escript
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FinleyDomain implements the AbstractContinuousDomain interface for the Finley library. More...
#include <FinleyDomain.h>
Public Types | |
typedef std::map< int, std::string > | FunctionSpaceNamesMapType |
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typedef int | StatusType |
Public Member Functions | |
FinleyDomain (const std::string &name, int numDim, escript::JMPI jmpi) | |
Constructor for FinleyDomain. More... | |
FinleyDomain (const FinleyDomain &in) | |
Copy constructor. More... | |
~FinleyDomain () | |
Destructor for FinleyDomain. More... | |
void | addDiracPoints (const std::vector< double > &points, const std::vector< int > &tags) |
adds Dirac delta points. Do NOT call this at any time other than construction! Using them later creates consistency problems More... | |
NodeFile * | getNodes () const |
returns a pointer to this domain's node file More... | |
void | setElements (ElementFile *elements) |
replaces the element file by elements More... | |
ElementFile * | getElements () const |
returns a pointer to this domain's element file More... | |
void | setFaceElements (ElementFile *elements) |
replaces the face element file by elements More... | |
ElementFile * | getFaceElements () const |
returns a pointer to this domain's face element file More... | |
void | setContactElements (ElementFile *elements) |
replaces the contact element file by elements More... | |
ElementFile * | getContactElements () const |
returns a pointer to this domain's contact element file More... | |
void | setPoints (ElementFile *elements) |
replaces the point element file by elements More... | |
ElementFile * | getPoints () const |
returns a pointer to this domain's point (nodal) element file More... | |
virtual escript::JMPI | getMPI () const |
returns a reference to the MPI information wrapper for this domain More... | |
virtual int | getMPISize () const |
returns the number of processors used for this domain More... | |
virtual int | getMPIRank () const |
returns the number MPI rank of this processor More... | |
virtual void | MPIBarrier () const |
If compiled for MPI then execute an MPI_Barrier, else do nothing. More... | |
virtual bool | onMasterProcessor () const |
returns true if on MPI processor 0, else false More... | |
MPI_Comm | getMPIComm () const |
get the communicator for this domain. Returns an integer on non-MPI builds Routine must be implemented by the DomainAdapter. More... | |
void | write (const std::string &fileName) const |
writes the current mesh to a file with the given name in the fly file format. More... | |
void | Print_Mesh_Info (bool full=false) const |
void | dump (const std::string &fileName) const |
dumps the mesh to a file with the given name. More... | |
int | getTagFromSampleNo (int functionSpaceType, index_t sampleNo) const |
Return the tag key for the given sample number. More... | |
const index_t * | borrowSampleReferenceIDs (int functionSpaceType) const |
Return the reference number of the given sample number. More... | |
virtual bool | isValidFunctionSpaceType (int functionSpaceType) const |
Returns true if the given integer is a valid function space type for this domain. More... | |
virtual std::string | getDescription () const |
Return a description for this domain. More... | |
virtual std::string | functionSpaceTypeAsString (int functionSpaceType) const |
Return a description for the given function space type code. More... | |
void | setFunctionSpaceTypeNames () |
Build the table of function space type names. More... | |
virtual int | getContinuousFunctionCode () const |
Return a continuous FunctionSpace code. More... | |
virtual int | getReducedContinuousFunctionCode () const |
Return a continuous on reduced order nodes FunctionSpace code. More... | |
virtual int | getFunctionCode () const |
Return a function FunctionSpace code. More... | |
virtual int | getReducedFunctionCode () const |
Return a function with reduced integration order FunctionSpace code. More... | |
virtual int | getFunctionOnBoundaryCode () const |
Return a function on boundary FunctionSpace code. More... | |
virtual int | getReducedFunctionOnBoundaryCode () const |
Return a function on boundary with reduced integration order FunctionSpace code. More... | |
virtual int | getFunctionOnContactZeroCode () const |
Return a FunctionOnContactZero code. More... | |
virtual int | getReducedFunctionOnContactZeroCode () const |
Return a FunctionOnContactZero code with reduced integration order. More... | |
virtual int | getFunctionOnContactOneCode () const |
Return a FunctionOnContactOne code. More... | |
virtual int | getReducedFunctionOnContactOneCode () const |
Return a FunctionOnContactOne code with reduced integration order. More... | |
virtual int | getSolutionCode () const |
Return a Solution code. More... | |
virtual int | getReducedSolutionCode () const |
Return a ReducedSolution code. More... | |
virtual int | getDiracDeltaFunctionsCode () const |
Return a DiracDeltaFunctions code. More... | |
virtual int | getDim () const |
returns the dimensionality of this domain More... | |
virtual StatusType | getStatus () const |
Returns a status indicator of the domain. The status identifier should be unique over the live time if the object but may be updated if changes to the domain happen, e.g. modifications to its geometry. More... | |
virtual dim_t | getNumDataPointsGlobal () const |
Return the number of data points summed across all MPI processes. More... | |
virtual std::pair< int, dim_t > | getDataShape (int functionSpaceCode) const |
Return the number of data points per sample, and the number of samples as a pair. More... | |
virtual void | setToX (escript::Data &arg) const |
copies the location of data points into arg. The domain of arg has to match this. has to be implemented by the actual Domain adapter. More... | |
virtual void | setTagMap (const std::string &name, int tag) |
sets a map from a clear tag name to a tag key More... | |
virtual int | getTag (const std::string &name) const |
Return the tag key for tag name. More... | |
virtual bool | isValidTagName (const std::string &name) const |
Returns true if name is a defined tag name. More... | |
virtual std::string | showTagNames () const |
Returns all tag names in a single string sperated by commas. More... | |
virtual void | setNewX (const escript::Data &arg) |
assigns new location to the domain More... | |
virtual void | interpolateOnDomain (escript::Data &target, const escript::Data &source) const |
interpolates data given on source onto target where source and target have to be given on the same domain. More... | |
virtual bool | probeInterpolationOnDomain (int functionSpaceType_source, int functionSpaceType_target) const |
True if interpolation is possible from source to target. More... | |
virtual signed char | preferredInterpolationOnDomain (int functionSpaceType_source, int functionSpaceType_target) const |
Preferred direction of interpolation. If you really need to test for a particular direction, then use probeInterpolation. More... | |
bool | commonFunctionSpace (const std::vector< int > &fs, int &resultcode) const |
given a vector of FunctionSpace typecodes, pass back a code which then can all be interpolated to. More... | |
virtual void | interpolateAcross (escript::Data &target, const escript::Data &source) const |
interpolates data given on source onto target where source and target are given on different domains. More... | |
virtual bool | probeInterpolationAcross (int functionSpaceType_source, const escript::AbstractDomain &targetDomain, int functionSpaceType_target) const |
determines whether interpolation from source to target is possible. More... | |
virtual void | setToNormal (escript::Data &out) const |
copies the surface normals at data points into out. The actual function space to be considered is defined by out. out has to be defined on this. More... | |
virtual void | setToSize (escript::Data &out) const |
copies the size of samples into out. The actual function space to be considered is defined by out. out has to be defined on this. More... | |
virtual void | setToGradient (escript::Data &grad, const escript::Data &arg) const |
copies the gradient of arg into grad. The actual function space to be considered for the gradient is defined by grad. arg and grad have to be defined on this. More... | |
virtual void | setToIntegrals (std::vector< double > &integrals, const escript::Data &arg) const |
copies the integrals of the function defined by arg into integrals. arg has to be defined on this. More... | |
virtual int | getSystemMatrixTypeId (const boost::python::object &options) const |
return the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package, preconditioner, and symmetric matrix is used. More... | |
virtual int | getTransportTypeId (int solver, int preconditioner, int package, bool symmetry) const |
return the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used. More... | |
virtual bool | isCellOriented (int functionSpaceCode) const |
returns true if data on this domain and a function space of type functionSpaceCode has to considered as cell centered data. More... | |
virtual bool | ownSample (int fsCode, index_t id) const |
virtual void | addPDEToSystem (escript::AbstractSystemMatrix &mat, escript::Data &rhs, const escript::Data &A, const escript::Data &B, const escript::Data &C, const escript::Data &D, const escript::Data &X, const escript::Data &Y, const escript::Data &d, const escript::Data &y, const escript::Data &d_contact, const escript::Data &y_contact, const escript::Data &d_dirac, const escript::Data &y_dirac) const |
adds a PDE onto the stiffness matrix mat and a rhs More... | |
virtual void | addPDEToLumpedSystem (escript::Data &mat, const escript::Data &D, const escript::Data &d, const escript::Data &d_dirac, bool useHRZ) const |
adds a PDE onto the lumped stiffness matrix matrix More... | |
virtual void | addPDEToRHS (escript::Data &rhs, const escript::Data &X, const escript::Data &Y, const escript::Data &y, const escript::Data &y_contact, const escript::Data &y_dirac) const |
adds a PDE onto the stiffness matrix mat and a rhs More... | |
virtual void | addPDEToTransportProblem (escript::AbstractTransportProblem &tp, escript::Data &source, const escript::Data &M, const escript::Data &A, const escript::Data &B, const escript::Data &C, const escript::Data &D, const escript::Data &X, const escript::Data &Y, const escript::Data &d, const escript::Data &y, const escript::Data &d_contact, const escript::Data &y_contact, const escript::Data &d_dirac, const escript::Data &y_dirac) const |
adds a PDE onto a transport problem More... | |
escript::ASM_ptr | newSystemMatrix (int row_blocksize, const escript::FunctionSpace &row_functionspace, int column_blocksize, const escript::FunctionSpace &column_functionspace, int type) const |
creates a stiffness matrix and initializes it with zeros More... | |
escript::ATP_ptr | newTransportProblem (int blocksize, const escript::FunctionSpace &functionspace, int type) const |
creates a TransportProblem More... | |
virtual escript::Data | getX () const |
returns locations in the FEM nodes More... | |
virtual escript::Data | getNormal () const |
returns boundary normals at the quadrature point on the face elements More... | |
virtual escript::Data | getSize () const |
returns the element size More... | |
virtual bool | operator== (const escript::AbstractDomain &other) const |
comparison operators More... | |
virtual bool | operator!= (const escript::AbstractDomain &other) const |
Return true if given domains are not equal. More... | |
virtual void | setTags (int functionSpaceType, int newTag, const escript::Data &mask) const |
assigns new tag newTag to all samples of functionspace with a positive value of mask for any its sample point. More... | |
virtual int | getNumberOfTagsInUse (int functionSpaceCode) const |
returns the number of tags in use and a pointer to an array with the number of tags in use More... | |
virtual const int * | borrowListOfTagsInUse (int functionSpaceCode) const |
virtual bool | canTag (int functionSpaceCode) const |
Checks if this domain allows tags for the specified functionSpace code. More... | |
virtual int | getApproximationOrder (int functionSpaceCode) const |
returns the approximation order used for a function space functionSpaceCode More... | |
virtual bool | supportsContactElements () const |
virtual escript::Data | randomFill (const escript::DataTypes::ShapeType &shape, const escript::FunctionSpace &what, long seed, const boost::python::tuple &filter) const |
Fills the data object with filtered random values. More... | |
const TagMap & | getTagMap () const |
returns a reference to the tag name->value map More... | |
void | createMappings (const IndexVector &dofDistribution, const IndexVector &nodeDistribution) |
void | glueFaces (double safetyFactor, double tolerance, bool optimize) |
void | joinFaces (double safetyFactor, double tolerance, bool optimize) |
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AbstractContinuousDomain () | |
Default constructor for AbstractContinuousDomain. More... | |
virtual | ~AbstractContinuousDomain () |
Destructor for AbstractContinuousDomain. More... | |
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Domain_ptr | getPtr () |
Returns smart pointer which is managing this object. If one does not exist yet it creates one. More... | |
const_Domain_ptr | getPtr () const |
virtual | ~AbstractDomain () |
Destructor for AbstractDomain. More... | |
virtual int | getTagFromSampleNo (int functionSpaceType, DataTypes::index_t sampleNo) const =0 |
Return the tag key for the given sample number. More... | |
virtual bool | ownSample (int fs_code, DataTypes::index_t id) const =0 |
True if this rank owns the sample(id) Must be implemented by the Domain adapter. More... | |
void | throwStandardException (const std::string &functionName) const |
Throw a standard exception. This function is called if any attempt is made to use a base class function. More... | |
virtual bool | supportsFilter (const boost::python::tuple &t) const |
true if this domain can handle to specified tuple of filter options. More... | |
Static Public Member Functions | |
static escript::Domain_ptr | load (const std::string &filename) |
recovers domain from a dump file More... | |
static escript::Domain_ptr | read (escript::JMPI mpiInfo, const std::string &fileName, int integrationOrder=-1, int reducedIntegrationOrder=-1, bool optimize=false) |
reads a mesh from a fly file. For MPI parallel runs fans out the mesh to multiple processes. More... | |
static escript::Domain_ptr | readGmsh (escript::JMPI mpiInfo, const std::string &filename, int numDim, int integrationOrder=-1, int reducedIntegrationOrder=-1, bool optimize=false, bool useMacroElements=false) |
reads a gmsh mesh file. More... | |
static escript::Domain_ptr | createRec4 (dim_t NE0, dim_t NE1, double L0, double L1, bool periodic0, bool periodic1, int order, int reducedOrder, bool useElementsOnFace, bool optimize, escript::JMPI jmpi) |
Creates a 2-dimensional rectangular domain with first order (Rec4) elements in the rectangle [0,L0] x [0,L1]. More... | |
static escript::Domain_ptr | createRec8 (dim_t NE0, dim_t NE1, double l0, double l1, bool periodic0, bool periodic1, int order, int reducedOrder, bool useElementsOnFace, bool useFullElementOrder, bool useMacroElements, bool optimize, escript::JMPI jmpi) |
Creates a 2-dimensional rectangular domain with second order (Rec8 or Rec9) elements in the rectangle [0,L0] x [0,L1]. More... | |
static escript::Domain_ptr | createHex8 (dim_t NE0, dim_t NE1, dim_t NE2, double l0, double l1, double l2, bool periodic0, bool periodic1, bool periodic2, int order, int reducedOrder, bool useElementsOnFace, bool optimize, escript::JMPI jmpi) |
Creates a 3-dimensional rectangular domain with first order (Hex8) elements. More... | |
static escript::Domain_ptr | createHex20 (dim_t NE0, dim_t NE1, dim_t NE2, double l0, double l1, double l2, bool periodic0, bool periodic1, bool periodic2, int order, int reducedOrder, bool useElementsOnFace, bool useFullElementOrder, bool useMacroElements, bool optimize, escript::JMPI jmpi) |
Creates a 3-dimensional rectangular domain with second order (Hex20 or Hex27) elements. More... | |
static FinleyDomain * | merge (const std::vector< const FinleyDomain *> &meshes) |
Private Member Functions | |
void | prepare (bool optimize) |
prepares the mesh for further use More... | |
void | setOrders () |
void | resolveNodeIds () |
void | relabelElementNodes (const IndexVector &newNode, index_t offset) |
void | createColoring (const IndexVector &dofMap) |
tries to reduce the number of colours for all element files More... | |
void | distributeByRankOfDOF (const IndexVector &distribution) |
void | markNodes (std::vector< short > &mask, index_t offset, bool useLinear) const |
void | optimizeDOFDistribution (IndexVector &distribution) |
void | optimizeDOFLabeling (const IndexVector &distribution) |
optimizes the labeling of the DOFs on each processor More... | |
void | optimizeElementOrdering () |
redistributes elements to minimize communication during assemblage More... | |
void | findMatchingFaces (double safetyFactor, double tolerance, int *numPairs, int *elem0, int *elem1, int *matchingNodes) const |
void | updateTagList () |
regenerates list of tags in use for node file and element files More... | |
void | printElementInfo (const ElementFile *e, const std::string &title, const std::string &defaultType, bool full) const |
void | writeElementInfo (std::ostream &stream, const ElementFile *e, const std::string &defaultType) const |
Private Attributes | |
escript::JMPI | m_mpiInfo |
MPI information. More... | |
std::string | m_name |
domain description More... | |
int | approximationOrder |
int | reducedApproximationOrder |
int | integrationOrder |
int | reducedIntegrationOrder |
NodeFile * | m_nodes |
the table of the nodes More... | |
ElementFile * | m_elements |
the table of the elements More... | |
ElementFile * | m_faceElements |
the table of face elements More... | |
ElementFile * | m_contactElements |
the table of contact elements More... | |
ElementFile * | m_points |
the table of points (treated as elements of dimension 0) More... | |
TagMap | m_tagMap |
the tag map mapping names to tag keys More... | |
Static Private Attributes | |
static FunctionSpaceNamesMapType | m_functionSpaceTypeNames |
FinleyDomain implements the AbstractContinuousDomain interface for the Finley library.
typedef std::map<int, std::string> finley::FinleyDomain::FunctionSpaceNamesMapType |
finley::FinleyDomain::FinleyDomain | ( | const std::string & | name, |
int | numDim, | ||
escript::JMPI | jmpi | ||
) |
Constructor for FinleyDomain.
name | a descriptive name for the domain |
numDim | dimensionality of the domain (2 or 3) |
jmpi | shared pointer to MPI Information to be used |
References m_mpiInfo, m_nodes, and setFunctionSpaceTypeNames().
Referenced by createHex20(), createHex8(), createRec4(), createRec8(), merge(), and read().
finley::FinleyDomain::FinleyDomain | ( | const FinleyDomain & | in | ) |
Copy constructor.
References setFunctionSpaceTypeNames().
finley::FinleyDomain::~FinleyDomain | ( | ) |
Destructor for FinleyDomain.
References m_contactElements, m_elements, m_faceElements, m_nodes, and m_points.
void finley::FinleyDomain::addDiracPoints | ( | const std::vector< double > & | points, |
const std::vector< int > & | tags | ||
) |
adds Dirac delta points. Do NOT call this at any time other than construction! Using them later creates consistency problems
References finley::ElementFile::allocTable(), finley::ElementFile::Color, finley::NodeFile::Coordinates, finley::NodeFile::degreesOfFreedomDistribution, getDim(), finley::NodeFile::getNumNodes(), finley::NodeFile::globalDegreesOfFreedom, finley::NodeFile::globalReducedDOFIndex, finley::ElementFile::Id, finley::NodeFile::Id, INDEX2, integrationOrder, paso::LARGE_POSITIVE_FLOAT, m_mpiInfo, m_nodes, m_points, finley::ElementFile::maxColor, finley::ElementFile::minColor, MPI_DOUBLE, finley::ElementFile::Nodes, finley::ElementFile::numElements, finley::ElementFile::Owner, finley::Point1, escript::DataTypes::real_t_max(), reducedIntegrationOrder, finley::ElementFile::referenceElementSet, and finley::ElementFile::Tag.
Referenced by finley::brick(), finley::readGmsh_driver(), finley::readMesh_driver(), and finley::rectangle().
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adds a PDE onto the lumped stiffness matrix matrix
References finley::Assemble_LumpedSystem(), m_elements, m_faceElements, m_nodes, and m_points.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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adds a PDE onto the stiffness matrix mat and a rhs
Reimplemented from escript::AbstractContinuousDomain.
References finley::Assemble_PDE(), m_contactElements, m_elements, m_faceElements, m_nodes, and m_points.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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adds a PDE onto the stiffness matrix mat and a rhs
Reimplemented from escript::AbstractContinuousDomain.
References finley::Assemble_PDE(), escript::AbstractSystemMatrix::getPtr(), m_contactElements, m_elements, m_faceElements, m_nodes, and m_points.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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adds a PDE onto a transport problem
Reimplemented from escript::AbstractContinuousDomain.
References finley::Assemble_PDE(), paso::TransportProblem::borrowMassMatrix(), paso::TransportProblem::borrowTransportMatrix(), escript::Data::expand(), m_contactElements, m_elements, m_faceElements, m_nodes, and m_points.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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Implements escript::AbstractDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, m_contactElements, m_elements, m_faceElements, m_nodes, m_points, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, finley::ReducedNodes, finley::ElementFile::tagsInUse, and finley::NodeFile::tagsInUse.
Referenced by getDim().
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Return the reference number of the given sample number.
functionSpaceType | Input - The function space type. |
Implements escript::AbstractDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::NodeFile::degreesOfFreedomId, finley::Elements, finley::FaceElements, getDescription(), finley::ElementFile::Id, finley::NodeFile::Id, m_contactElements, m_elements, m_faceElements, m_nodes, m_points, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::NodeFile::reducedDegreesOfFreedomId, finley::ReducedElements, finley::ReducedFaceElements, finley::ReducedNodes, and finley::NodeFile::reducedNodesId.
Referenced by getMPIComm().
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Checks if this domain allows tags for the specified functionSpace code.
Implements escript::AbstractDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::Elements, finley::FaceElements, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedElements, and finley::ReducedFaceElements.
Referenced by getDim().
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given a vector of FunctionSpace typecodes, pass back a code which then can all be interpolated to.
Implements escript::AbstractDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, and finley::ReducedNodes.
Referenced by getDim().
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private |
tries to reduce the number of colours for all element files
References finley::ElementFile::createColoring(), m_contactElements, m_elements, m_faceElements, and m_points.
Referenced by distributeByRankOfDOF(), and getTagMap().
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Creates a 3-dimensional rectangular domain with second order (Hex20 or Hex27) elements.
NE0 | Input - number of elements in first dimension |
NE1 | Input - number of elements in second dimension |
NE2 | Input - number of elements in third dimension |
l0 | Input - length of domain in first dimension (width) |
l1 | Input - length of domain in second dimension (height) |
l2 | Input - length of domain in third dimension (depth) |
periodic0 | Input - use periodic boundary in first dimension? |
periodic1 | Input - use periodic boundary in second dimension? |
periodic2 | Input - use periodic boundary in third dimension? |
order | Input - integration order (1 or 2) |
reducedOrder | Input - reduced integration order (1 or 2) |
useElementsOnFace | Input - whether to use rich face elements |
useFullElementOrder | Input - ignored |
useMacroElements | Input - whether to use Macro element type |
optimize | Input - whether to optimize node/DOF labelling |
jmpi | Input - Shared pointer to MPI Information to be used |
References finley::NodeFile::allocTable(), finley::ElementFile::allocTable(), finley::NodeFile::Coordinates, DIM, FinleyDomain(), getNodes(), escript::AbstractDomain::getPtr(), finley::NodeFile::globalDegreesOfFreedom, finley::Hex20, finley::Hex20Face, finley::Hex20Face_Contact, finley::Hex27, finley::Hex27Macro, finley::ElementFile::Id, finley::NodeFile::Id, INDEX2, MAX3, finley::ElementFile::Nodes, finley::ElementFile::numNodes, finley::ElementFile::Owner, finley::Point1, prepare(), finley::Rec8, finley::Rec8_Contact, finley::Rec9, finley::Rec9_Contact, finley::Rec9Macro, resolveNodeIds(), setContactElements(), setElements(), setFaceElements(), setPoints(), setTagMap(), finley::ElementFile::Tag, and finley::NodeFile::Tag.
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Creates a 3-dimensional rectangular domain with first order (Hex8) elements.
NE0 | Input - number of elements in first dimension |
NE1 | Input - number of elements in second dimension |
NE2 | Input - number of elements in third dimension |
l0 | Input - length of domain in first dimension (width) |
l1 | Input - length of domain in second dimension (height) |
l2 | Input - length of domain in third dimension (depth) |
periodic0 | Input - use periodic boundary in first dimension? |
periodic1 | Input - use periodic boundary in second dimension? |
periodic2 | Input - use periodic boundary in third dimension? |
order | Input - integration order (1 or 2) |
reducedOrder | Input - reduced integration order (1 or 2) |
useElementsOnFace | Input - whether to use rich face elements |
optimize | Input - whether to optimize node/DOF labelling |
jmpi | Input - Shared pointer to MPI Information to be used |
References finley::NodeFile::allocTable(), finley::ElementFile::allocTable(), finley::NodeFile::Coordinates, DIM, FinleyDomain(), getNodes(), escript::AbstractDomain::getPtr(), finley::NodeFile::globalDegreesOfFreedom, finley::Hex8, finley::Hex8Face, finley::Hex8Face_Contact, finley::ElementFile::Id, finley::NodeFile::Id, INDEX2, MAX3, finley::ElementFile::Nodes, finley::ElementFile::numNodes, finley::ElementFile::Owner, finley::Point1, prepare(), finley::Rec4, finley::Rec4_Contact, resolveNodeIds(), setContactElements(), setElements(), setFaceElements(), setPoints(), setTagMap(), finley::ElementFile::Tag, and finley::NodeFile::Tag.
void finley::FinleyDomain::createMappings | ( | const IndexVector & | dofDistribution, |
const IndexVector & | nodeDistribution | ||
) |
References finley::NodeFile::createNodeMappings(), finley::NodeFile::getNumNodes(), m_nodes, markNodes(), and finley::util::packMask().
Referenced by getTagMap(), and load().
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Creates a 2-dimensional rectangular domain with first order (Rec4) elements in the rectangle [0,L0] x [0,L1].
NE0 | Input - number of elements in first dimension |
NE1 | Input - number of elements in second dimension |
l0 | Input - length of domain in first dimension (width) |
l1 | Input - length of domain in second dimension (height) |
periodic0 | Input - use periodic boundary in first dimension? |
periodic1 | Input - use periodic boundary in second dimension? |
order | Input - accuracy of integration scheme (order 1 or 2) |
reducedOrder | Input - reduced integration order (1 or 2) |
useElementsOnFace | Input - whether to use rich face elements |
optimize | Input - whether to optimize node/DOF labelling |
jmpi | Input - Shared pointer to MPI Information to be used |
References finley::NodeFile::allocTable(), finley::ElementFile::allocTable(), finley::NodeFile::Coordinates, DIM, FinleyDomain(), getNodes(), escript::AbstractDomain::getPtr(), finley::NodeFile::globalDegreesOfFreedom, finley::ElementFile::Id, finley::NodeFile::Id, INDEX2, finley::Line2, finley::Line2_Contact, finley::ElementFile::Nodes, finley::ElementFile::numNodes, finley::ElementFile::Owner, finley::Point1, prepare(), finley::Rec4, finley::Rec4Face, finley::Rec4Face_Contact, resolveNodeIds(), setContactElements(), setElements(), setFaceElements(), setPoints(), setTagMap(), finley::ElementFile::Tag, and finley::NodeFile::Tag.
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Creates a 2-dimensional rectangular domain with second order (Rec8 or Rec9) elements in the rectangle [0,L0] x [0,L1].
NE0 | Input - number of elements in first dimension |
NE1 | Input - number of elements in second dimension |
l0 | Input - length of domain in first dimension (width) |
l1 | Input - length of domain in second dimension (height) |
periodic0 | Input - use periodic boundary in first dimension? |
periodic1 | Input - use periodic boundary in second dimension? |
order | Input - accuracy of integration scheme (order 1 or 2) |
reducedOrder | Input - reduced integration order (1 or 2) |
useElementsOnFace | Input - whether to use rich face elements |
useFullElementOrder | Input - if true the main element type will be Rec9 |
useMacroElements | Input - whether to use Macro element type |
optimize | Input - whether to optimize node/DOF labelling |
jmpi | Input - Shared pointer to MPI Information to be used |
References finley::NodeFile::allocTable(), finley::ElementFile::allocTable(), finley::NodeFile::Coordinates, DIM, FinleyDomain(), getNodes(), escript::AbstractDomain::getPtr(), finley::NodeFile::globalDegreesOfFreedom, finley::ElementFile::Id, finley::NodeFile::Id, INDEX2, finley::Line3, finley::Line3_Contact, finley::Line3Macro, finley::ElementFile::Nodes, finley::ElementFile::numNodes, finley::ElementFile::Owner, finley::Point1, prepare(), finley::Rec8, finley::Rec8Face, finley::Rec8Face_Contact, finley::Rec9, finley::Rec9Macro, resolveNodeIds(), setContactElements(), setElements(), setFaceElements(), setPoints(), setTagMap(), finley::ElementFile::Tag, and finley::NodeFile::Tag.
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redistributes the Nodes and Elements including overlap according to the DOF distribution. It will create an element colouring but will not create any mappings.
References finley::NodeFile::assignMPIRankToDOFs(), createColoring(), finley::ElementFile::distributeByRankOfDOF(), ESYS_ASSERT, finley::NodeFile::getDOFRange(), finley::NodeFile::getNumNodes(), finley::NodeFile::globalDegreesOfFreedom, finley::NodeFile::Id, m_contactElements, m_elements, m_faceElements, m_nodes, m_points, and resolveNodeIds().
Referenced by getTagMap(), and prepare().
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dumps the mesh to a file with the given name.
fileName | Input - The name of the file |
Implements escript::AbstractDomain.
References finley::ElementFile::Color, finley::NodeFile::Coordinates, finley::NodeFile::degreesOfFreedomDistribution, getMPIComm(), getMPIRank(), getMPISize(), finley::NodeFile::getNumNodes(), finley::NodeFile::globalDegreesOfFreedom, finley::NodeFile::globalNodesIndex, finley::NodeFile::globalReducedDOFIndex, finley::NodeFile::globalReducedNodesIndex, finley::ElementFile::Id, finley::NodeFile::Id, integrationOrder, m_contactElements, m_elements, m_faceElements, m_mpiInfo, m_name, m_nodes, m_points, m_tagMap, MPI_INT, finley::ElementFile::Nodes, finley::NodeFile::nodesDistribution, finley::NodeFile::numDim, finley::ElementFile::numElements, finley::ElementFile::numNodes, finley::ElementFile::Owner, reducedIntegrationOrder, finley::ElementFile::referenceElementSet, finley::ElementFile::Tag, and finley::NodeFile::Tag.
Referenced by BOOST_PYTHON_MODULE(), and getMPIComm().
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References finley::FaceCenterCompare(), finley::util::gather(), finley::getDist(), INDEX2, INDEX3, and finley::FaceCenter::x.
Referenced by getTagMap(), glueFaces(), and joinFaces().
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Return a description for the given function space type code.
Implements escript::AbstractDomain.
References m_functionSpaceTypeNames.
Referenced by getMPIComm().
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returns the approximation order used for a function space functionSpaceCode
Implements escript::AbstractDomain.
References approximationOrder, finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, integrationOrder, finley::Nodes, finley::Points, reducedApproximationOrder, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, reducedIntegrationOrder, and finley::ReducedNodes.
Referenced by getDim().
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returns a pointer to this domain's contact element file
References m_contactElements, and setPoints().
Referenced by weipa::FinleyDomain::initFromEscript(), and merge().
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Return a continuous FunctionSpace code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::Nodes.
Referenced by getMPIComm().
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Return the number of data points per sample, and the number of samples as a pair.
functionSpaceCode | Input - |
Reimplemented from escript::AbstractContinuousDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, getDescription(), finley::NodeFile::getNumDegreesOfFreedom(), finley::NodeFile::getNumNodes(), finley::NodeFile::getNumReducedDegreesOfFreedom(), finley::NodeFile::getNumReducedNodes(), m_contactElements, m_elements, m_faceElements, m_nodes, m_points, finley::Nodes, finley::ElementFile::numElements, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, finley::ReducedNodes, and finley::ElementFile::referenceElementSet.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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Return a description for this domain.
Reimplemented from escript::AbstractContinuousDomain.
Referenced by BOOST_PYTHON_MODULE(), borrowSampleReferenceIDs(), getDataShape(), getMPIComm(), and getTagFromSampleNo().
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returns the dimensionality of this domain
Implements escript::AbstractDomain.
References addPDEToLumpedSystem(), addPDEToRHS(), addPDEToSystem(), addPDEToTransportProblem(), borrowListOfTagsInUse(), canTag(), commonFunctionSpace(), getApproximationOrder(), getDataShape(), getNormal(), getNumberOfTagsInUse(), getNumDataPointsGlobal(), getSize(), getStatus(), getSystemMatrixTypeId(), getTag(), getTransportTypeId(), getX(), interpolateAcross(), interpolateOnDomain(), isCellOriented(), isValidTagName(), paso::M, m_nodes, newSystemMatrix(), newTransportProblem(), finley::NodeFile::numDim, operator!=(), operator==(), ownSample(), preferredInterpolationOnDomain(), probeInterpolationAcross(), probeInterpolationOnDomain(), setNewX(), setTagMap(), setTags(), setToGradient(), setToIntegrals(), setToNormal(), setToSize(), setToX(), and showTagNames().
Referenced by addDiracPoints(), BOOST_PYTHON_MODULE(), merge(), Print_Mesh_Info(), resolveNodeIds(), and write().
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Return a DiracDeltaFunctions code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::Points.
Referenced by getMPIComm().
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returns a pointer to this domain's element file
References m_elements, and setFaceElements().
Referenced by weipa::FinleyDomain::initFromEscript(), and merge().
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returns a pointer to this domain's face element file
References m_faceElements, and setContactElements().
Referenced by weipa::FinleyDomain::initFromEscript(), and merge().
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Return a function FunctionSpace code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::Elements.
Referenced by getMPIComm().
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Return a function on boundary FunctionSpace code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::FaceElements.
Referenced by getMPIComm().
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Return a FunctionOnContactOne code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::ContactElementsOne.
Referenced by getMPIComm().
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Return a FunctionOnContactZero code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::ContactElementsZero.
Referenced by getMPIComm().
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returns a reference to the MPI information wrapper for this domain
Implements escript::AbstractDomain.
References m_mpiInfo.
Referenced by getTransportTypeId().
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get the communicator for this domain. Returns an integer on non-MPI builds Routine must be implemented by the DomainAdapter.
Implements escript::AbstractDomain.
References borrowSampleReferenceIDs(), dump(), functionSpaceTypeAsString(), getContinuousFunctionCode(), getDescription(), getDiracDeltaFunctionsCode(), getFunctionCode(), getFunctionOnBoundaryCode(), getFunctionOnContactOneCode(), getFunctionOnContactZeroCode(), getReducedContinuousFunctionCode(), getReducedFunctionCode(), getReducedFunctionOnBoundaryCode(), getReducedFunctionOnContactOneCode(), getReducedFunctionOnContactZeroCode(), getReducedSolutionCode(), getSolutionCode(), getTagFromSampleNo(), isValidFunctionSpaceType(), m_mpiInfo, Print_Mesh_Info(), setFunctionSpaceTypeNames(), and write().
Referenced by dump(), and MPIBarrier().
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returns the number MPI rank of this processor
Implements escript::AbstractDomain.
References m_mpiInfo, and MPIBarrier().
Referenced by BOOST_PYTHON_MODULE(), dump(), onMasterProcessor(), and optimizeDOFLabeling().
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returns the number of processors used for this domain
Implements escript::AbstractDomain.
References m_mpiInfo.
Referenced by BOOST_PYTHON_MODULE(), dump(), getSystemMatrixTypeId(), interpolateOnDomain(), merge(), optimizeDOFLabeling(), ownSample(), and setToGradient().
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returns a pointer to this domain's node file
References m_nodes, and setElements().
Referenced by createHex20(), createHex8(), createRec4(), createRec8(), weipa::FinleyDomain::initFromEscript(), load(), merge(), and read().
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returns boundary normals at the quadrature point on the face elements
Implements escript::AbstractDomain.
References escript::functionOnBoundary(), and escript::FunctionSpace::getNormal().
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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returns the number of tags in use and a pointer to an array with the number of tags in use
Implements escript::AbstractDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, m_contactElements, m_elements, m_faceElements, m_nodes, m_points, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, finley::ReducedNodes, finley::ElementFile::tagsInUse, and finley::NodeFile::tagsInUse.
Referenced by getDim().
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Return the number of data points summed across all MPI processes.
Reimplemented from escript::AbstractContinuousDomain.
References finley::NodeFile::getGlobalNumNodes(), and m_nodes.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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Return a continuous on reduced order nodes FunctionSpace code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::ReducedNodes.
Referenced by getMPIComm().
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Return a function with reduced integration order FunctionSpace code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::ReducedElements.
Referenced by getMPIComm().
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Return a function on boundary with reduced integration order FunctionSpace code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::ReducedFaceElements.
Referenced by getMPIComm().
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Return a FunctionOnContactOne code with reduced integration order.
Reimplemented from escript::AbstractContinuousDomain.
References finley::ReducedContactElementsOne.
Referenced by getMPIComm().
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Return a FunctionOnContactZero code with reduced integration order.
Reimplemented from escript::AbstractContinuousDomain.
References finley::ReducedContactElementsZero.
Referenced by getMPIComm().
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Return a ReducedSolution code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::ReducedDegreesOfFreedom.
Referenced by getMPIComm().
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returns the element size
Implements escript::AbstractDomain.
References escript::function(), and escript::FunctionSpace::getSize().
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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Return a Solution code.
Reimplemented from escript::AbstractContinuousDomain.
References finley::DegreesOfFreedom.
Referenced by getMPIComm().
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Returns a status indicator of the domain. The status identifier should be unique over the live time if the object but may be updated if changes to the domain happen, e.g. modifications to its geometry.
Reimplemented from escript::AbstractDomain.
References m_nodes, and finley::NodeFile::status.
Referenced by getDim().
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return the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package, preconditioner, and symmetric matrix is used.
options | a SolverBuddy instance with the desired options set |
Reimplemented from escript::AbstractContinuousDomain.
References getMPISize(), escript::SolverBuddy::getPackage(), escript::SolverBuddy::getPreconditioner(), escript::SolverBuddy::getSolverMethod(), paso::SystemMatrix::getSystemMatrixTypeId(), escript::SolverBuddy::isComplex(), escript::isDirectSolver(), escript::SolverBuddy::isSymmetric(), m_mpiInfo, finley::SMT_COMPLEX, finley::SMT_PASO, finley::SMT_TRILINOS, finley::SMT_UNROLL, escript::SO_DEFAULT, escript::SO_METHOD_DIRECT, escript::SO_PACKAGE_TRILINOS, escript::SO_PRECONDITIONER_AMG, and escript::SO_PRECONDITIONER_ILUT.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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Return the tag key for tag name.
name | Input - tag name |
Implements escript::AbstractDomain.
References m_tagMap.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
int finley::FinleyDomain::getTagFromSampleNo | ( | int | functionSpaceType, |
index_t | sampleNo | ||
) | const |
Return the tag key for the given sample number.
functionSpaceType | Input - The function space type. |
sampleNo | Input - The sample number. |
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, getDescription(), m_contactElements, m_elements, m_faceElements, m_nodes, m_points, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, finley::ReducedNodes, finley::ElementFile::Tag, and finley::NodeFile::Tag.
Referenced by getMPIComm().
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returns a reference to the tag name->value map
References createColoring(), createMappings(), distributeByRankOfDOF(), findMatchingFaces(), glueFaces(), joinFaces(), m_tagMap, markNodes(), merge(), optimizeDOFDistribution(), optimizeDOFLabeling(), optimizeElementOrdering(), prepare(), printElementInfo(), relabelElementNodes(), resolveNodeIds(), setOrders(), updateTagList(), and writeElementInfo().
Referenced by finley::readGmsh_driver(), and finley::readMesh_driver().
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return the identifier of the transport problem type to be used when a particular solver, perconditioner, package and symmetric matrix is used.
solver | |
preconditioner | |
package | |
symmetry |
Reimplemented from escript::AbstractContinuousDomain.
References getMPI(), and paso::TransportProblem::getTypeId().
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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returns locations in the FEM nodes
Implements escript::AbstractDomain.
References escript::continuousFunction(), and escript::FunctionSpace::getX().
Referenced by BOOST_PYTHON_MODULE(), and getDim().
void finley::FinleyDomain::glueFaces | ( | double | safetyFactor, |
double | tolerance, | ||
bool | optimize | ||
) |
References finley::NodeFile::allocTable(), finley::ElementFile::allocTable(), findMatchingFaces(), finley::ElementFile::gather(), finley::NodeFile::gather(), finley::NodeFile::getNumNodes(), INDEX2, m_faceElements, m_mpiInfo, m_nodes, finley::ElementFile::Nodes, finley::NodeFile::numDim, finley::ElementFile::numElements, finley::ElementFile::numNodes, prepare(), finley::ElementFile::referenceElementSet, and relabelElementNodes().
Referenced by getTagMap(), and finley::glueFaces().
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interpolates data given on source onto target where source and target are given on different domains.
Implements escript::AbstractDomain.
Referenced by getDim().
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interpolates data given on source onto target where source and target have to be given on the same domain.
Implements escript::AbstractDomain.
References finley::Assemble_AverageElementData(), finley::Assemble_CopyElementData(), finley::Assemble_CopyNodalData(), finley::Assemble_interpolate(), finley::ContactElementsOne, finley::ContactElementsZero, escript::continuousFunction(), finley::DegreesOfFreedom, finley::Elements, escript::Data::expand(), finley::FaceElements, escript::FunctionSpace::getDomain(), escript::Data::getFunctionSpace(), getMPISize(), escript::FunctionSpace::getTypeCode(), m_contactElements, m_elements, m_faceElements, m_nodes, m_points, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, escript::reducedContinuousFunction(), finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, and finley::ReducedNodes.
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returns true if data on this domain and a function space of type functionSpaceCode has to considered as cell centered data.
Implements escript::AbstractDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, and finley::ReducedFaceElements.
Referenced by getDim().
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Returns true if the given integer is a valid function space type for this domain.
Reimplemented from escript::AbstractContinuousDomain.
References m_functionSpaceTypeNames.
Referenced by getMPIComm().
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Returns true if name is a defined tag name.
name | Input - tag name to be checked. |
Reimplemented from escript::AbstractDomain.
References m_tagMap.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
void finley::FinleyDomain::joinFaces | ( | double | safetyFactor, |
double | tolerance, | ||
bool | optimize | ||
) |
References finley::ElementFile::allocTable(), finley::ElementFile::Color, finley::ElementFile::copyTable(), findMatchingFaces(), finley::ElementFile::gather(), finley::ElementFile::Id, INDEX2, m_contactElements, m_faceElements, m_mpiInfo, finley::ElementFile::maxColor, finley::ElementFile::minColor, finley::ElementFile::Nodes, finley::ElementFile::numElements, finley::ElementFile::numNodes, prepare(), finley::ElementFile::referenceElementSet, and finley::ElementFile::Tag.
Referenced by getTagMap(), and finley::joinFaces().
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recovers domain from a dump file
filename | the name of the file |
References finley::NodeFile::allocTable(), finley::ElementFile::allocTable(), finley::cleanupAndThrow(), finley::ElementFile::Color, createMappings(), getNodes(), escript::AbstractDomain::getPtr(), finley::ElementFile::Id, INDEX2, escript::makeInfo(), finley::ElementFile::maxColor, finley::ElementFile::minColor, MPI_COMM_WORLD, finley::ElementFile::Nodes, finley::ElementFile::Owner, setContactElements(), setElements(), setFaceElements(), setPoints(), setTagMap(), finley::ElementFile::Tag, and finley::ElementFile::updateTagList().
Referenced by BOOST_PYTHON_MODULE().
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References m_contactElements, m_elements, m_faceElements, m_points, and finley::ElementFile::markNodes().
Referenced by createMappings(), getTagMap(), prepare(), and resolveNodeIds().
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takes nodes, elements, etc. of all input meshes and copies them into a new mesh. Ids of output are shifted by the maximum Id of inputs.
References finley::NodeFile::allocTable(), finley::ElementFile::allocTable(), finley::ElementFile::copyTable(), finley::NodeFile::copyTable(), FinleyDomain(), getContactElements(), getDim(), getElements(), getFaceElements(), finley::util::getMaxInt(), getMPISize(), getNodes(), getPoints(), integrationOrder, finley::NoRef, prepare(), reducedIntegrationOrder, setContactElements(), setElements(), setFaceElements(), and setPoints().
Referenced by getTagMap().
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If compiled for MPI then execute an MPI_Barrier, else do nothing.
Implements escript::AbstractDomain.
References getMPIComm().
Referenced by BOOST_PYTHON_MODULE(), and getMPIRank().
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creates a stiffness matrix and initializes it with zeros
Reimplemented from escript::AbstractContinuousDomain.
References finley::DegreesOfFreedom, escript::FunctionSpace::getDomain(), escript::FunctionSpace::getTypeCode(), m_mpiInfo, finley::ReducedDegreesOfFreedom, finley::SMT_COMPLEX, finley::SMT_PASO, finley::SMT_TRILINOS, and finley::SMT_UNROLL.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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creates a TransportProblem
Reimplemented from escript::AbstractContinuousDomain.
References finley::DegreesOfFreedom, escript::FunctionSpace::getDomain(), escript::FunctionSpace::getTypeCode(), and finley::ReducedDegreesOfFreedom.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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returns true if on MPI processor 0, else false
Implements escript::AbstractDomain.
References getMPIRank().
Referenced by BOOST_PYTHON_MODULE().
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Return true if given domains are not equal.
Implements escript::AbstractDomain.
References operator==().
Referenced by getDim().
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comparison operators
Implements escript::AbstractDomain.
References m_contactElements, m_elements, m_faceElements, m_nodes, and m_points.
Referenced by getDim(), and operator!=().
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optimizes the distribution of DOFs across processors using ParMETIS. On return a new distribution is given and the globalDOF are relabeled accordingly but the mesh has not been redistributed yet
References finley::NodeFile::Coordinates, finley::NodeFile::getNumNodes(), finley::NodeFile::globalDegreesOfFreedom, INDEX2, finley::IndexList_insertElementsWithRowRangeNoMainDiagonal(), m_contactElements, m_elements, m_faceElements, m_mpiInfo, m_nodes, m_points, and finley::NodeFile::numDim.
Referenced by getTagMap(), and prepare().
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optimizes the labeling of the DOFs on each processor
References paso::Pattern::fromIndexListArray(), getMPIRank(), getMPISize(), finley::NodeFile::getNumNodes(), finley::NodeFile::globalDegreesOfFreedom, finley::IndexList_insertElementsWithRowRangeNoMainDiagonal(), m_contactElements, m_elements, m_faceElements, m_mpiInfo, m_nodes, and m_points.
Referenced by getTagMap(), and prepare().
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redistributes elements to minimize communication during assemblage
References m_contactElements, m_elements, m_faceElements, m_points, and finley::ElementFile::optimizeOrdering().
Referenced by getTagMap(), and prepare().
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Preferred direction of interpolation. If you really need to test for a particular direction, then use probeInterpolation.
Implements escript::AbstractDomain.
References probeInterpolationOnDomain().
Referenced by getDim().
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prepares the mesh for further use
References finley::NodeFile::createDenseDOFLabeling(), finley::NodeFile::createDenseNodeLabeling(), finley::NodeFile::createDenseReducedLabeling(), finley::NodeFile::createNodeMappings(), distributeByRankOfDOF(), finley::NodeFile::getNumNodes(), m_mpiInfo, m_nodes, markNodes(), optimizeDOFDistribution(), optimizeDOFLabeling(), optimizeElementOrdering(), finley::util::packMask(), setOrders(), and updateTagList().
Referenced by createHex20(), createHex8(), createRec4(), createRec8(), getTagMap(), glueFaces(), joinFaces(), merge(), read(), and readGmsh().
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full | whether to include coordinate values and id's |
Reimplemented from escript::AbstractContinuousDomain.
References approximationOrder, finley::NodeFile::Coordinates, getDim(), finley::NodeFile::getNumNodes(), finley::NodeFile::globalDegreesOfFreedom, finley::NodeFile::globalNodesIndex, finley::NodeFile::globalReducedDOFIndex, finley::NodeFile::globalReducedNodesIndex, finley::NodeFile::Id, INDEX2, integrationOrder, m_contactElements, m_elements, m_faceElements, m_mpiInfo, m_name, m_nodes, m_points, m_tagMap, printElementInfo(), reducedApproximationOrder, reducedIntegrationOrder, and finley::NodeFile::Tag.
Referenced by BOOST_PYTHON_MODULE(), and getMPIComm().
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References finley::ElementFile::Color, finley::ElementFile::Id, finley::NodeFile::Id, INDEX2, m_mpiInfo, m_nodes, finley::ElementFile::Nodes, finley::ElementFile::numElements, finley::ElementFile::numNodes, finley::ElementFile::Owner, finley::ElementFile::referenceElementSet, and finley::ElementFile::Tag.
Referenced by getTagMap(), and Print_Mesh_Info().
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determines whether interpolation from source to target is possible.
Implements escript::AbstractDomain.
Referenced by getDim().
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True if interpolation is possible from source to target.
Implements escript::AbstractDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, and finley::ReducedNodes.
Referenced by getDim(), and preferredInterpolationOnDomain().
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Fills the data object with filtered random values.
Implements escript::AbstractDomain.
References escript::Data::getExpandedVectorReference(), and escript::randomFillArray().
Referenced by supportsContactElements().
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reads a mesh from a fly file. For MPI parallel runs fans out the mesh to multiple processes.
mpiInfo | the MPI information structure |
fileName | the name of the file |
integrationOrder | order of the quadrature scheme. If <0 the order is selected automatically. |
reducedIntegrationOrder | order of the reduced quadrature scheme. If <0 the order is selected automatically. |
optimize | whether to optimize the node labels |
References finley::NodeFile::allocTable(), finley::NodeFile::Coordinates, FinleyDomain(), getNodes(), escript::AbstractDomain::getPtr(), finley::NodeFile::globalDegreesOfFreedom, finley::NodeFile::Id, INDEX2, MPI_DOUBLE, MPI_INT, prepare(), resolveNodeIds(), setContactElements(), setElements(), setFaceElements(), setPoints(), setTagMap(), and finley::NodeFile::Tag.
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reads a gmsh mesh file.
mpiInfo | the MPI information structure |
filename | the name of the gmsh file |
numDim | spatial dimensionality |
integrationOrder | order of the quadrature scheme. If <0 the order is selected automatically. |
reducedIntegrationOrder | order of the reduced quadrature scheme. If <0 the order is selected automatically. |
optimize | whether to optimize the node labels |
useMacroElements | whether to use first order macro elements |
References escript::AbstractDomain::getPtr(), prepare(), and resolveNodeIds().
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private |
assigns new node reference numbers to all element files. If k is the old node, the new node is newNode[k-offset].
References m_contactElements, m_elements, m_faceElements, m_points, and finley::ElementFile::relabelNodes().
Referenced by getTagMap(), glueFaces(), and resolveNodeIds().
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Initially the element nodes refer to the numbering defined by the global id assigned to the nodes in the NodeFile. It is also not ensured that all nodes referred by an element are actually available on the process. At the output, a local node labeling is used and all nodes are available. In particular the numbering of the element nodes is between 0 and Nodes->numNodes. The function does not create a distribution of the degrees of freedom.
References finley::NodeFile::allocTable(), ESYS_ASSERT, finley::NodeFile::gather_global(), getDim(), finley::ElementFile::getNodeRange(), escript::DataTypes::index_t_max(), m_contactElements, m_elements, m_faceElements, m_mpiInfo, m_nodes, m_points, markNodes(), MPI_MAX, finley::util::packMask(), and relabelElementNodes().
Referenced by createHex20(), createHex8(), createRec4(), createRec8(), distributeByRankOfDOF(), getTagMap(), read(), and readGmsh().
void finley::FinleyDomain::setContactElements | ( | ElementFile * | elements | ) |
replaces the contact element file by elements
References m_contactElements.
Referenced by createHex20(), createHex8(), createRec4(), createRec8(), getFaceElements(), load(), merge(), and read().
void finley::FinleyDomain::setElements | ( | ElementFile * | elements | ) |
replaces the element file by elements
References m_elements.
Referenced by createHex20(), createHex8(), createRec4(), createRec8(), getNodes(), load(), merge(), and read().
void finley::FinleyDomain::setFaceElements | ( | ElementFile * | elements | ) |
replaces the face element file by elements
References m_faceElements.
Referenced by createHex20(), createHex8(), createRec4(), createRec8(), getElements(), load(), merge(), and read().
void finley::FinleyDomain::setFunctionSpaceTypeNames | ( | ) |
Build the table of function space type names.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, m_functionSpaceTypeNames, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, and finley::ReducedNodes.
Referenced by FinleyDomain(), and getMPIComm().
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assigns new location to the domain
Reimplemented from escript::AbstractContinuousDomain.
References escript::continuousFunction(), escript::FunctionSpace::getDomain(), escript::Data::getFunctionSpace(), m_nodes, and finley::NodeFile::setCoordinates().
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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References approximationOrder, integrationOrder, m_contactElements, m_elements, m_faceElements, m_mpiInfo, MPI_INT, MPI_MIN, finley::ElementFile::numElements, reducedApproximationOrder, reducedIntegrationOrder, and finley::ElementFile::referenceElementSet.
Referenced by getTagMap(), and prepare().
void finley::FinleyDomain::setPoints | ( | ElementFile * | elements | ) |
replaces the point element file by elements
References m_points.
Referenced by createHex20(), createHex8(), createRec4(), createRec8(), getContactElements(), load(), merge(), and read().
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sets a map from a clear tag name to a tag key
name | Input - tag name. |
tag | Input - tag key. |
Implements escript::AbstractDomain.
References m_tagMap.
Referenced by BOOST_PYTHON_MODULE(), createHex20(), createHex8(), createRec4(), createRec8(), getDim(), load(), read(), finley::readGmsh_driver(), and finley::readMesh_driver().
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assigns new tag newTag to all samples of functionspace with a positive value of mask for any its sample point.
Implements escript::AbstractDomain.
References finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, m_contactElements, m_elements, m_faceElements, m_nodes, m_points, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, finley::ReducedNodes, finley::ElementFile::setTags(), and finley::NodeFile::setTags().
Referenced by getDim().
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copies the gradient of arg into grad. The actual function space to be considered for the gradient is defined by grad. arg and grad have to be defined on this.
Implements escript::AbstractDomain.
References finley::Assemble_gradient(), finley::ContactElementsOne, finley::ContactElementsZero, escript::continuousFunction(), finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, escript::FunctionSpace::getDomain(), escript::Data::getFunctionSpace(), getMPISize(), escript::FunctionSpace::getTypeCode(), m_contactElements, m_elements, m_faceElements, m_nodes, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, escript::reducedContinuousFunction(), finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, and finley::ReducedNodes.
Referenced by getDim().
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copies the integrals of the function defined by arg into integrals. arg has to be defined on this.
Reimplemented from escript::AbstractContinuousDomain.
References finley::Assemble_integrate(), finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, escript::function(), escript::FunctionSpace::getDomain(), escript::Data::getFunctionSpace(), escript::FunctionSpace::getTypeCode(), m_contactElements, m_elements, m_faceElements, m_nodes, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, and finley::ReducedNodes.
Referenced by getDim().
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copies the surface normals at data points into out. The actual function space to be considered is defined by out. out has to be defined on this.
Implements escript::AbstractDomain.
References finley::Assemble_getNormal(), finley::ContactElementsOne, finley::ContactElementsZero, finley::FaceElements, escript::FunctionSpace::getDomain(), escript::Data::getFunctionSpace(), escript::FunctionSpace::getTypeCode(), m_contactElements, m_faceElements, m_nodes, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, and finley::ReducedFaceElements.
Referenced by getDim().
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copies the size of samples into out. The actual function space to be considered is defined by out. out has to be defined on this.
Implements escript::AbstractDomain.
References finley::Assemble_getSize(), finley::ContactElementsOne, finley::ContactElementsZero, finley::DegreesOfFreedom, finley::Elements, finley::FaceElements, escript::Data::getFunctionSpace(), escript::FunctionSpace::getTypeCode(), m_contactElements, m_elements, m_faceElements, m_nodes, finley::Nodes, finley::Points, finley::ReducedContactElementsOne, finley::ReducedContactElementsZero, finley::ReducedDegreesOfFreedom, finley::ReducedElements, finley::ReducedFaceElements, and finley::ReducedNodes.
Referenced by getDim().
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copies the location of data points into arg. The domain of arg has to match this. has to be implemented by the actual Domain adapter.
Implements escript::AbstractDomain.
References finley::Assemble_NodeCoordinates(), escript::continuousFunction(), escript::FunctionSpace::getDomain(), escript::Data::getFunctionSpace(), escript::FunctionSpace::getTypeCode(), interpolateOnDomain(), m_nodes, finley::Nodes, and escript::Vector().
Referenced by getDim().
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Returns all tag names in a single string sperated by commas.
Implements escript::AbstractDomain.
References m_tagMap.
Referenced by BOOST_PYTHON_MODULE(), and getDim().
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Implements escript::AbstractDomain.
References randomFill().
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regenerates list of tags in use for node file and element files
References m_contactElements, m_elements, m_faceElements, m_nodes, m_points, finley::NodeFile::updateTagList(), and finley::ElementFile::updateTagList().
Referenced by getTagMap(), and prepare().
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writes the current mesh to a file with the given name in the fly file format.
fileName | Input - The name of the file to write to. |
Implements escript::AbstractDomain.
References finley::NodeFile::Coordinates, getDim(), finley::NodeFile::getNumNodes(), finley::NodeFile::globalDegreesOfFreedom, finley::NodeFile::Id, INDEX2, m_contactElements, m_elements, m_faceElements, m_mpiInfo, m_name, m_nodes, m_points, m_tagMap, finley::NodeFile::Tag, and writeElementInfo().
Referenced by BOOST_PYTHON_MODULE(), and getMPIComm().
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Referenced by getApproximationOrder(), Print_Mesh_Info(), and setOrders().
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Referenced by addDiracPoints(), dump(), getApproximationOrder(), merge(), Print_Mesh_Info(), and setOrders().
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the table of contact elements
Referenced by addPDEToRHS(), addPDEToSystem(), addPDEToTransportProblem(), borrowListOfTagsInUse(), borrowSampleReferenceIDs(), createColoring(), distributeByRankOfDOF(), dump(), getContactElements(), getDataShape(), getNumberOfTagsInUse(), getTagFromSampleNo(), interpolateOnDomain(), joinFaces(), markNodes(), operator==(), optimizeDOFDistribution(), optimizeDOFLabeling(), optimizeElementOrdering(), Print_Mesh_Info(), relabelElementNodes(), resolveNodeIds(), setContactElements(), setOrders(), setTags(), setToGradient(), setToIntegrals(), setToNormal(), setToSize(), updateTagList(), write(), and ~FinleyDomain().
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the table of the elements
Referenced by addPDEToLumpedSystem(), addPDEToRHS(), addPDEToSystem(), addPDEToTransportProblem(), borrowListOfTagsInUse(), borrowSampleReferenceIDs(), createColoring(), distributeByRankOfDOF(), dump(), getDataShape(), getElements(), getNumberOfTagsInUse(), getTagFromSampleNo(), interpolateOnDomain(), markNodes(), operator==(), optimizeDOFDistribution(), optimizeDOFLabeling(), optimizeElementOrdering(), Print_Mesh_Info(), relabelElementNodes(), resolveNodeIds(), setElements(), setOrders(), setTags(), setToGradient(), setToIntegrals(), setToSize(), updateTagList(), write(), and ~FinleyDomain().
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the table of face elements
Referenced by addPDEToLumpedSystem(), addPDEToRHS(), addPDEToSystem(), addPDEToTransportProblem(), borrowListOfTagsInUse(), borrowSampleReferenceIDs(), createColoring(), distributeByRankOfDOF(), dump(), getDataShape(), getFaceElements(), getNumberOfTagsInUse(), getTagFromSampleNo(), glueFaces(), interpolateOnDomain(), joinFaces(), markNodes(), operator==(), optimizeDOFDistribution(), optimizeDOFLabeling(), optimizeElementOrdering(), Print_Mesh_Info(), relabelElementNodes(), resolveNodeIds(), setFaceElements(), setOrders(), setTags(), setToGradient(), setToIntegrals(), setToNormal(), setToSize(), updateTagList(), write(), and ~FinleyDomain().
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Referenced by functionSpaceTypeAsString(), isValidFunctionSpaceType(), and setFunctionSpaceTypeNames().
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MPI information.
Referenced by addDiracPoints(), dump(), FinleyDomain(), getMPI(), getMPIComm(), getMPIRank(), getMPISize(), getSystemMatrixTypeId(), glueFaces(), joinFaces(), newSystemMatrix(), optimizeDOFDistribution(), optimizeDOFLabeling(), prepare(), Print_Mesh_Info(), printElementInfo(), resolveNodeIds(), setOrders(), and write().
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domain description
Referenced by dump(), Print_Mesh_Info(), and write().
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the table of the nodes
Referenced by addDiracPoints(), addPDEToLumpedSystem(), addPDEToRHS(), addPDEToSystem(), addPDEToTransportProblem(), borrowListOfTagsInUse(), borrowSampleReferenceIDs(), createMappings(), distributeByRankOfDOF(), dump(), FinleyDomain(), getDataShape(), getDim(), getNodes(), getNumberOfTagsInUse(), getNumDataPointsGlobal(), getStatus(), getTagFromSampleNo(), glueFaces(), interpolateOnDomain(), operator==(), optimizeDOFDistribution(), optimizeDOFLabeling(), ownSample(), prepare(), Print_Mesh_Info(), printElementInfo(), resolveNodeIds(), setNewX(), setTags(), setToGradient(), setToIntegrals(), setToNormal(), setToSize(), setToX(), updateTagList(), write(), writeElementInfo(), and ~FinleyDomain().
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the table of points (treated as elements of dimension 0)
Referenced by addDiracPoints(), addPDEToLumpedSystem(), addPDEToRHS(), addPDEToSystem(), addPDEToTransportProblem(), borrowListOfTagsInUse(), borrowSampleReferenceIDs(), createColoring(), distributeByRankOfDOF(), dump(), getDataShape(), getNumberOfTagsInUse(), getPoints(), getTagFromSampleNo(), interpolateOnDomain(), markNodes(), operator==(), optimizeDOFDistribution(), optimizeDOFLabeling(), optimizeElementOrdering(), Print_Mesh_Info(), relabelElementNodes(), resolveNodeIds(), setPoints(), setTags(), updateTagList(), write(), and ~FinleyDomain().
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the tag map mapping names to tag keys
Referenced by dump(), getTag(), getTagMap(), isValidTagName(), Print_Mesh_Info(), setTagMap(), showTagNames(), and write().
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Referenced by getApproximationOrder(), Print_Mesh_Info(), and setOrders().
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Referenced by addDiracPoints(), dump(), getApproximationOrder(), merge(), Print_Mesh_Info(), and setOrders().