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

Inheritance diagram for ElectroPhysiology::OpAssembleStiffRhsV< dim >:

Collaboration diagram for ElectroPhysiology::OpAssembleStiffRhsV< dim >:

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 EntityHandle *	getConn ()
	get element connectivity More...

double	getVolume () const
	element volume (linear geometry) More...

double &	getVolume ()
	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...

VectorDouble &	getCoords ()
	nodal coordinates More...

VolumeElementForcesAndSourcesCore *	getVolumeFE () 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 NumeredEntFiniteElement >	getNumeredEntFiniteElementPtr () 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< SideNumber >	getSideNumberPtr (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 FEMethod *	getFEMethod () 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...

ForcesAndSourcesCore *	getPtrFE () const

ForcesAndSourcesCore *	getSidePtrFE () const

ForcesAndSourcesCore *	getRefinePtrFE () const

const PetscData::Switches &	getDataCtx () 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

MatrixDouble &	getGaussPts ()
	matrix of integration (Gauss) points for Volume Element More...

auto	getFTensor0IntegrationWeight ()
	Get integration weights. More...

MatrixDouble &	getCoordsAtGaussPts ()
	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...

double &	getMeasure ()
	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 call this function to loop over elements on the side of face. This function calls finite element with is operator to do calculations. More...

MoFEMErrorCode	loopThis (const string &fe_name, ForcesAndSourcesCore *parent_fe, const int verb=QUIET, const LogManager::SeverityLevel sev=Sev::noisy)
	User call this function to loop over parent elements. This function calls finite element with is 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 call this function to loop over parent elements. This function calls finite element with is 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 call this function to loop over parent elements. This function calls finite element with is 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...

VectorDouble &	getNormal ()
	get triangle normal More...

VectorDouble &	getTangent1 ()
	get triangle tangent 1 More...

VectorDouble &	getTangent2 ()
	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 EntityHandle *	getConn ()
	get element connectivity More...

VectorDouble &	getCoords ()
	get triangle coordinates More...

auto	getFTensor1Coords ()
	get get coords at gauss points More...

MatrixDouble &	getNormalsAtGaussPts ()
	if higher order geometry return normals at Gauss pts. More...

ublas::matrix_row< MatrixDouble >	getNormalsAtGaussPts (const int gg)
	if higher order geometry return normals at Gauss pts. More...

MatrixDouble &	getTangent1AtGaussPts ()
	if higher order geometry return tangent vector to triangle at Gauss pts. More...

MatrixDouble &	getTangent2AtGaussPts ()
	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...

FaceElementForcesAndSourcesCore *	getFaceFE ()
	return pointer to Generic Triangle Finite Element object More...

MoFEMErrorCode	loopSideVolumes (const string fe_name, VolumeElementForcesAndSourcesCoreOnSide &fe_method)

Public Attributes
Range &	stimRegion

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...

bool &	doVertices
	\deprectaed If false skip vertices More...

bool &	doEdges
	\deprectaed If false skip edges More...

bool &	doQuads
	\deprectaed More...

bool &	doTris
	\deprectaed More...

bool &	doTets
	\deprectaed More...

bool &	doPrisms
	\deprectaed More...

Private Attributes
boost::shared_ptr< PreviousData >	dataU

boost::shared_ptr< PreviousData >	dataV

VectorDouble	vecF

boost::shared_ptr< PreviousData >	commonDatau

boost::shared_ptr< PreviousData >	commonDatav

std::map< int, BlockData >	setOfBlock

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
ForcesAndSourcesCore *	ptrFE

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.

      : OpVolEle(mass_field, OpVolEle::OPROW)
      , dataU(data_u)
      , stimRegion(stim_region) {}

◆ 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.

      : OpFaceEle(flux_field, OpFaceEle::OPROW), commonDatau(datau),
        commonDatav(datav), setOfBlock(block_map), rhsU(rhs_u),
        stimRegion(stim_region) {}

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.

                                                                  {
    MoFEMFunctionBegin;
    const int nb_dofs = data.getIndices().size();
    // cerr << "In StiffRhsV ..." << endl;
    if (nb_dofs) {
 
      vecF.resize(nb_dofs, false);
      vecF.clear();
      const int nb_integration_pts = getGaussPts().size2();
      auto t_dot_u = getFTensor0FromVec(dataU->mass_dots);
 
 
      auto t_div_u = getFTensor0FromVec(dataU->flux_divs);
      auto t_row_v_base = data.getFTensor0N();
      auto t_w = getFTensor0IntegrationWeight();
      const double vol = getMeasure();
      const double c_time = getFEMethod()->ts_t;
 
      double dt;
      CHKERR TSGetTimeStep(getFEMethod()->ts, &dt);
 
      double stim = 0.0;
 
      double T = 627.0;
      double duration = 5.0;
 
      if (T - dt < c_time && c_time <= T + duration) {
        EntityHandle stim_ent = getFEEntityHandle();
        if (stimRegion.find(stim_ent) != stimRegion.end()) {
          stim = 40.0;
        } else {
          stim = 0.0;
        }
      }
 
      for (int gg = 0; gg < nb_integration_pts; ++gg) {
        const double a = vol * t_w;
        for (int rr = 0; rr < nb_dofs; ++rr) {
            vecF[rr] += t_row_v_base * (t_dot_u + t_div_u - stim) * a; 
          ++t_row_v_base;
        }
        ++t_dot_u;
        ++t_div_u;
        ++t_w;
      }
      CHKERR VecSetOption(getFEMethod()->ts_F, VEC_IGNORE_NEGATIVE_INDICES,
                          PETSC_TRUE);
      CHKERR VecSetValues(getFEMethod()->ts_F, data, &*vecF.begin(),
                          ADD_VALUES);
    }
    MoFEMFunctionReturn(0);
  }

◆ 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.

                                                                  {
    MoFEMFunctionBegin;
    const int nb_dofs = data.getIndices().size();
    // cerr << "In StiffRhsV ..." << endl;
    if (nb_dofs) {
      // auto find_block_data = [&]() {
      //   EntityHandle fe_ent = getFEEntityHandle();
      //   BlockData *block_raw_ptr = nullptr;
      //   for (auto &m : setOfBlock) {
      //     if (m.second.block_ents.find(fe_ent) != m.second.block_ents.end()) {
      //       block_raw_ptr = &m.second;
      //       break;
      //     }
      //   }
      //   return block_raw_ptr;
      // };
 
      // auto block_data_ptr = find_block_data();
      // if (!block_data_ptr)
      //   SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Block not found");
      // auto &block_data = *block_data_ptr;
 
      vecF.resize(nb_dofs, false);
      vecF.clear();
      const int nb_integration_pts = getGaussPts().size2();
      auto t_u_value = getFTensor0FromVec(commonDatau->mass_values);
      auto t_v_value = getFTensor0FromVec(commonDatav->mass_values);
 
      auto t_mass_dot = getFTensor0FromVec(commonDatau->mass_dots);
      auto t_flux_div = getFTensor0FromVec(commonDatau->flux_divs);
      auto t_row_v_base = data.getFTensor0N();
      auto t_w = getFTensor0IntegrationWeight();
      const double vol = getMeasure();
      auto t_coords = getFTensor1CoordsAtGaussPts();
 
      const double c_time = getFEMethod()->ts_t;
 
      double dt;
      CHKERR TSGetTimeStep(getFEMethod()->ts, &dt);
 
      double stim = 0.0;
 
      double T = 627.0;
      double duration = 5.0;
 
      if (T - dt < c_time && c_time <= T + duration) {
        EntityHandle stim_ent = getFEEntityHandle();
        if (stimRegion.find(stim_ent) != stimRegion.end()) {
          stim = 40.0;
        } else {
          stim = 0.0;
        }
      }
      for (int gg = 0; gg < nb_integration_pts; ++gg) {
        const double a = vol * t_w;
        // double u_dot = exactDot(t_coords(NX), t_coords(NY), ct);
        // double u_lap = exactLap(t_coords(NX), t_coords(NY), ct);
 
        // double f = u_dot - block_data.B0 * u_lap;
        double rhsu = rhsU(t_u_value, t_v_value);
        for (int rr = 0; rr < nb_dofs; ++rr) {
          vecF[rr] += (t_row_v_base * (t_mass_dot + t_flux_div - 0*rhsu - factor * stim)) * a;
          ++t_row_v_base;
        }
        ++t_mass_dot;
        ++t_flux_div;
        ++t_u_value;
        ++t_v_value;
        ++t_w;
        ++t_coords;
      }
      CHKERR VecSetOption(getFEMethod()->ts_F, VEC_IGNORE_NEGATIVE_INDICES,
                          PETSC_TRUE);
      CHKERR VecSetValues(getFEMethod()->ts_F, data, &*vecF.begin(),
                          ADD_VALUES);
    }
    MoFEMFunctionReturn(0);
  }