BidomainProblem< DIM > Class Template Reference

#include <BidomainProblem.hpp>

Inherits AbstractCardiacProblem< DIM, DIM, 2 >.

Collaboration diagram for BidomainProblem< DIM >:
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List of all members.

Public Member Functions

 BidomainProblem (AbstractCardiacCellFactory< DIM > *pCellFactory, bool hasBath=false)
 BidomainProblem ()
void SetFixedExtracellularPotentialNodes (std::vector< unsigned > nodes)
void SetNodeForAverageOfPhiZeroed (unsigned node)
BidomainPde< DIM > * GetBidomainPde ()
void WriteInfo (double time)
virtual void DefineWriterColumns (bool extending)
virtual void WriteOneStep (double time, Vec voltageVec)
void PreSolveChecks ()
void SetElectrodes (boost::shared_ptr< Electrodes< DIM > > pElectrodes)
void AtBeginningOfTimestep (double time)
void OnEndOfTimestep (double time)
void SetUpAdditionalStoppingTimes (std::vector< double > &rAdditionalStoppingTimes)
template<class Archive >
void LoadExtraArchiveForBidomain (Archive &archive, unsigned version)

Protected Member Functions

Vec CreateInitialCondition ()
void AnalyseMeshForBath ()
virtual AbstractCardiacPde< DIM > * CreateCardiacPde ()
virtual
AbstractDynamicAssemblerMixin
< DIM, DIM, 2 > * 		CreateAssembler ()

Protected Attributes

BidomainPde< DIM > * mpBidomainPde
std::vector< unsigned > mFixedExtracellularPotentialNodes
unsigned mExtracelluarColumnId
unsigned mRowForAverageOfPhiZeroed
bool mHasBath
boost::shared_ptr< Electrodes
< DIM > > 		mpElectrodes
BidomainDg0Assembler< DIM, DIM > * mpAssembler

Private Member Functions

template<class Archive >
void save (Archive &archive, const unsigned int version) const
template<class Archive >
void load (Archive &archive, const unsigned int version)

Friends

class boost::serialization::access
class TestBidomainWithBathAssembler
class TestCardiacSimulationArchiver

Detailed Description

template<unsigned DIM>
class BidomainProblem< DIM >

Class which specifies and solves a bidomain problem.

The solution vector is of the form: (V_1, phi_1, V_2, phi_2, ......, V_N, phi_N), where V_j is the voltage at node j and phi_j is the extracellular potential at node j.

Definition at line 59 of file BidomainProblem.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
BidomainProblem< DIM >::BidomainProblem ( AbstractCardiacCellFactory< DIM > *  pCellFactory,
bool  hasBath = false 
) [inline]

Constructor

Parameters:
pCellFactory User defined cell factory which shows how the pde should create cells.
hasBath Whether the simulation has a bath (if this is true, all elements with attribute = 1 will be set to be bath elements (the rest should have attribute = 0)).

Definition at line 186 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>
BidomainProblem< DIM >::BidomainProblem (  )  [inline]

Constructor just used for archiving

Definition at line 197 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

Member Function Documentation

template<unsigned DIM>
void BidomainProblem< DIM >::AnalyseMeshForBath (  )  [inline, protected]

Annotate bath nodes with the correct region code, if a bath is present. Will throw if mHasBath is set but no bath is present in the mesh.

Definition at line 41 of file BidomainProblem.cpp.

References HeartRegionCode::BATH, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetRegion(), BidomainProblem< DIM >::mHasBath, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and HeartRegionCode::TISSUE.

Referenced by BidomainProblem< DIM >::CreateCardiacPde(), and BidomainProblem< DIM >::load().

template<unsigned DIM>
void BidomainProblem< DIM >::AtBeginningOfTimestep ( double  time  )  [inline, virtual]

Called at beginning of each time step in the main time-loop in AbstractCardiacProblem::Solve(). Overloaded here to switch on the electrodes (if there are any).

Parameters:
time the current time

Todo:
#1159 #1324 heart/src/problem/AbstractCardiacProblem.hpp:657 expects both pointing at the same place when unarchiving

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 313 of file BidomainProblem.cpp.

References AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::GetLinearSystem(), BidomainProblem< DIM >::mpAssembler, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpDefaultBoundaryConditionsContainer, BidomainProblem< DIM >::mpElectrodes, and AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer().

template<unsigned DIM>
AbstractDynamicAssemblerMixin< DIM, DIM, 2 > * BidomainProblem< DIM >::CreateAssembler (  )  [inline, protected, virtual]

Create a suitable bidomain assembler

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 120 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes, BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpAssembler, BidomainProblem< DIM >::mpBidomainPde, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, BidomainProblem< DIM >::mRowForAverageOfPhiZeroed, AbstractCardiacProblem< DIM, DIM, 2 >::mUseMatrixBasedRhsAssembly, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed().

Referenced by BidomainProblem< DIM >::OnEndOfTimestep().

template<unsigned DIM>
AbstractCardiacPde< DIM > * BidomainProblem< DIM >::CreateCardiacPde (  )  [inline, protected, virtual]

Create our bidomain PDE object

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 112 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::mpBidomainPde, and AbstractCardiacProblem< DIM, DIM, 2 >::mpCellFactory.

template<unsigned DIM>
Vec BidomainProblem< DIM >::CreateInitialCondition (  )  [inline, protected, virtual]

Create normal initial condition but overwrite V to zero for bath nodes, if there are any.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 87 of file BidomainProblem.cpp.

References HeartRegionCode::BATH, DistributedVector::Begin(), DistributedVector::End(), BidomainProblem< DIM >::mHasBath, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and DistributedVector::Restore().

template<unsigned DIM>
void BidomainProblem< DIM >::DefineWriterColumns ( bool  extending  )  [inline, virtual]

Define what variables are written to the primary results file. Adds the extracellular potential.

Parameters:
extending whether we are extending an existing results file

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 259 of file BidomainProblem.cpp.

References AbstractCardiacProblem< DIM, DIM, 2 >::DefineExtraVariablesWriterColumns(), Hdf5DataWriter::DefineVariable(), Hdf5DataWriter::GetVariableByName(), BidomainProblem< DIM >::mExtracelluarColumnId, and AbstractCardiacProblem< DIM, DIM, 2 >::mpWriter.

template<unsigned DIM>
BidomainPde< DIM > * BidomainProblem< DIM >::GetBidomainPde (  )  [inline]

Get the pde. Can only be called after Initialise()

Definition at line 226 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mpBidomainPde.

template<unsigned DIM>
template<class Archive >
void BidomainProblem< DIM >::load ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Load the member variables from an archive.

Parameters:
archive 
version 

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 88 of file BidomainProblem.hpp.

References BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpBidomainPde, BidomainProblem< DIM >::mpElectrodes, and BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

template<unsigned DIM>
template<class Archive >
void BidomainProblem< DIM >::LoadExtraArchiveForBidomain ( Archive &  archive,
unsigned  version 
) [inline]

Used when loading a set of archives written by a parallel simulation onto a single process. Loads data from the given process-specific archive (written by a non-master process) and merges it into our data.

Parameters:
archive the archive to load
version the archive file version
Note:
The process-specific archives currently contain the following data. If the layout changes, then this method will need to be altered, since it hard-codes knowledge of the order in which things are archived.
  1. Stuff known by AbstractCardiacProblem
  2. mpElectrodes->mpBoundaryConditionsContainer

This gets called by AbstractCardiacProblem::LoadExtraArchive when it's done the generic stuff.

Todo:
#1159 sanity check that the contents of p_bcc and mpElectrodes->GetBoundaryConditionsContainer() match.

Definition at line 286 of file BidomainProblem.hpp.

References AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, and AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LoadExtraArchive().

template<unsigned DIM>
void BidomainProblem< DIM >::OnEndOfTimestep ( double  time  )  [inline, virtual]

Called at end of each time step in the main time-loop in AbstractCardiacProblem::Solve(). Overloaded here to switch off the electrodes (if there are any).

Parameters:
time the current time

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 354 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::mpAssembler, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpDefaultBoundaryConditionsContainer, BidomainProblem< DIM >::mpElectrodes, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer().

template<unsigned DIM>
void BidomainProblem< DIM >::PreSolveChecks (  )  [inline, virtual]

Performs a series of checks before solving. Checks that a suitable method of resolving the singularity is being used.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 282 of file BidomainProblem.cpp.

References HeartConfig::GetUseRelativeTolerance(), HeartConfig::Instance(), BidomainProblem< DIM >::mFixedExtracellularPotentialNodes, and BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

template<unsigned DIM>
template<class Archive >
void BidomainProblem< DIM >::save ( Archive &  archive,
const unsigned int  version 
) const [inline, private]

Save the member variables to an archive.

Parameters:
archive 
version 

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 71 of file BidomainProblem.hpp.

References BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpBidomainPde, BidomainProblem< DIM >::mpElectrodes, and BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

template<unsigned DIM>
void BidomainProblem< DIM >::SetElectrodes ( boost::shared_ptr< Electrodes< DIM > >  pElectrodes  )  [inline]

Set an electrode object (which provides boundary conditions). Only valid if there is a bath.

Parameters:
pElectrodes 

Definition at line 302 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mHasBath, and BidomainProblem< DIM >::mpElectrodes.

template<unsigned DIM>
void BidomainProblem< DIM >::SetFixedExtracellularPotentialNodes ( std::vector< unsigned >  nodes  )  [inline]

Set the nodes at which phi_e (the extracellular potential) is fixed to zero. This does not necessarily have to be called. If it is not, phi_e is only defined up to a constant.

Parameters:
nodes the nodes to be fixed.
Note:
currently, the value of phi_e at the fixed nodes cannot be set to be anything other than zero.

Definition at line 208 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>
void BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed ( unsigned  node  )  [inline]

Set which row of the linear system should be used to enforce the condition that the average of phi_e is zero. If not called, this condition will not be used.

Parameters:
node the mesh node index giving the row at which to impose the constraint

Definition at line 220 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

template<unsigned DIM>
void BidomainProblem< DIM >::SetUpAdditionalStoppingTimes ( std::vector< double > &  rAdditionalStoppingTimes  )  [inline, virtual]

Method to fill in a vector of additional stopping times consisting of the times when the electrodes are to be turned on and off

Parameters:
rAdditionalStoppingTimes reference to vector that will contain the on and off times for the electrodes

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 391 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mpElectrodes.

template<unsigned DIM>
void BidomainProblem< DIM >::WriteInfo ( double  time  )  [inline, virtual]

Print out time and max/min voltage/phi_e values at current time.

Parameters:
time current time.

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 233 of file BidomainProblem.cpp.

References PetscTools::AmMaster(), and AbstractCardiacProblem< DIM, DIM, 2 >::mSolution.

template<unsigned DIM>
void BidomainProblem< DIM >::WriteOneStep ( double  time,
Vec  voltageVec 
) [inline, virtual]

Write one timestep of output data to the primary results file. Adds the extracellular potential to the results.

Parameters:
time the current time
voltageVec the solution vector to write

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 274 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mExtracelluarColumnId, AbstractCardiacProblem< DIM, DIM, 2 >::mpWriter, AbstractCardiacProblem< DIM, DIM, 2 >::mVoltageColumnId, Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutUnlimitedVariable(), and AbstractCardiacProblem< DIM, DIM, 2 >::WriteExtraVariablesOneStep().

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 63 of file BidomainProblem.hpp.

Member Data Documentation

template<unsigned DIM>
unsigned BidomainProblem< DIM >::mExtracelluarColumnId [protected]

Used by the writer

Definition at line 115 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::DefineWriterColumns(), and BidomainProblem< DIM >::WriteOneStep().

template<unsigned DIM>
std::vector<unsigned> BidomainProblem< DIM >::mFixedExtracellularPotentialNodes [protected]

Nodes at which the extracellular voltage is fixed to zero (replicated)

Definition at line 113 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::BidomainProblem(), BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::PreSolveChecks(), and BidomainProblem< DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned DIM>
bool BidomainProblem< DIM >::mHasBath [protected]

Whether the mesh has a bath, ie whether this is a bath simulation

Definition at line 123 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::CreateInitialCondition(), BidomainProblem< DIM >::load(), BidomainProblem< DIM >::save(), and BidomainProblem< DIM >::SetElectrodes().

template<unsigned DIM>
BidomainDg0Assembler<DIM,DIM>* BidomainProblem< DIM >::mpAssembler [protected]

We need to save the assembler that is being used to be able to switch off the electrodes (by adding default boundary conditions to the assembler)

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 145 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::AtBeginningOfTimestep(), BidomainProblem< DIM >::CreateAssembler(), and BidomainProblem< DIM >::OnEndOfTimestep().

template<unsigned DIM>
BidomainPde<DIM>* BidomainProblem< DIM >::mpBidomainPde [protected]

The bidomain PDE

Definition at line 110 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::CreateCardiacPde(), BidomainProblem< DIM >::GetBidomainPde(), BidomainProblem< DIM >::load(), and BidomainProblem< DIM >::save().

template<unsigned DIM>
boost::shared_ptr<Electrodes<DIM> > BidomainProblem< DIM >::mpElectrodes [protected]

Electrodes used to provide a shock

Definition at line 126 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::AtBeginningOfTimestep(), BidomainProblem< DIM >::load(), BidomainProblem< DIM >::OnEndOfTimestep(), BidomainProblem< DIM >::save(), BidomainProblem< DIM >::SetElectrodes(), and BidomainProblem< DIM >::SetUpAdditionalStoppingTimes().

template<unsigned DIM>
unsigned BidomainProblem< DIM >::mRowForAverageOfPhiZeroed [protected]

Another method of resolving the singularity in the bidomain equations. Specifies a row of the matrix at which to impose an extra condition.

Definition at line 120 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::load(), BidomainProblem< DIM >::PreSolveChecks(), BidomainProblem< DIM >::save(), and BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed().

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