Chaste  Release::2018.1
CellBasedParabolicPdeSolver< DIM > Class Template Reference

#include <CellBasedParabolicPdeSolver.hpp>

+ Inheritance diagram for CellBasedParabolicPdeSolver< DIM >:
+ Collaboration diagram for CellBasedParabolicPdeSolver< DIM >:

Public Member Functions

 CellBasedParabolicPdeSolver (TetrahedralMesh< DIM, DIM > *pMesh, AbstractLinearParabolicPde< DIM, DIM > *pPde, BoundaryConditionsContainer< DIM, DIM, 1 > *pBoundaryConditions)
 
virtual ~CellBasedParabolicPdeSolver ()
 
- Public Member Functions inherited from SimpleLinearParabolicSolver< DIM, DIM >
 SimpleLinearParabolicSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, AbstractLinearParabolicPde< ELEMENT_DIM, SPACE_DIM > *pPde, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > *pBoundaryConditions)
 
- Public Member Functions inherited from AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, 1, NORMAL >
 AbstractAssemblerSolverHybrid (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *pBoundaryConditions)
 
virtual ~AbstractAssemblerSolverHybrid ()
 
void SetupGivenLinearSystem (Vec currentSolution, bool computeMatrix, LinearSystem *pLinearSystem)
 
- Public Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
 AbstractFeVolumeIntegralAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
 
virtual ~AbstractFeVolumeIntegralAssembler ()
 
- Public Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
 AbstractFeAssemblerCommon ()
 
void SetCurrentSolution (Vec currentSolution)
 
virtual ~AbstractFeAssemblerCommon ()
 
- Public Member Functions inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
 AbstractFeAssemblerInterface ()
 
void SetMatrixToAssemble (Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true)
 
void SetVectorToAssemble (Vec &rVecToAssemble, bool zeroVectorBeforeAssembly)
 
void Assemble ()
 
void AssembleMatrix ()
 
void AssembleVector ()
 
virtual ~AbstractFeAssemblerInterface ()
 
- Public Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
 AbstractDynamicLinearPdeSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
 
void SetTimes (double tStart, double tEnd)
 
void SetTimeStep (double dt)
 
void SetInitialCondition (Vec initialCondition)
 
virtual Vec Solve ()
 
void SetMatrixIsNotAssembled ()
 
void SetTimeAdaptivityController (AbstractTimeAdaptivityController *pTimeAdaptivityController)
 
void SetOutputToVtk (bool output)
 
void SetOutputToParallelVtk (bool output)
 
void SetOutputToTxt (bool output)
 
void SetOutputDirectoryAndPrefix (std::string outputDirectory, std::string prefix)
 
void SetPrintingTimestepMultiple (unsigned multiple)
 
- Public Member Functions inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
 AbstractLinearPdeSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)
 
virtual ~AbstractLinearPdeSolver ()
 
virtual void InitialiseForSolve (Vec initialSolution=nullptr)
 
virtual void PrepareForSetupLinearSystem (Vec currentSolution)
 
virtual void FinaliseLinearSystem (Vec currentSolution)
 
virtual void FollowingSolveLinearSystem (Vec currentSolution)
 
LinearSystemGetLinearSystem ()
 

Protected Member Functions

virtual c_vector< double,
1 *(DIM+1)> 
ComputeVectorTerm (c_vector< double, DIM+1 > &rPhi, c_matrix< double, DIM, DIM+1 > &rGradPhi, ChastePoint< DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, DIM > &rGradU, Element< DIM, DIM > *pElement)
 
virtual c_matrix< double,
1 *(DIM+1), 1 *(DIM+1)> 
ComputeMatrixTerm (c_vector< double, DIM+1 > &rPhi, c_matrix< double, DIM, DIM+1 > &rGradPhi, ChastePoint< DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, DIM > &rGradU, Element< DIM, DIM > *pElement)
 
void ResetInterpolatedQuantities ()
 
void IncrementInterpolatedQuantities (double phiI, const Node< DIM > *)
 
- Protected Member Functions inherited from SimpleLinearParabolicSolver< DIM, DIM >
virtual c_matrix< double,
1 *(ELEMENT_DIM+1),
1 *(ELEMENT_DIM+1)> 
ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
 
virtual c_vector< double,
1 *(ELEMENT_DIM+1)> 
ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
 
void SetupLinearSystem (Vec currentSolution, bool computeMatrix)
 
- Protected Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
void ComputeTransformedBasisFunctionDerivatives (const ChastePoint< ELEMENT_DIM > &rPoint, const c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rReturnValue)
 
void DoAssemble ()
 
virtual c_matrix< double,
PROBLEM_DIM *(ELEMENT_DIM+1),
PROBLEM_DIM *(ELEMENT_DIM+1)> 
ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
 
virtual c_vector< double,
PROBLEM_DIM *(ELEMENT_DIM+1)> 
ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)
 
virtual void AssembleOnElement (Element< ELEMENT_DIM, SPACE_DIM > &rElement, c_matrix< double, PROBLEM_DIM *(ELEMENT_DIM+1), PROBLEM_DIM *(ELEMENT_DIM+1) > &rAElem, c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)> &rBElem)
 
virtual bool ElementAssemblyCriterion (Element< ELEMENT_DIM, SPACE_DIM > &rElement)
 
- Protected Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
virtual double GetCurrentSolutionOrGuessValue (unsigned nodeIndex, unsigned indexOfUnknown)
 
virtual void IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)
 
virtual void IncrementInterpolatedGradientQuantities (const c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, unsigned phiIndex, const Node< SPACE_DIM > *pNode)
 
- Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
void InitialiseHdf5Writer ()
 
void WriteOneStep (double time, Vec solution)
 

Private Attributes

double mInterpolatedSourceTerm
 

Additional Inherited Members

- Protected Types inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
typedef LinearBasisFunction
< ELEMENT_DIM > 
BasisFunction
 
- Protected Attributes inherited from SimpleLinearParabolicSolver< DIM, DIM >
AbstractLinearParabolicPde
< ELEMENT_DIM, SPACE_DIM > * 
mpParabolicPde
 
- Protected Attributes inherited from AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, 1, NORMAL >
NaturalNeumannSurfaceTermAssembler
< ELEMENT_DIM, SPACE_DIM,
PROBLEM_DIM > 
mNaturalNeumannSurfaceTermAssembler
 
BoundaryConditionsContainer
< ELEMENT_DIM, SPACE_DIM,
PROBLEM_DIM > * 
mpBoundaryConditions
 
- Protected Attributes inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
AbstractTetrahedralMesh
< ELEMENT_DIM, SPACE_DIM > * 
mpMesh
 
GaussianQuadratureRule
< ELEMENT_DIM > * 
mpQuadRule
 
- Protected Attributes inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
ReplicatableVector mCurrentSolutionOrGuessReplicated
 
- Protected Attributes inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
Vec mVectorToAssemble
 
Mat mMatrixToAssemble
 
bool mAssembleMatrix
 
bool mAssembleVector
 
bool mZeroMatrixBeforeAssembly
 
bool mZeroVectorBeforeAssembly
 
PetscInt mOwnershipRangeLo
 
PetscInt mOwnershipRangeHi
 
- Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
double mTstart
 
double mTend
 
bool mTimesSet
 
Vec mInitialCondition
 
bool mMatrixIsAssembled
 
bool mMatrixIsConstant
 
double mIdealTimeStep
 
double mLastWorkingTimeStep
 
AbstractTimeAdaptivityControllermpTimeAdaptivityController
 
bool mOutputToVtk
 
bool mOutputToParallelVtk
 
bool mOutputToTxt
 
std::string mOutputDirectory
 
std::string mFilenamePrefix
 
unsigned mPrintingTimestepMultiple
 
Hdf5DataWritermpHdf5Writer
 
std::vector< int > mVariableColumnIds
 
- Protected Attributes inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
LinearSystemmpLinearSystem
 
AbstractTetrahedralMesh
< ELEMENT_DIM, SPACE_DIM > * 
mpMesh
 

Detailed Description

template<unsigned DIM>
class CellBasedParabolicPdeSolver< DIM >

A purpose-made parabolic solver that interpolates the source terms from node onto Gauss points, as for a cell-based simulation with PDEs the source will only be known at the cells (nodes), not the Gauss points.

Definition at line 48 of file CellBasedParabolicPdeSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
CellBasedParabolicPdeSolver< DIM >::CellBasedParabolicPdeSolver ( TetrahedralMesh< DIM, DIM > *  pMesh,
AbstractLinearParabolicPde< DIM, DIM > *  pPde,
BoundaryConditionsContainer< DIM, DIM, 1 > *  pBoundaryConditions 
)

Constructor.

Parameters
pMeshpointer to the mesh
pPdepointer to the PDE
pBoundaryConditionspointer to the boundary conditions

Definition at line 39 of file CellBasedParabolicPdeSolver.cpp.

template<unsigned DIM>
CellBasedParabolicPdeSolver< DIM >::~CellBasedParabolicPdeSolver ( )
virtual

Destructor.

Definition at line 47 of file CellBasedParabolicPdeSolver.cpp.

Member Function Documentation

template<unsigned DIM>
c_matrix< double, 1 *(DIM+1), 1 *(DIM+1)> CellBasedParabolicPdeSolver< DIM >::ComputeMatrixTerm ( c_vector< double, DIM+1 > &  rPhi,
c_matrix< double, DIM, DIM+1 > &  rGradPhi,
ChastePoint< DIM > &  rX,
c_vector< double, 1 > &  rU,
c_matrix< double, 1, DIM > &  rGradU,
Element< DIM, DIM > *  pElement 
)
protectedvirtual

The SimpleLinearParabolicSolver version of this method is overloaded using the interpolated source term.

Parameters
rPhiThe basis functions, rPhi(i) = phi_i, i=1..numBases
rGradPhiBasis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
rXThe point in space
rUThe unknown as a vector, u(i) = u_i
rGradUThe gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
pElementPointer to the element
Returns
The matrix term for the stiffness matrix

Definition at line 65 of file CellBasedParabolicPdeSolver.cpp.

References PdeSimulationTime::GetPdeTimeStepInverse().

template<unsigned DIM>
c_vector< double, 1 *(DIM+1)> CellBasedParabolicPdeSolver< DIM >::ComputeVectorTerm ( c_vector< double, DIM+1 > &  rPhi,
c_matrix< double, DIM, DIM+1 > &  rGradPhi,
ChastePoint< DIM > &  rX,
c_vector< double, 1 > &  rU,
c_matrix< double, 1, DIM > &  rGradU,
Element< DIM, DIM > *  pElement 
)
protectedvirtual

The SimpleLinearParabolicSolver version of this method is overloaded using the interpolated source term.

Parameters
rPhiThe basis functions, rPhi(i) = phi_i, i=1..numBases
rGradPhiBasis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
rXThe point in space
rUThe unknown as a vector, u(i) = u_i
rGradUThe gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
pElementPointer to the element
Returns
vector term.

Definition at line 52 of file CellBasedParabolicPdeSolver.cpp.

References PdeSimulationTime::GetPdeTimeStepInverse().

template<unsigned DIM>
void CellBasedParabolicPdeSolver< DIM >::IncrementInterpolatedQuantities ( double  phiI,
const Node< DIM > *  pNode 
)
protected

Overridden IncrementInterpolatedQuantities() method.

Parameters
phiI
pNode

Definition at line 87 of file CellBasedParabolicPdeSolver.cpp.

References Node< SPACE_DIM >::GetIndex().

template<unsigned DIM>
void CellBasedParabolicPdeSolver< DIM >::ResetInterpolatedQuantities ( void  )
protectedvirtual

Member Data Documentation

template<unsigned DIM>
double CellBasedParabolicPdeSolver< DIM >::mInterpolatedSourceTerm
private

The source term, interpolated onto the current point.

Definition at line 53 of file CellBasedParabolicPdeSolver.hpp.


The documentation for this class was generated from the following files: