AbstractUnstructuredGridDiscreteContinuumSolver< DIM > Class Template Reference

#include <AbstractUnstructuredGridDiscreteContinuumSolver.hpp>

Inheritance diagram for AbstractUnstructuredGridDiscreteContinuumSolver< DIM >:

Collaboration diagram for AbstractUnstructuredGridDiscreteContinuumSolver< DIM >:

Public Member Functions
	AbstractUnstructuredGridDiscreteContinuumSolver ()
virtual	~AbstractUnstructuredGridDiscreteContinuumSolver ()
boost::shared_ptr< DiscreteContinuumMesh< DIM > >	GetMesh ()
virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (const std::vector< DimensionalChastePoint< DIM > > &rSamplePoints)
virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (boost::shared_ptr< RegularGrid< DIM > > pGrid)
virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations (boost::shared_ptr< DiscreteContinuumMesh< DIM > > pMesh)
virtual std::vector< units::quantity< unit::concentration > >	GetConcentrationsAtCentroids ()
virtual std::vector< double >	GetSolution (const std::vector< DimensionalChastePoint< DIM > > &rSamplePoints)
virtual std::vector< double >	GetSolution (boost::shared_ptr< RegularGrid< DIM > > pGrid)
virtual std::vector< double >	GetSolution (boost::shared_ptr< DiscreteContinuumMesh< DIM > > pMesh)
virtual vtkSmartPointer< vtkUnstructuredGrid >	GetVtkSolution ()
void	SetMesh (boost::shared_ptr< DiscreteContinuumMesh< DIM, DIM > > pMesh)
virtual void	Setup ()
virtual void	UpdateSolution (const std::vector< double > &rData)
virtual void	UpdateElementSolution (const std::vector< double > &rData)
virtual void	UpdateSolution (const std::vector< units::quantity< unit::concentration > > &rData)
virtual void	UpdateCellData ()
virtual void	Update ()
virtual void	Solve ()=0
virtual void	Write ()
Public Member Functions inherited from AbstractDiscreteContinuumSolver< DIM >
	AbstractDiscreteContinuumSolver ()
virtual	~AbstractDiscreteContinuumSolver ()
void	AddBoundaryCondition (boost::shared_ptr< DiscreteContinuumBoundaryCondition< DIM > > pBoundaryCondition)
bool	CellPopulationIsSet ()
virtual std::vector< units::quantity< unit::concentration > >	GetConcentrations ()
const std::string &	GetLabel ()
boost::shared_ptr< AbstractDiscreteContinuumNonLinearEllipticPde< DIM, DIM > >	GetNonLinearPde ()
boost::shared_ptr< AbstractDiscreteContinuumLinearEllipticPde< DIM, DIM > >	GetPde ()
units::quantity< unit::concentration >	GetReferenceConcentration ()
virtual std::vector< double >	GetSolution ()
bool	HasRegularGrid ()
bool	HasUnstructuredGrid ()
void	SetCellPopulation (AbstractCellPopulation< DIM > &rCellPopulation, units::quantity< unit::length > cellPopulationReferenceLength, units::quantity< unit::concentration > cellPopulationReferenceConcentration)
void	SetFileHandler (boost::shared_ptr< OutputFileHandler > pOutputFileHandler)
void	SetFileName (const std::string &rFilename)
void	SetLabel (const std::string &rLabel)
void	SetPde (boost::shared_ptr< AbstractDiscreteContinuumLinearEllipticPde< DIM, DIM > > pPde)
void	SetNonLinearPde (boost::shared_ptr< AbstractDiscreteContinuumNonLinearEllipticPde< DIM, DIM > > pPde)
void	SetReferenceConcentration (units::quantity< unit::concentration > referenceConcentration)
void	SetVesselNetwork (boost::shared_ptr< VesselNetwork< DIM > > pNetwork)
void	SetWriteSolution (bool write=true)

Protected Attributes
vtkSmartPointer< vtkUnstructuredGrid >	mpVtkSolution
boost::shared_ptr< DiscreteContinuumMesh< DIM, DIM > >	mpMesh
Protected Attributes inherited from AbstractDiscreteContinuumSolver< DIM >
boost::shared_ptr< VesselNetwork< DIM > >	mpNetwork
AbstractCellPopulation< DIM > *	mpCellPopulation
units::quantity< unit::length >	mCellPopulationReferenceLength
units::quantity< unit::concentration >	mCellPopulationReferenceConcentration
boost::shared_ptr< OutputFileHandler >	mpOutputFileHandler
std::string	mFilename
std::string	mLabel
bool	IsSetupForSolve
bool	mWriteSolution
boost::shared_ptr< AbstractDiscreteContinuumLinearEllipticPde< DIM, DIM > >	mpPde
boost::shared_ptr< AbstractDiscreteContinuumNonLinearEllipticPde< DIM, DIM > >	mpNonLinearPde
std::vector< boost::shared_ptr< DiscreteContinuumBoundaryCondition< DIM > > >	mBoundaryConditions
units::quantity< unit::concentration >	mReferenceConcentration
std::vector< double >	mSolution
std::vector< units::quantity< unit::concentration > >	mConcentrations
bool	mHasRegularGrid
bool	mHasUnstructuredGrid

Detailed Description

template<unsigned DIM>
class AbstractUnstructuredGridDiscreteContinuumSolver< DIM >

An abstract solver class for DiscreteContinuum continuum-discrete problems using structured grids. Concrete classes can solve PDEs or perform other computations based on interpolation of discrete entities (points/cells, lines/vessels) onto structured grids.

Definition at line 57 of file AbstractUnstructuredGridDiscreteContinuumSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::AbstractUnstructuredGridDiscreteContinuumSolver

(

)

Constructor

Definition at line 46 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mHasUnstructuredGrid.

template<unsigned DIM>

AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::~AbstractUnstructuredGridDiscreteContinuumSolver ( )

virtual

Destructor

Definition at line 55 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

Member Function Documentation

template<unsigned DIM>

std::vector< units::quantity< unit::concentration > > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrations ( const std::vector< DimensionalChastePoint< DIM > > &  rSamplePoints )

virtual

Return the value of the field at the requested points

Parameters

rSamplePoints

a vector of sample points

Returns

the value of the field ordered according to input point order

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 118 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mLabel, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, AbstractDiscreteContinuumSolver< DIM >::mReferenceConcentration, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

template<unsigned DIM>

std::vector< units::quantity< unit::concentration > > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrations ( boost::shared_ptr< RegularGrid< DIM > >  pGrid )

virtual

Return the value of the field at the requested points

Parameters

pGrid

the sampling grid

Returns

the value of the field ordered according to grid order

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 166 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::GetConcentrations().

template<unsigned DIM>

std::vector< units::quantity< unit::concentration > > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrations ( boost::shared_ptr< DiscreteContinuumMesh< DIM > >  pMesh )

virtual

Return the value of the field on the nodes of the input mesh

Parameters

pMesh

the mesh from which nodes are sampled

Returns

the value of the field ordered according to mesh node ordering

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 172 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::GetConcentrations(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh.

template<unsigned DIM>

std::vector< units::quantity< unit::concentration > > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrationsAtCentroids ( )

virtual

Return the value of the field at the mesh centroids

Returns

the value of the field ordered according to element order

Definition at line 71 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mLabel, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, AbstractDiscreteContinuumSolver< DIM >::mReferenceConcentration, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

template<unsigned DIM>

boost::shared_ptr< DiscreteContinuumMesh< DIM > > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetMesh

(

)

Return the mesh

Returns

a pointer to the mesh

Definition at line 61 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh.

template<unsigned DIM>

std::vector< double > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetSolution ( const std::vector< DimensionalChastePoint< DIM > > &  rSamplePoints )

virtual

Return the value of the field at the requested points

Parameters

rSamplePoints

the points for sampling

Returns

the value of the field ordered according to input point order

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 185 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mLabel, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

template<unsigned DIM>

std::vector< double > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetSolution ( boost::shared_ptr< RegularGrid< DIM > >  pGrid )

virtual

Return the value of the field at all points on the supplied grid

Parameters

pGrid

the grid to be sampled

Returns

the value of the field ordered according to input point order

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 232 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::GetSolution().

template<unsigned DIM>

std::vector< double > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetSolution ( boost::shared_ptr< DiscreteContinuumMesh< DIM > >  pMesh )

virtual

Return the value of the field at all points on the supplied mesh nodes

Parameters

pMesh

the mesh for point sampling

Returns

the value of the field ordered according to mesh node order

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 238 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::GetSolution(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh.

template<unsigned DIM>

vtkSmartPointer< vtkUnstructuredGrid > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetVtkSolution ( )

virtual

Return the solution as vtk image data

Returns

the solution in vtk format

Definition at line 251 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

template<unsigned DIM>

void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::SetMesh

(

boost::shared_ptr< DiscreteContinuumMesh< DIM, DIM > >

pMesh

)

Set the mesh

Parameters

pMesh

the finite element mesh

Definition at line 261 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh.

template<unsigned DIM>

void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup ( )

virtual

Overridden Setup method.

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 267 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh, AbstractDiscreteContinuumSolver< DIM >::mpNetwork, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, and AbstractDiscreteContinuumSolver< DIM >::mSolution.

Referenced by AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrations(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrationsAtCentroids(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetSolution(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetVtkSolution(), FiniteElementSolver< DIM >::Solve(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateCellData(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateElementSolution(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateSolution(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Write().

template<unsigned DIM>

virtual void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Solve ( )

pure virtual

Overridden Update method.

Implements AbstractDiscreteContinuumSolver< DIM >.

Implemented in FiniteElementSolver< DIM >.

template<unsigned DIM>

void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Update ( )

virtual

Overridden Update method.

Implements AbstractDiscreteContinuumSolver< DIM >.

Reimplemented in FiniteElementSolver< DIM >.

Definition at line 383 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

template<unsigned DIM>

void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateCellData ( )

virtual

Update the cell data as passed in

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 358 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::CellPopulationIsSet(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

template<unsigned DIM>

void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateElementSolution ( const std::vector< double > &  rData )

virtual

Update the element solution using dimensionless data

Parameters

rData

the data

Definition at line 313 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::GetLabel(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

template<unsigned DIM>

void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateSolution ( const std::vector< double > &  rData )

virtual

Update the solution using dimensionless data

Parameters

rData

the data

Reimplemented from AbstractDiscreteContinuumSolver< DIM >.

Definition at line 287 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::GetLabel(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, AbstractDiscreteContinuumSolver< DIM >::mSolution, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

Referenced by FiniteElementSolver< DIM >::Solve().

template<unsigned DIM>

void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateSolution ( const std::vector< units::quantity< unit::concentration > > &  rData )

virtual

Update the solution using concentration data

Parameters

rData

the data

Reimplemented from AbstractDiscreteContinuumSolver< DIM >.

Definition at line 332 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::GetLabel(), AbstractDiscreteContinuumSolver< DIM >::mConcentrations, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, AbstractDiscreteContinuumSolver< DIM >::mReferenceConcentration, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

template<unsigned DIM>

void AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Write ( )

virtual

Overridden Write method. Writes the solution to file

Implements AbstractDiscreteContinuumSolver< DIM >.

Definition at line 389 of file AbstractUnstructuredGridDiscreteContinuumSolver.cpp.

References AbstractDiscreteContinuumSolver< DIM >::mFilename, AbstractDiscreteContinuumSolver< DIM >::mpOutputFileHandler, AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution, and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup().

Referenced by FiniteElementSolver< DIM >::Solve().

Member Data Documentation

template<unsigned DIM>

boost::shared_ptr<DiscreteContinuumMesh<DIM, DIM> > AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpMesh

protected

The finite element mesh

Definition at line 73 of file AbstractUnstructuredGridDiscreteContinuumSolver.hpp.

Referenced by AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrations(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrationsAtCentroids(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetMesh(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetSolution(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::SetMesh(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup(), and FiniteElementSolver< DIM >::Solve().

template<unsigned DIM>

vtkSmartPointer<vtkUnstructuredGrid> AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::mpVtkSolution

protected

The solution in VTK form

Definition at line 68 of file AbstractUnstructuredGridDiscreteContinuumSolver.hpp.

Referenced by AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrations(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetConcentrationsAtCentroids(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetSolution(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::GetVtkSolution(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Setup(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateCellData(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateElementSolution(), AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::UpdateSolution(), and AbstractUnstructuredGridDiscreteContinuumSolver< DIM >::Write().

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

• projects/MicrovesselChaste/src/pde/solvers/AbstractUnstructuredGridDiscreteContinuumSolver.hpp
• projects/MicrovesselChaste/src/pde/solvers/AbstractUnstructuredGridDiscreteContinuumSolver.cpp