
304 Vmath::Vsub(n, outarray[0], 1, tmp_I_Ca_L, 1, outarray[0], 1);
305
306 // Na-K Pump Current
307 Array<OneD, NekDouble> &tmp_f_Na_k = outarray[14];
308 Vmath::Smul(n, -F / R / T, inarray[0], 1, tmp_f_Na_k, 1);
309 Vmath::Vexp(n, tmp_f_Na_k, 1, tmp, 1);
310 Vmath::Smul(n, 0.0365 * sigma, tmp, 1, tmp, 1);
311 Vmath::Smul(n, -0.1 * F / R / T, inarray[0], 1, tmp_f_Na_k, 1);
312 Vmath::Vexp(n, tmp_f_Na_k, 1, tmp_f_Na_k, 1);
313 Vmath::Smul(n, 0.1245, tmp_f_Na_k, 1, tmp_f_Na_k, 1);
314 Vmath::Vadd(n, tmp_f_Na_k, 1, tmp, 1, tmp_f_Na_k, 1);
315 Vmath::Sadd(n, 1.0, tmp_f_Na_k, 1, tmp_f_Na_k, 1);
316
317 Array<OneD, NekDouble> &tmp_I_Na_K = outarray[15];
318 Vmath::Sdiv(n, K_m_Na_i, inarray[16], 1, tmp_I_Na_K, 1);
319 Vmath::Vpow(n, tmp_I_Na_K, 1, 1.5, tmp_I_Na_K, 1);
320 Vmath::Sadd(n, 1.0, tmp_I_Na_K, 1, tmp_I_Na_K, 1);
321 Vmath::Vmul(n, tmp_f_Na_k, 1, tmp_I_Na_K, 1, tmp_I_Na_K, 1);
322 Vmath::Sdiv(n, C_m * I_Na_K_max * K_o / (K_o + K_i), tmp_I_Na_K, 1,
323 tmp_I_Na_K, 1);
324 Vmath::Vsub(n, outarray[0], 1, tmp_I_Na_K, 1, outarray[0], 1);
325 Vmath::Svtvp(n, -3.0, tmp_I_Na_K, 1, outarray[16], 1, outarray[16], 1);
326 Vmath::Svtvp(n, 2.0, tmp_I_Na_K, 1, outarray[18], 1, outarray[18], 1);
327
328 // Na-Ca exchanger current
329 Array<OneD, NekDouble> &tmp_I_Na_Ca = outarray[3];
330 Vmath::Smul(n, (gamma - 1) * F / R / T, inarray[0], 1, tmp, 1);
331 Vmath::Vexp(n, tmp, 1, tmp, 1);
332 Vmath::Smul(n, K_sat, tmp, 1, tmp_I_Na_Ca, 1);
333 Vmath::Sadd(n, 1.0, tmp_I_Na_Ca, 1, tmp_I_Na_Ca, 1);
334 Vmath::Smul(
335 n, (K_m_Na * K_m_Na * K_m_Na + Na_o * Na_o * Na_o) * (K_m_Ca + Ca_o),
336 tmp_I_Na_Ca, 1, tmp_I_Na_Ca, 1);
337
338 Vmath::Smul(n, Na_o * Na_o * Na_o, tmp, 1, tmp2, 1);
339 Vmath::Vmul(n, tmp2, 1, inarray[17], 1, tmp2, 1);
340 Vmath::Smul(n, gamma * F / R / T, inarray[0], 1, tmp, 1);
341 Vmath::Vexp(n, tmp, 1, tmp, 1);
342 Vmath::Vmul(n, inarray[16], 1, tmp, 1, tmp, 1);
343 Vmath::Vmul(n, inarray[16], 1, tmp, 1, tmp, 1);
344 Vmath::Vmul(n, inarray[16], 1, tmp, 1, tmp, 1);
345 Vmath::Svtvm(n, Ca_o, tmp, 1, tmp2, 1, tmp, 1);
346 Vmath::Smul(n, C_m * I_NaCa_max, tmp, 1, tmp, 1);
347 Vmath::Vdiv(n, tmp, 1, tmp_I_Na_Ca, 1, tmp_I_Na_Ca, 1);
348 Vmath::Vsub(n, outarray[0], 1, tmp_I_Na_Ca, 1, outarray[0], 1);
349 Vmath::Svtvp(n, -3.0, tmp_I_Na_Ca, 1, outarray[16], 1, outarray[16], 1);
350
351 // Calcium Pump current
352 Array<OneD, NekDouble> &tmp_I_p_Ca = outarray[4];
353 Vmath::Sadd(n, 0.0005, inarray[17], 1, tmp_I_p_Ca, 1);
354 Vmath::Vdiv(n, inarray[17], 1, tmp_I_p_Ca, 1, tmp_I_p_Ca, 1);
355 Vmath::Smul(n, C_m * I_p_Ca_max, tmp_I_p_Ca, 1, tmp_I_p_Ca, 1);
356 Vmath::Vsub(n, outarray[0], 1, tmp_I_p_Ca, 1, outarray[0], 1);
357
358 // Scale currents by capacitance
359 Vmath::Smul(n, 1.0 / C_m, outarray[0], 1, outarray[0], 1);
360
361 // Scale sodium and potassium by FV_i
362 Vmath::Smul(n, 1.0 / F / V_i, outarray[16], 1, outarray[16], 1);
363 Vmath::Smul(n, 1.0 / F / V_i, outarray[18], 1, outarray[18], 1);
364
365 // I_tr
366 Array<OneD, NekDouble> &tmp_I_tr = outarray[5];
367 Vmath::Vsub(n, inarray[20], 1, inarray[19], 1, tmp_I_tr, 1);
368 Vmath::Smul(n, 1.0 / tau_tr, tmp_I_tr, 1, tmp_I_tr, 1);
369
370 // I_up_leak
371 Array<OneD, NekDouble> &tmp_I_up_leak = outarray[6];
372 Vmath::Smul(n, NSR_I_up_max / NSR_I_Ca_max, inarray[20], 1, tmp_I_up_leak,
373 1);
374
375 // I_up
376 Array<OneD, NekDouble> &tmp_I_up = outarray[7];
377 Vmath::Sdiv(n, NSR_K_up, inarray[17], 1, tmp_I_up, 1);
378 Vmath::Sadd(n, 1.0, tmp_I_up, 1, tmp_I_up, 1);
379 Vmath::Sdiv(n, NSR_I_up_max, tmp_I_up, 1, tmp_I_up, 1);
380
381 // I_rel
382 Array<OneD, NekDouble> &tmp_I_rel = outarray[8];
383 Vmath::Vsub(n, inarray[19], 1, inarray[17], 1, tmp_I_rel, 1);
384 Vmath::Vmul(n, tmp_I_rel, 1, inarray[13], 1, tmp_I_rel, 1);
385 Vmath::Vmul(n, tmp_I_rel, 1, inarray[13], 1, tmp_I_rel, 1);
386 Vmath::Vmul(n, tmp_I_rel, 1, inarray[14], 1, tmp_I_rel, 1);
387 Vmath::Vmul(n, tmp_I_rel, 1, inarray[15], 1, tmp_I_rel, 1);
388 Vmath::Smul(n, JSR_K_rel, tmp_I_rel, 1, tmp_I_rel, 1);
389
390 // B1
391 Array<OneD, NekDouble> &tmp_B1 = outarray[9];
392 Vmath::Svtvm(n, 2.0, tmp_I_Na_Ca, 1, tmp_I_p_Ca, 1, tmp_B1, 1);
393 Vmath::Vsub(n, tmp_B1, 1, tmp_I_Ca_L, 1, tmp_B1, 1);
394 Vmath::Vsub(n, tmp_B1, 1, tmp_I_b_Ca, 1, tmp_B1, 1);
395 Vmath::Smul(n, 0.5 / F, tmp_B1, 1, tmp_B1, 1);
396 Vmath::Svtvp(n, JSR_V_up, tmp_I_up_leak, 1, tmp_B1, 1, tmp_B1, 1);
397 Vmath::Svtvp(n, -JSR_V_up, tmp_I_up, 1, tmp_B1, 1, tmp_B1, 1);
398 Vmath::Svtvp(n, JSR_V_rel, tmp_I_rel, 1, tmp_B1, 1, tmp_B1, 1);
399 Vmath::Smul(n, 1.0 / V_i, tmp_B1, 1, tmp_B1, 1);
400
401 // B2
402 Array<OneD, NekDouble> &tmp_B2 = outarray[10];
403 Vmath::Sadd(n, Km_Cmdn, inarray[17], 1, tmp_B2, 1);
404 Vmath::Vmul(n, tmp_B2, 1, tmp_B2, 1, tmp_B2, 1);
405 Vmath::Sdiv(n, Cmdn_max * Km_Cmdn, tmp_B2, 1, tmp_B2, 1);
406 Vmath::Sadd(n, Km_Trpn, inarray[17], 1, tmp, 1);
407 Vmath::Vmul(n, tmp, 1, tmp, 1, tmp, 1);
408 Vmath::Sdiv(n, Trpn_max * Km_Trpn, tmp, 1, tmp, 1);
409 Vmath::Vadd(n, tmp, 1, tmp_B2, 1, tmp_B2, 1);
410 Vmath::Sadd(n, 1.0, tmp_B2, 1, tmp_B2, 1);
411
412 // Calcium concentration (18)
413 Vmath::Vdiv(n, tmp_B1, 1, tmp_B2, 1, outarray[17], 1);
414
415 // Calcium up (21)
416 Vmath::Vsub(n, tmp_I_up, 1, tmp_I_up_leak, 1, outarray[20], 1);
417 Vmath::Svtvp(n, -JSR_V_rel / JSR_V_up, tmp_I_tr, 1, outarray[20], 1,
418 outarray[20], 1);
419
420 // Calcium rel (20)
421 Vmath::Vsub(n, tmp_I_tr, 1, tmp_I_rel, 1, tmp, 1);
422 Vmath::Sadd(n, Km_Csqn, inarray[19], 1, outarray[19], 1);
423 Vmath::Vmul(n, outarray[19], 1, outarray[19], 1, outarray[19], 1);
424 Vmath::Sdiv(n, Csqn_max * Km_Csqn, outarray[19], 1, outarray[19], 1);
425 Vmath::Sadd(n, 1.0, outarray[19], 1, outarray[19], 1);
426 Vmath::Vdiv(n, tmp, 1, outarray[19], 1, outarray[19], 1);
427
428 // Process gating variables
429 const NekDouble *v;
430 const NekDouble *x;
431 NekDouble *x_tau;
432 NekDouble *x_new;
433 // m
434 for (i = 0, v = &inarray[0][0], x = &inarray[1][0], x_new = &outarray[1][0],
435 x_tau = &m_gates_tau[0][0];
436 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
437 {
438 alpha = (*v == (-47.13)) ? 3.2
439 : (0.32 * (*v + 47.13)) /
440 (1.0 - exp((-0.1) * (*v + 47.13)));
441 beta = 0.08 * exp(-(*v) / 11.0);
442 *x_tau = 1.0 / (alpha + beta);
443 *x_new = alpha * (*x_tau);
444 }
445 // h
446 for (i = 0, v = &inarray[0][0], x = &inarray[2][0], x_new = &outarray[2][0],
447 x_tau = &m_gates_tau[1][0];
448 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
449 {
450 alpha = (*v >= -40.0) ? 0.0 : 0.135 * exp(-((*v) + 80.0) / 6.8);
451 beta = (*v >= -40.0)
452 ? 1.0 / (0.13 * (1.0 + exp(-(*v + 10.66) / 11.1)))
453 : 3.56 * exp(0.079 * (*v)) + 310000.0 * exp(0.35 * (*v));
454 *x_tau = 1.0 / (alpha + beta);
455 *x_new = alpha * (*x_tau);
456 }
457 // j
458 for (i = 0, v = &inarray[0][0], x = &inarray[3][0], x_new = &outarray[3][0],
459 x_tau = &m_gates_tau[2][0];
460 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
461 {
462 alpha =
463 (*v >= -40.0)
464 ? 0.0
465 : (-127140.0 * exp(0.2444 * (*v)) -
466 3.474e-05 * exp(-0.04391 * (*v))) *
467 (((*v) + 37.78) / (1.0 + exp(0.311 * ((*v) + 79.23))));
468 beta = (*v >= -40.0) ? (0.3 * exp(-2.535e-07 * (*v)) /
469 (1.0 + exp(-0.1 * (*v + 32.0))))
470 : 0.1212 * exp(-0.01052 * (*v)) /
471 (1.0 + exp(-0.1378 * (*v + 40.14)));
472 *x_tau = 1.0 / (alpha + beta);
473 *x_new = alpha * (*x_tau);
474 }
475 // oa
476 for (i = 0, v = &inarray[0][0], x = &inarray[4][0], x_new = &outarray[4][0],
477 x_tau = &m_gates_tau[3][0];
478 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
479 {
480 alpha = 0.65 / (exp(-(*v + 10.0) / 8.5) + exp(-(*v - 30.0) / 59.0));
481 beta = 0.65 / (2.5 + exp((*v + 82.0) / 17.0));
482 *x_tau = 1.0 / K_Q10 / (alpha + beta);
483 *x_new = (1.0 / (1.0 + exp(-(*v + 20.47) / 17.54)));
484 }
485 // oi
486 for (i = 0, v = &inarray[0][0], x = &inarray[5][0], x_new = &outarray[5][0],
487 x_tau = &m_gates_tau[4][0];
488 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
489 {
490 alpha = 1.0 / (18.53 + exp((*v + 113.7) / 10.95));
491 beta = 1.0 / (35.56 + exp(-(*v + 1.26) / 7.44));
492 *x_tau = 1.0 / K_Q10 / (alpha + beta);
493 *x_new = (1.0 / (1.0 + exp((*v + 43.1) / 5.3)));
494 }
495 // ua
496 for (i = 0, v = &inarray[0][0], x = &inarray[6][0], x_new = &outarray[6][0],
497 x_tau = &m_gates_tau[5][0];
498 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
499 {
500 alpha = 0.65 / (exp(-(*v + 10.0) / 8.5) + exp(-(*v - 30.0) / 59.0));
501 beta = 0.65 / (2.5 + exp((*v + 82.0) / 17.0));
502 *x_tau = 1.0 / K_Q10 / (alpha + beta);
503 *x_new = 1.0 / (1.0 + exp(-(*v + 30.3) / 9.6));
504 }
505 // ui
506 for (i = 0, v = &inarray[0][0], x = &inarray[7][0], x_new = &outarray[7][0],
507 x_tau = &m_gates_tau[6][0];
508 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
509 {
510 alpha = 1.0 / (21.0 + exp(-(*v - 185.0) / 28.0));
511 beta = exp((*v - 158.0) / 16.0);
512 *x_tau = 1.0 / K_Q10 / (alpha + beta);
513 *x_new = 1.0 / (1.0 + exp((*v - 99.45) / 27.48));
514 }
515 // xr
516 for (i = 0, v = &inarray[0][0], x = &inarray[8][0], x_new = &outarray[8][0],
517 x_tau = &m_gates_tau[7][0];
518 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
519 {
520 alpha = 0.0003 * (*v + 14.1) / (1 - exp(-(*v + 14.1) / 5.0));
521 beta = 7.3898e-5 * (*v - 3.3328) / (exp((*v - 3.3328) / 5.1237) - 1.0);
522 *x_tau = 1.0 / (alpha + beta);
523 *x_new = 1.0 / (1 + exp(-(*v + 14.1) / 6.5));
524 }
525 // xs
526 for (i = 0, v = &inarray[0][0], x = &inarray[9][0], x_new = &outarray[9][0],
527 x_tau = &m_gates_tau[8][0];
528 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
529 {
530 alpha = 4e-5 * (*v - 19.9) / (1.0 - exp(-(*v - 19.9) / 17.0));
531 beta = 3.5e-5 * (*v - 19.9) / (exp((*v - 19.9) / 9.0) - 1.0);
532 *x_tau = 0.5 / (alpha + beta);
533 *x_new = 1.0 / sqrt(1.0 + exp(-(*v - 19.9) / 12.7));
534 }
535 // d
536 for (i = 0, v = &inarray[0][0], x = &inarray[10][0],
537 x_new = &outarray[10][0], x_tau = &m_gates_tau[9][0];
538 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
539 {
540 *x_tau = (1 - exp(-(*v + 10.0) / 6.24)) /
541 (0.035 * (*v + 10.0) * (1 + exp(-(*v + 10.0) / 6.24)));
542 *x_new = 1.0 / (1.0 + exp(-(*v + 10) / 8.0));
543 }
544 // f
545 for (i = 0, v = &inarray[0][0], x = &inarray[11][0],
546 x_new = &outarray[11][0], x_tau = &m_gates_tau[10][0];
547 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
548 {
549 // alpha = 1.0/(1.0 + exp((*v+28.0)/6.9));
550 *x_tau =
551 9.0 /
552 (0.0197 * exp(-0.0337 * 0.0337 * (*v + 10.0) * (*v + 10.0)) + 0.02);
553 *x_new = exp((-(*v + 28.0)) / 6.9) / (1.0 + exp((-(*v + 28.0)) / 6.9));
554 }
555 // f_Ca
556 for (i = 0, v = &inarray[0][0], x = &inarray[12][0],
557 x_new = &outarray[12][0], x_tau = &m_gates_tau[11][0];
558 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
559 {
560 *x_tau = 2.0;
561 *x_new = 1.0 / (1.0 + inarray[17][i] / 0.00035);
562 }
563
564 Array<OneD, NekDouble> &tmp_Fn = outarray[15];
565 Vmath::Svtsvtp(n, 0.5 * 5e-13 / F, tmp_I_Ca_L, 1, -0.2 * 5e-13 / F,
566 tmp_I_Na_Ca, 1, tmp_Fn, 1);
567 Vmath::Svtvm(n, 1e-12 * JSR_V_rel, tmp_I_rel, 1, tmp_Fn, 1, tmp_Fn, 1);
568
569 // u
570 for (i = 0, v = &tmp_Fn[0], x = &inarray[13][0], x_new = &outarray[13][0],
571 x_tau = &m_gates_tau[12][0];
572 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
573 {
574 *x_tau = 8.0;
575 *x_new = 1.0 / (1.0 + exp(-(*v - 3.4175e-13) / 1.367e-15));
576 }
577 // v
578 for (i = 0, v = &tmp_Fn[0], x = &inarray[14][0], x_new = &outarray[14][0],
579 x_tau = &m_gates_tau[13][0];
580 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
581 {
582 *x_tau = 1.91 + 2.09 / (1.0 + exp(-(*v - 3.4175e-13) / 13.67e-16));
583 *x_new = 1.0 - 1.0 / (1.0 + exp(-(*v - 6.835e-14) / 13.67e-16));
584 }
585 // w
586 for (i = 0, v = &inarray[0][0], x = &inarray[15][0],
587 x_new = &outarray[15][0], x_tau = &m_gates_tau[14][0];
588 i < n; ++i, ++v, ++x, ++x_new, ++x_tau)
589 {
590 *x_tau = 6.0 * (1.0 - exp(-(*v - 7.9) / 5.0)) /
591 (1.0 + 0.3 * exp(-(*v - 7.9) / 5.0)) / (*v - 7.9);
592 *x_new = 1.0 - 1.0 / (1.0 + exp(-(*v - 40.0) / 17.0));
593 }
594}
595
596/**
597 *
598 */
599void CourtemancheRamirezNattel98::v_GenerateSummary(SummaryList &s)
600{
601 SolverUtils::AddSummaryItem(s, "Cell model", "CourtemancheRamirezNattel98");
602 SolverUtils::AddSummaryItem(s, "Cell model var.", lookupIds[model_variant]);
603}
604
605void CourtemancheRamirezNattel98::v_SetInitialConditions()
606{
607 Vmath::Fill(m_nq, -81.0, m_cellSol[0], 1);
608 Vmath::Fill(m_nq, 2.908e-03, m_cellSol[1], 1);
609 Vmath::Fill(m_nq, 9.649e-01, m_cellSol[2], 1);
610 Vmath::Fill(m_nq, 9.775e-01, m_cellSol[3], 1);
611 Vmath::Fill(m_nq, 3.043e-02, m_cellSol[4], 1);
612 Vmath::Fill(m_nq, 9.992e-01, m_cellSol[5], 1);
613 Vmath::Fill(m_nq, 4.966e-03, m_cellSol[6], 1);
614 Vmath::Fill(m_nq, 9.986e-01, m_cellSol[7], 1);
615 Vmath::Fill(m_nq, 3.296e-05, m_cellSol[8], 1);
616 Vmath::Fill(m_nq, 1.869e-02, m_cellSol[9], 1);
617 Vmath::Fill(m_nq, 1.367e-04, m_cellSol[10], 1);
618 Vmath::Fill(m_nq, 9.996e-01, m_cellSol[11], 1);
619 Vmath::Fill(m_nq, 7.755e-01, m_cellSol[12], 1);
620 Vmath::Fill(m_nq, 2.35e-112, m_cellSol[13], 1);
621 Vmath::Fill(m_nq, 1.0, m_cellSol[14], 1);
622 Vmath::Fill(m_nq, 0.9992, m_cellSol[15], 1);
623 Vmath::Fill(m_nq, 1.117e+01, m_cellSol[16], 1);
624 Vmath::Fill(m_nq, 1.013e-04, m_cellSol[17], 1);
625 Vmath::Fill(m_nq, 1.39e+02, m_cellSol[18], 1);
626 Vmath::Fill(m_nq, 1.488, m_cellSol[19], 1);
627 Vmath::Fill(m_nq, 1.488, m_cellSol[20], 1);
628}
629
630std::string CourtemancheRamirezNattel98::v_GetCellVarName(size_t idx)
631{
632 switch (idx)
633 {
634 case 0:
635 return "u";
636 case 1:
637 return "m";
638 case 2:
639 return "h";
640 case 3:
641 return "j";
642 case 4:
643 return "o_a";
644 case 5:
645 return "o_i";
646 case 6:
647 return "u_a";
648 case 7:
649 return "u_i";
650 case 8:
651 return "x_r";
652 case 9:
653 return "x_s";
654 case 10:
655 return "d";
656 case 11:
657 return "f";
658 case 12:
659 return "f_Ca";
660 case 13:
661 return "U";
662 case 14:
663 return "V";
664 case 15:
665 return "W";
666 case 16:
667 return "Na_i";
668 case 17:
669 return "Ca_i";
670 case 18:
671 return "K_i";
672 case 19:
673 return "Ca_rel";
674 case 20:
675 return "Ca_up";
676 default:
677 return "unknown";
678 }
679}
680
681} // namespace Nektar
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:208
Nektar::CellModel
Cell model base class.
Definition: CellModel.h:66
Nektar::CellModel::m_cellSol
Array< OneD, Array< OneD, NekDouble > > m_cellSol
Cell model solution variables.
Definition: CellModel.h:126
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::m_nq
size_t m_nq
Number of physical points.
Definition: CellModel.h:117
Nektar::CellModel::m_nvar
size_t m_nvar
Number of variables in cell model (inc. transmembrane voltage)
Definition: CellModel.h:119
Nektar::CellModel::m_gates_tau
Array< OneD, Array< OneD, NekDouble > > m_gates_tau
Storage for gate tau values.
Definition: CellModel.h:143
Nektar::CourtemancheRamirezNattel98::v_GenerateSummary
void v_GenerateSummary(SummaryList &s) override
Prints a summary of the model parameters.
Definition: CourtemancheRamirezNattel98.cpp:599
Nektar::CourtemancheRamirezNattel98::CourtemancheRamirezNattel98
CourtemancheRamirezNattel98(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Constructor.
Definition: CourtemancheRamirezNattel98.cpp:65
Nektar::CourtemancheRamirezNattel98::create
static CellModelSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Creates an instance of this class.
Definition: CourtemancheRamirezNattel98.h:47
Nektar::CourtemancheRamirezNattel98::v_Update
void v_Update(const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time) override
Computes the reaction terms $f(u,v)$ and $g(u,v)$.
Definition: CourtemancheRamirezNattel98.cpp:160
Nektar::CourtemancheRamirezNattel98::v_GetCellVarName
std::string v_GetCellVarName(size_t idx) override
Definition: CourtemancheRamirezNattel98.cpp:630
Nektar::CourtemancheRamirezNattel98::className
static std::string className
Name of class.
Definition: CourtemancheRamirezNattel98.h:56
Nektar::LibUtilities::NekFactory::RegisterCreatorFunction
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, std::string pDesc="")
Register a class with the factory.
Definition: BasicUtils/NekFactory.hpp:197
Nektar::LibUtilities::SessionReader::RegisterEnumValue
static std::string RegisterEnumValue(std::string pEnum, std::string pString, int pEnumValue)
Registers an enumeration value.
Definition: SessionReader.h:560
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:594
Nektar::LibUtilities::SessionReaderSharedPtr
std::shared_ptr< SessionReader > SessionReaderSharedPtr
Definition: SessionReader.h:113
Nektar::LibUtilities::beta
@ beta
Gauss Radau pinned at x=-1,.
Definition: PointsType.h:59
Nektar::MultiRegions::ExpListSharedPtr
std::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
Definition: LocTraceToTraceMap.h:56
Nektar::SolverUtils::SummaryList
std::vector< std::pair< std::string, std::string > > SummaryList
Definition: Misc.h:46
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
Nektar::GetCellModelFactory
CellModelFactory & GetCellModelFactory()
Definition: CellModel.cpp:46
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:43
Vmath::Svtsvtp
void Svtsvtp(int n, const T alpha, const T *x, int incx, const T beta, const T *y, int incy, T *z, int incz)
Svtsvtp (scalar times vector plus scalar times vector):
Definition: Vmath.hpp:473
Vmath::Vmul
void Vmul(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Multiply vector z = x*y.
Definition: Vmath.hpp:72
Vmath::Vlog
void Vlog(int n, const T *x, const int incx, T *y, const int incy)
log y = log(x)
Definition: Vmath.hpp:303
Vmath::Vexp
void Vexp(int n, const T *x, const int incx, T *y, const int incy)
exp y = exp(x)
Definition: Vmath.hpp:315
Vmath::Svtvp
void Svtvp(int n, const T alpha, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Svtvp (scalar times vector plus vector): z = alpha*x + y.
Definition: Vmath.hpp:396
Vmath::Svtvm
void Svtvm(int n, const T alpha, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Svtvm (scalar times vector minus vector): z = alpha*x - y.
Definition: Vmath.hpp:424
Vmath::Vadd
void Vadd(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Add vector z = x+y.
Definition: Vmath.hpp:180
Vmath::Smul
void Smul(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha*x.
Definition: Vmath.hpp:100
Vmath::Sdiv
void Sdiv(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha/x.
Definition: Vmath.hpp:154
Vmath::Vdiv
void Vdiv(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Multiply vector z = x/y.
Definition: Vmath.hpp:126
Vmath::Zero
void Zero(int n, T *x, const int incx)
Zero vector.
Definition: Vmath.hpp:273
Vmath::Fill
void Fill(int n, const T alpha, T *x, const int incx)
Fill a vector with a constant value.
Definition: Vmath.hpp:54
Vmath::Sadd
void Sadd(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Add vector y = alpha + x.
Definition: Vmath.hpp:194
Vmath::Vsub
void Vsub(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Subtract vector z = x-y.
Definition: Vmath.hpp:220
Vmath::Vpow
void Vpow(int n, const T *x, const int incx, const T f, T *y, const int incy)
pow y = pow(x, f)
Definition: Vmath.hpp:327
std
STL namespace.
tinysimd::sqrt
scalarT< T > sqrt(scalarT< T > in)
Definition: scalar.hpp:294
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