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Nektar::CellModelAlievPanfilov Class Reference

Aliev Panfilov model. More...

#include <AlievPanfilov.h>

Inheritance diagram for Nektar::CellModelAlievPanfilov:
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Collaboration diagram for Nektar::CellModelAlievPanfilov:
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Public Member Functions

 CellModelAlievPanfilov (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
 
virtual ~CellModelAlievPanfilov ()
 
- 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, NekDoubleGetCellSolutionCoeffs (unsigned int idx)
 
Array< OneD, NekDoubleGetCellSolution (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)
 
virtual void v_GenerateSummary (SummaryList &s)
 
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_a
 Trigger parameter a. More...
 
NekDouble m_k
 Scaling parameter k. More...
 
NekDouble m_mu1
 Restitution parameter $\mu_1$. More...
 
NekDouble m_mu2
 Restitution parameter $\mu_2$. More...
 
NekDouble m_eps
 Restitution parameter $\epsilon$. More...
 
Array< OneD, NekDoublem_uu
 Temporary space for storing $u^2$ when computing reaction term. More...
 
Array< OneD, NekDoublem_uuu
 Temporary space for storing $u^3$ when computing reaction term. More...
 
Array< OneD, NekDoublem_tmp1
 Workspace for computing reaction term. More...
 
Array< OneD, NekDoublem_tmp2
 Workspace for computing reaction term. More...
 

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

Aliev Panfilov model.

Definition at line 44 of file AlievPanfilov.h.

Constructor & Destructor Documentation

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

Definition at line 53 of file AlievPanfilov.cpp.

References m_a, Nektar::CellModel::m_concentrations, m_eps, m_k, m_mu1, m_mu2, Nektar::CellModel::m_nq, Nektar::CellModel::m_nvar, m_tmp1, m_tmp2, m_uu, and m_uuu.

56  : CellModel(pSession, pField)
57  {
58  pSession->LoadParameter("k", m_k, 0.0);
59  pSession->LoadParameter("a", m_a, 0.0);
60  pSession->LoadParameter("mu1", m_mu1, 0.0);
61  pSession->LoadParameter("mu2", m_mu2, 0.0);
62  pSession->LoadParameter("eps", m_eps, 0.0);
63 
64  m_uu = Array<OneD, NekDouble>(m_nq, 0.0);
65  m_uuu = Array<OneD, NekDouble>(m_nq, 0.0);
66  m_tmp1 = Array<OneD, NekDouble>(m_nq, 0.0);
67  m_tmp2 = Array<OneD, NekDouble>(m_nq, 0.0);
68 
69  m_nvar = 2;
70  m_concentrations.push_back(1);
71  }
NekDouble m_a
Trigger parameter a.
Definition: AlievPanfilov.h:75
Array< OneD, NekDouble > m_uu
Temporary space for storing when computing reaction term.
Definition: AlievPanfilov.h:86
Array< OneD, NekDouble > m_tmp2
Workspace for computing reaction term.
Definition: AlievPanfilov.h:92
int m_nq
Number of physical points.
Definition: CellModel.h:117
CellModel(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Definition: CellModel.cpp:69
std::vector< int > m_concentrations
Indices of cell model variables which are concentrations.
Definition: CellModel.h:139
int m_nvar
Number of variables in cell model (inc. transmembrane voltage)
Definition: CellModel.h:119
NekDouble m_eps
Restitution parameter .
Definition: AlievPanfilov.h:83
NekDouble m_k
Scaling parameter k.
Definition: AlievPanfilov.h:77
NekDouble m_mu1
Restitution parameter .
Definition: AlievPanfilov.h:79
Array< OneD, NekDouble > m_tmp1
Workspace for computing reaction term.
Definition: AlievPanfilov.h:90
Array< OneD, NekDouble > m_uuu
Temporary space for storing when computing reaction term.
Definition: AlievPanfilov.h:88
NekDouble m_mu2
Restitution parameter .
Definition: AlievPanfilov.h:81
virtual Nektar::CellModelAlievPanfilov::~CellModelAlievPanfilov ( )
inlinevirtual

Definition at line 61 of file AlievPanfilov.h.

61 {}

Member Function Documentation

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

Creates an instance of this class.

Definition at line 48 of file AlievPanfilov.h.

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

50  {
52  }
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
void Nektar::CellModelAlievPanfilov::v_GenerateSummary ( SummaryList s)
protectedvirtual

Implements Nektar::CellModel.

Definition at line 186 of file AlievPanfilov.cpp.

References Nektar::SolverUtils::AddSummaryItem(), m_a, m_eps, m_k, m_mu1, and m_mu2.

187  {
188  SolverUtils::AddSummaryItem(s, "Cell model","Aliev-Panfilov");
194  }
NekDouble m_a
Trigger parameter a.
Definition: AlievPanfilov.h:75
void AddSummaryItem(SummaryList &l, const std::string &name, const std::string &value)
Adds a summary item to the summary info list.
Definition: Misc.cpp:50
NekDouble m_eps
Restitution parameter .
Definition: AlievPanfilov.h:83
NekDouble m_k
Scaling parameter k.
Definition: AlievPanfilov.h:77
NekDouble m_mu1
Restitution parameter .
Definition: AlievPanfilov.h:79
NekDouble m_mu2
Restitution parameter .
Definition: AlievPanfilov.h:81
void Nektar::CellModelAlievPanfilov::v_SetInitialConditions ( )
protectedvirtual

Implements Nektar::CellModel.

Definition at line 200 of file AlievPanfilov.cpp.

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

201  {
202  Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
203  Vmath::Fill(m_nq, 0.0, m_cellSol[1], 1);
204  }
int m_nq
Number of physical points.
Definition: CellModel.h:117
void Fill(int n, const T alpha, T *x, const int incx)
Fill a vector with a constant value.
Definition: Vmath.cpp:46
Array< OneD, Array< OneD, NekDouble > > m_cellSol
Cell model solution variables.
Definition: CellModel.h:126
void Nektar::CellModelAlievPanfilov::v_Update ( const Array< OneD, const Array< OneD, NekDouble > > &  inarray,
Array< OneD, Array< OneD, NekDouble > > &  outarray,
const NekDouble  time 
)
protectedvirtual

Implements Nektar::CellModel.

Definition at line 74 of file AlievPanfilov.cpp.

References m_a, m_eps, m_k, m_mu1, m_mu2, Nektar::CellModel::m_nq, m_tmp1, m_tmp2, m_uu, m_uuu, Vmath::Neg(), Vmath::Sadd(), Vmath::Smul(), Vmath::Svtvp(), Vmath::Vadd(), Vmath::Vdiv(), Vmath::Vmul(), and Vmath::Vvtvp().

78  {
79  // inarray[0] holds initial physical u values throughout
80  // inarray[1] holds initial physical v values throughout
81 
82  // compute u^2: m_u = u*u
83  Vmath::Vmul(m_nq, &inarray[0][0], 1, &inarray[0][0], 1, &m_uu[0], 1);
84 
85  // compute u^3: m_u = u*u*u
86  Vmath::Vmul(m_nq, &inarray[0][0], 1, &m_uu[0], 1, &m_uuu[0], 1);
87 
88  // --------------------------------------
89  // Compute reaction term f(u,v)
90  // --------------------------------------
91 // if (m_spatialParameters->Exists("a"))
92 // {
93 // Vmath::Vmul(m_nq, &m_spatialParameters->GetData("a")->GetPhys()[0], 1,
94 // &inarray[0][0], 1, &m_tmp1[0], 1);
95 //
96 // Vmath::Vvtvm(m_nq, &m_spatialParameters->GetData("a")->GetPhys()[0], 1,
97 // &m_uu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
98 //
99 // Vmath::Svtvm(m_nq, -1.0, &m_uu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
100 // }
101 // else
102 // {
103  // Ru = au
104  Vmath::Smul(m_nq, m_a, &inarray[0][0], 1, &m_tmp1[0], 1);
105  // Ru = (-1-a)u*u + au
106  Vmath::Svtvp(m_nq, (-1.0-m_a), &m_uu[0], 1, &m_tmp1[0], 1,
107  &m_tmp1[0], 1);
108 // }
109  // Ru = u*u*u - (1+a)u*u + au
110  Vmath::Vadd(m_nq, &m_uuu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
111  // Ru = k(u*u*u - (1+a)u*u + au)
112 // if (m_spatialParameters->Exists("k"))
113 // {
114 // Vmath::Vmul(m_nq, &m_spatialParameters->GetData("k")->GetPhys()[0], 1,
115 // &m_tmp1[0], 1, &m_tmp1[0], 1);
116 // }
117 // else
118 // {
119  Vmath::Smul(m_nq, m_k, &m_tmp1[0], 1, &m_tmp1[0], 1);
120 // }
121 
122  // Ru = k(u*u*u - (1+a)u*u + au) + I_stim
123  Vmath::Vadd(m_nq, &outarray[0][0], 1, &m_tmp1[0], 1, &outarray[0][0], 1);
124 
125  // Ru = k(u*u*u - (1+a)u*u + au) + uv + I_stim
126  Vmath::Vvtvp(m_nq, &inarray[0][0], 1, &inarray[1][0], 1, &m_tmp1[0], 1,
127  &outarray[0][0], 1);
128  // Ru = -k(u*u*u - (1+a)u*u + au) - uv - I_stim
129  Vmath::Neg(m_nq, &outarray[0][0], 1);
130 
131 
132  // --------------------------------------
133  // Compute reaction term g(u,v)
134  // --------------------------------------
135  // tmp2 = mu2 + u
136  Vmath::Sadd(m_nq, m_mu2, &inarray[0][0], 1, &m_tmp2[0], 1);
137 
138  // tmp2 = v/(mu2 + u)
139  Vmath::Vdiv(m_nq, &inarray[1][0], 1, &m_tmp2[0], 1, &m_tmp2[0], 1);
140 
141  // tmp2 = mu1*v/(mu2 + u)
142  Vmath::Smul(m_nq, m_mu1, &m_tmp2[0], 1, &m_tmp2[0], 1);
143 
144  // tmp1 = Eps + mu1*v/(mu2+u)
145  Vmath::Sadd(m_nq, m_eps, &m_tmp2[0], 1, &m_tmp2[0], 1);
146 
147  // tmp1 = (-a-1) + u
148 // if (m_spatialParameters->Exists("a"))
149 // {
150 // Vmath::Vsub(m_nq, &inarray[0][0], 1,
151 // &m_spatialParameters->GetData("a")->GetPhys()[0], 1,
152 // &m_tmp1[0], 1);
153 //
154 // Vmath::Sadd(m_nq, -1.0, &inarray[0][0], 1, &m_tmp1[0], 1);
155 // }
156 // else
157 // {
158  Vmath::Sadd(m_nq, (-m_a-1), &inarray[0][0], 1, &m_tmp1[0], 1);
159 // }
160 
161  // tmp1 = k(u-a-1)
162 // if (m_spatialParameters->Exists("k"))
163 // {
164 // Vmath::Vmul(m_nq, &m_spatialParameters->GetData("k")->GetPhys()[0], 1,
165 // &m_tmp1[0], 1, &m_tmp1[0], 1);
166 // }
167 // else
168 // {
169  Vmath::Smul(m_nq, m_k, &m_tmp1[0], 1, &m_tmp1[0], 1);
170 // }
171 
172  // tmp1 = ku(u-a-1) + v
173  Vmath::Vvtvp(m_nq, &inarray[0][0], 1, &m_tmp1[0], 1, &inarray[1][0], 1,
174  &m_tmp1[0], 1);
175 
176  // tmp1 = -ku(u-a-1)-v
177  Vmath::Neg(m_nq, &m_tmp1[0], 1);
178 
179  // outarray = [Eps + mu1*v/(mu2+u)] * [-ku(u-a-1)-v]
180  Vmath::Vmul(m_nq, &m_tmp1[0], 1, &m_tmp2[0], 1, &outarray[1][0], 1);
181  }
NekDouble m_a
Trigger parameter a.
Definition: AlievPanfilov.h:75
Array< OneD, NekDouble > m_uu
Temporary space for storing when computing reaction term.
Definition: AlievPanfilov.h:86
Array< OneD, NekDouble > m_tmp2
Workspace for computing reaction term.
Definition: AlievPanfilov.h:92
int m_nq
Number of physical points.
Definition: CellModel.h:117
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.cpp:471
void Vvtvp(int n, const T *w, const int incw, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
vvtvp (vector times vector plus vector): z = w*x + y
Definition: Vmath.cpp:428
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.cpp:227
void Smul(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha*y.
Definition: Vmath.cpp:199
void Neg(int n, T *x, const int incx)
Negate x = -x.
Definition: Vmath.cpp:382
NekDouble m_eps
Restitution parameter .
Definition: AlievPanfilov.h:83
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.cpp:301
NekDouble m_k
Scaling parameter k.
Definition: AlievPanfilov.h:77
NekDouble m_mu1
Restitution parameter .
Definition: AlievPanfilov.h:79
Array< OneD, NekDouble > m_tmp1
Workspace for computing reaction term.
Definition: AlievPanfilov.h:90
Array< OneD, NekDouble > m_uuu
Temporary space for storing when computing reaction term.
Definition: AlievPanfilov.h:88
NekDouble m_mu2
Restitution parameter .
Definition: AlievPanfilov.h:81
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.cpp:285
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.cpp:169

Member Data Documentation

std::string Nektar::CellModelAlievPanfilov::className
static
Initial value:
"AlievPanfilov",
"Phenomological model of canine cardiac electrophysiology.")

Name of class.

Registers the class with the Factory.

Definition at line 55 of file AlievPanfilov.h.

NekDouble Nektar::CellModelAlievPanfilov::m_a
private

Trigger parameter a.

Definition at line 75 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), v_GenerateSummary(), and v_Update().

NekDouble Nektar::CellModelAlievPanfilov::m_eps
private

Restitution parameter $\epsilon$.

Definition at line 83 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), v_GenerateSummary(), and v_Update().

NekDouble Nektar::CellModelAlievPanfilov::m_k
private

Scaling parameter k.

Definition at line 77 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), v_GenerateSummary(), and v_Update().

NekDouble Nektar::CellModelAlievPanfilov::m_mu1
private

Restitution parameter $\mu_1$.

Definition at line 79 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), v_GenerateSummary(), and v_Update().

NekDouble Nektar::CellModelAlievPanfilov::m_mu2
private

Restitution parameter $\mu_2$.

Definition at line 81 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), v_GenerateSummary(), and v_Update().

Array<OneD, NekDouble> Nektar::CellModelAlievPanfilov::m_tmp1
private

Workspace for computing reaction term.

Definition at line 90 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), and v_Update().

Array<OneD, NekDouble> Nektar::CellModelAlievPanfilov::m_tmp2
private

Workspace for computing reaction term.

Definition at line 92 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), and v_Update().

Array<OneD, NekDouble> Nektar::CellModelAlievPanfilov::m_uu
private

Temporary space for storing $u^2$ when computing reaction term.

Definition at line 86 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), and v_Update().

Array<OneD, NekDouble> Nektar::CellModelAlievPanfilov::m_uuu
private

Temporary space for storing $u^3$ when computing reaction term.

Definition at line 88 of file AlievPanfilov.h.

Referenced by CellModelAlievPanfilov(), and v_Update().