48 string BidomainRoth::className =
50 "BidomainRoth", BidomainRoth::create,
51 "Bidomain Roth model of cardiac electrophysiology.");
72 std::string vCellModel;
73 m_session->LoadSolverInfo(
"CELLMODEL", vCellModel,
"");
75 ASSERTL0(vCellModel !=
"",
"Cell Model not specified.");
87 std::string varCoeffString[6] = {
"xx",
"xy",
"yy",
"xz",
"yz",
"zz"};
88 std::string aniso_var[3] = {
"fx",
"fy",
"fz"};
90 const int nq =
m_fields[0]->GetNpoints();
95 for (
int j = 0; j < i + 1; ++j)
115 if (
m_session->DefinesFunction(
"ExtracellularAnisotropicConductivity"))
117 if (
m_session->DefinesCmdLineArgument(
"verbose"))
119 cout <<
"Loading Extracellular Anisotropic Fibre map." << endl;
149 "ExtracellularAnisotropicConductivity", aniso_var[j]),
150 "Function 'AnisotropicConductivity' not correctly "
153 GetFunction(
"ExtracellularAnisotropicConductivity")
154 ->Evaluate(aniso_var[j], vTemp_j);
157 for (
int i = 0; i < j + 1; ++i)
161 "ExtracellularAnisotropicConductivity", aniso_var[i]),
162 "Function 'ExtracellularAnisotropicConductivity' not "
163 "correctly defined.");
165 GetFunction(
"ExtracellularAnisotropicConductivity")
166 ->Evaluate(aniso_var[i], vTemp_i);
185 if (
m_session->DefinesFunction(
"IntracellularAnisotropicConductivity"))
187 if (
m_session->DefinesCmdLineArgument(
"verbose"))
189 cout <<
"Loading Anisotropic Fibre map." << endl;
219 "IntracellularAnisotropicConductivity", aniso_var[j]),
220 "Function 'IntracellularAnisotropicConductivity' not "
221 "correctly defined.");
223 GetFunction(
"IntracellularAnisotropicConductivity")
224 ->Evaluate(aniso_var[j], vTemp_j);
227 for (
int i = 0; i < j + 1; ++i)
231 "IntracellularAnisotropicConductivity", aniso_var[i]),
232 "Function 'IntracellularAnisotropicConductivity' not "
233 "correctly defined.");
234 GetFunction(
"IntracellularAnisotropicConductivity")
235 ->Evaluate(aniso_var[i], vTemp_i);
262 for (
int i = 0; i < j + 1; ++i)
267 std::stringstream filenamei;
268 filenamei <<
"IConductivity_" << varCoeffString[k] <<
".fld";
274 std::stringstream filenamee;
275 filenamee <<
"EConductivity_" << varCoeffString[k] <<
".fld";
286 if (x.first ==
"CheckpointCellModel")
288 std::shared_ptr<FilterCheckpointCellModel> c =
289 std::dynamic_pointer_cast<FilterCheckpointCellModel>(x.second);
345 outarray[0] =
m_fields[0]->GetPhys();
358 m_cell->TimeIntegrate(inarray, outarray, time);
361 for (
unsigned int i = 0; i <
m_stimulus.size(); ++i)
373 m_fields[0]->PhysDeriv(inarray[0], ggrad0, ggrad1, ggrad2);
374 m_fields[0]->PhysDeriv(0, ggrad0, ggrad0);
375 m_fields[0]->PhysDeriv(1, ggrad1, ggrad1);
376 m_fields[0]->PhysDeriv(2, ggrad2, ggrad2);
377 if (
m_session->DefinesFunction(
"IntracellularAnisotropicConductivity") &&
378 m_session->DefinesFunction(
"ExtracellularAnisotropicConductivity"))
405 m_fields[1]->PhysDeriv(0, ggrad0, ggrad0);
406 m_fields[1]->PhysDeriv(1, ggrad1, ggrad1);
407 m_fields[1]->PhysDeriv(2, ggrad2, ggrad2);
408 if (
m_session->DefinesFunction(
"IntracellularAnisotropicConductivity") &&
409 m_session->DefinesFunction(
"ExtracellularAnisotropicConductivity"))
422 Vmath::Vadd(nq, ggrad, 1, outarray[0], 1, outarray[0], 1);
429 bool dumpInitialConditions,
443 m_cell->GenerateSummary(s);
#define ASSERTL0(condition, msg)
virtual ~BidomainRoth()
Desctructor.
virtual void v_GenerateSummary(SummaryList &s)
Prints a summary of the model parameters.
StdRegions::VarCoeffMap m_vardiffi
std::vector< StimulusSharedPtr > m_stimulus
void DoImplicitSolve(const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, NekDouble time, NekDouble lambda)
Solve for the diffusion term.
CellModelSharedPtr m_cell
Cell model.
virtual void v_SetInitialConditions(NekDouble initialtime, bool dumpInitialConditions, const int domain)
Sets a custom initial condition.
StdRegions::VarCoeffMap m_vardiffie
virtual void v_InitObject()
void DoOdeRhs(const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time)
Computes the reaction terms and .
StdRegions::VarCoeffMap m_vardiffe
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, std::string pDesc="")
Register a class with the factory.
tBaseSharedPtr CreateInstance(tKey idKey, tParam... args)
Create an instance of the class referred to by idKey.
void DefineOdeRhs(FuncPointerT func, ObjectPointerT obj)
void DefineImplicitSolve(FuncPointerT func, ObjectPointerT obj)
int m_spacedim
Spatial dimension (>= expansion dim).
virtual SOLVER_UTILS_EXPORT void v_SetInitialConditions(NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
SOLVER_UTILS_EXPORT void WriteFld(const std::string &outname)
Write field data to the given filename.
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
SOLVER_UTILS_EXPORT SessionFunctionSharedPtr GetFunction(std::string name, const MultiRegions::ExpListSharedPtr &field=MultiRegions::NullExpListSharedPtr, bool cache=false)
Get a SessionFunction by name.
Base class for unsteady solvers.
LibUtilities::TimeIntegrationSchemeOperators m_ode
The time integration scheme operators to use.
std::vector< std::pair< std::string, FilterSharedPtr > > m_filters
bool m_explicitDiffusion
Indicates if explicit or implicit treatment of diffusion is used.
virtual SOLVER_UTILS_EXPORT void v_InitObject(bool DeclareField=true)
Init object for UnsteadySystem class.
virtual SOLVER_UTILS_EXPORT void v_GenerateSummary(SummaryList &s)
Print a summary of time stepping parameters.
std::vector< int > m_intVariables
static std::vector< StimulusSharedPtr > LoadStimuli(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
std::shared_ptr< SessionReader > SessionReaderSharedPtr
std::vector< std::pair< std::string, std::string > > SummaryList
EquationSystemFactory & GetEquationSystemFactory()
std::shared_ptr< MeshGraph > MeshGraphSharedPtr
std::map< ConstFactorType, NekDouble > ConstFactorMap
The above copyright notice and this permission notice shall be included.
CellModelFactory & GetCellModelFactory()
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.
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.
void Smul(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha*x.
void Sadd(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Add vector y = alpha - x.