definition of volume element More...

#include <users_modules/gels/src/Gels.hpp>

Inheritance diagram for GelModule::Gel::GelFE:

Collaboration diagram for GelModule::Gel::GelFE:

Public Member Functions
	GelFE (MoFEM::Interface &m_field, CommonData &common_data)

int	getRule (int order)

PetscErrorCode	preProcess ()
	function is run at the beginning of loop More...

PetscErrorCode	postProcess ()
	function is run at the end of loop More...

Public Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCore
	VolumeElementForcesAndSourcesCore (Interface &m_field, const EntityType type=MBTET)

MoFEMErrorCode	operator() ()
	function is run for every finite element More...

Public Member Functions inherited from MoFEM::ForcesAndSourcesCore
	ForcesAndSourcesCore (Interface &m_field)

boost::ptr_deque< UserDataOperator > &	getOpPtrVector ()
	Use to push back operator for row operator. More...

auto &	getElementPolynomialBase ()
	Get the Entity Polynomial Base object. More...

auto &	getUserPolynomialBase ()
	Get the User Polynomial Base object. More...

int	getMaxDataOrder () const
	Get max order of approximation for data fields. More...

int	getMaxRowOrder () const
	Get max order of approximation for field in rows. More...

int	getMaxColOrder () const
	Get max order of approximation for field in columns. More...

auto &	getEntData (const FieldSpace space, const EntityType type, const int side)
	Get the entity data. More...

auto &	getDataOnElementBySpaceArray ()
	Get data on entities and space. More...

auto &	getDerivedDataOnElementBySpaceArray ()
	Get derived data on entities and space. More...

Public Member Functions inherited from MoFEM::FEMethod
MoFEMErrorCode	query_interface (boost::typeindex::type_index type_index, UnknownInterface **iface) const

	FEMethod ()=default

auto	getFEName () const
	get finite element name More...

auto	getDataDofsPtr () const

auto	getDataVectorDofsPtr () const

const FieldEntity_vector_view &	getDataFieldEnts () const

boost::shared_ptr< FieldEntity_vector_view > &	getDataFieldEntsPtr () const

auto &	getRowFieldEnts () const

auto &	getRowFieldEntsPtr () const

auto &	getColFieldEnts () const

auto &	getColFieldEntsPtr () const

auto	getRowDofsPtr () const

auto	getColDofsPtr () const

auto	getNumberOfNodes () const

EntityHandle	getFEEntityHandle () const

MoFEMErrorCode	getNodeData (const std::string field_name, VectorDouble &data, const bool reset_dofs=true)

Public Member Functions inherited from MoFEM::BasicMethod
	BasicMethod ()

virtual	~BasicMethod ()=default

int	getNinTheLoop () const
	get number of evaluated element in the loop More...

int	getLoopSize () const
	get loop size More...

auto	getLoHiFERank () const
	Get lo and hi processor rank of iterated entities. More...

auto	getLoFERank () const
	Get upper rank in loop for iterating elements. More...

auto	getHiFERank () const
	Get upper rank in loop for iterating elements. More...

unsigned int	getFieldBitNumber (std::string field_name) const

MoFEMErrorCode	copyBasicMethod (const BasicMethod &basic)
	Copy data from other base method to this base method. More...

boost::weak_ptr< CacheTuple >	getCacheWeakPtr () const
	Get the cache weak ptr object. More...

Public Member Functions inherited from MoFEM::KspMethod
	KspMethod ()

virtual	~KspMethod ()=default

MoFEMErrorCode	copyKsp (const KspMethod &ksp)
	copy data form another method More...

Public Member Functions inherited from MoFEM::PetscData
	PetscData ()

virtual	~PetscData ()=default

MoFEMErrorCode	copyPetscData (const PetscData &petsc_data)

Public Member Functions inherited from MoFEM::UnknownInterface
template<class IFACE >
MoFEMErrorCode	registerInterface (bool error_if_registration_failed=true)
	Register interface. More...

template<class IFACE >
MoFEMErrorCode	getInterface (IFACE *&iface) const
	Get interface reference to pointer of interface. More...

template<class IFACE >
MoFEMErrorCode	getInterface (IFACE **const iface) const
	Get interface pointer to pointer of interface. More...

template<class IFACE , typename boost::enable_if< boost::is_pointer< IFACE >, int >::type = 0>
IFACE	getInterface () const
	Get interface pointer to pointer of interface. More...

template<class IFACE , typename boost::enable_if< boost::is_reference< IFACE >, int >::type = 0>
IFACE	getInterface () const
	Get reference to interface. More...

template<class IFACE >
IFACE *	getInterface () const
	Function returning pointer to interface. More...

virtual	~UnknownInterface ()=default

Public Member Functions inherited from MoFEM::SnesMethod
	SnesMethod ()

virtual	~SnesMethod ()=default

MoFEMErrorCode	copySnes (const SnesMethod &snes)
	Copy snes data. More...

Public Member Functions inherited from MoFEM::TSMethod
	TSMethod ()

virtual	~TSMethod ()=default

MoFEMErrorCode	copyTs (const TSMethod &ts)
	Copy TS solver data. More...

Public Attributes
CommonData &	commonData

int	addToRule
	Takes into account HO geometry. More...

Public Attributes inherited from MoFEM::VolumeElementForcesAndSourcesCore
std::string	meshPositionsFieldName

Public Attributes inherited from MoFEM::ForcesAndSourcesCore
Interface &	mField

RuleHookFun	getRuleHook
	Hook to get rule. More...

GaussHookFun	setRuleHook
	Set function to calculate integration rule. More...

MatrixDouble	gaussPts
	Matrix of integration points. More...

Public Attributes inherited from MoFEM::FEMethod
std::string	feName
	Name of finite element. More...

boost::shared_ptr< const NumeredEntFiniteElement >	numeredEntFiniteElementPtr

boost::function< bool(FEMethod *fe_method_ptr)>	exeTestHook
	Tet if element to skip element. More...

Public Attributes inherited from MoFEM::BasicMethod
int	nInTheLoop
	number currently of processed method More...

int	loopSize
	local number oe methods to process More...

std::pair< int, int >	loHiFERank
	Llo and hi processor rank of iterated entities. More...

int	rAnk
	processor rank More...

int	sIze
	number of processors in communicator More...

const RefEntity_multiIndex *	refinedEntitiesPtr
	container of mofem dof entities More...

const RefElement_multiIndex *	refinedFiniteElementsPtr
	container of mofem finite element entities More...

const Problem *	problemPtr
	raw pointer to problem More...

const Field_multiIndex *	fieldsPtr
	raw pointer to fields container More...

const FieldEntity_multiIndex *	entitiesPtr
	raw pointer to container of field entities More...

const DofEntity_multiIndex *	dofsPtr
	raw pointer container of dofs More...

const FiniteElement_multiIndex *	finiteElementsPtr
	raw pointer to container finite elements More...

const EntFiniteElement_multiIndex *	finiteElementsEntitiesPtr

const FieldEntityEntFiniteElementAdjacencyMap_multiIndex *	adjacenciesPtr

boost::function< MoFEMErrorCode()>	preProcessHook
	Hook function for pre-processing. More...

boost::function< MoFEMErrorCode()>	postProcessHook
	Hook function for post-processing. More...

boost::function< MoFEMErrorCode()>	operatorHook
	Hook function for operator. More...

boost::movelib::unique_ptr< bool >	vecAssembleSwitch

boost::movelib::unique_ptr< bool >	matAssembleSwitch

boost::weak_ptr< CacheTuple >	cacheWeakPtr

Public Attributes inherited from MoFEM::KspMethod
KSPContext	ksp_ctx
	Context. More...

KSP	ksp
	KSP solver. More...

Vec &	ksp_f

Mat &	ksp_A

Mat &	ksp_B

Public Attributes inherited from MoFEM::PetscData
Switches	data_ctx

Vec	f

Mat	A

Mat	B

Vec	x

Vec	x_t

Vec	x_tt

Public Attributes inherited from MoFEM::SnesMethod
SNESContext	snes_ctx

SNES	snes
	snes solver More...

Vec &	snes_x
	state vector More...

Vec &	snes_f
	residual More...

Mat &	snes_A
	jacobian matrix More...

Mat &	snes_B
	preconditioner of jacobian matrix More...

Public Attributes inherited from MoFEM::TSMethod
TS	ts
	time solver More...

TSContext	ts_ctx

PetscInt	ts_step
	time step number More...

PetscReal	ts_a
	shift for U_t (see PETSc Time Solver) More...

PetscReal	ts_aa
	shift for U_tt shift for U_tt More...

PetscReal	ts_t
	time More...

PetscReal	ts_dt
	time step size More...

Vec &	ts_u
	state vector More...

Vec &	ts_u_t
	time derivative of state vector More...

Vec &	ts_u_tt
	second time derivative of state vector More...

Vec &	ts_F
	residual vector More...

Mat &	ts_A

Mat &	ts_B
	Preconditioner for ts_A. More...

Additional Inherited Members
Public Types inherited from MoFEM::VolumeElementForcesAndSourcesCore
enum	Switches

Public Types inherited from MoFEM::ForcesAndSourcesCore
typedef boost::function< int(int order_row, int order_col, int order_data)>	RuleHookFun

typedef boost::function< MoFEMErrorCode(ForcesAndSourcesCore *fe_raw_ptr, int order_row, int order_col, int order_data)>	GaussHookFun

Public Types inherited from MoFEM::KspMethod
enum	KSPContext { CTX_SETFUNCTION, CTX_OPERATORS, CTX_KSPNONE }
	pass information about context of KSP/DM for with finite element is computed More...

Public Types inherited from MoFEM::PetscData
enum	DataContext { CTX_SET_NONE = 0, CTX_SET_F = 1 << 0, CTX_SET_A = 1 << 1, CTX_SET_B = 1 << 2, CTX_SET_X = 1 << 3, CTX_SET_X_T = 1 << 4, CTX_SET_X_TT = 1 << 6, CTX_SET_TIME = 1 << 7 }

using	Switches = std::bitset< 8 >

Public Types inherited from MoFEM::SnesMethod
enum	SNESContext { CTX_SNESSETFUNCTION, CTX_SNESSETJACOBIAN, CTX_SNESNONE }

Public Types inherited from MoFEM::TSMethod
enum	TSContext { CTX_TSSETRHSFUNCTION, CTX_TSSETRHSJACOBIAN, CTX_TSSETIFUNCTION, CTX_TSSETIJACOBIAN, CTX_TSTSMONITORSET, CTX_TSNONE }

Static Public Member Functions inherited from MoFEM::UnknownInterface
static MoFEMErrorCode	getLibVersion (Version &version)
	Get library version. More...

static MoFEMErrorCode	getFileVersion (moab::Interface &moab, Version &version)
	Get database major version. More...

static MoFEMErrorCode	setFileVersion (moab::Interface &moab, Version version=Version(MoFEM_VERSION_MAJOR, MoFEM_VERSION_MINOR, MoFEM_VERSION_BUILD))
	Get database major version. More...

static MoFEMErrorCode	getInterfaceVersion (Version &version)
	Get database major version. More...

Static Public Attributes inherited from MoFEM::PetscData
static constexpr Switches	CtxSetNone = PetscData::Switches(CTX_SET_NONE)

static constexpr Switches	CtxSetF = PetscData::Switches(CTX_SET_F)

static constexpr Switches	CtxSetA = PetscData::Switches(CTX_SET_A)

static constexpr Switches	CtxSetB = PetscData::Switches(CTX_SET_B)

static constexpr Switches	CtxSetX = PetscData::Switches(CTX_SET_X)

static constexpr Switches	CtxSetX_T = PetscData::Switches(CTX_SET_X_T)

static constexpr Switches	CtxSetX_TT = PetscData::Switches(CTX_SET_X_TT)

static constexpr Switches	CtxSetTime = PetscData::Switches(CTX_SET_TIME)

Protected Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCore
virtual MoFEMErrorCode	setIntegrationPts ()
	Set integration points. More...

virtual MoFEMErrorCode	calculateVolumeAndJacobian ()
	Calculate element volume and Jacobian. More...

virtual MoFEMErrorCode	calculateCoordinatesAtGaussPts ()
	Calculate coordinate at integration points. More...

virtual MoFEMErrorCode	getSpaceBaseAndOrderOnElement ()
	Determine approximation space and order of base functions. More...

virtual MoFEMErrorCode	transformBaseFunctions ()
	Transform base functions based on geometric element Jacobian. More...

Protected Member Functions inherited from MoFEM::ForcesAndSourcesCore
MoFEMErrorCode	getEntitySense (const EntityType type, boost::ptr_vector< EntitiesFieldData::EntData > &data) const
	get sense (orientation) of entity More...

MoFEMErrorCode	getEntityDataOrder (const EntityType type, const FieldSpace space, boost::ptr_vector< EntitiesFieldData::EntData > &data) const
	Get the entity data order. More...

template<EntityType type>
MoFEMErrorCode	getEntitySense (EntitiesFieldData &data) const
	Get the entity sense (orientation) More...

template<EntityType type>
MoFEMErrorCode	getEntityDataOrder (EntitiesFieldData &data, const FieldSpace space) const
	Get the entity data order for given space. More...

MoFEMErrorCode	getFaceNodes (EntitiesFieldData &data) const
	Get nodes on faces. More...

MoFEMErrorCode	getSpacesAndBaseOnEntities (EntitiesFieldData &data) const
	Get field approximation space and base on entities. More...

virtual int	getRule (int order_row, int order_col, int order_data)
	another variant of getRule More...

virtual MoFEMErrorCode	setGaussPts (int order_row, int order_col, int order_data)
	set user specific integration rule More...

MoFEMErrorCode	calHierarchicalBaseFunctionsOnElement (const FieldApproximationBase b)
	Calculate base functions. More...

MoFEMErrorCode	calHierarchicalBaseFunctionsOnElement ()
	Calculate base functions. More...

MoFEMErrorCode	calBernsteinBezierBaseFunctionsOnElement ()
	Calculate Bernstein-Bezier base. More...

MoFEMErrorCode	createDataOnElement (EntityType type)
	Create a entity data on element object. More...

MoFEMErrorCode	loopOverOperators ()
	Iterate user data operators. More...

template<typename EXTRACTOR >
MoFEMErrorCode	getNodesIndices (const int bit_number, FieldEntity_vector_view &ents_field, VectorInt &nodes_indices, VectorInt &local_nodes_indices, EXTRACTOR &&extractor) const
	get node indices More...

MoFEMErrorCode	getRowNodesIndices (EntitiesFieldData &data, const int bit_number) const
	get row node indices from FENumeredDofEntity_multiIndex More...

MoFEMErrorCode	getColNodesIndices (EntitiesFieldData &data, const int bit_number) const
	get col node indices from FENumeredDofEntity_multiIndex More...

template<typename EXTRACTOR >
MoFEMErrorCode	getEntityIndices (EntitiesFieldData &data, const int bit_number, FieldEntity_vector_view &ents_field, const EntityType type_lo, const EntityType type_hi, EXTRACTOR &&extractor) const

MoFEMErrorCode	getEntityRowIndices (EntitiesFieldData &data, const int bit_number, const EntityType type_lo=MBVERTEX, const EntityType type_hi=MBPOLYHEDRON) const

MoFEMErrorCode	getEntityColIndices (EntitiesFieldData &data, const int bit_number, const EntityType type_lo=MBVERTEX, const EntityType type_hi=MBPOLYHEDRON) const

MoFEMErrorCode	getNoFieldIndices (const int bit_number, boost::shared_ptr< FENumeredDofEntity_multiIndex > dofs, VectorInt &nodes_indices) const
	get NoField indices More...

MoFEMErrorCode	getNoFieldRowIndices (EntitiesFieldData &data, const int bit_number) const
	get col NoField indices More...

MoFEMErrorCode	getNoFieldColIndices (EntitiesFieldData &data, const int bit_number) const
	get col NoField indices More...

MoFEMErrorCode	getBitRefLevelOnData ()

MoFEMErrorCode	getNoFieldFieldData (const int bit_number, VectorDouble &ent_field_data, VectorDofs &ent_field_dofs, VectorFieldEntities &ent_field) const
	Get field data on nodes. More...

MoFEMErrorCode	getNoFieldFieldData (EntitiesFieldData &data, const int bit_number) const

MoFEMErrorCode	getNodesFieldData (EntitiesFieldData &data, const int bit_number) const
	Get data on nodes. More...

MoFEMErrorCode	getEntityFieldData (EntitiesFieldData &data, const int bit_number, const EntityType type_lo=MBVERTEX, const EntityType type_hi=MBPOLYHEDRON) const

MoFEMErrorCode	getProblemNodesIndices (const std::string &field_name, const NumeredDofEntity_multiIndex &dofs, VectorInt &nodes_indices) const
	get indices of nodal indices which are declared for problem but not this particular element More...

MoFEMErrorCode	getProblemTypeIndices (const std::string &field_name, const NumeredDofEntity_multiIndex &dofs, EntityType type, int side_number, VectorInt &indices) const
	get indices by type (generic function) which are declared for problem but not this particular element More...

MoFEMErrorCode	getProblemNodesRowIndices (const std::string &field_name, VectorInt &nodes_indices) const

MoFEMErrorCode	getProblemTypeRowIndices (const std::string &field_name, EntityType type, int side_number, VectorInt &indices) const

MoFEMErrorCode	getProblemNodesColIndices (const std::string &field_name, VectorInt &nodes_indices) const

MoFEMErrorCode	getProblemTypeColIndices (const std::string &field_name, EntityType type, int side_number, VectorInt &indices) const

virtual MoFEMErrorCode	setGaussPts (int order)

Protected Attributes inherited from MoFEM::VolumeElementForcesAndSourcesCore
VectorDouble	coords

MatrixDouble3by3	jAc

MatrixDouble3by3	invJac

OpSetInvJacH1	opSetInvJacH1

OpSetContravariantPiolaTransform	opContravariantPiolaTransform

OpSetCovariantPiolaTransform	opCovariantPiolaTransform

OpSetInvJacHdivAndHcurl	opSetInvJacHdivAndHcurl

double &	vOlume

int	num_nodes

const EntityHandle *	conn

FTensor::Tensor2< double *, 3, 3 >	tJac

FTensor::Tensor2< double *, 3, 3 >	tInvJac

Protected Attributes inherited from MoFEM::ForcesAndSourcesCore
const std::array< boost::shared_ptr< EntitiesFieldData >, LASTSPACE >	dataOnElement
	Entity data on element entity rows fields. More...

const std::array< boost::shared_ptr< EntitiesFieldData >, LASTSPACE >	derivedDataOnElement
	Entity data on element entity columns fields. More...

EntitiesFieldData &	dataNoField

EntitiesFieldData &	dataH1

EntitiesFieldData &	dataHcurl

EntitiesFieldData &	dataHdiv

EntitiesFieldData &	dataL2

boost::ptr_deque< UserDataOperator >	opPtrVector
	Vector of finite element users data operators. More...

EntityType	lastEvaluatedElementEntityType
	Last evaluated type of element entity. More...

MatrixDouble	coordsAtGaussPts
	coordinated at gauss points More...

double	elementMeasure

Detailed Description

definition of volume element

Definition at line 379 of file Gels.hpp.

Constructor & Destructor Documentation

◆ GelFE()

GelModule::Gel::GelFE::GelFE	(	MoFEM::Interface &	m_field,
		CommonData &	common_data
	)

inline

Definition at line 384 of file Gels.hpp.

                                                           :
     MoFEM::VolumeElementForcesAndSourcesCore(m_field),
     commonData(common_data),
     addToRule(1) {
     }

Member Function Documentation

◆ getRule()

int GelModule::Gel::GelFE::getRule ( int order )

inlinevirtual

Deprecated:: Use getRule(int row_order, int col_order, int data order)

Reimplemented from MoFEM::ForcesAndSourcesCore.

Definition at line 390 of file Gels.hpp.

                            {
       return 2*(order-1)+addToRule;
     }

◆ postProcess()

PetscErrorCode GelModule::Gel::GelFE::postProcess ( )

inlinevirtual

function is run at the end of loop

It is used to assembly matrices and vectors, calculating global variables, f.e. total internal energy, ect.

Iterating over dofs: Example1 iterating over dofs in row by name of the field for(IT_GET_FEROW_BY_NAME_DOFS_FOR_LOOP(this,"DISPLACEMENT",it)) { ... }

Reimplemented from MoFEM::ForcesAndSourcesCore.

Definition at line 416 of file Gels.hpp.

                                  {
       
       PetscFunctionBegin;
  
       ierr = MoFEM::VolumeElementForcesAndSourcesCore::postProcess(); CHKERRQ(ierr);
  
       if(ts_ctx == CTX_TSSETIFUNCTION) {
         ierr = VecAssemblyBegin(ts_F); CHKERRQ(ierr);
         ierr = VecAssemblyEnd(ts_F); CHKERRQ(ierr);
       }
       if(ts_ctx == CTX_TSSETIJACOBIAN) {
         ierr = MatAssemblyBegin(ts_B,MAT_FLUSH_ASSEMBLY); CHKERRQ(ierr);
         ierr = MatAssemblyEnd(ts_B,MAT_FLUSH_ASSEMBLY); CHKERRQ(ierr);
       }
  
       PetscFunctionReturn(0);
     }

◆ preProcess()

PetscErrorCode GelModule::Gel::GelFE::preProcess ( )

inlinevirtual

function is run at the beginning of loop

It is used to zeroing matrices and vectors, calculation of shape functions on reference element, preprocessing boundary conditions, etc.

Reimplemented from MoFEM::ForcesAndSourcesCore.

Definition at line 394 of file Gels.hpp.

                                 {
       
       PetscFunctionBegin;
       ierr = MoFEM::VolumeElementForcesAndSourcesCore::preProcess(); CHKERRQ(ierr);
  
       if(ts_ctx == CTX_TSSETIFUNCTION) {
  
         ierr = mField.set_other_local_ghost_vector(
           problemPtr,commonData.spatialPositionName,commonData.spatialPositionNameDot,COL,ts_u_t,INSERT_VALUES,SCATTER_REVERSE
         ); CHKERRQ(ierr);
         ierr = mField.set_other_local_ghost_vector(
           problemPtr,commonData.muName,commonData.muNameDot,COL,ts_u_t,INSERT_VALUES,SCATTER_REVERSE
         ); CHKERRQ(ierr);
         ierr = mField.set_other_local_ghost_vector(
           problemPtr,commonData.strainHatName,commonData.strainHatNameDot,COL,ts_u_t,INSERT_VALUES,SCATTER_REVERSE
         ); CHKERRQ(ierr);
  
       }
  
       PetscFunctionReturn(0);
     }

Member Data Documentation

◆ addToRule

int GelModule::Gel::GelFE::addToRule

Takes into account HO geometry.

Definition at line 382 of file Gels.hpp.

◆ commonData

CommonData& GelModule::Gel::GelFE::commonData

Definition at line 381 of file Gels.hpp.

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

users_modules/gels/src/Gels.hpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GelFE()

Member Function Documentation

◆ getRule()

◆ postProcess()

◆ preProcess()

Member Data Documentation

◆ addToRule

◆ commonData