MyTransport Struct Reference

Application of mix transport data structure. More...

Inheritance diagram for MyTransport:

Collaboration diagram for MyTransport:

Public Member Functions
	MyTransport (MoFEM::Interface &m_field)
MoFEMErrorCode	getSource (EntityHandle ent, const double x, const double y, const double z, double &flux)
	set source term More...
MoFEMErrorCode	getBcOnValues (const EntityHandle ent, const double x, const double y, const double z, double &value)
MoFEMErrorCode	getBcOnFluxes (const EntityHandle ent, const double x, const double y, const double z, double &flux)
	essential (Neumann) boundary condition (set fluxes) More...
	MyTransport (MoFEM::Interface &m_field, BcFluxMap &bc_flux_map)
MoFEMErrorCode	getSource (EntityHandle ent, const double x, const double y, const double z, double &flux)
	set source term More...
MoFEMErrorCode	getBcOnValues (const EntityHandle ent, const double x, const double y, const double z, double &value)
	natural (Dirihlet) boundary conditions (set values) More...
MoFEMErrorCode	getBcOnFluxes (const EntityHandle ent, const double x, const double y, const double z, double &flux)
	essential (Neumann) boundary condition (set fluxes) More...
MoFEMErrorCode	addBoundaryElements (BitRefLevel &ref_level)
	set-up boundary conditions More...
MoFEMErrorCode	refineMesh (MixTransportElement &ufe, const int nb_levels, const int order)
	Refine mesh. More...
MoFEMErrorCode	squashBits ()
	Squash bits of entities. More...
MoFEMErrorCode	updateMeshsetsFieldsAndElements (const int nb_levels)
	update meshsets with new entities after mesh refinement More...
Public Member Functions inherited from MixTransport::MixTransportElement
	MixTransportElement (MoFEM::Interface &m_field)
	construction of this data structure More...
virtual	~MixTransportElement ()
	destructor More...
MoFEMErrorCode	getDirichletBCIndices (IS *is)
	get dof indices where essential boundary conditions are applied More...
virtual MoFEMErrorCode	getSource (const EntityHandle ent, const double x, const double y, const double z, double &flux)
	set source term More...
virtual MoFEMErrorCode	getResistivity (const EntityHandle ent, const double x, const double y, const double z, MatrixDouble3by3 &inv_k)
	natural (Dirichlet) boundary conditions (set values) More...
virtual MoFEMErrorCode	getBcOnValues (const EntityHandle ent, const int gg, const double x, const double y, const double z, double &value)
	evaluate natural (Dirichlet) boundary conditions More...
virtual MoFEMErrorCode	getBcOnFluxes (const EntityHandle ent, const double x, const double y, const double z, double &flux)
	essential (Neumann) boundary condition (set fluxes) More...
MoFEMErrorCode	addFields (const std::string &values, const std::string &fluxes, const int order)
	Add fields to database. More...
MoFEMErrorCode	addFiniteElements (const std::string &fluxes_name, const std::string &values_name)
	add finite elements More...
MoFEMErrorCode	buildProblem (BitRefLevel &ref_level)
	Build problem. More...
MoFEMErrorCode	postProc (const string out_file)
	Post process results. More...
MoFEMErrorCode	createMatrices ()
	create matrices More...
MoFEMErrorCode	solveLinearProblem ()
	solve problem More...
MoFEMErrorCode	calculateResidual ()
	calculate residual More...
MoFEMErrorCode	evaluateError ()
	Calculate error on elements. More...
MoFEMErrorCode	destroyMatrices ()
	destroy matrices More...

Public Attributes
BcFluxMap &	bcFluxMap
EntityHandle	lastEnt
double	lastFlux
Public Attributes inherited from MixTransport::MixTransportElement
MoFEM::Interface &	mField
MyVolumeFE	feVol
	Instance of volume element. More...
MyTriFE	feTri
	Instance of surface element. More...
VectorDouble	valuesAtGaussPts
	values at integration points on element More...
MatrixDouble	valuesGradientAtGaussPts
	gradients at integration points on element More...
VectorDouble	divergenceAtGaussPts
	divergence at integration points on element More...
MatrixDouble	fluxesAtGaussPts
	fluxes at integration points on element More...
set< int >	bcIndices
std::map< int, BlockData >	setOfBlocks
	maps block set id with appropriate BlockData More...
Vec	D
Vec	D0
Vec	F
Mat	Aij
map< double, EntityHandle >	errorMap
double	sumErrorFlux
double	sumErrorDiv
double	sumErrorJump

Detailed Description

Application of mix transport data structure.

define sources and other stuff

MixTransportElement is a class collecting functions, operators and data for mix implementation of transport element. See there to learn how elements are created or how operators look like.

Some methods in MixTransportElement are abstract, f.e. user need to implement own source therm.

MixTransportElement is a class collecting functions, operators and data for mix implementation of transport element. See there to learn how elements are created or how operators look like.

Some methods in MixTransportElement are abstract, f.e. user need to implement own source therm.

Definition at line 24 of file mix_transport.cpp.

Constructor & Destructor Documentation

MyTransport() [1/2]

MyTransport::MyTransport ( MoFEM::Interface &  m_field )

inline

Definition at line 26 of file mix_transport.cpp.

: MixTransportElement(m_field){};

MyTransport() [2/2]

MyTransport::MyTransport ( MoFEM::Interface &  m_field, BcFluxMap &  bc_flux_map  )

inline

Definition at line 53 of file h_adaptive_transport.cpp.

      : MixTransportElement(m_field), bcFluxMap(bc_flux_map), lastEnt(0),
        lastFlux(0) {}

Member Function Documentation

addBoundaryElements()

MoFEMErrorCode MyTransport::addBoundaryElements ( BitRefLevel &  ref_level )

inline

set-up boundary conditions

Parameters

ref_level

mesh refinement level

Note

It is assumed that user would like to something non-standard with boundary conditions, have a own type of data structures to pass to functions calculating values and fluxes on boundary. For example BcFluxMap. That way this function is implemented here not in generic class MixTransportElement.

Returns

error code

Definition at line 129 of file h_adaptive_transport.cpp.

                                                             {
    MoFEMFunctionBegin;
    Range tets;
    CHKERR mField.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        ref_level, BitRefLevel().set(), MBTET, tets);
    Skinner skin(&mField.get_moab());
    Range skin_faces; // skin faces from 3d ents
    CHKERR skin.find_skin(0, tets, false, skin_faces);
    // note: what is essential (dirichlet) is natural (neumann) for mix-FE
    // compared to classical FE
    Range natural_bc;
    for (_IT_CUBITMESHSETS_BY_BCDATA_TYPE_FOR_LOOP_(
             mField, NODESET | TEMPERATURESET, it)) {
      Range tris;
      CHKERR it->getMeshsetIdEntitiesByDimension(mField.get_moab(), 2, tris,
                                                 true);
      natural_bc.insert(tris.begin(), tris.end());
    }
    for (_IT_CUBITMESHSETS_BY_BCDATA_TYPE_FOR_LOOP_(
             mField, SIDESET | HEATFLUXSET, it)) {
      HeatFluxCubitBcData mydata;
      CHKERR it->getBcDataStructure(mydata);
      if (mydata.data.flag1 == 1) {
        Range tris;
        CHKERR it->getMeshsetIdEntitiesByDimension(mField.get_moab(), 2, tris,
                                                   true);
        bcFluxMap[it->getMeshsetId()].eNts = tris;
        bcFluxMap[it->getMeshsetId()].fLux = mydata.data.value1;
        // cerr << bcFluxMap[it->getMeshsetId()].eNts << endl;
        // cerr << bcFluxMap[it->getMeshsetId()].fLux << endl;
      }
    }
    Range essential_bc = subtract(skin_faces, natural_bc);
    Range bit_tris;
    CHKERR mField.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        ref_level, BitRefLevel().set(), MBTRI, bit_tris);
    essential_bc = intersect(bit_tris, essential_bc);
    natural_bc = intersect(bit_tris, natural_bc);
    CHKERR mField.add_ents_to_finite_element_by_type(essential_bc, MBTRI,
                                                     "MIX_BCFLUX");
    CHKERR mField.add_ents_to_finite_element_by_type(natural_bc, MBTRI,
                                                     "MIX_BCVALUE");
    // CHKERR
    // mField.add_ents_to_finite_element_by_type(skin_faces,MBTRI,"MIX_BCVALUE");
    MoFEMFunctionReturn(0);
  }

getBcOnFluxes() [1/2]

MoFEMErrorCode MyTransport::getBcOnFluxes ( const EntityHandle  ent, const double  x, const double  y, const double  z, double &  flux  )

inlinevirtual

essential (Neumann) boundary condition (set fluxes)

Parameters

ent	handle to finite element entity
x	coord
y	coord
z	coord
flux	reference to flux which is set by function

Returns

[description]

Reimplemented from MixTransport::MixTransportElement.

Definition at line 43 of file mix_transport.cpp.

                                                                             {
    MoFEMFunctionBeginHot;
    flux = 0;
    MoFEMFunctionReturnHot(0);
  }

getBcOnFluxes() [2/2]

MoFEMErrorCode MyTransport::getBcOnFluxes ( const EntityHandle  ent, const double  x, const double  y, const double  z, double &  flux  )

inlinevirtual

essential (Neumann) boundary condition (set fluxes)

Parameters

ent	handle to finite element entity
x	coord
y	coord
z	coord
flux	reference to flux which is set by function

Returns

[description]

Reimplemented from MixTransport::MixTransportElement.

Definition at line 98 of file h_adaptive_transport.cpp.

                                                                             {
    MoFEMFunctionBeginHot;
    if (lastEnt == ent) {
      flux = lastFlux;
    } else {
      flux = 0;
      for (BcFluxMap::iterator mit = bcFluxMap.begin(); mit != bcFluxMap.end();
           mit++) {
        Range &tris = mit->second.eNts;
        if (tris.find(ent) != tris.end()) {
          flux = mit->second.fLux;
        }
      }
      lastEnt = ent;
      lastFlux = flux;
    }
    MoFEMFunctionReturnHot(0);
  }

getBcOnValues() [1/2]

MoFEMErrorCode MyTransport::getBcOnValues ( const EntityHandle  ent, const double  x, const double  y, const double  z, double &  value  )

inline

Definition at line 36 of file mix_transport.cpp.

                                                                              {
    MoFEMFunctionBeginHot;
    value = 1;
    MoFEMFunctionReturnHot(0);
  }

getBcOnValues() [2/2]

MoFEMErrorCode MyTransport::getBcOnValues ( const EntityHandle  ent, const double  x, const double  y, const double  z, double &  value  )

inline

natural (Dirihlet) boundary conditions (set values)

Parameters

ent	handle to finite element entity
x	coord
y	coord
z	coord
value	reference to value set by function

Returns

error code

Definition at line 82 of file h_adaptive_transport.cpp.

                                                                              {
    MoFEMFunctionBeginHot;
    value = 0;
    MoFEMFunctionReturnHot(0);
  }

getSource() [1/2]

MoFEMErrorCode MyTransport::getSource ( EntityHandle  ent, const double  x, const double  y, const double  z, double &  flux  )

inlinevirtual

set source term

Parameters

ent	handle to entity on which function is evaluated
x	coord
y	coord
z	coord
flux	reference to source term set by function

Returns

error code

Reimplemented from MixTransport::MixTransportElement.

Definition at line 28 of file mix_transport.cpp.

                                                         {
    MoFEMFunctionBeginHot;
    // double d = std::sqrt(x*x+y*y+z*z);
    flux = 1; //-pow(d,5./4.);
    MoFEMFunctionReturnHot(0);
  }

getSource() [2/2]

MoFEMErrorCode MyTransport::getSource ( EntityHandle  ent, const double  x, const double  y, const double  z, double &  flux  )

inlinevirtual

set source term

Parameters

ent	handle to entity on which function is evaluated
x	coord
y	coord
z	coord
flux	reference to source term set by function

Returns

error code

Reimplemented from MixTransport::MixTransportElement.

Definition at line 66 of file h_adaptive_transport.cpp.

                                                         {
    MoFEMFunctionBeginHot;
    flux = 0;
    MoFEMFunctionReturnHot(0);
  }

refineMesh()

MoFEMErrorCode MyTransport::refineMesh ( MixTransportElement &  ufe, const int  nb_levels, const int  order  )

inline

Refine mesh.

Parameters

ufe	general data structure
nb_levels	number of refinement levels
order	set order of approximation

Returns

errpr code

Refinement of could result in distorted mesh, for example, imagine when you have two levels of non-uniform refinement. Some tetrahedra on the mesh at first refinement instance are only refined by splitting subset of edges on it. Then refined child tetrahedra usually will have worse quality than quality of parent element. Refining such element in subsequent mesh refinement, potentially will deteriorate elements quality even worse. To prevent that adding new refinement level, recreate whole hierarchy of meshes.

Note on subsequent improvement could include refinement of tetrahedra from different levels, including initial mesh. So refinement two could split elements created during refinement one and also split elements from an initial mesh.

That adding the new refinement level creates refinement hierarchy of meshes from a scratch, not adding to existing one.

Entities from previous hierarchy are used in that process, but bit levels on those entities are squashed.

Definition at line 203 of file h_adaptive_transport.cpp.

                                             {
    MeshRefinement *refine_ptr;
    MoFEMFunctionBegin;
    // get refined edges having child vertex
    auto ref_ents_ptr = mField.get_ref_ents();
    typedef RefEntity_multiIndex::index<
        Composite_EntType_and_ParentEntType_mi_tag>::type RefEntsByComposite;
    const RefEntsByComposite &ref_ents =
        ref_ents_ptr->get<Composite_EntType_and_ParentEntType_mi_tag>();
    RefEntsByComposite::iterator rit, hi_rit;
    rit = ref_ents.lower_bound(boost::make_tuple(MBVERTEX, MBEDGE));
    hi_rit = ref_ents.upper_bound(boost::make_tuple(MBVERTEX, MBEDGE));
    Range refined_edges;
    // thist loop is over vertices which parent is edge
    for (; rit != hi_rit; rit++) {
      refined_edges.insert((*rit)->getParentEnt()); // get parent edge
    }
    // get tets which has large error
    Range tets_to_refine;
    const double max_error = ufe.errorMap.rbegin()->first;
    // int size = ((double)5/6)*ufe.errorMap.size();
    for (map<double, EntityHandle>::iterator mit = ufe.errorMap.begin();
         mit != ufe.errorMap.end(); mit++) {
      // cerr << mit->first << " " << mit->second << endl;
      // if((size--)>0) continue;
      if (mit->first < 0.25 * max_error)
        continue;
      tets_to_refine.insert(mit->second);
    }
    Range tets_to_refine_edges;
    CHKERR mField.get_moab().get_adjacencies(
        tets_to_refine, 1, false, tets_to_refine_edges, moab::Interface::UNION);
    refined_edges.merge(tets_to_refine_edges);
    CHKERR mField.getInterface(refine_ptr);
    for (int ll = 0; ll != nb_levels; ll++) {
      Range edges;
      CHKERR mField.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
          BitRefLevel().set(ll), BitRefLevel().set(), MBEDGE, edges);
      edges = intersect(edges, refined_edges);
      // add edges to refine at current level edges (some of the where refined
      // before)
      CHKERR refine_ptr->addVerticesInTheMiddleOfEdges(
          edges, BitRefLevel().set(ll + 1));
      //  get tets at current level
      Range tets;
      CHKERR mField.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
          BitRefLevel().set(ll), BitRefLevel().set(), MBTET, tets);
      CHKERR refine_ptr->refineTets(tets, BitRefLevel().set(ll + 1));
      CHKERR updateMeshsetsFieldsAndElements(ll + 1);
    }
 
    // update fields and elements
    EntityHandle ref_meshset;
    CHKERR mField.get_moab().create_meshset(MESHSET_SET, ref_meshset);
    {
      // cerr << BitRefLevel().set(nb_levels) << endl;
      CHKERR mField.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
          BitRefLevel().set(nb_levels), BitRefLevel().set(), MBTET,
          ref_meshset);
 
      Range ref_tets;
      CHKERR mField.get_moab().get_entities_by_type(ref_meshset, MBTET,
                                                    ref_tets);
 
      // add entities to field
      CHKERR mField.add_ents_to_field_by_type(ref_meshset, MBTET, "FLUXES");
      CHKERR mField.add_ents_to_field_by_type(ref_meshset, MBTET, "VALUES");
      CHKERR mField.set_field_order(0, MBTET, "FLUXES", order + 1);
      CHKERR mField.set_field_order(0, MBTRI, "FLUXES", order + 1);
      CHKERR mField.set_field_order(0, MBTET, "VALUES", order);
 
      // add entities to skeleton
      Range ref_tris;
      CHKERR mField.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
          BitRefLevel().set(nb_levels), BitRefLevel().set(), MBTRI, ref_tris);
      CHKERR mField.add_ents_to_finite_element_by_type(ref_tris, MBTRI,
                                                       "MIX_SKELETON");
 
      // add entities to finite elements
      for (_IT_CUBITMESHSETS_BY_BCDATA_TYPE_FOR_LOOP_(
               mField, BLOCKSET | MAT_THERMALSET, it)) {
        Mat_Thermal temp_data;
        CHKERR it->getAttributeDataStructure(temp_data);
        setOfBlocks[it->getMeshsetId()].cOnductivity =
            temp_data.data.Conductivity;
        setOfBlocks[it->getMeshsetId()].cApacity = temp_data.data.HeatCapacity;
        CHKERR mField.get_moab().get_entities_by_type(
            it->meshset, MBTET, setOfBlocks[it->getMeshsetId()].tEts, true);
        setOfBlocks[it->getMeshsetId()].tEts =
            intersect(ref_tets, setOfBlocks[it->getMeshsetId()].tEts);
        CHKERR mField.add_ents_to_finite_element_by_type(
            setOfBlocks[it->getMeshsetId()].tEts, MBTET, "MIX");
      }
    }
    CHKERR mField.get_moab().delete_entities(&ref_meshset, 1);
    MoFEMFunctionReturn(0);
  }

squashBits()

MoFEMErrorCode MyTransport::squashBits ( )

inline

Squash bits of entities.

Information about hierarchy of meshsets is lost, but entities are not deleted from the mesh. After squash entities bits, new hierarchy can be created.

Returns

error code

Definition at line 310 of file h_adaptive_transport.cpp.

                              {
    MoFEMFunctionBegin;
    BitRefLevel all_but_0;
    all_but_0.set(0);
    all_but_0.flip();
    BitRefLevel garbage_bit;
    garbage_bit.set(BITREFLEVEL_SIZE - 1); // Garbage level
    auto ref_ents_ptr = mField.get_ref_ents();
    RefEntity_multiIndex::iterator mit = ref_ents_ptr->begin();
    for (; mit != ref_ents_ptr->end(); mit++) {
      if (mit->get()->getEntType() == MBENTITYSET)
        continue;
      BitRefLevel bit = mit->get()->getBitRefLevel();
      if ((all_but_0 & bit) == bit) {
        *(const_cast<RefEntity *>(mit->get())->getBitRefLevelPtr()) =
            garbage_bit;
      } else {
        *(const_cast<RefEntity *>(mit->get())->getBitRefLevelPtr()) =
            BitRefLevel().set(0);
      }
    }
    MoFEMFunctionReturn(0);
  }

updateMeshsetsFieldsAndElements()

MoFEMErrorCode MyTransport::updateMeshsetsFieldsAndElements ( const int  nb_levels )

inline

update meshsets with new entities after mesh refinement

Parameters

nb_levels	nb_levels
order	appropriate order

Returns

error code

Definition at line 340 of file h_adaptive_transport.cpp.

                                                                      {
    BitRefLevel ref_level;
    MoFEMFunctionBegin;
    ref_level.set(nb_levels);
    for (_IT_CUBITMESHSETS_FOR_LOOP_(mField, it)) {
      EntityHandle meshset = it->meshset;
      CHKERR mField.getInterface<BitRefManager>()
          ->updateMeshsetByEntitiesChildren(meshset, ref_level, meshset,
                                            MBMAXTYPE, true);
    }
    MoFEMFunctionReturn(0);
  }

Member Data Documentation

bcFluxMap

BcFluxMap& MyTransport::bcFluxMap

Definition at line 49 of file h_adaptive_transport.cpp.

lastEnt

EntityHandle MyTransport::lastEnt

Definition at line 50 of file h_adaptive_transport.cpp.

lastFlux

double MyTransport::lastFlux

Definition at line 51 of file h_adaptive_transport.cpp.

---

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

• users_modules/tutorials/cor-0to1/atom_tests/mix_transport.cpp
• users_modules/tutorials/cor-0to1/h_adaptive_transport.cpp