Class FEMechanicsBase provides core finite element mechanics functionality and data management. More...

#include <ibamr/FEMechanicsBase.h>

Inheritance diagram for IBAMR::FEMechanicsBase:

[legend]

Classes
struct	CoordinateMappingFcnData

struct	InitialVelocityFcnData

struct	LagBodyForceFcnData

struct	LagSurfaceForceFcnData

struct	LagSurfacePressureFcnData

struct	PK1StressFcnData

Public Types
using	CoordinateMappingFcnPtr = void()(libMesh::Point &x, const libMesh::Point &X, void ctx)

using	InitialVelocityFcnPtr = void()(libMesh::VectorValue< double > &U0, const libMesh::Point &X0, void ctx)

using	PK1StressFcnPtr = IBTK::TensorMeshFcnPtr

using	LagBodyForceFcnPtr = IBTK::VectorMeshFcnPtr

using	LagSurfacePressureFcnPtr = IBTK::ScalarSurfaceFcnPtr

using	LagSurfaceForceFcnPtr = IBTK::VectorSurfaceFcnPtr

using	VolumetricEnergyDerivativeFcn = double(*)(double)

Public Member Functions
	FEMechanicsBase (const std::string &object_name, const SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > &input_db, libMesh::MeshBase *mesh, bool register_for_restart=true, const std::string &restart_read_dirname="", unsigned int restart_restore_number=0)

	FEMechanicsBase (const std::string &object_name, const SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > &input_db, const std::vector< libMesh::MeshBase * > &meshes, bool register_for_restart=true, const std::string &restart_read_dirname="", unsigned int restart_restore_number=0)

	FEMechanicsBase ()=delete

	FEMechanicsBase (const FEMechanicsBase &from)=delete

FEMechanicsBase &	operator= (const FEMechanicsBase &that)=delete

virtual	~FEMechanicsBase () override

libMesh::EquationSystems *	getEquationSystems (unsigned int part=0) const

const std::string &	getCurrentCoordinatesSystemName () const

const std::string &	getDisplacementSystemName () const

const std::string &	getForceSystemName () const

const std::string &	getPressureSystemName () const

const std::string &	getVelocitySystemName () const

std::shared_ptr< IBTK::FEData >	getFEData (unsigned int part=0) const

virtual void	registerInitialCoordinateMappingFunction (const CoordinateMappingFcnData &data, unsigned int part=0)

CoordinateMappingFcnData	getInitialCoordinateMappingFunction (unsigned int part=0) const

virtual void	registerInitialVelocityFunction (const InitialVelocityFcnData &data, unsigned int part=0)

InitialVelocityFcnData	getInitialVelocityFunction (unsigned int part=0) const

virtual void	registerPK1StressFunction (const PK1StressFcnData &data, unsigned int part=0)

std::vector< PK1StressFcnData >	getPK1StressFunction (unsigned int part=0) const

virtual void	registerLagBodyForceFunction (const LagBodyForceFcnData &data, unsigned int part=0)

LagBodyForceFcnData	getLagBodyForceFunction (unsigned int part=0) const

virtual void	registerLagSurfacePressureFunction (const LagSurfacePressureFcnData &data, unsigned int part=0)

LagSurfacePressureFcnData	getLagSurfacePressureFunction (unsigned int part=0) const

virtual void	registerLagSurfaceForceFunction (const LagSurfaceForceFcnData &data, unsigned int part=0)

LagSurfaceForceFcnData	getLagSurfaceForceFunction (unsigned int part=0) const

virtual void	registerStaticPressurePart (PressureProjectionType projection_type=CONSISTENT_PROJECTION, VolumetricEnergyDerivativeFcn dU_dJ_fcn=nullptr, unsigned int part=0)

virtual void	registerDynamicPressurePart (PressureProjectionType projection_type=CONSISTENT_PROJECTION, VolumetricEnergyDerivativeFcn d2U_dJ2_fcn=nullptr, unsigned int part=0)

bool	partHasPressure (unsigned int part=0)

virtual void	preprocessIntegrateData (double current_time, double new_time, int num_cycles)

virtual void	postprocessIntegrateData (double current_time, double new_time, int num_cycles)

virtual void	initializeFEEquationSystems ()

virtual void	initializeFEData ()

virtual void	reinitializeFEData ()

virtual void	putToDatabase (SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db) override

virtual void	writeFEDataToRestartFile (const std::string &restart_dump_dirname, unsigned int time_step_number)

Static Public Attributes
static const std::string	COORDS_SYSTEM_NAME

static const std::string	COORD_MAPPING_SYSTEM_NAME

static const std::string	FORCE_SYSTEM_NAME

static const std::string	PRESSURE_SYSTEM_NAME

static const std::string	VELOCITY_SYSTEM_NAME

Protected Member Functions
virtual void	doInitializeFEEquationSystems ()

virtual void	doInitializeFESystemVectors ()

virtual void	doInitializeFEData (bool use_present_data)

void	computeStaticPressure (libMesh::PetscVector< double > &P_vec, libMesh::PetscVector< double > &X_vec, double data_time, unsigned int part)
	Compute the static pressure field. More...

void	computeDynamicPressureRateOfChange (libMesh::PetscVector< double > &dP_dt_vec, libMesh::PetscVector< double > &X_vec, libMesh::PetscVector< double > &U_vec, double data_time, unsigned int part)
	Compute the dynamic pressure time rate of change. More...

virtual void	assembleInteriorForceDensityRHS (libMesh::PetscVector< double > &F_rhs_vec, libMesh::PetscVector< double > &X_vec, libMesh::PetscVector< double > *P_vec, double data_time, unsigned int part)

virtual void	initializeCoordinates (unsigned int part)

virtual void	updateCoordinateMapping (unsigned int part)

virtual void	initializeVelocity (unsigned int part)

virtual std::string	getLibMeshRestartFileName (const std::string &restart_dump_dirname, unsigned int time_step_number, unsigned int part, const std::string &extension) const

Static Protected Member Functions
static void	setup_system_vectors (libMesh::EquationSystems *equation_systems, const std::vector< std::string > &system_names, const std::vector< std::string > &vector_names)

static void	setup_system_vector (libMesh::System &system, const std::string &vector_name)

Protected Attributes
SAMRAI::tbox::Pointer< SAMRAI::tbox::Database >	d_fe_projector_db

bool	d_do_log = false

double	d_current_time = std::numeric_limits<double>::quiet_NaN()

double	d_new_time = std::numeric_limits<double>::quiet_NaN()

double	d_half_time = std::numeric_limits<double>::quiet_NaN()

std::vector< libMesh::MeshBase * >	d_meshes

libMesh::CouplingMatrix	d_diagonal_system_coupling

std::vector< std::unique_ptr< libMesh::EquationSystems > >	d_equation_systems

const std::string	d_current_coordinates_system_name
	System names for key variables. More...

const std::string	d_displacement_system_name

const std::string	d_force_system_name

const std::string	d_pressure_system_name

const std::string	d_velocity_system_name

std::vector< std::shared_ptr< IBTK::FEData > >	d_fe_data
	FEData objects provide key FE data management. More...

std::vector< std::shared_ptr< IBTK::FEProjector > >	d_fe_projectors
	FEProjector objects provide L2 projection functionality. More...

std::vector< libMesh::ExplicitSystem * >	d_X_systems

std::vector< libMesh::ExplicitSystem * >	d_U_systems

std::vector< libMesh::ExplicitSystem * >	d_F_systems

std::vector< libMesh::ExplicitSystem * >	d_P_systems

std::unique_ptr< IBTK::LibMeshSystemVectors >	d_X_vecs

std::unique_ptr< IBTK::LibMeshSystemVectors >	d_U_vecs

std::unique_ptr< IBTK::LibMeshSystemVectors >	d_F_vecs

std::unique_ptr< IBTK::LibMeshSystemVectors >	d_P_vecs

bool	d_fe_equation_systems_initialized = false

bool	d_fe_data_initialized = false

LibmeshPartitionerType	d_libmesh_partitioner_type = LIBMESH_DEFAULT

bool	d_libmesh_use_amr = false

std::vector< libMesh::Order >	d_fe_order_position

std::vector< libMesh::Order >	d_fe_order_force

std::vector< libMesh::Order >	d_fe_order_pressure

std::vector< libMesh::FEFamily >	d_fe_family_position

std::vector< libMesh::FEFamily >	d_fe_family_force

std::vector< libMesh::FEFamily >	d_fe_family_pressure

std::vector< libMesh::QuadratureType >	d_default_quad_type_stress

std::vector< libMesh::QuadratureType >	d_default_quad_type_force

std::vector< libMesh::QuadratureType >	d_default_quad_type_pressure

std::vector< libMesh::Order >	d_default_quad_order_stress

std::vector< libMesh::Order >	d_default_quad_order_force

std::vector< libMesh::Order >	d_default_quad_order_pressure

bool	d_use_consistent_mass_matrix = true

bool	d_allow_rules_with_negative_weights = true

bool	d_include_normal_stress_in_weak_form = false

bool	d_include_tangential_stress_in_weak_form = false

bool	d_include_normal_surface_forces_in_weak_form = true

bool	d_include_tangential_surface_forces_in_weak_form = true

std::vector< CoordinateMappingFcnData >	d_coordinate_mapping_fcn_data

std::vector< InitialVelocityFcnData >	d_initial_velocity_fcn_data

std::vector< std::vector< PK1StressFcnData > >	d_PK1_stress_fcn_data

std::vector< LagBodyForceFcnData >	d_lag_body_force_fcn_data

std::vector< LagSurfacePressureFcnData >	d_lag_surface_pressure_fcn_data

std::vector< LagSurfaceForceFcnData >	d_lag_surface_force_fcn_data

double	d_static_pressure_kappa = 0.0

double	d_static_pressure_stab_param = 0.0

bool	d_has_static_pressure_parts = false

std::vector< bool >	d_static_pressure_part

std::vector< PressureProjectionType >	d_static_pressure_proj_type

std::vector< VolumetricEnergyDerivativeFcn >	d_static_pressure_dU_dJ_fcn

double	d_dynamic_pressure_kappa = 0.0

double	d_dynamic_pressure_stab_param = 0.0

bool	d_has_dynamic_pressure_parts = false

std::vector< bool >	d_dynamic_pressure_part

std::vector< PressureProjectionType >	d_dynamic_pressure_proj_type

std::vector< VolumetricEnergyDerivativeFcn >	d_dynamic_pressure_d2U_dJ2_fcn

std::string	d_object_name

bool	d_registered_for_restart

std::string	d_libmesh_restart_read_dir

unsigned int	d_libmesh_restart_restore_number

std::string	d_libmesh_restart_file_extension

Private Member Functions
void	commonConstructor (const std::string &object_name, const SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > &input_db, const std::vector< libMesh::MeshBase * > &meshes, bool register_for_restart, const std::string &restart_read_dirname, unsigned int restart_restore_number)

void	getFromInput (const SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > &db, bool is_from_restart)

void	getFromRestart ()

Detailed Description

Parameters read from the input database

FEProjector: Input database passed along to the object responsible for computing projections onto the finite element space. See the documentation of IBTK::FEProjector for more information.

Member Typedef Documentation

◆ CoordinateMappingFcnPtr

using IBAMR::FEMechanicsBase::CoordinateMappingFcnPtr = void (*)(libMesh::Point& x, const libMesh::Point& X, void* ctx)

Typedef specifying interface for coordinate mapping function.

◆ InitialVelocityFcnPtr

using IBAMR::FEMechanicsBase::InitialVelocityFcnPtr = void (*)(libMesh::VectorValue<double>& U0, const libMesh::Point& X0, void* ctx)

Typedef specifying interface for initial velocity specification function.

◆ PK1StressFcnPtr

using IBAMR::FEMechanicsBase::PK1StressFcnPtr = IBTK::TensorMeshFcnPtr

Typedef specifying interface for PK1 stress tensor function.

◆ LagBodyForceFcnPtr

using IBAMR::FEMechanicsBase::LagBodyForceFcnPtr = IBTK::VectorMeshFcnPtr

Typedef specifying interface for Lagrangian body force distribution function.

◆ LagSurfacePressureFcnPtr

using IBAMR::FEMechanicsBase::LagSurfacePressureFcnPtr = IBTK::ScalarSurfaceFcnPtr

Typedef specifying interface for Lagrangian pressure force distribution function.

◆ LagSurfaceForceFcnPtr

using IBAMR::FEMechanicsBase::LagSurfaceForceFcnPtr = IBTK::VectorSurfaceFcnPtr

Typedef specifying interface for Lagrangian surface force distribution function.

◆ VolumetricEnergyDerivativeFcn

using IBAMR::FEMechanicsBase::VolumetricEnergyDerivativeFcn = double (*)(double)

Function signature for specifying the energy functional that determines the pressure.

Constructor & Destructor Documentation

◆ FEMechanicsBase() [1/4]

IBAMR::FEMechanicsBase::FEMechanicsBase	(	const std::string &	object_name,
		const SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > &	input_db,
		libMesh::MeshBase *	mesh,
		bool	register_for_restart = `true`,
		const std::string &	restart_read_dirname = `""`,
		unsigned int	restart_restore_number = `0`
	)

Constructor for a single-part model.

◆ FEMechanicsBase() [2/4]

IBAMR::FEMechanicsBase::FEMechanicsBase	(	const std::string &	object_name,
		const SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > &	input_db,
		const std::vector< libMesh::MeshBase * > &	meshes,
		bool	register_for_restart = `true`,
		const std::string &	restart_read_dirname = `""`,
		unsigned int	restart_restore_number = `0`
	)

Constructor for a multi-part model.

◆ FEMechanicsBase() [3/4]

IBAMR::FEMechanicsBase::FEMechanicsBase ( )

delete

Deleted default constructor.

◆ FEMechanicsBase() [4/4]

IBAMR::FEMechanicsBase::FEMechanicsBase ( const FEMechanicsBase & from )

delete

Deleted copy constructor.

◆ ~FEMechanicsBase()

virtual IBAMR::FEMechanicsBase::~FEMechanicsBase ( )

overridevirtual

Destructor.

Member Function Documentation

◆ operator=()

FEMechanicsBase& IBAMR::FEMechanicsBase::operator= ( const FEMechanicsBase & that )

delete

Deleted assignment operator.

◆ getEquationSystems()

libMesh::EquationSystems* IBAMR::FEMechanicsBase::getEquationSystems ( unsigned int part = 0 ) const

Return a pointer to the equations system object for the specified part.

◆ getCurrentCoordinatesSystemName()

const std::string& IBAMR::FEMechanicsBase::getCurrentCoordinatesSystemName ( ) const

inline

Return the current coordinates system name.

◆ getDisplacementSystemName()

const std::string& IBAMR::FEMechanicsBase::getDisplacementSystemName ( ) const

inline

Return the displacement system name.

◆ getForceSystemName()

const std::string& IBAMR::FEMechanicsBase::getForceSystemName ( ) const

inline

Return the force system name.

◆ getPressureSystemName()

const std::string& IBAMR::FEMechanicsBase::getPressureSystemName ( ) const

inline

Return the pressure system name.

◆ getVelocitySystemName()

const std::string& IBAMR::FEMechanicsBase::getVelocitySystemName ( ) const

inline

Return the velocity system name.

◆ getFEData()

std::shared_ptr<IBTK::FEData> IBAMR::FEMechanicsBase::getFEData ( unsigned int part = 0 ) const

Return a pointer to the FEData object for the specified part.

◆ registerInitialCoordinateMappingFunction()

virtual void IBAMR::FEMechanicsBase::registerInitialCoordinateMappingFunction	(	const CoordinateMappingFcnData &	data,
		unsigned int	part = `0`
	)

virtual

Register the (optional) function used to initialize the physical coordinates from the Lagrangian coordinates.

Note: If no function is provided, the initial physical coordinates are taken to be the same as the Lagrangian coordinate system, i.e., the initial coordinate mapping is assumed to be the identity mapping.

◆ getInitialCoordinateMappingFunction()

CoordinateMappingFcnData IBAMR::FEMechanicsBase::getInitialCoordinateMappingFunction ( unsigned int part = 0 ) const

Get the initial coordinate mapping function data.

◆ registerInitialVelocityFunction()

virtual void IBAMR::FEMechanicsBase::registerInitialVelocityFunction	(	const InitialVelocityFcnData &	data,
		unsigned int	part = `0`
	)

virtual

Register the (optional) function used to initialize the velocity of the solid mesh.

Note: If no function is provided, the initial velocity is taken to be zero.

◆ getInitialVelocityFunction()

InitialVelocityFcnData IBAMR::FEMechanicsBase::getInitialVelocityFunction ( unsigned int part = 0 ) const

Get the initial velocity function data.

◆ registerPK1StressFunction()

virtual void IBAMR::FEMechanicsBase::registerPK1StressFunction	(	const PK1StressFcnData &	data,
		unsigned int	part = `0`
	)

virtual

Register the (optional) function to compute the first Piola-Kirchhoff stress tensor, used to compute the forces on the Lagrangian finite element mesh.

Note: It is possible to register multiple PK1 stress functions with this class. This is intended to be used to implement selective reduced integration.

◆ getPK1StressFunction()

std::vector<PK1StressFcnData> IBAMR::FEMechanicsBase::getPK1StressFunction ( unsigned int part = 0 ) const

Get the PK1 stress function data.

◆ registerLagBodyForceFunction()

virtual void IBAMR::FEMechanicsBase::registerLagBodyForceFunction	(	const LagBodyForceFcnData &	data,
		unsigned int	part = `0`
	)

virtual

Register the (optional) function to compute body force distributions on the Lagrangian finite element mesh.

Note: It is NOT possible to register multiple body force functions with this class.

◆ getLagBodyForceFunction()

LagBodyForceFcnData IBAMR::FEMechanicsBase::getLagBodyForceFunction ( unsigned int part = 0 ) const

Get the Lagrangian body force function data.

◆ registerLagSurfacePressureFunction()

virtual void IBAMR::FEMechanicsBase::registerLagSurfacePressureFunction	(	const LagSurfacePressureFcnData &	data,
		unsigned int	part = `0`
	)

virtual

Register the (optional) function to compute surface pressure distributions on the Lagrangian finite element mesh.

Note: It is NOT possible to register multiple pressure functions with this class.

◆ getLagSurfacePressureFunction()

LagSurfacePressureFcnData IBAMR::FEMechanicsBase::getLagSurfacePressureFunction ( unsigned int part = 0 ) const

Get the Lagrangian surface pressure function data.

◆ registerLagSurfaceForceFunction()

virtual void IBAMR::FEMechanicsBase::registerLagSurfaceForceFunction	(	const LagSurfaceForceFcnData &	data,
		unsigned int	part = `0`
	)

virtual

Register the (optional) function to compute surface force distributions on the Lagrangian finite element mesh.

Note: It is NOT possible to register multiple surface force functions with this class.

◆ getLagSurfaceForceFunction()

LagSurfaceForceFcnData IBAMR::FEMechanicsBase::getLagSurfaceForceFunction ( unsigned int part = 0 ) const

Get the Lagrangian surface force function data.

◆ registerStaticPressurePart()

virtual void IBAMR::FEMechanicsBase::registerStaticPressurePart	(	PressureProjectionType	projection_type = `CONSISTENT_PROJECTION`,
		VolumetricEnergyDerivativeFcn	dU_dJ_fcn = `nullptr`,
		unsigned int	part = `0`
	)

virtual

Indicate that a part should include a static pressure.

The pressure is determined via (P, Q) = (U'(J), Q), using either a consistent or lumped mass matrix, or via a locally stabilized projection of the form (P, Q) + epsilon (P - Pi P, Q - Pi Q) = (U'(J), Q), in which P is the pressure and Q is an arbitrary test function.

Users can provide a function to evaluate U'(J). If no function is provided, we default to using U(J) = -kappa (J ln(J) − J + 1), so that U'(J) = -kappa ln J. (Ref: C.H. Liu, G. Hofstetter, H.A. Mang, 3D finite element analysis of rubber-like materials at finite strains, Eng. Comput. 11 (2) (1994) 111–128.)

The sign convention used in the implementation generates a PK1 stress of the form PP = -J P FF^{-T}.

Note: The same part cannot have both static and dynamic pressures.

See also: registerDynamicPressurePart

Reimplemented in IBAMR::IBFEMethod.

◆ registerDynamicPressurePart()

virtual void IBAMR::FEMechanicsBase::registerDynamicPressurePart	(	PressureProjectionType	projection_type = `CONSISTENT_PROJECTION`,
		VolumetricEnergyDerivativeFcn	d2U_dJ2_fcn = `nullptr`,
		unsigned int	part = `0`
	)

virtual

Indicate that a part should include a dynamic pressure.

The pressure is determined via (P-dot, Q) = (J U''(J) (FF : Grad U), Q), using either a consistent or lumped mass matrix, or via a locally stabilized projection of the form (P, Q) + epsilon (P - Pi P, Q - Pi Q) = (U'(J), Q), in which P is the pressure and Q is an arbitrary test function.

Users can provide a function to evaluate U''(J). If no function is provided, we default to using U(J) = -kappa (J ln(J) − J + 1), so that U'(J) = -kappa ln J and U''(J) = -kappa J^{-1}. (Ref: C.H. Liu, G. Hofstetter, H.A. Mang, 3D finite element analysis of rubber-like materials at finite strains, Eng. Comput. 11 (2) (1994) 111–128.)

The sign convention used in the implementation generates a PK1 stress of the form PP = -J P FF^{-T}.

Note: The same part cannot have both static and dynamic pressures.

See also: registerStaticPressurePart

◆ partHasPressure()

bool IBAMR::FEMechanicsBase::partHasPressure ( unsigned int part = 0 )

inline

Indicate whether there is a static or dynamic pressure associated with the specified FE mesh part.

◆ preprocessIntegrateData()

virtual void IBAMR::FEMechanicsBase::preprocessIntegrateData	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

virtual

Method to prepare to advance data from current_time to new_time.

Reimplemented in IBAMR::IBFEMethod, and IBAMR::FEMechanicsExplicitIntegrator.

◆ postprocessIntegrateData()

virtual void IBAMR::FEMechanicsBase::postprocessIntegrateData	(	double	current_time,
		double	new_time,
		int	num_cycles
	)

virtual

Method to clean up data following call(s) to integrateHierarchy().

Reimplemented in IBAMR::IBFEMethod, and IBAMR::FEMechanicsExplicitIntegrator.

◆ initializeFEEquationSystems()

virtual void IBAMR::FEMechanicsBase::initializeFEEquationSystems ( )

virtual

Initialize the FE equation systems objects. This method must be called prior to calling initializeFEData().

◆ initializeFEData()

virtual void IBAMR::FEMechanicsBase::initializeFEData ( )

virtual

Initialize FE data. This method must be called prior to calling IBHierarchyIntegrator::initializePatchHierarchy().

◆ reinitializeFEData()

virtual void IBAMR::FEMechanicsBase::reinitializeFEData ( )

virtual

Reinitialize FE data by calling reinit on each part's EquationSystem, reassembling the system matrices, and setting boundary conditions.

◆ putToDatabase()

virtual void IBAMR::FEMechanicsBase::putToDatabase ( SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > db )

overridevirtual

Write out object state to the given database.

Implements SAMRAI::tbox::Serializable.

Reimplemented in IBAMR::IBFEMethod, and IBAMR::FEMechanicsExplicitIntegrator.

◆ writeFEDataToRestartFile()

virtual void IBAMR::FEMechanicsBase::writeFEDataToRestartFile	(	const std::string &	restart_dump_dirname,
		unsigned int	time_step_number
	)

virtual

For technical reasons this class does not use SAMRAI's RestartManager, so restart files must be separately written for the FE objects. This function saves the solutions to the defined EquationSystems in an xdr file in restart_dump_dirname for each FE part. An example snippet is included below to show the distinct FE restart data saving step. The data will then be automatically read back into the system along with the RestartManager data during restart.

if (dump_restart_data && (iteration_num % restart_dump_interval == 0 || last_step))
{
    RestartManager::getManager()->writeRestartFile(restart_dump_dirname, iteration_num);
    fe_mechanics_base->writeFEDataToRestartFile(restart_dump_dirname, iteration_num);
}

◆ doInitializeFEEquationSystems()

virtual void IBAMR::FEMechanicsBase::doInitializeFEEquationSystems ( )

protectedvirtual

Do the actual work in initializeFEEquationSystems.

Reimplemented in IBAMR::IBFEMethod, and IBAMR::FEMechanicsExplicitIntegrator.

◆ doInitializeFESystemVectors()

virtual void IBAMR::FEMechanicsBase::doInitializeFESystemVectors ( )

protectedvirtual

Do the actual work of setting up libMesh system vectors.

Reimplemented in IBAMR::IBFEMethod, and IBAMR::FEMechanicsExplicitIntegrator.

◆ doInitializeFEData()

virtual void IBAMR::FEMechanicsBase::doInitializeFEData ( bool use_present_data )

protectedvirtual

Do the actual work in reinitializeFEData and initializeFEData. if use_present_data is true then the current content of the solution vectors is used: more exactly, the coordinates and velocities (computed by initializeCoordinates and initializeVelocity) are considered as being up to date.

Reimplemented in IBAMR::IBFEMethod, and IBAMR::FEMechanicsExplicitIntegrator.

◆ computeStaticPressure()

void IBAMR::FEMechanicsBase::computeStaticPressure	(	libMesh::PetscVector< double > &	P_vec,
		libMesh::PetscVector< double > &	X_vec,
		double	data_time,
		unsigned int	part
	)

protected

◆ computeDynamicPressureRateOfChange()

void IBAMR::FEMechanicsBase::computeDynamicPressureRateOfChange	(	libMesh::PetscVector< double > &	dP_dt_vec,
		libMesh::PetscVector< double > &	X_vec,
		libMesh::PetscVector< double > &	U_vec,
		double	data_time,
		unsigned int	part
	)

protected

◆ assembleInteriorForceDensityRHS()

virtual void IBAMR::FEMechanicsBase::assembleInteriorForceDensityRHS	(	libMesh::PetscVector< double > &	F_rhs_vec,
		libMesh::PetscVector< double > &	X_vec,
		libMesh::PetscVector< double > *	P_vec,
		double	data_time,
		unsigned int	part
	)

protectedvirtual

Assemble the RHS for the interior elastic density, possibly splitting off the normal component of the transmission force along the physical boundary of the Lagrangian structure.

◆ initializeCoordinates()

virtual void IBAMR::FEMechanicsBase::initializeCoordinates ( unsigned int part )

protectedvirtual

Initialize the physical coordinates using the supplied coordinate mapping function. If no function is provided, the initial coordinates are taken to be the Lagrangian coordinates.

◆ updateCoordinateMapping()

virtual void IBAMR::FEMechanicsBase::updateCoordinateMapping ( unsigned int part )

protectedvirtual

Compute dX = x - X, useful mainly for visualization purposes.

◆ initializeVelocity()

virtual void IBAMR::FEMechanicsBase::initializeVelocity ( unsigned int part )

protectedvirtual

Initialize the velocity field using the supplied initial velocity specification function. If no function is provided, the initial velocity is taken to be zero.

◆ getLibMeshRestartFileName()

virtual std::string IBAMR::FEMechanicsBase::getLibMeshRestartFileName	(	const std::string &	restart_dump_dirname,
		unsigned int	time_step_number,
		unsigned int	part,
		const std::string &	extension
	)		const

protectedvirtual

Get the libMesh restart file name.

◆ setup_system_vectors()

static void IBAMR::FEMechanicsBase::setup_system_vectors	(	libMesh::EquationSystems *	equation_systems,
		const std::vector< std::string > &	system_names,
		const std::vector< std::string > &	vector_names
	)

staticprotected

Convenience function to setup system vectors and, if necessary, convert PARALLEL vectors into GHOSTED vectors for a collection of Systems.

Deprecated:: use IBTK::setup_system_vectors instead.

◆ setup_system_vector()

static void IBAMR::FEMechanicsBase::setup_system_vector	(	libMesh::System &	system,
		const std::string &	vector_name
	)

staticprotected

Convenience function to setup a system vector and, if necessary, convert a PARALLEL vector into a GHOSTED vector.

Deprecated:: use IBTK::setup_system_vector instead.

◆ commonConstructor()

void IBAMR::FEMechanicsBase::commonConstructor	(	const std::string &	object_name,
		const SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > &	input_db,
		const std::vector< libMesh::MeshBase * > &	meshes,
		bool	register_for_restart,
		const std::string &	restart_read_dirname,
		unsigned int	restart_restore_number
	)

private

Implementation of class constructor.

◆ getFromInput()

void IBAMR::FEMechanicsBase::getFromInput	(	const SAMRAI::tbox::Pointer< SAMRAI::tbox::Database > &	db,
		bool	is_from_restart
	)

private

Read input values from a given database.

◆ getFromRestart()

void IBAMR::FEMechanicsBase::getFromRestart ( )

private

Read object state from the restart file and initialize class data members.

Member Data Documentation

◆ COORDS_SYSTEM_NAME

const std::string IBAMR::FEMechanicsBase::COORDS_SYSTEM_NAME

static

◆ COORD_MAPPING_SYSTEM_NAME

const std::string IBAMR::FEMechanicsBase::COORD_MAPPING_SYSTEM_NAME

static

◆ FORCE_SYSTEM_NAME

const std::string IBAMR::FEMechanicsBase::FORCE_SYSTEM_NAME

static

◆ PRESSURE_SYSTEM_NAME

const std::string IBAMR::FEMechanicsBase::PRESSURE_SYSTEM_NAME

static

◆ VELOCITY_SYSTEM_NAME

const std::string IBAMR::FEMechanicsBase::VELOCITY_SYSTEM_NAME

static

◆ d_fe_projector_db

SAMRAI::tbox::Pointer<SAMRAI::tbox::Database> IBAMR::FEMechanicsBase::d_fe_projector_db

protected

Cached input databases.

◆ d_do_log

bool IBAMR::FEMechanicsBase::d_do_log = false

protected

Indicates whether the integrator should output logging messages.

◆ d_current_time

double IBAMR::FEMechanicsBase::d_current_time = std::numeric_limits<double>::quiet_NaN()

protected

◆ d_new_time

double IBAMR::FEMechanicsBase::d_new_time = std::numeric_limits<double>::quiet_NaN()

protected

◆ d_half_time

double IBAMR::FEMechanicsBase::d_half_time = std::numeric_limits<double>::quiet_NaN()

protected

◆ d_meshes

std::vector<libMesh::MeshBase*> IBAMR::FEMechanicsBase::d_meshes

protected

Meshes provided to this object. These are set up and managed outside this class. These meshes are modified by FEMechanicsBase since this class creates several libMesh Systems (and hence stores DoF information in these meshes).

◆ d_diagonal_system_coupling

libMesh::CouplingMatrix IBAMR::FEMechanicsBase::d_diagonal_system_coupling

protected

The libMesh Systems set up by this system (for example, for velocity projection) consist of one variable per spatial component. By default, libMesh assumes that all variables in a given System couple to each other which, since we only ever solve projection problems in this class, is not the case. Hence we can save some memory by explicitly informing libMesh that the variables in a system only couple to themselves by providing a diagonal coupling matrix to each System.

◆ d_equation_systems

std::vector<std::unique_ptr<libMesh::EquationSystems> > IBAMR::FEMechanicsBase::d_equation_systems

protected

EquationSystems objects, one per part. These contain the actual matrices and solution vectors for each relevant libMesh system.

◆ d_current_coordinates_system_name

const std::string IBAMR::FEMechanicsBase::d_current_coordinates_system_name

protected

◆ d_displacement_system_name

const std::string IBAMR::FEMechanicsBase::d_displacement_system_name

protected

◆ d_force_system_name

const std::string IBAMR::FEMechanicsBase::d_force_system_name

protected

◆ d_pressure_system_name

const std::string IBAMR::FEMechanicsBase::d_pressure_system_name

protected

◆ d_velocity_system_name

const std::string IBAMR::FEMechanicsBase::d_velocity_system_name

protected

◆ d_fe_data

std::vector<std::shared_ptr<IBTK::FEData> > IBAMR::FEMechanicsBase::d_fe_data

protected

◆ d_fe_projectors

std::vector<std::shared_ptr<IBTK::FEProjector> > IBAMR::FEMechanicsBase::d_fe_projectors

protected

◆ d_X_systems

std::vector<libMesh::ExplicitSystem*> IBAMR::FEMechanicsBase::d_X_systems

protected

Vectors of pointers to the systems for each part (for position, velocity, force, and pressure).

◆ d_U_systems

std::vector<libMesh::ExplicitSystem*> IBAMR::FEMechanicsBase::d_U_systems

protected

◆ d_F_systems

std::vector<libMesh::ExplicitSystem*> IBAMR::FEMechanicsBase::d_F_systems

protected

◆ d_P_systems

std::vector<libMesh::ExplicitSystem*> IBAMR::FEMechanicsBase::d_P_systems

protected

◆ d_X_vecs

std::unique_ptr<IBTK::LibMeshSystemVectors> IBAMR::FEMechanicsBase::d_X_vecs

protected

Object managing access to libMesh system vectors for the position.

◆ d_U_vecs

std::unique_ptr<IBTK::LibMeshSystemVectors> IBAMR::FEMechanicsBase::d_U_vecs

protected

Object managing access to libMesh system vectors for the velocity.

◆ d_F_vecs

std::unique_ptr<IBTK::LibMeshSystemVectors> IBAMR::FEMechanicsBase::d_F_vecs

protected

Object managing access to libMesh system vectors for the force.

◆ d_P_vecs

std::unique_ptr<IBTK::LibMeshSystemVectors> IBAMR::FEMechanicsBase::d_P_vecs

protected

Object managing access to libMesh system vectors for the pressure.

◆ d_fe_equation_systems_initialized

bool IBAMR::FEMechanicsBase::d_fe_equation_systems_initialized = false

protected

Whether or not the libMesh equation systems objects have been initialized (i.e., whether or not initializeFEEquationSystems has been called).

◆ d_fe_data_initialized

bool IBAMR::FEMechanicsBase::d_fe_data_initialized = false

protected

Whether or not all finite element data (including that initialized by initializeFEEquationSystems), such system matrices, is available.

◆ d_libmesh_partitioner_type

LibmeshPartitionerType IBAMR::FEMechanicsBase::d_libmesh_partitioner_type = LIBMESH_DEFAULT

protected

Type of partitioner to use. See the main documentation of this class for more information.

◆ d_libmesh_use_amr

bool IBAMR::FEMechanicsBase::d_libmesh_use_amr = false

protected

Whether or not to use AMR in the finite element discretization. This feature is not yet implemented and currently defaults to false.

◆ d_fe_order_position

std::vector<libMesh::Order> IBAMR::FEMechanicsBase::d_fe_order_position

protected

Method parameters.

◆ d_fe_order_force

std::vector<libMesh::Order> IBAMR::FEMechanicsBase::d_fe_order_force

protected

◆ d_fe_order_pressure

std::vector<libMesh::Order> IBAMR::FEMechanicsBase::d_fe_order_pressure

protected

◆ d_fe_family_position

std::vector<libMesh::FEFamily> IBAMR::FEMechanicsBase::d_fe_family_position

protected

◆ d_fe_family_force

std::vector<libMesh::FEFamily> IBAMR::FEMechanicsBase::d_fe_family_force

protected

◆ d_fe_family_pressure

std::vector<libMesh::FEFamily> IBAMR::FEMechanicsBase::d_fe_family_pressure

protected

◆ d_default_quad_type_stress

std::vector<libMesh::QuadratureType> IBAMR::FEMechanicsBase::d_default_quad_type_stress

protected

◆ d_default_quad_type_force

std::vector<libMesh::QuadratureType> IBAMR::FEMechanicsBase::d_default_quad_type_force

protected

◆ d_default_quad_type_pressure

std::vector<libMesh::QuadratureType> IBAMR::FEMechanicsBase::d_default_quad_type_pressure

protected

◆ d_default_quad_order_stress

std::vector<libMesh::Order> IBAMR::FEMechanicsBase::d_default_quad_order_stress

protected

◆ d_default_quad_order_force

std::vector<libMesh::Order> IBAMR::FEMechanicsBase::d_default_quad_order_force

protected

◆ d_default_quad_order_pressure

std::vector<libMesh::Order> IBAMR::FEMechanicsBase::d_default_quad_order_pressure

protected

◆ d_use_consistent_mass_matrix

bool IBAMR::FEMechanicsBase::d_use_consistent_mass_matrix = true

protected

◆ d_allow_rules_with_negative_weights

bool IBAMR::FEMechanicsBase::d_allow_rules_with_negative_weights = true

protected

◆ d_include_normal_stress_in_weak_form

bool IBAMR::FEMechanicsBase::d_include_normal_stress_in_weak_form = false

protected

◆ d_include_tangential_stress_in_weak_form

bool IBAMR::FEMechanicsBase::d_include_tangential_stress_in_weak_form = false

protected

◆ d_include_normal_surface_forces_in_weak_form

bool IBAMR::FEMechanicsBase::d_include_normal_surface_forces_in_weak_form = true

protected

◆ d_include_tangential_surface_forces_in_weak_form

bool IBAMR::FEMechanicsBase::d_include_tangential_surface_forces_in_weak_form = true

protected

◆ d_coordinate_mapping_fcn_data

std::vector<CoordinateMappingFcnData> IBAMR::FEMechanicsBase::d_coordinate_mapping_fcn_data

protected

Functions used to compute the initial coordinates of the Lagrangian mesh.

◆ d_initial_velocity_fcn_data

std::vector<InitialVelocityFcnData> IBAMR::FEMechanicsBase::d_initial_velocity_fcn_data

protected

Functions used to compute the initial coordinates of the Lagrangian mesh.

◆ d_PK1_stress_fcn_data

std::vector<std::vector<PK1StressFcnData> > IBAMR::FEMechanicsBase::d_PK1_stress_fcn_data

protected

Functions used to compute the first Piola-Kirchhoff stress tensor.

◆ d_lag_body_force_fcn_data

std::vector<LagBodyForceFcnData> IBAMR::FEMechanicsBase::d_lag_body_force_fcn_data

protected

Functions used to compute additional body and surface forces on the Lagrangian mesh.

◆ d_lag_surface_pressure_fcn_data

std::vector<LagSurfacePressureFcnData> IBAMR::FEMechanicsBase::d_lag_surface_pressure_fcn_data

protected

◆ d_lag_surface_force_fcn_data

std::vector<LagSurfaceForceFcnData> IBAMR::FEMechanicsBase::d_lag_surface_force_fcn_data

protected

◆ d_static_pressure_kappa

double IBAMR::FEMechanicsBase::d_static_pressure_kappa = 0.0

protected

Data related to handling static pressures.

◆ d_static_pressure_stab_param

double IBAMR::FEMechanicsBase::d_static_pressure_stab_param = 0.0

protected

◆ d_has_static_pressure_parts

bool IBAMR::FEMechanicsBase::d_has_static_pressure_parts = false

protected

◆ d_static_pressure_part

std::vector<bool> IBAMR::FEMechanicsBase::d_static_pressure_part

protected

◆ d_static_pressure_proj_type

std::vector<PressureProjectionType> IBAMR::FEMechanicsBase::d_static_pressure_proj_type

protected

◆ d_static_pressure_dU_dJ_fcn

std::vector<VolumetricEnergyDerivativeFcn> IBAMR::FEMechanicsBase::d_static_pressure_dU_dJ_fcn

protected

◆ d_dynamic_pressure_kappa

double IBAMR::FEMechanicsBase::d_dynamic_pressure_kappa = 0.0

protected

Data related to handling dynamic pressures.

◆ d_dynamic_pressure_stab_param

double IBAMR::FEMechanicsBase::d_dynamic_pressure_stab_param = 0.0

protected

◆ d_has_dynamic_pressure_parts

bool IBAMR::FEMechanicsBase::d_has_dynamic_pressure_parts = false

protected

◆ d_dynamic_pressure_part

std::vector<bool> IBAMR::FEMechanicsBase::d_dynamic_pressure_part

protected

◆ d_dynamic_pressure_proj_type

std::vector<PressureProjectionType> IBAMR::FEMechanicsBase::d_dynamic_pressure_proj_type

protected

◆ d_dynamic_pressure_d2U_dJ2_fcn

std::vector<VolumetricEnergyDerivativeFcn> IBAMR::FEMechanicsBase::d_dynamic_pressure_d2U_dJ2_fcn

protected

◆ d_object_name

std::string IBAMR::FEMechanicsBase::d_object_name

protected

The object name is used as a handle to databases stored in restart files and for error reporting purposes.

◆ d_registered_for_restart

bool IBAMR::FEMechanicsBase::d_registered_for_restart

protected

A boolean value indicating whether the class is registered with the restart database.

◆ d_libmesh_restart_read_dir

std::string IBAMR::FEMechanicsBase::d_libmesh_restart_read_dir

protected

Directory and time step number to use when restarting.

◆ d_libmesh_restart_restore_number

unsigned int IBAMR::FEMechanicsBase::d_libmesh_restart_restore_number

protected

◆ d_libmesh_restart_file_extension

std::string IBAMR::FEMechanicsBase::d_libmesh_restart_file_extension

protected

Restart file type for libMesh equation systems (e.g. xda or xdr).

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

include/ibamr/FEMechanicsBase.h

Classes

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Parameters read from the input database

Member Typedef Documentation

◆ CoordinateMappingFcnPtr

◆ InitialVelocityFcnPtr

◆ PK1StressFcnPtr

◆ LagBodyForceFcnPtr

◆ LagSurfacePressureFcnPtr

◆ LagSurfaceForceFcnPtr

◆ VolumetricEnergyDerivativeFcn

Constructor & Destructor Documentation

◆ FEMechanicsBase() [1/4]

◆ FEMechanicsBase() [2/4]

◆ FEMechanicsBase() [3/4]

◆ FEMechanicsBase() [4/4]

◆ ~FEMechanicsBase()

Member Function Documentation

◆ operator=()

◆ getEquationSystems()

◆ getCurrentCoordinatesSystemName()

◆ getDisplacementSystemName()

◆ getForceSystemName()

◆ getPressureSystemName()

◆ getVelocitySystemName()

◆ getFEData()

◆ registerInitialCoordinateMappingFunction()

◆ getInitialCoordinateMappingFunction()

◆ registerInitialVelocityFunction()

◆ getInitialVelocityFunction()

◆ registerPK1StressFunction()

◆ getPK1StressFunction()

◆ registerLagBodyForceFunction()

◆ getLagBodyForceFunction()

◆ registerLagSurfacePressureFunction()

◆ getLagSurfacePressureFunction()

◆ registerLagSurfaceForceFunction()

◆ getLagSurfaceForceFunction()

◆ registerStaticPressurePart()

◆ registerDynamicPressurePart()

◆ partHasPressure()

◆ preprocessIntegrateData()

◆ postprocessIntegrateData()

◆ initializeFEEquationSystems()

◆ initializeFEData()

◆ reinitializeFEData()

◆ putToDatabase()

◆ writeFEDataToRestartFile()

◆ doInitializeFEEquationSystems()

◆ doInitializeFESystemVectors()

◆ doInitializeFEData()

◆ computeStaticPressure()

◆ computeDynamicPressureRateOfChange()

◆ assembleInteriorForceDensityRHS()

◆ initializeCoordinates()

◆ updateCoordinateMapping()

◆ initializeVelocity()

◆ getLibMeshRestartFileName()

◆ setup_system_vectors()

◆ setup_system_vector()

◆ commonConstructor()

◆ getFromInput()

◆ getFromRestart()

Member Data Documentation

◆ COORDS_SYSTEM_NAME

◆ COORD_MAPPING_SYSTEM_NAME

◆ FORCE_SYSTEM_NAME

◆ PRESSURE_SYSTEM_NAME

◆ VELOCITY_SYSTEM_NAME

◆ d_fe_projector_db

◆ d_do_log

◆ d_current_time

◆ d_new_time