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Public Member Functions | Private Attributes | List of all members
ElectroPhysiology::OpAssembleLhsTauTau< dim > Struct Template Reference

#include <users_modules/softmech/chemo_mech/src/ElecPhysOperators.hpp>

Inheritance diagram for ElectroPhysiology::OpAssembleLhsTauTau< dim >:
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Collaboration diagram for ElectroPhysiology::OpAssembleLhsTauTau< dim >:
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Public Member Functions

 OpAssembleLhsTauTau (std::string flux_field)
 
MoFEMErrorCode doWork (int row_side, int col_side, EntityType row_type, EntityType col_type, EntData &row_data, EntData &col_data)
 
 OpAssembleLhsTauTau (std::string flux_field, boost::shared_ptr< PreviousData > &commonData, std::map< int, BlockData > &block_map)
 
MoFEMErrorCode doWork (int row_side, int col_side, EntityType row_type, EntityType col_type, EntData &row_data, EntData &col_data)
 
- Public Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator
int getNumNodes ()
 get element number of nodes More...
 
const EntityHandlegetConn ()
 get element connectivity More...
 
double getVolume () const
 element volume (linear geometry) More...
 
doublegetVolume ()
 element volume (linear geometry) More...
 
FTensor::Tensor2< double *, 3, 3 > & getJac ()
 get element Jacobian More...
 
FTensor::Tensor2< double *, 3, 3 > & getInvJac ()
 get element inverse Jacobian More...
 
VectorDoublegetCoords ()
 nodal coordinates More...
 
VolumeElementForcesAndSourcesCoregetVolumeFE () const
 return pointer to Generic Volume Finite Element object More...
 
- Public Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
 UserDataOperator (const FieldSpace space, const char type=OPSPACE, const bool symm=true)
 
 UserDataOperator (const std::string field_name, const char type, const bool symm=true)
 
 UserDataOperator (const std::string row_field_name, const std::string col_field_name, const char type, const bool symm=true)
 
boost::shared_ptr< const NumeredEntFiniteElementgetNumeredEntFiniteElementPtr () const
 Return raw pointer to NumeredEntFiniteElement. More...
 
EntityHandle getFEEntityHandle () const
 Return finite element entity handle. More...
 
int getFEDim () const
 Get dimension of finite element. More...
 
EntityType getFEType () const
 Get dimension of finite element. More...
 
boost::weak_ptr< SideNumbergetSideNumberPtr (const int side_number, const EntityType type)
 Get the side number pointer. More...
 
EntityHandle getSideEntity (const int side_number, const EntityType type)
 Get the side entity. More...
 
int getNumberOfNodesOnElement () const
 Get the number of nodes on finite element. More...
 
MoFEMErrorCode getProblemRowIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 Get row indices. More...
 
MoFEMErrorCode getProblemColIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 Get col indices. More...
 
const FEMethodgetFEMethod () const
 Return raw pointer to Finite Element Method object. More...
 
int getOpType () const
 Get operator types. More...
 
void setOpType (const OpType type)
 Set operator type. More...
 
void addOpType (const OpType type)
 Add operator type. More...
 
int getNinTheLoop () const
 get number of finite element in the loop More...
 
int getLoopSize () const
 get size of elements in the loop More...
 
std::string getFEName () const
 Get name of the element. More...
 
ForcesAndSourcesCoregetPtrFE () const
 
ForcesAndSourcesCoregetSidePtrFE () const
 
ForcesAndSourcesCoregetRefinePtrFE () const
 
const PetscData::SwitchesgetDataCtx () const
 
const KspMethod::KSPContext getKSPCtx () const
 
const SnesMethod::SNESContext getSNESCtx () const
 
const TSMethod::TSContext getTSCtx () const
 
Vec getKSPf () const
 
Mat getKSPA () const
 
Mat getKSPB () const
 
Vec getSNESf () const
 
Vec getSNESx () const
 
Mat getSNESA () const
 
Mat getSNESB () const
 
Vec getTSu () const
 
Vec getTSu_t () const
 
Vec getTSu_tt () const
 
Vec getTSf () const
 
Mat getTSA () const
 
Mat getTSB () const
 
int getTSstep () const
 
double getTStime () const
 
double getTStimeStep () const
 
double getTSa () const
 
double getTSaa () const
 
MatrixDoublegetGaussPts ()
 matrix of integration (Gauss) points for Volume Element More...
 
auto getFTensor0IntegrationWeight ()
 Get integration weights. More...
 
MatrixDoublegetCoordsAtGaussPts ()
 Gauss points and weight, matrix (nb. of points x 3) More...
 
auto getFTensor1CoordsAtGaussPts ()
 Get coordinates at integration points assuming linear geometry. More...
 
double getMeasure () const
 get measure of element More...
 
doublegetMeasure ()
 get measure of element More...
 
MoFEMErrorCode loopSide (const string &fe_name, ForcesAndSourcesCore *side_fe, const size_t dim, const EntityHandle ent_for_side=0, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy, AdjCache *adj_cache=nullptr)
 User calls this function to loop over elements on the side of face. This function calls finite element with its operator to do calculations. More...
 
MoFEMErrorCode loopThis (const string &fe_name, ForcesAndSourcesCore *this_fe, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy)
 User calls this function to loop over the same element using a different set of integration points. This function calls finite element with its operator to do calculations. More...
 
MoFEMErrorCode loopParent (const string &fe_name, ForcesAndSourcesCore *parent_fe, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy)
 User calls this function to loop over parent elements. This function calls finite element with its operator to do calculations. More...
 
MoFEMErrorCode loopChildren (const string &fe_name, ForcesAndSourcesCore *child_fe, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy)
 User calls this function to loop over parent elements. This function calls finite element with its operator to do calculations. More...
 
- Public Member Functions inherited from MoFEM::DataOperator
 DataOperator (const bool symm=true)
 
virtual ~DataOperator ()=default
 
virtual MoFEMErrorCode doWork (int row_side, int col_side, EntityType row_type, EntityType col_type, EntitiesFieldData::EntData &row_data, EntitiesFieldData::EntData &col_data)
 Operator for bi-linear form, usually to calculate values on left hand side. More...
 
virtual MoFEMErrorCode opLhs (EntitiesFieldData &row_data, EntitiesFieldData &col_data)
 
virtual MoFEMErrorCode doWork (int side, EntityType type, EntitiesFieldData::EntData &data)
 Operator for linear form, usually to calculate values on right hand side. More...
 
virtual MoFEMErrorCode opRhs (EntitiesFieldData &data, const bool error_if_no_base=false)
 
bool getSymm () const
 Get if operator uses symmetry of DOFs or not. More...
 
void setSymm ()
 set if operator is executed taking in account symmetry More...
 
void unSetSymm ()
 unset if operator is executed for non symmetric problem More...
 
- Public Member Functions inherited from MoFEM::FaceElementForcesAndSourcesCore::UserDataOperator
double getArea ()
 get area of face More...
 
VectorDoublegetNormal ()
 get triangle normal More...
 
VectorDoublegetTangent1 ()
 get triangle tangent 1 More...
 
VectorDoublegetTangent2 ()
 get triangle tangent 2 More...
 
auto getFTensor1Normal ()
 get normal as tensor More...
 
auto getFTensor1Tangent1 ()
 get tangentOne as tensor More...
 
auto getFTensor1Tangent2 ()
 get tangentTwo as tensor More...
 
int getNumNodes ()
 get element number of nodes More...
 
const EntityHandlegetConn ()
 get element connectivity More...
 
VectorDoublegetCoords ()
 get triangle coordinates More...
 
auto getFTensor1Coords ()
 get get coords at gauss points More...
 
MatrixDoublegetNormalsAtGaussPts ()
 if higher order geometry return normals at Gauss pts. More...
 
ublas::matrix_row< MatrixDoublegetNormalsAtGaussPts (const int gg)
 if higher order geometry return normals at Gauss pts. More...
 
MatrixDoublegetTangent1AtGaussPts ()
 if higher order geometry return tangent vector to triangle at Gauss pts. More...
 
MatrixDoublegetTangent2AtGaussPts ()
 if higher order geometry return tangent vector to triangle at Gauss pts. More...
 
auto getFTensor1NormalsAtGaussPts ()
 get normal at integration points More...
 
auto getFTensor1Tangent1AtGaussPts ()
 get tangent 1 at integration points More...
 
auto getFTensor1Tangent2AtGaussPts ()
 get tangent 2 at integration points More...
 
FaceElementForcesAndSourcesCoregetFaceFE ()
 return pointer to Generic Triangle Finite Element object More...
 
MoFEMErrorCode loopSideVolumes (const string fe_name, VolumeElementForcesAndSourcesCoreOnSide &fe_method)
 

Private Attributes

MatrixDouble mat
 
MatrixDouble transMat
 
boost::shared_ptr< PreviousDatacommonData
 
Range essential_bd_ents
 
std::map< int, BlockDatasetOfBlock
 

Additional Inherited Members

- Public Types inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
enum  OpType {
  OPROW = 1 << 0 , OPCOL = 1 << 1 , OPROWCOL = 1 << 2 , OPSPACE = 1 << 3 ,
  OPLAST = 1 << 3
}
 Controls loop over entities on element. More...
 
using AdjCache = std::map< EntityHandle, std::vector< boost::weak_ptr< NumeredEntFiniteElement > > >
 
- Public Types inherited from MoFEM::DataOperator
using DoWorkLhsHookFunType = boost::function< MoFEMErrorCode(DataOperator *op_ptr, int row_side, int col_side, EntityType row_type, EntityType col_type, EntitiesFieldData::EntData &row_data, EntitiesFieldData::EntData &col_data)>
 
using DoWorkRhsHookFunType = boost::function< MoFEMErrorCode(DataOperator *op_ptr, int side, EntityType type, EntitiesFieldData::EntData &data)>
 
- Public Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
char opType
 
std::string rowFieldName
 
std::string colFieldName
 
FieldSpace sPace
 
- Public Attributes inherited from MoFEM::DataOperator
DoWorkLhsHookFunType doWorkLhsHook
 
DoWorkRhsHookFunType doWorkRhsHook
 
bool sYmm
 If true assume that matrix is symmetric structure. More...
 
std::array< bool, MBMAXTYPE > doEntities
 If true operator is executed for entity. More...
 
booldoVertices
 \deprectaed If false skip vertices More...
 
booldoEdges
 \deprectaed If false skip edges More...
 
booldoQuads
 \deprectaed More...
 
booldoTris
 \deprectaed More...
 
booldoTets
 \deprectaed More...
 
booldoPrisms
 \deprectaed More...
 
- Static Public Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
static const char *const OpTypeNames []
 
- Protected Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator
MoFEMErrorCode setPtrFE (ForcesAndSourcesCore *ptr)
 
virtual MoFEMErrorCode setPtrFE (ForcesAndSourcesCore *ptr)
 
- Protected Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCoreptrFE
 

Detailed Description

template<int dim>
struct ElectroPhysiology::OpAssembleLhsTauTau< dim >

Definition at line 548 of file ElecPhysOperators.hpp.

Constructor & Destructor Documentation

◆ OpAssembleLhsTauTau() [1/2]

template<int dim>
ElectroPhysiology::OpAssembleLhsTauTau< dim >::OpAssembleLhsTauTau ( std::string  flux_field)
inline

Definition at line 550 of file ElecPhysOperators.hpp.

551 : OpVolEle(flux_field, flux_field, OpVolEle::OPROWCOL) {
552 sYmm = true;
553 }
VolEle::UserDataOperator OpVolEle
bool sYmm
If true assume that matrix is symmetric structure.
@ OPROWCOL
operator doWork is executed on FE rows &columns

◆ OpAssembleLhsTauTau() [2/2]

template<int dim>
ElectroPhysiology::OpAssembleLhsTauTau< dim >::OpAssembleLhsTauTau ( std::string  flux_field,
boost::shared_ptr< PreviousData > &  commonData,
std::map< int, BlockData > &  block_map 
)
inline

Definition at line 594 of file ElecPhysOperators2D.hpp.

597 : OpFaceEle(flux_field, flux_field, OpFaceEle::OPROWCOL),
598 setOfBlock(block_map), commonData(commonData) {
599 sYmm = true;
600 }
FaceEle::UserDataOperator OpFaceEle
boost::shared_ptr< PreviousData > commonData

Member Function Documentation

◆ doWork() [1/2]

template<int dim>
MoFEMErrorCode ElectroPhysiology::OpAssembleLhsTauTau< dim >::doWork ( int  row_side,
int  col_side,
EntityType  row_type,
EntityType  col_type,
EntData row_data,
EntData col_data 
)
inline

Definition at line 555 of file ElecPhysOperators.hpp.

557 {
559 const int nb_row_dofs = row_data.getIndices().size();
560 const int nb_col_dofs = col_data.getIndices().size();
561
562 if (nb_row_dofs && nb_col_dofs) {
563
564 mat.resize(nb_row_dofs, nb_col_dofs, false);
565 mat.clear();
566 const int nb_integration_pts = getGaussPts().size2();
567
568 auto t_row_tau_base = row_data.getFTensor1N<3>();
569
570 auto t_w = getFTensor0IntegrationWeight();
571 const double vol = getMeasure();
572
573 for (int gg = 0; gg != nb_integration_pts; ++gg) {
574 const double a = vol * t_w;
575 const double K_inv = 1. / D_tilde;
576 for (int rr = 0; rr != nb_row_dofs; ++rr) {
577 auto t_col_tau_base = col_data.getFTensor1N<3>(gg, 0);
578 for (int cc = 0; cc != nb_col_dofs; ++cc) {
579 mat(rr, cc) += (K_inv * t_row_tau_base(i) * t_col_tau_base(i)) * a;
580 ++t_col_tau_base;
581 }
582 ++t_row_tau_base;
583 }
584 ++t_w;
585 }
586 CHKERR MatSetValues(getFEMethod()->ts_B, row_data, col_data, &mat(0, 0),
587 ADD_VALUES);
588 if (row_side != col_side || row_type != col_type) {
589 transMat.resize(nb_col_dofs, nb_row_dofs, false);
590 noalias(transMat) = trans(mat);
591 CHKERR MatSetValues(getFEMethod()->ts_B, col_data, row_data,
592 &transMat(0, 0), ADD_VALUES);
593 }
594 }
596 }
constexpr double a
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:346
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:416
#define CHKERR
Inline error check.
Definition: definitions.h:535
FTensor::Index< 'i', 3 > i
MoFEMErrorCode MatSetValues(Mat M, const EntitiesFieldData::EntData &row_data, const EntitiesFieldData::EntData &col_data, const double *ptr, InsertMode iora)
Assemble PETSc matrix.
FTensor::Tensor1< FTensor::PackPtr< double *, Tensor_Dim >, Tensor_Dim > getFTensor1N(FieldApproximationBase base)
Get base functions for Hdiv/Hcurl spaces.
const VectorInt & getIndices() const
Get global indices of dofs on entity.
auto getFTensor0IntegrationWeight()
Get integration weights.
double getMeasure() const
get measure of element
const FEMethod * getFEMethod() const
Return raw pointer to Finite Element Method object.
MatrixDouble & getGaussPts()
matrix of integration (Gauss) points for Volume Element

◆ doWork() [2/2]

template<int dim>
MoFEMErrorCode ElectroPhysiology::OpAssembleLhsTauTau< dim >::doWork ( int  row_side,
int  col_side,
EntityType  row_type,
EntityType  col_type,
EntData row_data,
EntData col_data 
)
inline

Definition at line 602 of file ElecPhysOperators2D.hpp.

604 {
606 const int nb_row_dofs = row_data.getIndices().size();
607 const int nb_col_dofs = col_data.getIndices().size();
608
609 if (nb_row_dofs && nb_col_dofs) {
610 // auto find_block_data = [&]() {
611 // EntityHandle fe_ent = getFEEntityHandle();
612 // BlockData *block_raw_ptr = nullptr;
613 // for (auto &m : setOfBlock) {
614 // if (m.second.block_ents.find(fe_ent) != m.second.block_ents.end()) {
615 // block_raw_ptr = &m.second;
616 // break;
617 // }
618 // }
619 // return block_raw_ptr;
620 // };
621
622 // auto block_data_ptr = find_block_data();
623 // if (!block_data_ptr)
624 // SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Block not found");
625 // auto &block_data = *block_data_ptr;
626
627 mat.resize(nb_row_dofs, nb_col_dofs, false);
628 mat.clear();
629 const int nb_integration_pts = getGaussPts().size2();
630 auto t_mass_value = getFTensor0FromVec(commonData->mass_values);
631
632 auto t_row_tau_base = row_data.getFTensor1N<3>();
633
634 auto t_w = getFTensor0IntegrationWeight();
635 const double vol = getMeasure();
636
637 for (int gg = 0; gg != nb_integration_pts; ++gg) {
638 const double a = vol * t_w;
639 const double K = B_epsilon + (block.B0 + B * t_mass_value);
640 const double K_inv = 1. / K;
641 for (int rr = 0; rr != nb_row_dofs; ++rr) {
642 auto t_col_tau_base = col_data.getFTensor1N<3>(gg, 0);
643 for (int cc = 0; cc != nb_col_dofs; ++cc) {
644 mat(rr, cc) += (K_inv * t_row_tau_base(i) * t_col_tau_base(i)) * a;
645 ++t_col_tau_base;
646 }
647 ++t_row_tau_base;
648 }
649 ++t_mass_value;
650 ++t_w;
651 }
652 CHKERR MatSetValues(getFEMethod()->ts_B, row_data, col_data, &mat(0, 0),
653 ADD_VALUES);
654 if (row_side != col_side || row_type != col_type) {
655 transMat.resize(nb_col_dofs, nb_row_dofs, false);
656 noalias(transMat) = trans(mat);
657 CHKERR MatSetValues(getFEMethod()->ts_B, col_data, row_data,
658 &transMat(0, 0), ADD_VALUES);
659 }
660 }
662 }
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:135

Member Data Documentation

◆ commonData

template<int dim>
boost::shared_ptr<PreviousData> ElectroPhysiology::OpAssembleLhsTauTau< dim >::commonData
private

Definition at line 665 of file ElecPhysOperators2D.hpp.

◆ essential_bd_ents

template<int dim>
Range ElectroPhysiology::OpAssembleLhsTauTau< dim >::essential_bd_ents
private

Definition at line 667 of file ElecPhysOperators2D.hpp.

◆ mat

template<int dim>
MatrixDouble ElectroPhysiology::OpAssembleLhsTauTau< dim >::mat
private

Definition at line 599 of file ElecPhysOperators.hpp.

◆ setOfBlock

template<int dim>
std::map<int, BlockData> ElectroPhysiology::OpAssembleLhsTauTau< dim >::setOfBlock
private

Definition at line 668 of file ElecPhysOperators2D.hpp.

◆ transMat

template<int dim>
MatrixDouble ElectroPhysiology::OpAssembleLhsTauTau< dim >::transMat
private

Definition at line 599 of file ElecPhysOperators.hpp.


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