GCC Code Coverage Report

Directory: ./
File: Solver/courtemancheSolver.hpp
Date: 2024-04-14 07:32:34
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1 // ______ ______ _ _ _____ ______
2 // | ____| ____| | (_)/ ____| | ____|
3 // | |__ | |__ | | _| (___ ___| |__
4 // | __| | __| | | | |\___ \ / __| __|
5 // | | | |____| |____| |____) | (__| |____
6 // |_| |______|______|_|_____/ \___|______|
7 // Finite Elements for Life Sciences and Engineering
8 //
9 // License: LGL2.1 License
10 // FELiScE default license: LICENSE in root folder
11 //
12 // Main authors: A. Collin
13 //
14
15 #ifndef _COURTEMANCHESOLVER_HPP
16 #define _COURTEMANCHESOLVER_HPP
17
18 // System includes
19
20 // External includes
21 #include "Core/NoThirdPartyWarning/Petsc/vec.hpp"
22 #include "Core/NoThirdPartyWarning/Petsc/ao.hpp"
23
24 // Project includes
25 #include "Model/model.hpp"
26 #include "Core/felisce.hpp"
27 #include "Solver/bdf.hpp"
28 #include "Core/felisceParam.hpp"
29 #include "Core/felisceTransient.hpp"
30 #include "Solver/cardiacFunction.hpp"
31
32 namespace felisce
33 {
34 class CourtemancheSolver {
35 public:
36 /// Constructor.
37 CourtemancheSolver(FelisceTransient::Pointer fstransient);
38 /// Destructor.
39 ~CourtemancheSolver();
40
41 void defineSizeAndMappingOfIonicProblem(felInt size, ISLocalToGlobalMapping& mapping, AO ao=FELISCE_PETSC_NULLPTR);
42
43 void initializeExtrap(PetscVector& V_0);
44 void updateExtrap(PetscVector& V_1);
45
46 /// Compute Iion with value_uExtrap.
47 double iIonTotal(double v, felInt pos);
48 /// Update ion concentrations.
49 void updateConcentrations();
50 void initializeConcentrationsAndGateConditions(PetscVector& m,PetscVector& h, PetscVector& j, PetscVector& ao, PetscVector& io, PetscVector& ua, PetscVector& ui, PetscVector& xr, PetscVector& xs, PetscVector& d, PetscVector& f, PetscVector& fca, PetscVector& urel, PetscVector& vrel, PetscVector& wrel, PetscVector& nai, PetscVector& nao, PetscVector& cao, PetscVector& ki, PetscVector& ko, PetscVector& cai, PetscVector& naiont, PetscVector& kiont, PetscVector& caiont, PetscVector& ileak, PetscVector& iup, PetscVector& itr, PetscVector& irel, PetscVector& cmdn, PetscVector& trpn, PetscVector& nsr, PetscVector& jsr, PetscVector& csqn);
51
52 PetscVector& ionicVariable(int iVar);
53
54 void computeIon();
55
56 /// Access function.
57 inline const PetscVector& ion() const {
58 return m_ion;
59 }
60 ✗ inline PetscVector& ion() {
61 ✗ return m_ion;
62 }
63
64 inline const HeteroCourtModelIto& fctCourtCondIto() const {
65 return m_heteroCourtModelIto;
66 }
67 ✗ inline HeteroCourtModelIto& fctCourtCondIto() {
68 ✗ return m_heteroCourtModelIto;
69 }
70
71 inline const std::vector<double>& courtCondIto() const {
72 return m_courtCondIto;
73 }
74 ✗ inline std::vector<double>& courtCondIto() {
75 ✗ return m_courtCondIto;
76 }
77
78 inline const HeteroCourtModelICaL& fctCourtCondICaL() const {
79 return m_heteroCourtModelICaL;
80 }
81 ✗ inline HeteroCourtModelICaL& fctCourtCondICaL() {
82 ✗ return m_heteroCourtModelICaL;
83 }
84
85 inline const std::vector<double>& courtCondICaL() const {
86 return m_courtCondICaL;
87 }
88 ✗ inline std::vector<double>& courtCondICaL() {
89 ✗ return m_courtCondICaL;
90 }
91
92 inline const HeteroCourtModelMultCoeff& fctCourtCondMultCoeff() const {
93 return m_heteroCourtModelMultCoeff;
94 }
95 ✗ inline HeteroCourtModelMultCoeff& fctCourtCondMultCoeff() {
96 ✗ return m_heteroCourtModelMultCoeff;
97 }
98
99 inline const std::vector<double>& courtCondMultCoeff() const {
100 return m_courtCondMultCoeff;
101 }
102 ✗ inline std::vector<double>& courtCondMultCoeff() {
103 ✗ return m_courtCondMultCoeff;
104 }
105
106 protected:
107 /// User data file of Felisce (only transient parameters).
108 FelisceTransient::Pointer m_fstransient;
109 /// Number of Dof for the trans membrane potential.
110 felInt m_size;
111
112 ISLocalToGlobalMapping m_localDofToGlobalDof;
113
114 private:
115 //Gate conditions
116 // INa
117 PetscVector m_m;
118 PetscVector m_h;
119 PetscVector m_j;
120 // ITo
121 PetscVector m_ao;
122 PetscVector m_io;
123 // IKur
124 PetscVector m_ua;
125 PetscVector m_ui;
126 // IKr
127 PetscVector m_xr;
128 // IKs
129 PetscVector m_xs;
130 // ICaL
131 PetscVector m_d;
132 PetscVector m_f;
133 PetscVector m_fca;
134 // Irel
135 PetscVector m_urel;
136 PetscVector m_vrel;
137 PetscVector m_wrel;
138
139 // Ion concentrations
140 PetscVector m_nai;
141 PetscVector m_nao;
142 PetscVector m_cao;
143 PetscVector m_ki;
144 PetscVector m_ko;
145 PetscVector m_cai;
146 //Currents
147 PetscVector m_naiont;
148 PetscVector m_kiont;
149 PetscVector m_caiont;
150 PetscVector m_ileak;
151 PetscVector m_iup;
152 PetscVector m_itr;
153 PetscVector m_irel;
154 // Ca:
155 PetscVector m_cmdn; /* Calmodulin Buffered Ca Concentration (mM) */
156 PetscVector m_trpn; /* Troponin Buffered Ca Concentration (mM) */
157 PetscVector m_nsr; /* NSR Ca Concentration (mM) */
158 PetscVector m_jsr; /* JSR Ca Concentration (mM) */
159 PetscVector m_csqn; /* Calsequestrin Buffered Ca Concentration (mM) */
160
161 //Gate conditions
162 // INa
163 double m_value_m;
164 double m_value_h;
165 double m_value_j;
166 // ITo
167 double m_valuem_ao;
168 double m_value_io;
169 // IKur
170 double m_value_ua;
171 double m_value_ui;
172 // IKr
173 double m_value_xr;
174 // IKs
175 double m_value_xs;
176 // ICaL
177 double m_value_d;
178 double m_value_f;
179 double m_value_fca;
180 // Irel
181 double m_value_urel;
182 double m_value_vrel;
183 double m_value_wrel;
184
185 // Ion concentrations
186 double m_value_nai;
187 double m_value_nao;
188 double m_value_cao;
189 double m_value_ki;
190 double m_value_ko;
191 double m_value_cai;
192 //Currents
193 double m_value_naiont;
194 double m_value_kiont;
195 double m_value_caiont;
196 double m_value_ileak;
197 double m_value_iup;
198 double m_value_itr;
199 double m_value_irel;
200 // Ca:
201 double m_value_cmdn; /* Calmodulin Buffered Ca Concentration (mM) */
202 double m_value_trpn; /* Troponin Buffered Ca Concentration (mM) */
203 double m_value_nsr; /* NSR Ca Concentration (mM) */
204 double m_value_jsr; /* JSR Ca Concentration (mM) */
205 double m_value_csqn; /* Calsequestrin Buffered Ca Concentration (mM) */
206
207
208 // Ionic current
209 PetscVector m_ion;
210 /// Extrapolate vector.
211 PetscVector m_uExtrap;
212
213 HeteroCourtModelIto m_heteroCourtModelIto;
214 std::vector<double> m_courtCondIto;
215
216 HeteroCourtModelICaL m_heteroCourtModelICaL;
217 std::vector<double> m_courtCondICaL;
218
219 HeteroCourtModelMultCoeff m_heteroCourtModelMultCoeff;
220 std::vector<double> m_courtCondMultCoeff;
221
222 AO m_aoPetsc;
223
224 };
225 }
226
227 #endif
228