#include <AbstractContinuumMechanicsSolver.hpp>

Inheritance diagram for AbstractContinuumMechanicsSolver< DIM >:

Collaboration diagram for AbstractContinuumMechanicsSolver< DIM >:

Public Member Functions
	AbstractContinuumMechanicsSolver (AbstractTetrahedralMesh< DIM, DIM > &rQuadMesh, ContinuumMechanicsProblemDefinition< DIM > &rProblemDefinition, std::string outputDirectory, CompressibilityType compressibilityType)

virtual	~AbstractContinuumMechanicsSolver ()

void	WriteCurrentSpatialSolution (std::string fileName, std::string fileExtension, int counterToAppend=-1)

void	WriteCurrentPressureSolution (int counterToAppend=-1)

void	SetWriteOutput (bool writeOutput=true)

void	CreateVtkOutput (std::string spatialSolutionName="Spatial solution")

std::vector< double > &	rGetCurrentSolution ()

virtual std::vector< c_vector < double, DIM > > &	rGetSpatialSolution ()=0

std::vector< double > &	rGetPressures ()

Protected Member Functions
void	AllocateMatrixMemory ()

void	ApplyDirichletBoundaryConditions (ApplyDirichletBcsType type, bool symmetricProblem)

void	AddIdentityBlockForDummyPressureVariables (ApplyDirichletBcsType type)

void	RemovePressureDummyValuesThroughLinearInterpolation ()

Protected Attributes
AbstractTetrahedralMesh< DIM, DIM > &	mrQuadMesh

ContinuumMechanicsProblemDefinition < DIM > &	mrProblemDefinition

bool	mWriteOutput

std::string	mOutputDirectory

OutputFileHandler *	mpOutputFileHandler

std::vector< c_vector< double, DIM > >	mSpatialSolution

std::vector< double >	mPressureSolution

std::vector< double >	mCurrentSolution

GaussianQuadratureRule< DIM > *	mpQuadratureRule

GaussianQuadratureRule< DIM-1 > *	mpBoundaryQuadratureRule

CompressibilityType	mCompressibilityType

unsigned	mProblemDimension

unsigned	mNumDofs

bool	mVerbose

Vec	mResidualVector

Vec	mLinearSystemRhsVector

Mat	mSystemLhsMatrix

Vec	mDirichletBoundaryConditionsVector

Mat	mPreconditionMatrix

Friends
class	StressRecoveror< DIM >

class	VtkNonlinearElasticitySolutionWriter< DIM >

Detailed Description

template<unsigned DIM>
class AbstractContinuumMechanicsSolver< DIM >

General base class for continuum mechanics solvers. Deals with memory allocation, writing to file, applying boundary conditions, and adding an identity block (see below)

Note: the PROBLEM DIMENSION depends on DIM and whether a compressible or incompressible problem is being solved. (i) Compressible: mProblemDimension is set to DIM, and the ordering of the unknowns is, for 2D say: [U1 V1 U2 V2 .. Un Vn] (ii) Incompressible: Here we have spatial unknowns (at all nodes of the QuadraticMesh) and pressure unknowns (only at the vertices, as linear bases are). We choose mProblemDim = DIM+1, use (for parallelisation reasons) the ordering [U1 V1 P1 , .. , Un Vn, Pn], introducing dummy variables for pressure unknowns at internal hences, with the equation Pi=0 at these nodes, hence the need for an identity block to be added the corresponding parts of the matrix.

Definition at line 87 of file AbstractContinuumMechanicsSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver	(	AbstractTetrahedralMesh< DIM, DIM > &	rQuadMesh,
		ContinuumMechanicsProblemDefinition< DIM > &	rProblemDefinition,
		std::string	outputDirectory,
		CompressibilityType	compressibilityType
	)

Constructor

Parameters

rQuadMesh	the mesh
rProblemDefinition	problem definition object
outputDirectory	output directory name
compressibilityType	'INCOMPRESSIBLE' or 'COMPRESSIBLE'

Definition at line 376 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

AbstractContinuumMechanicsSolver< DIM >::~AbstractContinuumMechanicsSolver ( )

virtual

Destructor

Definition at line 430 of file AbstractContinuumMechanicsSolver.hpp.

References PetscTools::Destroy().

Member Function Documentation

template<unsigned DIM>

void AbstractContinuumMechanicsSolver< DIM >::AddIdentityBlockForDummyPressureVariables ( ApplyDirichletBcsType type )

protected

For incompressible problems, we use the following ordering: [U0 V0 W0 P0 U1 V1 W1 P1 .. Un Vn Wn Pn] where (U V W) is the displacement, and P is the pressure. Therefore P is defined at every node; however for the solve, linear basis functions are used for the pressure, so pressure is solved for at each vertex, not at internal nodes (which are for quadratic basis functions).

The pressure variables for non-vertex nodes are therefore dummy variables. This method enforces the condition P_i=0, where i corresponds to a non-vertex node.

The first input parameter should be one of the following LINEAR_PROBLEM – indicating the overall problem is linear, and in which case the matrix will be altered (1 on diagonal, zeros assumed on rest of row) and the rhs vector will be set to 0.

NONLINEAR_PROBLEM_APPLY_TO_RESIDUAL_ONLY – indicating the overall problem is nonlinear and here only the residual vector will be altered (sets the residual value of the appropriate rows to P_i-0.0.

NONLINEAR_PROBLEM_APPLY_TO_EVERYTHING – indicating the overall problem is nonlinear, and here, the residual vector will be altered, as will the matrix and RHS vector (see documentation on mResidualVector for why there is a separate residual vector and RHS vector).

Note the row (and columns) for the dummy variables are not explicitly zeroed, as they are assumed to be zero already - in a finite element assembly nothing will have been written to the rows or columns corresponding to dummy variables. Hence this method always maintains symmetry.

Parameters

type see above

Definition at line 796 of file AbstractContinuumMechanicsSolver.hpp.

References PetscMatTools::SetElement(), and PetscVecTools::SetElement().

template<unsigned DIM>

void AbstractContinuumMechanicsSolver< DIM >::AllocateMatrixMemory ( )

protected

Allocates memory for the matrices and vectors

We want to allocate different numbers of non-zeros per row, which means PetscTools::SetupMat isn't that useful. We could call

but we would get warnings due to the lack allocation

Definition at line 828 of file AbstractContinuumMechanicsSolver.hpp.

References PetscTools::Destroy(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), PetscTools::IsSequential(), and PetscTools::SetupMat().

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

void AbstractContinuumMechanicsSolver< DIM >::ApplyDirichletBoundaryConditions	(	ApplyDirichletBcsType	type,
		bool	symmetricProblem
	)

protected

Apply the Dirichlet boundary conditions to the linear system.

The first input parameter should be one of the following LINEAR_PROBLEM – indicating the overall problem is linear, and in which case the BCs will be applied to both the matrix and vector of the linear system

NONLINEAR_PROBLEM_APPLY_TO_RESIDUAL_ONLY – indicating the overall problem is nonlinear and here only the residual vector will be altered (apply the Dirichlet boundary conditions to the residual vector involves setting appropriate components to the difference between the current value and the correct value).

NONLINEAR_PROBLEM_APPLY_TO_EVERYTHING – indicating the overall problem is nonlinear, and here, the residual vector will be altered, as will the matrix and RHS vector (see documentation on mResidualVector for why there is a separate residual vector and RHS vector).

The second parameter should be true if the overall problem is symmetric, in which case boundary conditions will be applied keeping the matrix symmetric (if the matrix is being altered). See in-code comments for how this is done.

Parameters

type	see above
symmetricProblem	see above

Definition at line 672 of file AbstractContinuumMechanicsSolver.hpp.

References PetscVecTools::AddScaledVector(), PetscTools::Destroy(), PetscMatTools::Finalise(), PetscMatTools::GetMatrixRowDistributed(), PetscVecTools::SetElement(), PetscVecTools::Zero(), PetscMatTools::ZeroRowsAndColumnsWithValueOnDiagonal(), and PetscMatTools::ZeroRowsWithValueOnDiagonal().

template<unsigned DIM>

void AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput ( std::string spatialSolutionName = "Spatial solution" )

Convert the output to vtk format (placed in a folder called vtk in the output directory).

Parameters

spatialSolutionName is used to identify the spatial solution as a velocity, displacement...

** TO BE DEPRECATED - see #2321 **

Definition at line 547 of file AbstractContinuumMechanicsSolver.hpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddCellData(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), EXCEPTION, and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned DIM>

void AbstractContinuumMechanicsSolver< DIM >::RemovePressureDummyValuesThroughLinearInterpolation ( )

protected

For incompressible problems, we use the following ordering: [U0 V0 W0 P0 U1 V1 W1 P1 .. Un Vn Wn Pn] where (U V W) is the displacement, and P is the pressure. Therefore P is defined at every node; however for the solve, linear basis functions are used for the pressure, so pressure is solved for at each vertex, not at internal nodes (which are for quadratic basis functions).

The above method, AddIdentityBlockForDummyPressureVariables(), enforces the condition P_i=0, where i corresponds to a non-vertex node.

AFTER the solve, this method can be used to remove the dummy values, but looping over all edges, and linearly interpolating the pressure at the two vertices onto the internal node.

This method assumes each internal node is midway between the two vertices.

Definition at line 593 of file AbstractContinuumMechanicsSolver.hpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin().

template<unsigned DIM>

std::vector<double>& AbstractContinuumMechanicsSolver< DIM >::rGetCurrentSolution ( )

inline

Returns: the current solution vector (advanced use only - for getting the deformed position use rGetDeformedPosition()).

Definition at line 353 of file AbstractContinuumMechanicsSolver.hpp.

References AbstractContinuumMechanicsSolver< DIM >::mCurrentSolution.

template<unsigned DIM>

std::vector< double > & AbstractContinuumMechanicsSolver< DIM >::rGetPressures ( )

Returns: the pressure, for each NODE in the mesh. If the node is an internal node of the quadratic mesh the pressure is not computed at this node (as linear basis functions are used for the pressure, so pressures unknowns are only present at vertices), so a dummy pressure value of 0 is returned in this vector.

Only valid if mCompressibilityType==INCOMPRESSIBLE

Definition at line 578 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

virtual std::vector<c_vector<double,DIM> >& AbstractContinuumMechanicsSolver< DIM >::rGetSpatialSolution ( )

pure virtual

Returns: the spatial solution. For solids problems this will be the deformed position, for fluids problems this will be the flow.

Implemented in AbstractNonlinearElasticitySolver< DIM >, and StokesFlowSolver< DIM >.

template<unsigned DIM>

void AbstractContinuumMechanicsSolver< DIM >::SetWriteOutput ( bool writeOutput = true )

Set whether to write any output.

Parameters

writeOutput (defaults to true)

Definition at line 536 of file AbstractContinuumMechanicsSolver.hpp.

References EXCEPTION.

template<unsigned DIM>

void AbstractContinuumMechanicsSolver< DIM >::WriteCurrentPressureSolution ( int counterToAppend = -1 )

Write the pressure solution. Only valid if mCompressibilityType==INCOMPRESSIBLE. Writes the pressure for ALL nodes on the mesh, including internal nodes (as these are not assumed to be have indices greater than vertex nodes). As linear basis functions are used for pressure, the pressure solution is only computed at the vertices, and pressure dummy variables are used at internal nodes, hence for each internal node, 0 will be written to file.

Parameters

counterToAppend append a counter to the file name

WriteCurrentPressureSolution() –> file called "pressure.txt" WriteCurrentPressureSolution(3) –> file called "pressure_3.txt"

Definition at line 500 of file AbstractContinuumMechanicsSolver.hpp.

References PetscTools::AmMaster(), and PetscTools::Barrier().

template<unsigned DIM>

void AbstractContinuumMechanicsSolver< DIM >::WriteCurrentSpatialSolution	(	std::string	fileName,
		std::string	fileExtension,
		int	counterToAppend = `-1`
	)

Write the spatial solution (deformed position if solids, flow if fluids) at the nodes

Parameters

fileName	(stem)
fileExtension	to append at end.
counterToAppend	append a counter to the file name (defaults to nothing appended).

For example: WriteCurrentSpatialSolution("solution","nodes") –> file called "solution.nodes" WriteCurrentSpatialSolution("solution","nodes",3) –> file called "solution_3.nodes"

Definition at line 458 of file AbstractContinuumMechanicsSolver.hpp.

References PetscTools::AmMaster(), and PetscTools::Barrier().

Member Data Documentation

template<unsigned DIM>

CompressibilityType AbstractContinuumMechanicsSolver< DIM >::mCompressibilityType

protected

This is equal to either COMPRESSIBLE or INCOMPRESSIBLE (see enumeration class) and is only used in computing mNumDofs and allocating matrix memory.

Definition at line 138 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

std::vector<double> AbstractContinuumMechanicsSolver< DIM >::mCurrentSolution

protected

The current solution, in the form (assuming 2d): Incompressible problem: [u1 v1 u2 v2 ... uN vN p1 p2 .. pM] Compressible problem: [u1 v1 u2 v2 ... uN vN] where there are N total nodes and M vertices.

Definition at line 126 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver(), and AbstractContinuumMechanicsSolver< DIM >::rGetCurrentSolution().

template<unsigned DIM>

Vec AbstractContinuumMechanicsSolver< DIM >::mDirichletBoundaryConditionsVector

protected

Helper vector (see ApplyDirichletBoundaryConditions code).

Definition at line 197 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

Vec AbstractContinuumMechanicsSolver< DIM >::mLinearSystemRhsVector

protected

The RHS side in the linear system that is solved each Newton iteration.

Definition at line 187 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

unsigned AbstractContinuumMechanicsSolver< DIM >::mNumDofs

protected

Number of degrees of freedom (equal to mProblemDim*num_nodes)

Definition at line 153 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

std::string AbstractContinuumMechanicsSolver< DIM >::mOutputDirectory

protected

Where to write output, relative to CHASTE_TEST_OUTPUT.

Definition at line 106 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

GaussianQuadratureRule<DIM-1>* AbstractContinuumMechanicsSolver< DIM >::mpBoundaryQuadratureRule

protected

Boundary Gaussian quadrature rule.

Definition at line 132 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

OutputFileHandler* AbstractContinuumMechanicsSolver< DIM >::mpOutputFileHandler

protected

Output file handler.

Definition at line 109 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

GaussianQuadratureRule<DIM>* AbstractContinuumMechanicsSolver< DIM >::mpQuadratureRule

protected

Gaussian quadrature rule.

Definition at line 129 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

Mat AbstractContinuumMechanicsSolver< DIM >::mPreconditionMatrix

protected

Precondition matrix for the linear system.

Definition at line 202 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

std::vector<double> AbstractContinuumMechanicsSolver< DIM >::mPressureSolution

protected

Pressures solution at each vertex of the mesh. Only valid if mCompressibilityType==INCOMPRESSIBLE.

Definition at line 117 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

unsigned AbstractContinuumMechanicsSolver< DIM >::mProblemDimension

protected

The problem dimension - the number of unknowns at each node. For compressible problems, where only the deformation/flow is computed at each node, this is equal to DIM For incompressible problems, where pressure is computed as well, this is equal to DIM+1 (there is a pressure variable defined even for internal nodes at which pressure is not computed, this is a dummy pressure variable – done like this for parallelisation reasons. See above).

Definition at line 148 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

Vec AbstractContinuumMechanicsSolver< DIM >::mResidualVector

protected

Residual vector nonlinear problems.

Since the residual in nonlinear problems is usually also the RHS vector in the linear system, it may seem unncessary to also have the member variable mLinearSystemRhsVector.

However: Newton's method is Ju = f, where J is the Jacobian, u the (negative of the) update and f the residual, but when applying Dirichlet boundary conditions in the compressible case, we alter the rows of the matrix and also alter the columns in order to maintain symmetry. This requires making further changes to the right-hand vector, meaning that it no longer properly represents the residual. Hence, we have to use two vectors.

Overall, this can be represents as

compute residual f
compute Jacobian J
apply BCs to f.
alter the linear system from Ju=f to (J*)u=f* which enforces the dirichlet boundary conditions but enforces them symmetrically.

mLinearSystemRhsVector below represents f*.

Definition at line 182 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

ContinuumMechanicsProblemDefinition<DIM>& AbstractContinuumMechanicsSolver< DIM >::mrProblemDefinition

protected

Problem definition class - contains info on boundary conditions, etc

Definition at line 100 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

AbstractTetrahedralMesh<DIM, DIM>& AbstractContinuumMechanicsSolver< DIM >::mrQuadMesh

protected

The mesh to be solved on. Requires 6 nodes per triangle (or 10 per tetrahedron) as quadratic bases are used.

Definition at line 97 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver(), and StokesFlowSolver< DIM >::StokesFlowSolver().

template<unsigned DIM>

std::vector<c_vector<double,DIM> > AbstractContinuumMechanicsSolver< DIM >::mSpatialSolution

protected

Spatial solution: For solids problems, mSpatialSolution[i](j) = x_j (new position) for node i. For fluids problems, mSpatialSolution[i](j) = u_j (flow) for node i.

Definition at line 114 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

Mat AbstractContinuumMechanicsSolver< DIM >::mSystemLhsMatrix

protected

Jacobian matrix of the nonlinear system, LHS matrix for the linear system.

Definition at line 192 of file AbstractContinuumMechanicsSolver.hpp.

template<unsigned DIM>

bool AbstractContinuumMechanicsSolver< DIM >::mVerbose

protected

If SetVerboseDuringSolve() is called on the problem definition class, or the command line argument "-mech_verbose" or "-mech_very_verbose" is given, than this bool will be set to true and lots of details about each nonlinear solve (including timing breakdowns) will be printed out

Definition at line 160 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

template<unsigned DIM>

bool AbstractContinuumMechanicsSolver< DIM >::mWriteOutput

protected

Whether to write any output.

Definition at line 103 of file AbstractContinuumMechanicsSolver.hpp.

Referenced by AbstractContinuumMechanicsSolver< DIM >::AbstractContinuumMechanicsSolver().

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