This is the abstract base class for the matrix free implementation of parabolic and elliptic BVP's, and supports MPI, threads and vectorization (Hybrid Parallel). This class contains the parallel data structures, mesh (referred to as triangulation), parallel degrees of freedom distribution, constraints, and general utility methods. More...

#include <matrixFreePDE.h>

Inheritance diagram for MatrixFreePDE< dim, degree >:

Public Member Functions
	MatrixFreePDE (userInputParameters< dim >)
	Class contructor.

	~MatrixFreePDE () override
	Class destructor.

virtual void	init ()
	Initializes the mesh, degrees of freedom, constraints and data structures using the user provided inputs in the application parameters file.

virtual void	create_triangulation (parallel::distributed::Triangulation< dim > &tria) const
	Create the mesh with the user provided domain sizes.

void	initForTests (std::vector< Field< dim > > _fields)
	Initializes the data structures for enabling unit tests.

void	solve ()
	This method implements the time stepping algorithm and invokes the solveIncrement() method.

void	vmult (dealii::LinearAlgebra::distributed::Vector< double > &dst, const dealii::LinearAlgebra::distributed::Vector< double > &src) const
	This method essentially converts the MatrixFreePDE object into a matrix object which can be used with matrix free iterative solvers. Provides the A*x functionality for solving the system of equations Ax=b.

void	buildFields ()
	Create the vector of all physical fields in the problem.

virtual void	setInitialCondition (const Point< dim > &p, const unsigned int index, double &scalar_IC, Vector< double > &vector_IC)=0
	Set the initial condition for all fields. This function is overriden in each application.

virtual void	setNonUniformDirichletBCs (const Point< dim > &p, const unsigned int index, const unsigned int direction, const double time, double &scalar_BC, Vector< double > &vector_BC)=0
	Set the spatially or temporally non-uniform boundary conditions. This function is overriden in each application.

Public Attributes
std::vector< Field< dim > >	fields
	Vector of all the physical fields in the problem. Fields are identified by dimentionality (SCALAR/VECTOR), the kind of PDE (ELLIPTIC/PARABOLIC) used to compute them and a character identifier (e.g.: "c" for composition) which is used to write the fields to the output files.

ConditionalOStream	pcout
	Parallel message stream.

Protected Member Functions
void	reinit ()

void	reassignGrains ()

virtual void	solveIncrement (bool skip_time_dependent)

void	outputResults ()

void	computeInvM ()

void	updateExplicitSolution (unsigned int fieldIndex)

bool	updateImplicitSolution (unsigned int fieldIndex, unsigned int nonlinear_iteration_index)

void	applyBCs (unsigned int fieldIndex)

void	compute_element_volume ()
	Compute element volume for the triangulation.

void	computeExplicitRHS ()

void	computeNonexplicitRHS ()

void	getLHS (const MatrixFree< dim, double > &data, dealii::LinearAlgebra::distributed::Vector< double > &dst, const dealii::LinearAlgebra::distributed::Vector< double > &src, const std::pair< unsigned int, unsigned int > &cell_range) const

void	getLaplaceLHS (const MatrixFree< dim, double > &data, dealii::LinearAlgebra::distributed::Vector< double > &dst, const dealii::LinearAlgebra::distributed::Vector< double > &src, const std::pair< unsigned int, unsigned int > &cell_range) const

void	setNonlinearEqInitialGuess ()

void	computeLaplaceRHS (unsigned int fieldIndex)

void	getLaplaceRHS (const MatrixFree< dim, double > &data, dealii::LinearAlgebra::distributed::Vector< double > &dst, const dealii::LinearAlgebra::distributed::Vector< double > &src, const std::pair< unsigned int, unsigned int > &cell_range) const

void	getExplicitRHS (const MatrixFree< dim, double > &data, std::vector< dealii::LinearAlgebra::distributed::Vector< double > * > &dst, const std::vector< dealii::LinearAlgebra::distributed::Vector< double > * > &src, const std::pair< unsigned int, unsigned int > &cell_range) const

void	getNonexplicitRHS (const MatrixFree< dim, double > &data, std::vector< dealii::LinearAlgebra::distributed::Vector< double > * > &dst, const std::vector< dealii::LinearAlgebra::distributed::Vector< double > * > &src, const std::pair< unsigned int, unsigned int > &cell_range) const

virtual void	explicitEquationRHS (variableContainer< dim, degree, VectorizedArray< double > > &variable_list, const Point< dim, VectorizedArray< double > > q_point_loc, const VectorizedArray< double > element_volume) const =0

virtual void	nonExplicitEquationRHS (variableContainer< dim, degree, VectorizedArray< double > > &variable_list, const Point< dim, VectorizedArray< double > > q_point_loc, const VectorizedArray< double > element_volume) const =0

virtual void	equationLHS (variableContainer< dim, degree, VectorizedArray< double > > &variable_list, const Point< dim, VectorizedArray< double > > q_point_loc, const VectorizedArray< double > element_volume) const =0

virtual void	postProcessedFields (const variableContainer< dim, degree, VectorizedArray< double > > &variable_list, variableContainer< dim, degree, VectorizedArray< double > > &pp_variable_list, const Point< dim, VectorizedArray< double > > q_point_loc, const VectorizedArray< double > element_volume) const

void	computePostProcessedFields (std::vector< dealii::LinearAlgebra::distributed::Vector< double > * > &postProcessedSet)

void	getPostProcessedFields (const MatrixFree< dim, double > &data, std::vector< dealii::LinearAlgebra::distributed::Vector< double > * > &dst, const std::vector< dealii::LinearAlgebra::distributed::Vector< double > * > &src, const std::pair< unsigned int, unsigned int > &cell_range)

void	markBoundaries (parallel::distributed::Triangulation< dim > &) const

void	applyDirichletBCs ()

void	applyNeumannBCs ()

void	setPeriodicity ()

void	setPeriodicityConstraints (AffineConstraints< double > , const DoFHandler< dim > ) const

void	set_rigid_body_mode_constraints (AffineConstraints< double > constraints, const DoFHandler< dim > dof_handler, const Point< dim > target_point=Point< dim >()) const
	Set constraints to pin the solution to 0 at a certain vertex. This is automatically done at the origin if no value terms are detected in your dependencies in a time_independent or implicit solve.

void	applyInitialConditions ()

void	save_checkpoint ()

void	load_checkpoint_triangulation ()

void	load_checkpoint_fields ()

void	load_checkpoint_time_info ()

void	move_file (const std::string &, const std::string &)

void	verify_checkpoint_file_exists (const std::string &filename)

void	updateNucleiList ()

std::vector< nucleus< dim > >	getNewNuclei ()

void	getLocalNucleiList (std::vector< nucleus< dim > > &newnuclei) const

void	safetyCheckNewNuclei (std::vector< nucleus< dim > > newnuclei, std::vector< unsigned int > &conflict_ids)

void	refineMeshNearNuclei (std::vector< nucleus< dim > > newnuclei)

double	weightedDistanceFromNucleusCenter (const Point< dim, double > center, const std::vector< double > &semiaxes, const Point< dim, double > q_point_loc, const unsigned int var_index) const

VectorizedArray< double >	weightedDistanceFromNucleusCenter (const Point< dim, double > center, const std::vector< double > &semiaxes, const Point< dim, VectorizedArray< double > > q_point_loc, const unsigned int var_index) const

virtual double	getNucleationProbability (variableValueContainer, double, Point< dim >, unsigned int variable_index) const

unsigned int	getFieldIndex (std::string _name)

void	computeIntegral (double &integratedField, int index, std::vector< dealii::LinearAlgebra::distributed::Vector< double > * > variableSet)

Protected Attributes
userInputParameters< dim >	userInputs

unsigned int	totalDOFs

const AttributesList &	var_attributes

const AttributesList &	pp_attributes

std::vector< SimplifiedGrainRepresentation< dim > >	simplified_grain_representations

parallel::distributed::Triangulation< dim >	triangulation

std::vector< FESystem< dim > * >	FESet

std::vector< const AffineConstraints< double > * >	constraintsDirichletSet

std::vector< const AffineConstraints< double > * >	constraintsOtherSet

std::vector< const DoFHandler< dim > * >	dofHandlersSet

std::vector< const IndexSet * >	locally_relevant_dofsSet

std::vector< AffineConstraints< double > * >	constraintsDirichletSet_nonconst

std::vector< AffineConstraints< double > * >	constraintsOtherSet_nonconst

std::vector< DoFHandler< dim > * >	dofHandlersSet_nonconst

std::vector< IndexSet * >	locally_relevant_dofsSet_nonconst

std::vector< dealii::LinearAlgebra::distributed::Vector< double > * >	solutionSet

std::vector< dealii::LinearAlgebra::distributed::Vector< double > * >	residualSet

std::vector< parallel::distributed::SolutionTransfer< dim, dealii::LinearAlgebra::distributed::Vector< double > > * >	soltransSet

MatrixFree< dim, double >	matrixFreeObject

dealii::LinearAlgebra::distributed::Vector< double >	invMscalar

dealii::LinearAlgebra::distributed::Vector< double >	invMvector

dealii::LinearAlgebra::distributed::Vector< double >	dU_vector

dealii::LinearAlgebra::distributed::Vector< double >	dU_scalar

unsigned int	currentFieldIndex

dealii::AlignedVector< dealii::VectorizedArray< double > >	element_volume
	Vector that stores element volumes.

bool	generatingInitialGuess

std::vector< std::map< types::global_dof_index, double > * >	valuesDirichletSet

std::vector< nucleus< dim > >	nuclei

bool	isTimeDependentBVP

bool	isEllipticBVP

bool	hasExplicitEquation

bool	hasNonExplicitEquation

double	currentTime

unsigned int	currentIncrement

unsigned int	currentOutput

unsigned int	currentCheckpoint

unsigned int	current_grain_reassignment

TimerOutput	computing_timer

bool	first_integrated_var_output_complete

double	integrated_var

unsigned int	integral_index

std::mutex	assembler_lock

AdaptiveRefinement< dim, degree >	AMR

Static Protected Attributes
static const unsigned int	CIJ_tensor_size = 2 * dim - 1 + dim / 3

Detailed Description

template<int dim, int degree>
class MatrixFreePDE< dim, degree >

This is the abstract base class for the matrix free implementation of parabolic and elliptic BVP's, and supports MPI, threads and vectorization (Hybrid Parallel). This class contains the parallel data structures, mesh (referred to as triangulation), parallel degrees of freedom distribution, constraints, and general utility methods.

All the physical models in this package inherit this base class.

Template Parameters

dim	The number of dimensions in the problem.
degree	The polynomial degree of the shape functions.

Member Function Documentation

◆ applyDirichletBCs()

template<int dim, int degree>

void MatrixFreePDE< dim, degree >::applyDirichletBCs ( )

protected

Method for applying Dirichlet boundary conditions.

◆ applyNeumannBCs()

template<int dim, int degree>

void MatrixFreePDE< dim, degree >::applyNeumannBCs ( )

protected

Method for applying Neumann boundary conditions.

◆ create_triangulation()

template<int dim, int degree>

void MatrixFreePDE< dim, degree >::create_triangulation ( parallel::distributed::Triangulation< dim > & tria ) const

virtual

Create the mesh with the user provided domain sizes.

Parameters

tria	Triangulation object. It must be empty prior to calling this function.

◆ initForTests()

template<int dim, int degree>

void MatrixFreePDE< dim, degree >::initForTests ( std::vector< Field< dim > > _fields )

Initializes the data structures for enabling unit tests.

This method initializes the MatrixFreePDE object with a fixed geometry, discretization and other custom selected options specifically to help with unit tests, and should not be called in any of the physical models.

Parameters

_fields Vector of PDE descriptions (e.g., scalar/vector) for each field.

◆ reassignGrains()

template<int dim, int degree>

void MatrixFreePDE< dim, degree >::reassignGrains ( )

protected

Method to reassign grains when multiple grains are stored in a single order parameter.

◆ set_rigid_body_mode_constraints()

template<int dim, int degree>

void MatrixFreePDE< dim, degree >::set_rigid_body_mode_constraints	(	AffineConstraints< double > *	constraints,
		const DoFHandler< dim > *	dof_handler,
		const Point< dim >	target_point = `Point<dim>()`
	)		const

protected

Set constraints to pin the solution to 0 at a certain vertex. This is automatically done at the origin if no value terms are detected in your dependencies in a time_independent or implicit solve.

Parameters

constraints	The constraint set.
dof_handler	The list of the degrees of freedom.
target_point	The point where the solution is constrained. This is the origin by default.

◆ setInitialCondition()

template<int dim, int degree>

virtual void MatrixFreePDE< dim, degree >::setInitialCondition	(	const Point< dim > &	p,
		const unsigned int	index,
		double &	scalar_IC,
		Vector< double > &	vector_IC
	)

pure virtual

Set the initial condition for all fields. This function is overriden in each application.

Parameters

p	The point at which the initial condition is evaluated.
index	The index of the field being evaluated.
scalar_IC	Return variable for scalar fields.
vector_IC	Return variable for vector fields.

◆ setNonUniformDirichletBCs()

template<int dim, int degree>

virtual void MatrixFreePDE< dim, degree >::setNonUniformDirichletBCs	(	const Point< dim > &	p,
		const unsigned int	index,
		const unsigned int	direction,
		const double	time,
		double &	scalar_BC,
		Vector< double > &	vector_BC
	)

pure virtual

Set the spatially or temporally non-uniform boundary conditions. This function is overriden in each application.

Parameters

p	The point at which the boundary condition is evaluated.
index	The index of the field being evaluated.
direction	The face of the boundary condition.
time	The time at which the boundary condition is evaluated.
scalar_BC	Return variable for scalar fields.
vector_BC	Return variable for vector fields.

◆ solveIncrement()

template<int dim, int degree>

void MatrixFreePDE< dim, degree >::solveIncrement ( bool skip_time_dependent )

protectedvirtual

Method to solve each time increment of a time-dependent problem. For time-independent problems this method is called only once. This method solves for all the fields in a staggered manner (one after another) and also invokes the corresponding solvers: Explicit solver for Parabolic problems, Implicit (matrix-free) solver for Elliptic problems.

◆ vmult()

template<int dim, int degree>

void MatrixFreePDE< dim, degree >::vmult	(	dealii::LinearAlgebra::distributed::Vector< double > &	dst,
		const dealii::LinearAlgebra::distributed::Vector< double > &	src
	)		const

This method essentially converts the MatrixFreePDE object into a matrix object which can be used with matrix free iterative solvers. Provides the A*x functionality for solving the system of equations Ax=b.

Parameters

dst	The destination vector.
src	The source vector.

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

/home/runner/work/phaseField/phaseField/include/core/matrixFreePDE.h
/home/runner/work/phaseField/phaseField/src/core/boundary_conditions/boundaryConditions.cc
/home/runner/work/phaseField/phaseField/src/core/boundary_conditions/markBoundaries.cc
/home/runner/work/phaseField/phaseField/src/core/buildFields.cc
/home/runner/work/phaseField/phaseField/src/core/checkpoint.cc
/home/runner/work/phaseField/phaseField/src/core/init.cc
/home/runner/work/phaseField/phaseField/src/core/initial_conditions/initialConditions.cc
/home/runner/work/phaseField/phaseField/src/core/invM.cc
/home/runner/work/phaseField/phaseField/src/core/matrixFreePDE.cc
/home/runner/work/phaseField/phaseField/src/core/outputResults.cc
/home/runner/work/phaseField/phaseField/src/core/postprocessing/computeIntegral.cc
/home/runner/work/phaseField/phaseField/src/core/postprocessing/postprocessor.cc
/home/runner/work/phaseField/phaseField/src/core/reinit.cc
/home/runner/work/phaseField/phaseField/src/core/solvers/computeLHS.cc
/home/runner/work/phaseField/phaseField/src/core/solvers/computeRHS.cc
/home/runner/work/phaseField/phaseField/src/core/solvers/setNonlinearEqInitialGuess.cc
/home/runner/work/phaseField/phaseField/src/core/solvers/solve.cc
/home/runner/work/phaseField/phaseField/src/core/solvers/solveIncrement.cc
/home/runner/work/phaseField/phaseField/src/grains/reassignGrains.cc
/home/runner/work/phaseField/phaseField/src/nucleation/nucleation.cc
/home/runner/work/phaseField/phaseField/src/utilities/utilities.cc

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Function Documentation

◆ applyDirichletBCs()

◆ applyNeumannBCs()

◆ create_triangulation()

◆ initForTests()

◆ reassignGrains()

◆ set_rigid_body_mode_constraints()

◆ setInitialCondition()

◆ setNonUniformDirichletBCs()

◆ solveIncrement()

◆ vmult()