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

Inheritance diagram for GelModule::Gel::OpJacobian:

Collaboration diagram for GelModule::Gel::OpJacobian:

Public Member Functions
	OpJacobian (const string field_name, vector< int > tags, boost::shared_ptr< Gel::ConstitutiveEquation< adouble > > ce, CommonData &common_data, bool calculate_residual, bool calculate_jacobian)

PetscErrorCode	recordStressTotal ()

PetscErrorCode	recordSolventFlux ()

PetscErrorCode	recordSolventConcentrationDot ()

PetscErrorCode	recordResidualStrainHat ()

PetscErrorCode	calculateFunction (TagEvaluate te, double *ptr)

PetscErrorCode	calculateJacobian (TagEvaluate te)

PetscErrorCode	calculateAtIntPtsStressTotal ()

PetscErrorCode	calculateAtIntPtsSolventFlux ()

PetscErrorCode	calculateAtIntPtsSolventDot ()

PetscErrorCode	calculateAtIntPtrsResidualStrainHat ()

PetscErrorCode	doWork (int row_side, EntityType row_type, DataForcesAndSurcesCore::EntData &row_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 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 Attributes
vector< int >	tagS

boost::shared_ptr< Gel::ConstitutiveEquation< adouble > >	cE

CommonData &	commonData

bool	calculateResidualBool

bool	calculateJacobianBool

bool &	recordOn

map< int, int > &	nbActiveVariables

map< int, int > &	nbActiveResults

int	nbGaussPts

VectorDouble	activeVariables

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...

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)>

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)

Protected Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCore *	ptrFE

Detailed Description

Definition at line 541 of file Gels.hpp.

Constructor & Destructor Documentation

◆ OpJacobian()

GelModule::Gel::OpJacobian::OpJacobian	(	const string	field_name,
		vector< int >	tags,
		boost::shared_ptr< Gel::ConstitutiveEquation< adouble > >	ce,
		CommonData &	common_data,
		bool	calculate_residual,
		bool	calculate_jacobian
	)

inline

Definition at line 553 of file Gels.hpp.

      :
     MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator(
       field_name,UserDataOperator::OPROW
     ),
     tagS(tags),
     cE(ce),
     commonData(common_data),
     calculateResidualBool(calculate_residual),
     calculateJacobianBool(calculate_jacobian),
     recordOn(common_data.recordOn),
     nbActiveVariables(common_data.nbActiveVariables),
     nbActiveResults(common_data.nbActiveResults) {
     }

Member Function Documentation

◆ calculateAtIntPtrsResidualStrainHat()

PetscErrorCode GelModule::Gel::OpJacobian::calculateAtIntPtrsResidualStrainHat ( )

inline

Definition at line 1006 of file Gels.hpp.

                                                          {
       PetscFunctionBegin;
  
       try {
         if(tagS[RESIDUALSTRAINHAT]<0) {
           PetscFunctionReturn(0);
         }
         
         activeVariables.resize(nbActiveVariables[tagS[RESIDUALSTRAINHAT]]);
         for(int gg = 0;gg<nbGaussPts;gg++) {
           MatrixDouble &F = (commonData.gradAtGaussPts[commonData.spatialPositionName])[gg];
           VectorDouble &strain_hat = (commonData.dataAtGaussPts[commonData.strainHatName])[gg];
           VectorDouble &strain_hat_dot = (commonData.dataAtGaussPts[commonData.strainHatNameDot])[gg];
           int nb_active_variables = 0;
           // Activate gradient of defamation
           for(int dd1 = 0;dd1<3;dd1++) {
             for(int dd2 = 0;dd2<3;dd2++) {
               activeVariables[nb_active_variables++] = F(dd1,dd2);
             }
           }
           // Using vector notation to store hatStrain
           // xx,yy,zz,2xy,2yz,2zy
           for(int ii = 0;ii<6;ii++) {
             activeVariables[nb_active_variables++] = strain_hat[ii];
           }
           // Using vector notation to store hatStrainDot
           for(int ii = 0;ii<6;ii++) {
             activeVariables[nb_active_variables++] = strain_hat_dot[ii];
           }
           if(nb_active_variables!=nbActiveVariables[tagS[RESIDUALSTRAINHAT]]) {
             SETERRQ(
               PETSC_COMM_SELF,MOFEM_IMPOSIBLE_CASE,"Number of active variables does not much"
             );
           }
           if(calculateResidualBool) {
             if(gg == 0) {
               commonData.residualStrainHat.resize(nbGaussPts);
             }
             commonData.residualStrainHat[gg].resize(6,false);
             ierr = calculateFunction(
               RESIDUALSTRAINHAT,&commonData.residualStrainHat[gg][0]
             ); CHKERRQ(ierr);
           }
           if(calculateJacobianBool) {
             if(gg == 0) {
               commonData.jacStrainHat.resize(nbGaussPts);
               commonData.jacRowPtr.resize(nbActiveResults[tagS[RESIDUALSTRAINHAT]]);
             }
             commonData.jacStrainHat[gg].resize(
               nbActiveResults[tagS[RESIDUALSTRAINHAT]],
               nbActiveVariables[tagS[RESIDUALSTRAINHAT]],
               false
             );
             for(int dd = 0;dd<nbActiveResults[tagS[RESIDUALSTRAINHAT]];dd++) {
               commonData.jacRowPtr[dd] = &commonData.jacStrainHat[gg](dd,0);
             }
             ierr = calculateJacobian(RESIDUALSTRAINHAT); CHKERRQ(ierr);
           }
         }
  
  
       } catch (const std::exception& ex) {
         ostringstream ss;
         ss << "throw in method: " << ex.what() << endl;
         SETERRQ(PETSC_COMM_SELF,1,ss.str().c_str());
       }
  
       PetscFunctionReturn(0);
     }

◆ calculateAtIntPtsSolventDot()

PetscErrorCode GelModule::Gel::OpJacobian::calculateAtIntPtsSolventDot ( )

inline

Definition at line 958 of file Gels.hpp.

                                                  {
       PetscFunctionBegin;
  
       if(tagS[SOLVENTRATE]<0) {
         PetscFunctionReturn(0);
       }
  
       
  
       activeVariables.resize(nbActiveVariables[tagS[SOLVENTRATE]],false);
  
       for(int gg = 0;gg<nbGaussPts;gg++) {
         MatrixDouble &F = (commonData.gradAtGaussPts[commonData.spatialPositionName])[gg];
         MatrixDouble &F_dot = (commonData.gradAtGaussPts[commonData.spatialPositionNameDot])[gg];
         int nb_active_variables = 0;
         // Activate gradient of defamation
         for(int dd1 = 0;dd1<3;dd1++) {
           for(int dd2 = 0;dd2<3;dd2++) {
             activeVariables[nb_active_variables++] = F(dd1,dd2);
           }
         }
         for(int dd1 = 0;dd1<3;dd1++) {
           for(int dd2 = 0;dd2<3;dd2++) {
             activeVariables[nb_active_variables++] = F_dot(dd1,dd2);
           }
         }
         if(nb_active_variables!=nbActiveVariables[tagS[SOLVENTRATE]]) {
           SETERRQ(
             PETSC_COMM_SELF,MOFEM_IMPOSIBLE_CASE,"Number of active variables does not much"
           );
         }
         if(calculateResidualBool) {
           ierr = calculateFunction(SOLVENTRATE,&commonData.solventConcentrationDot[gg]); CHKERRQ(ierr);
         }
         if(calculateJacobianBool) {
           if(gg == 0) {
             commonData.jacSolventDot.resize(nbGaussPts);
             commonData.jacRowPtr.resize(nbActiveResults[tagS[SOLVENTRATE]]);
           }
           commonData.jacSolventDot[gg].resize(nbActiveVariables[tagS[SOLVENTRATE]]);
           commonData.jacRowPtr[0] = &commonData.jacSolventDot[gg][0];
           ierr = calculateJacobian(SOLVENTRATE); CHKERRQ(ierr);
         }
       }
  
       PetscFunctionReturn(0);
     }

◆ calculateAtIntPtsSolventFlux()

PetscErrorCode GelModule::Gel::OpJacobian::calculateAtIntPtsSolventFlux ( )

inline

Definition at line 908 of file Gels.hpp.

                                                   {
       PetscFunctionBegin;
  
       if(tagS[SOLVENTFLUX]<0) {
         PetscFunctionReturn(0);
       }
  
       
  
       activeVariables.resize(nbActiveResults[tagS[SOLVENTFLUX]]);
  
       for(int gg = 0;gg<nbGaussPts;gg++) {
         MatrixDouble &gradient_mu = (commonData.gradAtGaussPts[commonData.muName])[gg];
         int nb_active_variables = 0;
         // Activate rate of gradient of defamation
         for(int ii = 0;ii<3;ii++) {
           activeVariables[nb_active_variables++] = gradient_mu(0,ii);
         }
         if(nb_active_variables!=nbActiveVariables[tagS[SOLVENTFLUX]]) {
           SETERRQ(
             PETSC_COMM_SELF,MOFEM_IMPOSIBLE_CASE,"Number of active variables does not much"
           );
         }
         if(calculateResidualBool) {
           commonData.solventFlux[gg].resize(3,false);
           ierr = calculateFunction(
             SOLVENTFLUX,
             &(commonData.solventFlux[gg][0])
           ); CHKERRQ(ierr);
         }
         if(calculateJacobianBool) {
           if(gg == 0) {
             commonData.jacSolventFlux.resize(nbGaussPts);
             commonData.jacRowPtr.resize(nbActiveResults[tagS[SOLVENTFLUX]]);
           }
           commonData.jacSolventFlux[gg].resize(
             nbActiveResults[tagS[SOLVENTFLUX]],
             nbActiveVariables[tagS[SOLVENTFLUX]],
             false
           );
           for(int dd = 0;dd<nbActiveResults[tagS[SOLVENTFLUX]];dd++) {
             commonData.jacRowPtr[dd] = &(commonData.jacSolventFlux[gg](dd,0));
           }
           ierr = calculateJacobian(SOLVENTFLUX); CHKERRQ(ierr);
         }
       }
  
       PetscFunctionReturn(0);
     }

◆ calculateAtIntPtsStressTotal()

PetscErrorCode GelModule::Gel::OpJacobian::calculateAtIntPtsStressTotal ( )

inline

Definition at line 833 of file Gels.hpp.

                                                   {
       PetscFunctionBegin;
  
       try {
  
         if(tagS[STRESSTOTAL]<0) {
           PetscFunctionReturn(0);
         }
  
  
         
         activeVariables.resize(nbActiveVariables[tagS[STRESSTOTAL]],false);
  
         for(int gg = 0;gg<nbGaussPts;gg++) {
  
           MatrixDouble &F = (commonData.gradAtGaussPts[commonData.spatialPositionName])[gg];
           VectorDouble &strain_hat = (commonData.dataAtGaussPts[commonData.strainHatName])[gg];
           double mu = (commonData.dataAtGaussPts[commonData.muName])[gg][0];
           int nb_active_variables = 0;
           // Activate gradient of defamation
           for(int dd1 = 0;dd1<3;dd1++) {
             for(int dd2 = 0;dd2<3;dd2++) {
               activeVariables[nb_active_variables++] = F(dd1,dd2);
             }
           }
           // Using vector notation to store hatStrain
           // xx,yy,zz,2xy,2yz,2zy
           for(int ii = 0;ii<6;ii++) {
             activeVariables[nb_active_variables++] = strain_hat[ii];
           }
           // chemical load
           activeVariables[nb_active_variables++] = mu;
  
           if(nb_active_variables!=nbActiveVariables[tagS[STRESSTOTAL]]) {
             SETERRQ(
               PETSC_COMM_SELF,MOFEM_IMPOSIBLE_CASE,
               "Number of active variables does not much"
             );
           }
  
           if(calculateResidualBool) {
             if(gg == 0) {
               commonData.stressTotal.resize(nbGaussPts);
             }
             commonData.stressTotal[gg].resize(3,3,false);
             ierr = calculateFunction(STRESSTOTAL,&commonData.stressTotal[gg](0,0)); CHKERRQ(ierr);
           }
  
           if(calculateJacobianBool) {
             if(gg == 0) {
               commonData.jacStressTotal.resize(nbGaussPts);
               commonData.jacRowPtr.resize(nbActiveResults[tagS[STRESSTOTAL]]);
             }
             commonData.jacStressTotal[gg].resize(
               nbActiveResults[tagS[STRESSTOTAL]],
               nbActiveVariables[tagS[STRESSTOTAL]],
               false
             );
             for(int dd = 0;dd<nbActiveResults[tagS[STRESSTOTAL]];dd++) {
               commonData.jacRowPtr[dd] = &commonData.jacStressTotal[gg](dd,0);
             }
             ierr = calculateJacobian(STRESSTOTAL); CHKERRQ(ierr);
           }
  
         }
  
       } catch (const std::exception& ex) {
         ostringstream ss;
         ss << "throw in method: " << ex.what() << endl;
         SETERRQ(PETSC_COMM_SELF,1,ss.str().c_str());
       }
  
       PetscFunctionReturn(0);
     }

◆ calculateFunction()

PetscErrorCode GelModule::Gel::OpJacobian::calculateFunction	(	TagEvaluate	te,
		double *	ptr
	)

inline

Definition at line 786 of file Gels.hpp.

                                                                  {
       PetscFunctionBegin;
  
       int r;
       //play recorder for values
       r = ::function(
         tagS[te],
         nbActiveResults[tagS[te]],
         nbActiveVariables[tagS[te]],
         &activeVariables[0],
         ptr
       );
       if(r<3) { // function is locally analytic
         SETERRQ1(
           PETSC_COMM_SELF,MOFEM_OPERATION_UNSUCCESSFUL,
           "ADOL-C function evaluation with error r = %d",r
         );
       }
  
       PetscFunctionReturn(0);
     }

◆ calculateJacobian()

PetscErrorCode GelModule::Gel::OpJacobian::calculateJacobian ( TagEvaluate te )

inline

Definition at line 808 of file Gels.hpp.

                                                      {
       PetscFunctionBegin;
       try {
         int r;
         r = jacobian(
           tagS[te],
           nbActiveResults[tagS[te]],
           nbActiveVariables[tagS[te]],
           &activeVariables[0],
           &(commonData.jacRowPtr[0])
         );
         if(r<3) {
           SETERRQ(
             PETSC_COMM_SELF,MOFEM_OPERATION_UNSUCCESSFUL,
             "ADOL-C function evaluation with error"
           );
         }
       } catch (const std::exception& ex) {
         ostringstream ss;
         ss << "throw in method: " << ex.what() << endl;
         SETERRQ(PETSC_COMM_SELF,1,ss.str().c_str());
       }
       PetscFunctionReturn(0);
     }

◆ doWork()

PetscErrorCode GelModule::Gel::OpJacobian::doWork	(	int	row_side,
		EntityType	row_type,
		DataForcesAndSurcesCore::EntData &	row_data
	)

inline

Definition at line 1076 of file Gels.hpp.

       {
       PetscFunctionBegin;
       
       
  
       if(row_type != MBVERTEX) PetscFunctionReturn(0);
       nbGaussPts = row_data.getN().size1();
  
       Tag th_block_id;
       EntityHandle ent = getNumeredEntFiniteElementPtr()->getEnt();
       rval = getVolumeFE()->
       mField.get_moab().tag_get_handle("BLOCK_ID",th_block_id); CHKERRQ_MOAB(rval);
       rval = getVolumeFE()->
       mField.get_moab().tag_get_data(th_block_id,&ent,1,&(cE->iD)); CHKERRQ_MOAB(rval);
  
       try {
  
         if(recordOn) {
           ierr = recordStressTotal(); CHKERRQ(ierr);
           ierr = recordSolventFlux(); CHKERRQ(ierr);
           ierr = recordSolventConcentrationDot(); CHKERRQ(ierr);
           ierr = recordResidualStrainHat(); CHKERRQ(ierr);
         }
  
         ierr = calculateAtIntPtsStressTotal(); CHKERRQ(ierr);
         ierr = calculateAtIntPtsSolventFlux(); CHKERRQ(ierr);
         ierr = calculateAtIntPtsSolventDot(); CHKERRQ(ierr);
         ierr = calculateAtIntPtrsResidualStrainHat(); CHKERRQ(ierr);
  
       } catch (const std::exception& ex) {
         ostringstream ss;
         ss << "throw in method: " << ex.what() << endl;
         SETERRQ(PETSC_COMM_SELF,1,ss.str().c_str());
       }
  
       PetscFunctionReturn(0);
     }

◆ recordResidualStrainHat()

PetscErrorCode GelModule::Gel::OpJacobian::recordResidualStrainHat ( )

inline

Definition at line 719 of file Gels.hpp.

                                              {
       PetscFunctionBegin;
  
       if(tagS[RESIDUALSTRAINHAT]<0) {
         PetscFunctionReturn(0);
       }
  
       
  
       cE->F.resize(3,3,false);
       cE->strainHat.resize(3,3,false);
       cE->strainHatDot.resize(3,3,false);
       MatrixDouble &F = (commonData.gradAtGaussPts[commonData.spatialPositionName])[0];
       VectorDouble &strain_hat = (commonData.dataAtGaussPts[commonData.strainHatName])[0];
       VectorDouble &strain_hat_dot = (commonData.dataAtGaussPts[commonData.strainHatNameDot])[0];
       trace_on(tagS[RESIDUALSTRAINHAT]);
       {
         // Activate gradient of defamation
         nbActiveVariables[tagS[RESIDUALSTRAINHAT]] = 0;
         for(int dd1 = 0;dd1<3;dd1++) {
           for(int dd2 = 0;dd2<3;dd2++) {
             cE->F(dd1,dd2) <<= F(dd1,dd2);
             nbActiveVariables[tagS[RESIDUALSTRAINHAT]]++;
           }
         }
         // Using vector notation to store hatStrain
         // xx,yy,zz,2xy,2yz,2zy
         cE->strainHat(0,0) <<= strain_hat[0];
         cE->strainHat(1,1) <<= strain_hat[1];
         cE->strainHat(2,2) <<= strain_hat[2];
         cE->strainHat(0,1) <<= strain_hat[3];
         cE->strainHat(1,2) <<= strain_hat[4];
         cE->strainHat(0,2) <<= strain_hat[5];
         nbActiveVariables[tagS[RESIDUALSTRAINHAT]] += 6;
         cE->strainHat(1,0) = cE->strainHat(0,1);
         cE->strainHat(2,1) = cE->strainHat(1,2);
         cE->strainHat(2,0) = cE->strainHat(0,2);
         // Activate strain hat dot
         cE->strainHatDot(0,0) <<= strain_hat_dot[0];
         cE->strainHatDot(1,1) <<= strain_hat_dot[1];
         cE->strainHatDot(2,2) <<= strain_hat_dot[2];
         cE->strainHatDot(0,1) <<= strain_hat_dot[3];
         cE->strainHatDot(1,2) <<= strain_hat_dot[4];
         cE->strainHatDot(0,2) <<= strain_hat_dot[5];
         nbActiveVariables[tagS[RESIDUALSTRAINHAT]] += 6;
         cE->strainHatDot(1,0) = cE->strainHatDot(0,1);
         cE->strainHatDot(2,1) = cE->strainHatDot(1,2);
         cE->strainHatDot(2,0) = cE->strainHatDot(0,2);
         ierr = cE->calculateStrainTotal(); CHKERRQ(ierr);
         ierr = cE->calculateStressBeta(); CHKERRQ(ierr);
         ierr = cE->calculateStrainHatFlux(); CHKERRQ(ierr);
         ierr = cE->calculateResidualStrainHat(); CHKERRQ(ierr);
         nbActiveResults[tagS[RESIDUALSTRAINHAT]] = 0;
         commonData.residualStrainHat.resize(nbGaussPts);
         commonData.residualStrainHat[0].resize(6,false);
         cE->residualStrainHat(0,0) >>= commonData.residualStrainHat[0][nbActiveResults[tagS[RESIDUALSTRAINHAT]]++];
         cE->residualStrainHat(1,1) >>= commonData.residualStrainHat[0][nbActiveResults[tagS[RESIDUALSTRAINHAT]]++];
         cE->residualStrainHat(2,2) >>= commonData.residualStrainHat[0][nbActiveResults[tagS[RESIDUALSTRAINHAT]]++];
         cE->residualStrainHat(0,1) >>= commonData.residualStrainHat[0][nbActiveResults[tagS[RESIDUALSTRAINHAT]]++];
         cE->residualStrainHat(1,2) >>= commonData.residualStrainHat[0][nbActiveResults[tagS[RESIDUALSTRAINHAT]]++];
         cE->residualStrainHat(0,2) >>= commonData.residualStrainHat[0][nbActiveResults[tagS[RESIDUALSTRAINHAT]]++];
       }
       trace_off();
  
       PetscFunctionReturn(0);
     }

◆ recordSolventConcentrationDot()

PetscErrorCode GelModule::Gel::OpJacobian::recordSolventConcentrationDot ( )

inline

Definition at line 677 of file Gels.hpp.

                                                    {
       PetscFunctionBegin;
  
       if(tagS[SOLVENTRATE]<0) {
         PetscFunctionReturn(0);
       }
  
       
  
       MatrixDouble &F = (commonData.gradAtGaussPts[commonData.spatialPositionName])[0];
       MatrixDouble &F_dot = (commonData.gradAtGaussPts[commonData.spatialPositionNameDot])[0];
  
       trace_on(tagS[SOLVENTRATE]);
       {
         // Activate rate of gradient of defamation
         nbActiveVariables[tagS[SOLVENTRATE]] = 0;
         cE->F.resize(3,3,false);
         for(int dd1 = 0;dd1<3;dd1++) {
           for(int dd2 = 0;dd2<3;dd2++) {
             cE->F(dd1,dd2) <<= F(dd1,dd2);
             nbActiveVariables[tagS[SOLVENTRATE]]++;
           }
         }
         cE->FDot.resize(3,3,false);
         for(int dd1 = 0;dd1<3;dd1++) {
           for(int dd2 = 0;dd2<3;dd2++) {
             cE->FDot(dd1,dd2) <<= F_dot(dd1,dd2);
             nbActiveVariables[tagS[SOLVENTRATE]]++;
           }
         }
         ierr = cE->calculateTraceStrainTotalDot(); CHKERRQ(ierr);
         ierr = cE->calculateSolventConcentrationDot(); CHKERRQ(ierr);
         nbActiveResults[tagS[SOLVENTRATE]] = 0;
         commonData.solventConcentrationDot.resize(nbGaussPts);
         cE->solventConcentrationDot >>= commonData.solventConcentrationDot[0];
         nbActiveResults[tagS[SOLVENTRATE]]++;
       }
       trace_off();
  
       PetscFunctionReturn(0);
     }

◆ recordSolventFlux()

PetscErrorCode GelModule::Gel::OpJacobian::recordSolventFlux ( )

inline

Definition at line 641 of file Gels.hpp.

                                        {
       PetscFunctionBegin;
       try {
         if(tagS[SOLVENTFLUX]<0) {
           PetscFunctionReturn(0);
         }
         
         cE->gradientMu.resize(3,false);
         MatrixDouble &gradient_mu = (commonData.gradAtGaussPts[commonData.muName])[0];
         trace_on(tagS[SOLVENTFLUX]);
         {
           // Activate rate of gradient of defamation
           nbActiveVariables[tagS[SOLVENTFLUX]] = 0;
           for(int ii = 0;ii<3;ii++) {
             cE->gradientMu[ii] <<= gradient_mu(0,ii);
             nbActiveVariables[tagS[SOLVENTFLUX]]++;
           }
           ierr = cE->calculateSolventFlux(); CHKERRQ(ierr);
           nbActiveResults[tagS[SOLVENTFLUX]] = 0;
           commonData.solventFlux.resize(nbGaussPts);
           commonData.solventFlux[0].resize(3,false);
           for(int d1 = 0;d1<3;d1++) {
             cE->solventFlux[d1] >>= commonData.solventFlux[0][d1];
             nbActiveResults[tagS[SOLVENTFLUX]]++;
           }
         }
         trace_off();
       } catch (const std::exception& ex) {
         ostringstream ss;
         ss << "throw in method: " << ex.what() << endl;
         SETERRQ(PETSC_COMM_SELF,1,ss.str().c_str());
       }
  
       PetscFunctionReturn(0);
     }

◆ recordStressTotal()

PetscErrorCode GelModule::Gel::OpJacobian::recordStressTotal ( )

inline

Definition at line 577 of file Gels.hpp.

                                        {
       
       PetscFunctionBegin;
  
       try {
         if(tagS[STRESSTOTAL]<0) {
           PetscFunctionReturn(0);
         }
         cE->F.resize(3,3,false);
         cE->strainHat.resize(3,3,false);
         MatrixDouble &F = (commonData.gradAtGaussPts[commonData.spatialPositionName])[0];
         VectorDouble &strain_hat = (commonData.dataAtGaussPts[commonData.strainHatName])[0];
         VectorDouble mu = (commonData.dataAtGaussPts[commonData.muName])[0];
         trace_on(tagS[STRESSTOTAL]);
         {
           // Activate gradient of defamation
           nbActiveVariables[tagS[STRESSTOTAL]] = 0;
           for(int dd1 = 0;dd1<3;dd1++) {
             for(int dd2 = 0;dd2<3;dd2++) {
               cE->F(dd1,dd2) <<= F(dd1,dd2);
               nbActiveVariables[tagS[STRESSTOTAL]]++;
             }
           }
           // Using vector notation to store hatStrain
           // xx,yy,zz,2xy,2yz,2zy
           cE->strainHat(0,0) <<= strain_hat[0];
           cE->strainHat(1,1) <<= strain_hat[1];
           cE->strainHat(2,2) <<= strain_hat[2];
           cE->strainHat(0,1) <<= strain_hat[3];
           cE->strainHat(1,2) <<= strain_hat[4];
           cE->strainHat(0,2) <<= strain_hat[5];
           nbActiveVariables[tagS[STRESSTOTAL]] += 6;
           cE->strainHat(1,0) = cE->strainHat(0,1);
           cE->strainHat(2,1) = cE->strainHat(1,2);
           cE->strainHat(2,0) = cE->strainHat(0,2);
           cE->mU <<= mu[0];
           nbActiveVariables[tagS[STRESSTOTAL]]++;
           // Do calculations
           ierr = cE->calculateStrainTotal(); CHKERRQ(ierr);
           ierr = cE->calculateStressAlpha(); CHKERRQ(ierr);
           ierr = cE->calculateStressBeta(); CHKERRQ(ierr);
           ierr = cE->calculateStressBetaHat(); CHKERRQ(ierr);
           // Finally calculate result
           ierr = cE->calculateStressTotal(); CHKERRQ(ierr);
           // Results
           nbActiveResults[tagS[STRESSTOTAL]] = 0;
           commonData.stressTotal.resize(nbGaussPts);
           commonData.stressTotal[0].resize(3,3,false);
           for(int d1 = 0;d1<3;d1++) {
             for(int d2 = 0;d2<3;d2++) {
               cE->stressTotal(d1,d2) >>= (commonData.stressTotal[0])(d1,d2);
               nbActiveResults[tagS[STRESSTOTAL]]++;
             }
           }
         }
         trace_off();
       } catch (const std::exception& ex) {
         ostringstream ss;
         ss << "throw in method: " << ex.what() << endl;
         SETERRQ(PETSC_COMM_SELF,1,ss.str().c_str());
       }
       PetscFunctionReturn(0);
     }

Member Data Documentation

◆ activeVariables

VectorDouble GelModule::Gel::OpJacobian::activeVariables

Definition at line 575 of file Gels.hpp.

◆ calculateJacobianBool

bool GelModule::Gel::OpJacobian::calculateJacobianBool

Definition at line 548 of file Gels.hpp.

◆ calculateResidualBool

bool GelModule::Gel::OpJacobian::calculateResidualBool

Definition at line 547 of file Gels.hpp.

◆ cE

boost::shared_ptr<Gel::ConstitutiveEquation<adouble> > GelModule::Gel::OpJacobian::cE

Definition at line 544 of file Gels.hpp.

◆ commonData

CommonData& GelModule::Gel::OpJacobian::commonData

Definition at line 545 of file Gels.hpp.

◆ nbActiveResults

map<int,int>& GelModule::Gel::OpJacobian::nbActiveResults

Definition at line 551 of file Gels.hpp.

◆ nbActiveVariables

map<int,int>& GelModule::Gel::OpJacobian::nbActiveVariables

Definition at line 550 of file Gels.hpp.

◆ nbGaussPts

int GelModule::Gel::OpJacobian::nbGaussPts

Definition at line 574 of file Gels.hpp.

◆ recordOn

bool& GelModule::Gel::OpJacobian::recordOn

Definition at line 549 of file Gels.hpp.

◆ tagS

vector<int> GelModule::Gel::OpJacobian::tagS

Definition at line 543 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

◆ OpJacobian()

Member Function Documentation

◆ calculateAtIntPtrsResidualStrainHat()

◆ calculateAtIntPtsSolventDot()

◆ calculateAtIntPtsSolventFlux()

◆ calculateAtIntPtsStressTotal()

◆ calculateFunction()

◆ calculateJacobian()

◆ doWork()

◆ recordResidualStrainHat()

◆ recordSolventConcentrationDot()

◆ recordSolventFlux()

◆ recordStressTotal()

Member Data Documentation

◆ activeVariables

◆ calculateJacobianBool

◆ calculateResidualBool

◆ cE

◆ commonData

◆ nbActiveResults

◆ nbActiveVariables

◆ nbGaussPts

◆ recordOn

◆ tagS