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

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

Inheritance diagram for ElectroPhysiology::OpAssembleStiffRhsV< dim >:
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Collaboration diagram for ElectroPhysiology::OpAssembleStiffRhsV< dim >:
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Public Types

typedef boost::function< double(const double, const double)> FUval
 
- 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 Member Functions

 OpAssembleStiffRhsV (std::string mass_field, boost::shared_ptr< PreviousData > &data_u, Range &stim_region)
 
MoFEMErrorCode doWork (int side, EntityType type, EntData &data)
 
 OpAssembleStiffRhsV (std::string flux_field, boost::shared_ptr< PreviousData > &datau, boost::shared_ptr< PreviousData > &datav, FUval rhs_u, std::map< int, BlockData > &block_map, Range &stim_region)
 
MoFEMErrorCode doWork (int side, EntityType type, EntData &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)
 

Public Attributes

RangestimRegion
 
FUval rhsU
 
- 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...
 

Private Attributes

boost::shared_ptr< PreviousDatadataU
 
boost::shared_ptr< PreviousDatadataV
 
VectorDouble vecF
 
boost::shared_ptr< PreviousDatacommonDatau
 
boost::shared_ptr< PreviousDatacommonDatav
 
std::map< int, BlockDatasetOfBlock
 
FTensor::Number< 0 > NX
 
FTensor::Number< 1 > NY
 

Additional Inherited Members

- 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::OpAssembleStiffRhsV< dim >

Definition at line 474 of file ElecPhysOperators.hpp.

Member Typedef Documentation

◆ FUval

template<int dim>
typedef boost::function<double(const double, const double)> ElectroPhysiology::OpAssembleStiffRhsV< dim >::FUval

Definition at line 484 of file ElecPhysOperators2D.hpp.

Constructor & Destructor Documentation

◆ OpAssembleStiffRhsV() [1/2]

template<int dim>
ElectroPhysiology::OpAssembleStiffRhsV< dim >::OpAssembleStiffRhsV ( std::string  mass_field,
boost::shared_ptr< PreviousData > &  data_u,
Range stim_region 
)
inline

Definition at line 476 of file ElecPhysOperators.hpp.

479 : OpVolEle(mass_field, OpVolEle::OPROW)
480 , dataU(data_u)
481 , stimRegion(stim_region) {}
VolEle::UserDataOperator OpVolEle
boost::shared_ptr< PreviousData > dataU
@ OPROW
operator doWork function is executed on FE rows

◆ OpAssembleStiffRhsV() [2/2]

template<int dim>
ElectroPhysiology::OpAssembleStiffRhsV< dim >::OpAssembleStiffRhsV ( std::string  flux_field,
boost::shared_ptr< PreviousData > &  datau,
boost::shared_ptr< PreviousData > &  datav,
FUval  rhs_u,
std::map< int, BlockData > &  block_map,
Range stim_region 
)
inline

Definition at line 485 of file ElecPhysOperators2D.hpp.

489 : OpFaceEle(flux_field, OpFaceEle::OPROW), commonDatau(datau),
490 commonDatav(datav), setOfBlock(block_map), rhsU(rhs_u),
491 stimRegion(stim_region) {}
FaceEle::UserDataOperator OpFaceEle
boost::shared_ptr< PreviousData > commonDatau
boost::shared_ptr< PreviousData > commonDatav

Member Function Documentation

◆ doWork() [1/2]

template<int dim>
MoFEMErrorCode ElectroPhysiology::OpAssembleStiffRhsV< dim >::doWork ( int  side,
EntityType  type,
EntData data 
)
inline

Definition at line 485 of file ElecPhysOperators.hpp.

485 {
487 const int nb_dofs = data.getIndices().size();
488 // cerr << "In StiffRhsV ..." << endl;
489 if (nb_dofs) {
490
491 vecF.resize(nb_dofs, false);
492 vecF.clear();
493 const int nb_integration_pts = getGaussPts().size2();
494 auto t_dot_u = getFTensor0FromVec(dataU->mass_dots);
495
496
497 auto t_div_u = getFTensor0FromVec(dataU->flux_divs);
498 auto t_row_v_base = data.getFTensor0N();
499 auto t_w = getFTensor0IntegrationWeight();
500 const double vol = getMeasure();
501 const double c_time = getFEMethod()->ts_t;
502
503 double dt;
504 CHKERR TSGetTimeStep(getFEMethod()->ts, &dt);
505
506 double stim = 0.0;
507
508 double T = 627.0;
509 double duration = 5.0;
510
511 if (T - dt < c_time && c_time <= T + duration) {
512 EntityHandle stim_ent = getFEEntityHandle();
513 if (stimRegion.find(stim_ent) != stimRegion.end()) {
514 stim = 40.0;
515 } else {
516 stim = 0.0;
517 }
518 }
519
520 for (int gg = 0; gg < nb_integration_pts; ++gg) {
521 const double a = vol * t_w;
522 for (int rr = 0; rr < nb_dofs; ++rr) {
523 vecF[rr] += t_row_v_base * (t_dot_u + t_div_u - stim) * a;
524 ++t_row_v_base;
525 }
526 ++t_dot_u;
527 ++t_div_u;
528 ++t_w;
529 }
530 CHKERR VecSetOption(getFEMethod()->ts_F, VEC_IGNORE_NEGATIVE_INDICES,
531 PETSC_TRUE);
532 CHKERR VecSetValues(getFEMethod()->ts_F, data, &*vecF.begin(),
533 ADD_VALUES);
534 }
536 }
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
double dt
Definition: heat_method.cpp:26
const double T
static auto getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:135
MoFEMErrorCode VecSetValues(Vec V, const EntitiesFieldData::EntData &data, const double *ptr, InsertMode iora)
Assemble PETSc vector.
FTensor::Tensor0< FTensor::PackPtr< double *, 1 > > getFTensor0N(const FieldApproximationBase base)
Get base function as Tensor0.
const VectorInt & getIndices() const
Get global indices of dofs on entity.
EntityHandle getFEEntityHandle() const
Return finite element entity handle.
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
PetscReal ts_t
time

◆ doWork() [2/2]

template<int dim>
MoFEMErrorCode ElectroPhysiology::OpAssembleStiffRhsV< dim >::doWork ( int  side,
EntityType  type,
EntData data 
)
inline

Definition at line 495 of file ElecPhysOperators2D.hpp.

495 {
497 const int nb_dofs = data.getIndices().size();
498 // cerr << "In StiffRhsV ..." << endl;
499 if (nb_dofs) {
500 // auto find_block_data = [&]() {
501 // EntityHandle fe_ent = getFEEntityHandle();
502 // BlockData *block_raw_ptr = nullptr;
503 // for (auto &m : setOfBlock) {
504 // if (m.second.block_ents.find(fe_ent) != m.second.block_ents.end()) {
505 // block_raw_ptr = &m.second;
506 // break;
507 // }
508 // }
509 // return block_raw_ptr;
510 // };
511
512 // auto block_data_ptr = find_block_data();
513 // if (!block_data_ptr)
514 // SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Block not found");
515 // auto &block_data = *block_data_ptr;
516
517 vecF.resize(nb_dofs, false);
518 vecF.clear();
519 const int nb_integration_pts = getGaussPts().size2();
520 auto t_u_value = getFTensor0FromVec(commonDatau->mass_values);
521 auto t_v_value = getFTensor0FromVec(commonDatav->mass_values);
522
523 auto t_mass_dot = getFTensor0FromVec(commonDatau->mass_dots);
524 auto t_flux_div = getFTensor0FromVec(commonDatau->flux_divs);
525 auto t_row_v_base = data.getFTensor0N();
526 auto t_w = getFTensor0IntegrationWeight();
527 const double vol = getMeasure();
528 auto t_coords = getFTensor1CoordsAtGaussPts();
529
530 const double c_time = getFEMethod()->ts_t;
531
532 double dt;
533 CHKERR TSGetTimeStep(getFEMethod()->ts, &dt);
534
535 double stim = 0.0;
536
537 double T = 627.0;
538 double duration = 5.0;
539
540 if (T - dt < c_time && c_time <= T + duration) {
541 EntityHandle stim_ent = getFEEntityHandle();
542 if (stimRegion.find(stim_ent) != stimRegion.end()) {
543 stim = 40.0;
544 } else {
545 stim = 0.0;
546 }
547 }
548 for (int gg = 0; gg < nb_integration_pts; ++gg) {
549 const double a = vol * t_w;
550 // double u_dot = exactDot(t_coords(NX), t_coords(NY), ct);
551 // double u_lap = exactLap(t_coords(NX), t_coords(NY), ct);
552
553 // double f = u_dot - block_data.B0 * u_lap;
554 double rhsu = rhsU(t_u_value, t_v_value);
555 for (int rr = 0; rr < nb_dofs; ++rr) {
556 vecF[rr] += (t_row_v_base * (t_mass_dot + t_flux_div - 0*rhsu - factor * stim)) * a;
557 ++t_row_v_base;
558 }
559 ++t_mass_dot;
560 ++t_flux_div;
561 ++t_u_value;
562 ++t_v_value;
563 ++t_w;
564 ++t_coords;
565 }
566 CHKERR VecSetOption(getFEMethod()->ts_F, VEC_IGNORE_NEGATIVE_INDICES,
567 PETSC_TRUE);
568 CHKERR VecSetValues(getFEMethod()->ts_F, data, &*vecF.begin(),
569 ADD_VALUES);
570 }
572 }
auto getFTensor1CoordsAtGaussPts()
Get coordinates at integration points assuming linear geometry.

Member Data Documentation

◆ commonDatau

template<int dim>
boost::shared_ptr<PreviousData> ElectroPhysiology::OpAssembleStiffRhsV< dim >::commonDatau
private

Definition at line 575 of file ElecPhysOperators2D.hpp.

◆ commonDatav

template<int dim>
boost::shared_ptr<PreviousData> ElectroPhysiology::OpAssembleStiffRhsV< dim >::commonDatav
private

Definition at line 576 of file ElecPhysOperators2D.hpp.

◆ dataU

template<int dim>
boost::shared_ptr<PreviousData> ElectroPhysiology::OpAssembleStiffRhsV< dim >::dataU
private

Definition at line 539 of file ElecPhysOperators.hpp.

◆ dataV

template<int dim>
boost::shared_ptr<PreviousData> ElectroPhysiology::OpAssembleStiffRhsV< dim >::dataV
private

Definition at line 540 of file ElecPhysOperators.hpp.

◆ NX

template<int dim>
FTensor::Number<0> ElectroPhysiology::OpAssembleStiffRhsV< dim >::NX
private

Definition at line 584 of file ElecPhysOperators2D.hpp.

◆ NY

template<int dim>
FTensor::Number<1> ElectroPhysiology::OpAssembleStiffRhsV< dim >::NY
private

Definition at line 585 of file ElecPhysOperators2D.hpp.

◆ rhsU

template<int dim>
FUval ElectroPhysiology::OpAssembleStiffRhsV< dim >::rhsU

Definition at line 494 of file ElecPhysOperators2D.hpp.

◆ setOfBlock

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

Definition at line 578 of file ElecPhysOperators2D.hpp.

◆ stimRegion

template<int dim>
Range & ElectroPhysiology::OpAssembleStiffRhsV< dim >::stimRegion

Definition at line 483 of file ElecPhysOperators.hpp.

◆ vecF

template<int dim>
VectorDouble ElectroPhysiology::OpAssembleStiffRhsV< dim >::vecF
private

Definition at line 541 of file ElecPhysOperators.hpp.


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