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finley/src/FinleyDomain.h
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1 
2 /*****************************************************************************
3 *
4 * Copyright (c) 2003-2018 by The University of Queensland
5 * http://www.uq.edu.au
6 *
7 * Primary Business: Queensland, Australia
8 * Licensed under the Apache License, version 2.0
9 * http://www.apache.org/licenses/LICENSE-2.0
10 *
11 * Development until 2012 by Earth Systems Science Computational Center (ESSCC)
12 * Development 2012-2013 by School of Earth Sciences
13 * Development from 2014 by Centre for Geoscience Computing (GeoComp)
14 *
15 *****************************************************************************/
16 
17 #ifndef __FINLEY_DOMAIN_H__
18 #define __FINLEY_DOMAIN_H__
19 
20 /****************************************************************************
21 
22  Finley: Domain
23 
24  A mesh is built from nodes and elements which describe the domain, surface,
25  and point sources (the latter are needed to establish links with other
26  codes, in particular particle codes). The nodes are stored in a NodeFile
27  and elements in ElementFiles. Finley domains have four ElementFiles
28  containing the elements, surface, contact and point sources, respectively.
29  Notice that the surface elements do not necessarily cover the entire
30  surface of the domain.
31 
32  The element type is fixed by the reference element, see ReferenceElement.h.
33  The numbering of the nodes starts with 0.
34 
35  Important: it is assumed that every node appears in at least one element or
36  surface element and that any node used in an element, surface element or as
37  a point is specified in the NodeFile, see also resolveNodeIds.
38 
39  In some cases it is useful to refer to a mesh entirely built from
40  order 1 (=linear) elements. The linear version of the mesh can be
41  accessed by referring to the first few nodes of each element
42  (thanks to the way the nodes are ordered). As the numbering of
43  these nodes is not continuous a relabeling vector is introduced
44  in the NodeFile. This feature is not fully implemented yet.
45 
46  All nodes and elements are tagged. The tag allows to group nodes and
47  elements. A typical application is to mark surface elements on a
48  certain portion of the domain with the same tag. All these surface
49  elements can then be assigned the same value e.g. for the pressure.
50 
51  The spatial dimensionality is determined by the type of elements
52  used and can be queried using getDim(). Notice that the element type
53  also determines the type of surface elements to be used.
54 
55 *****************************************************************************/
56 
57 #include <finley/Finley.h>
58 #include <finley/ElementFile.h>
59 #include <finley/NodeFile.h>
60 #include <finley/Util.h>
61 
62 #include <escript/AbstractContinuousDomain.h>
63 #include <escript/FunctionSpace.h>
64 #include <escript/FunctionSpaceFactory.h>
65 
66 #ifdef ESYS_HAVE_PASO
67 #include <paso/SystemMatrixPattern.h>
68 #endif
69 #ifdef ESYS_HAVE_TRILINOS
70 #include <trilinoswrap/types.h>
71 #endif
72 
73 #include <map>
74 #include <string>
75 #include <vector>
76 
77 namespace finley {
78 
79 typedef std::map<std::string, int> TagMap;
80 
81 enum SystemMatrixType {
82  SMT_PASO = 1<<8,
83  SMT_TRILINOS = 1<<10,
84  SMT_COMPLEX = 1<<16,
85  SMT_UNROLL = 1<<17
86 };
87 
93 class FinleyDomain : public escript::AbstractContinuousDomain
94 {
95 public:
101  static escript::Domain_ptr load(const std::string& filename);
102 
115  static escript::Domain_ptr read(escript::JMPI mpiInfo,
116  const std::string& fileName,
117  int integrationOrder = -1,
118  int reducedIntegrationOrder = -1,
119  bool optimize = false);
120 
135  const std::string& filename,
136  int numDim, int integrationOrder = -1,
138  bool optimize = false,
139  bool useMacroElements = false);
140 
158  static escript::Domain_ptr createRec4(dim_t NE0, dim_t NE1,
159  double L0, double L1,
160  bool periodic0, bool periodic1, int order,
161  int reducedOrder, bool useElementsOnFace,
162  bool optimize, escript::JMPI jmpi);
163 
184  static escript::Domain_ptr createRec8(dim_t NE0, dim_t NE1,
185  double l0, double l1,
186  bool periodic0, bool periodic1, int order,
187  int reducedOrder, bool useElementsOnFace,
188  bool useFullElementOrder,
189  bool useMacroElements, bool optimize,
190  escript::JMPI jmpi);
191 
212  static escript::Domain_ptr createHex8(dim_t NE0, dim_t NE1, dim_t NE2,
213  double l0, double l1, double l2,
214  bool periodic0, bool periodic1, bool periodic2,
215  int order, int reducedOrder,
216  bool useElementsOnFace,
217  bool optimize, escript::JMPI jmpi);
218 
241  static escript::Domain_ptr createHex20(dim_t NE0, dim_t NE1, dim_t NE2,
242  double l0, double l1, double l2,
243  bool periodic0, bool periodic1, bool periodic2,
244  int order, int reducedOrder,
245  bool useElementsOnFace,
246  bool useFullElementOrder,
247  bool useMacroElements, bool optimize,
248  escript::JMPI jmpi);
249 
258  FinleyDomain(const std::string& name, int numDim, escript::JMPI jmpi);
259 
264  FinleyDomain(const FinleyDomain& in);
265 
270  ~FinleyDomain();
271 
277  void addDiracPoints(const std::vector<double>& points,
278  const std::vector<int>& tags);
279 
284  NodeFile* getNodes() const { return m_nodes; }
285 
290  void setElements(ElementFile* elements);
291 
296  ElementFile* getElements() const { return m_elements; }
297 
302  void setFaceElements(ElementFile* elements);
303 
308  ElementFile* getFaceElements() const { return m_faceElements; }
309 
314  void setContactElements(ElementFile* elements);
315 
320  ElementFile* getContactElements() const { return m_contactElements; }
321 
326  void setPoints(ElementFile* elements);
327 
332  ElementFile* getPoints() const { return m_points; }
333 
338  virtual escript::JMPI getMPI() const { return m_mpiInfo; }
339 
344  virtual int getMPISize() const { return m_mpiInfo->size; }
345 
350  virtual int getMPIRank() const { return m_mpiInfo->rank; }
351 
356  virtual void MPIBarrier() const;
357 
362  virtual bool onMasterProcessor() const { return getMPIRank() == 0; }
363 
364  MPI_Comm getMPIComm() const { return m_mpiInfo->comm; }
365 
372  void write(const std::string& fileName) const;
373 
378  void Print_Mesh_Info(bool full=false) const;
379 
385  void dump(const std::string& fileName) const;
386 
393  int getTagFromSampleNo(int functionSpaceType, index_t sampleNo) const;
394 
400  const index_t* borrowSampleReferenceIDs(int functionSpaceType) const;
401 
407  virtual bool isValidFunctionSpaceType(int functionSpaceType) const;
408 
413  virtual std::string getDescription() const;
414 
419  virtual std::string functionSpaceTypeAsString(int functionSpaceType) const;
420 
426 
431  virtual int getContinuousFunctionCode() const;
432 
437  virtual int getReducedContinuousFunctionCode() const;
438 
443  virtual int getFunctionCode() const;
444 
449  virtual int getReducedFunctionCode() const;
450 
455  virtual int getFunctionOnBoundaryCode() const;
456 
461  virtual int getReducedFunctionOnBoundaryCode() const;
462 
467  virtual int getFunctionOnContactZeroCode() const;
468 
473  virtual int getReducedFunctionOnContactZeroCode() const;
474 
479  virtual int getFunctionOnContactOneCode() const;
480 
485  virtual int getReducedFunctionOnContactOneCode() const;
486 
491  virtual int getSolutionCode() const;
492 
497  virtual int getReducedSolutionCode() const;
498 
503  virtual int getDiracDeltaFunctionsCode() const;
504 
508  typedef std::map<int, std::string> FunctionSpaceNamesMapType;
509 
513  virtual int getDim() const { return m_nodes->numDim; }
514 
521  virtual StatusType getStatus() const;
522 
527  virtual dim_t getNumDataPointsGlobal() const;
528 
534  virtual std::pair<int,dim_t> getDataShape(int functionSpaceCode) const;
535 
541  virtual void setToX(escript::Data& arg) const;
542 
549  virtual void setTagMap(const std::string& name, int tag);
550 
556  virtual int getTag(const std::string& name) const;
557 
563  virtual bool isValidTagName(const std::string& name) const;
564 
569  virtual std::string showTagNames() const;
570 
575  virtual void setNewX(const escript::Data& arg);
576 
581  virtual void interpolateOnDomain(escript::Data& target,
582  const escript::Data& source) const;
583 
584  virtual bool probeInterpolationOnDomain(int functionSpaceType_source,
585  int functionSpaceType_target) const;
586 
587  virtual signed char preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const;
588 
593  bool commonFunctionSpace(const std::vector<int>& fs, int& resultcode) const;
594 
599  virtual void interpolateAcross(escript::Data& target, const escript::Data& source) const;
600 
604  virtual bool probeInterpolationAcross(int functionSpaceType_source,
605  const escript::AbstractDomain& targetDomain,
606  int functionSpaceType_target) const;
607 
613  virtual void setToNormal(escript::Data& out) const;
614 
620  virtual void setToSize(escript::Data& out) const;
621 
627  virtual void setToGradient(escript::Data& grad, const escript::Data& arg) const;
628 
634  virtual void setToIntegrals(std::vector<escript::DataTypes::real_t>& integrals,
635  const escript::Data& arg) const;
636  virtual void setToIntegrals(std::vector<escript::DataTypes::cplx_t>& integrals,
637  const escript::Data& arg) const;
638 
647  virtual int getSystemMatrixTypeId(const boost::python::object& options) const;
648 
658  virtual int getTransportTypeId(int solver, int preconditioner, int package,
659  bool symmetry) const;
660 
666  virtual bool isCellOriented(int functionSpaceCode) const;
667 
668  virtual bool ownSample(int fsCode, index_t id) const;
669 
674  virtual void addPDEToSystem(
676  const escript::Data& A, const escript::Data& B,
677  const escript::Data& C, const escript::Data& D,
678  const escript::Data& X, const escript::Data& Y,
679  const escript::Data& d, const escript::Data& y,
680  const escript::Data& d_contact,
681  const escript::Data& y_contact,
682  const escript::Data& d_dirac,
683  const escript::Data& y_dirac) const;
684 
689  virtual void addPDEToLumpedSystem(escript::Data& mat,
690  const escript::Data& D,
691  const escript::Data& d,
692  const escript::Data& d_dirac,
693  bool useHRZ) const;
694 
699  virtual void addPDEToRHS(escript::Data& rhs, const escript::Data& X,
700  const escript::Data& Y, const escript::Data& y,
701  const escript::Data& y_contact,
702  const escript::Data& y_dirac) const;
703 
708  virtual void addPDEToTransportProblem(
710  escript::Data& source, const escript::Data& M,
711  const escript::Data& A, const escript::Data& B,
712  const escript::Data& C, const escript::Data& D,
713  const escript::Data& X, const escript::Data& Y,
714  const escript::Data& d, const escript::Data& y,
715  const escript::Data& d_contact,
716  const escript::Data& y_contact,
717  const escript::Data& d_dirac,
718  const escript::Data& y_dirac) const;
719 
725  int row_blocksize,
726  const escript::FunctionSpace& row_functionspace,
727  int column_blocksize,
728  const escript::FunctionSpace& column_functionspace,
729  int type) const;
730 
736  const escript::FunctionSpace& functionspace,
737  int type) const;
738 
742  virtual escript::Data getX() const;
743 
748  virtual escript::Data getNormal() const;
749 
753  virtual escript::Data getSize() const;
754 
758  virtual bool operator==(const escript::AbstractDomain& other) const;
759  virtual bool operator!=(const escript::AbstractDomain& other) const;
760 
765  virtual void setTags(int functionSpaceType, int newTag,
766  const escript::Data& mask) const;
767 
773  virtual int getNumberOfTagsInUse(int functionSpaceCode) const;
774 
775  virtual const int* borrowListOfTagsInUse(int functionSpaceCode) const;
776 
781  virtual bool canTag(int functionSpaceCode) const;
782 
786  virtual int getApproximationOrder(int functionSpaceCode) const;
787 
788  virtual bool supportsContactElements() const { return true; }
789 
791  const escript::FunctionSpace& what, long seed,
792  const boost::python::tuple& filter) const;
793 
798  const TagMap& getTagMap() const { return m_tagMap; }
799 
800  void createMappings(const IndexVector& dofDistribution,
801  const IndexVector& nodeDistribution);
802 
803 #ifdef ESYS_HAVE_PASO
804  paso::SystemMatrixPattern_ptr getPasoPattern(bool reducedRowOrder,
806  bool reducedColOrder) const;
807 #endif
808 
809 #ifdef ESYS_HAVE_TRILINOS
810  esys_trilinos::const_TrilinosGraph_ptr getTrilinosGraph(bool reducedOrder) const;
812 #endif
813 
814  void glueFaces(double safetyFactor, double tolerance, bool optimize);
815 
816  void joinFaces(double safetyFactor, double tolerance, bool optimize);
817 
820  static FinleyDomain* merge(const std::vector<const FinleyDomain*>& meshes);
821 
822 private:
823  void prepare(bool optimize);
824 
825  void setOrders();
826 
834  void resolveNodeIds();
835 
838  void relabelElementNodes(const IndexVector& newNode, index_t offset);
839 
840  template<typename Scalar>
841  void setToIntegralsWorker(std::vector<Scalar>& integrals,
842  const escript::Data& arg) const;
843 
844 #ifdef ESYS_HAVE_PASO
845  paso::SystemMatrixPattern_ptr makePasoPattern(bool reducedRowOrder,
846  bool reducedColOrder) const;
847 #endif
848 #ifdef ESYS_HAVE_TRILINOS
849  esys_trilinos::GraphType* createTrilinosGraph(bool reducedOrder) const;
850 #endif
851  void createColoring(const IndexVector& dofMap);
852  void distributeByRankOfDOF(const IndexVector& distribution);
853  void markNodes(std::vector<short>& mask, index_t offset, bool useLinear) const;
854  void optimizeDOFDistribution(IndexVector& distribution);
855  void optimizeDOFLabeling(const IndexVector& distribution);
857  void findMatchingFaces(double safetyFactor, double tolerance, int* numPairs,
858  int* elem0, int* elem1, int* matchingNodes) const;
859  void updateTagList();
860  void printElementInfo(const ElementFile* e, const std::string& title,
861  const std::string& defaultType, bool full) const;
862 
863  void writeElementInfo(std::ostream& stream, const ElementFile* e,
864  const std::string& defaultType) const;
865 
869  std::string m_name;
870  int approximationOrder;
872  int integrationOrder;
875  NodeFile* m_nodes;
886 #ifdef ESYS_HAVE_PASO
887  // pointer to the sparse matrix patterns
888  mutable paso::SystemMatrixPattern_ptr FullFullPattern;
889  mutable paso::SystemMatrixPattern_ptr FullReducedPattern;
890  mutable paso::SystemMatrixPattern_ptr ReducedFullPattern;
891  mutable paso::SystemMatrixPattern_ptr ReducedReducedPattern;
892 #endif
893 #ifdef ESYS_HAVE_TRILINOS
894  mutable esys_trilinos::TrilinosGraph_ptr m_fullGraph;
895  mutable esys_trilinos::TrilinosGraph_ptr m_reducedGraph;
896 #endif
897 
899 };
900 
901 } // end of namespace
902 
903 #endif // __FINLEY_DOMAIN_H__
904 
finley::FinleyDomain::optimizeDOFLabeling
void optimizeDOFLabeling(const IndexVector &distribution)
optimizes the labeling of the DOFs on each processor
Definition: finley/src/FinleyDomain.cpp:2787
finley::FinleyDomain::getNumDataPointsGlobal
virtual dim_t getNumDataPointsGlobal() const
Return the number of data points summed across all MPI processes.
Definition: finley/src/FinleyDomain.cpp:1046
finley::NodeFile::updateTagList
void updateTagList()
Definition: finley/src/NodeFile.h:324
finley::FinleyDomain::setContactElements
void setContactElements(ElementFile *elements)
replaces the contact element file by elements
Definition: finley/src/FinleyDomain.cpp:132
dudley::DudleyDomain::getFaceElements
ElementFile * getFaceElements() const
returns a pointer to this domain's face element file
Definition: DudleyDomain.h:234
finley::brick_driver
Domain_ptr brick_driver(const bp::list &args)
Definition: finley/src/DomainFactory.cpp:1103
escript::SolverOptions
SolverOptions
Definition: SolverOptions.h:90
MPI_Status
int MPI_Status
Definition: EsysMPI.h:43
escript::SolverBuddy
Definition: SolverOptions.h:168
finley::FinleyDomain::randomFill
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.
Definition: finley/src/FinleyDomain.cpp:2666
escript::Data::isComplex
bool isComplex() const
True if components of this data are stored as complex.
Definition: Data.cpp:1163
finley::FinleyDomain::addPDEToLumpedSystem
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
Definition: finley/src/FinleyDomain.cpp:1170
finley::FinleyDomain::setToX
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 implement...
Definition: finley/src/FinleyDomain.cpp:1644
escript::FunctionSpace::getSize
escript::Data getSize() const
Returns the sample size (e.g. the diameter of elements, radius of particles).
Definition: FunctionSpace.cpp:245
finley::FinleyDomain::joinFaces
void joinFaces(double safetyFactor, double tolerance, bool optimize)
Definition: Mesh_joinFaces.cpp:47
finley::FinleyDomain
FinleyDomain implements the AbstractContinuousDomain interface for the Finley library.
Definition: finley/src/FinleyDomain.h:137
finley::FinleyDomain::relabelElementNodes
void relabelElementNodes(const IndexVector &newNode, index_t offset)
Definition: finley/src/FinleyDomain.cpp:201
finley::Assemble_NodeCoordinates
void Assemble_NodeCoordinates(const NodeFile *nodes, escript::Data &x)
copies node coordinates into expanded Data object x
Definition: finley/src/Assemble_NodeCoordinates.cpp:46
finley::SMT_COMPLEX
Definition: finley/src/FinleyDomain.h:128
finley::FaceElements
Definition: Finley.h:80
finley::NodeFile::globalReducedNodesIndex
index_t * globalReducedNodesIndex
Definition: finley/src/NodeFile.h:179
escript::DataTypes::real_t
double real_t
type of all real-valued scalars in escript
Definition: DataTypes.h:73
finley::FinleyDomain::approximationOrder
int approximationOrder
Definition: finley/src/FinleyDomain.h:914
REGISTER_ESCRIPT_EXCEPTION_TRANSLATORS
#define REGISTER_ESCRIPT_EXCEPTION_TRANSLATORS
Definition: ExceptionTranslators.h:24
finley::FinleyDomain::createRec8
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...
Definition: Mesh_rec8.cpp:24
finley::FinleyDomain::m_mpiInfo
escript::JMPI m_mpiInfo
MPI information.
Definition: finley/src/FinleyDomain.h:911
finley::FinleyDomain::functionSpaceTypeAsString
virtual std::string functionSpaceTypeAsString(int functionSpaceType) const
Return a description for the given function space type code.
Definition: finley/src/FinleyDomain.cpp:930
weipa::FinleyDomain::writeToSilo
virtual bool writeToSilo(DBfile *dbfile, const std::string &pathInSilo, const StringVec &labels, const StringVec &units, bool writeMeshData)
Writes the domain to a Silo file.
Definition: weipa/src/FinleyDomain.cpp:505
escript::reducedContinuousFunction
FunctionSpace reducedContinuousFunction(const AbstractDomain &domain)
Return a continuous with reduced order FunctionSpace (overlapped node values on reduced element order...
Definition: FunctionSpaceFactory.cpp:47
finley::Rec9
Definition: ReferenceElements.h:47
weipa::FinleyDomain::~FinleyDomain
virtual ~FinleyDomain()
Definition: weipa/src/FinleyDomain.cpp:77
finley::FinleyDomain::m_tagMap
TagMap m_tagMap
the tag map mapping names to tag keys
Definition: finley/src/FinleyDomain.h:929
FINLEY_REDUCED_FACE_ELEMENTS
#define FINLEY_REDUCED_FACE_ELEMENTS
Definition: Finley.h:69
finley::FinleyDomain::setTags
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 samp...
Definition: finley/src/FinleyDomain.cpp:2467
finley::FinleyDomain::updateTagList
void updateTagList()
regenerates list of tags in use for node file and element files
Definition: finley/src/FinleyDomain.cpp:2968
finley::NodeFile::createDenseDOFLabeling
dim_t createDenseDOFLabeling()
Definition: finley/src/NodeFile.cpp:535
finley::FinleyDomain::getSolutionCode
virtual int getSolutionCode() const
Return a Solution code.
Definition: finley/src/FinleyDomain.cpp:1028
paso::SystemMatrix
this class holds a (distributed) stiffness matrix
Definition: SystemMatrix.h:58
finley::FinleyDomain::borrowListOfTagsInUse
virtual const int * borrowListOfTagsInUse(int functionSpaceCode) const
Definition: finley/src/FinleyDomain.cpp:2569
finley::Assemble_integrate
void Assemble_integrate(const NodeFile *nodes, const ElementFile *elements, const escript::Data &data, Scalar *integrals)
integrates data on quadrature points
Definition: finley/src/Assemble_integrate.cpp:45
paso::Pattern::fromIndexListArray
static Pattern_ptr fromIndexListArray(dim_t n0, dim_t n, const escript::IndexList *index_list_array, index_t range_min, index_t range_max, index_t index_offset)
Definition: Pattern.cpp:100
finley::NodeFile::globalDegreesOfFreedom
index_t * globalDegreesOfFreedom
Definition: finley/src/NodeFile.h:171
weipa::FinleyDomain::removeGhostZones
virtual void removeGhostZones(int ownIndex)
Removes 'ghost' elements and nodes.
Definition: weipa/src/FinleyDomain.cpp:486
escript::SO_METHOD_DIRECT
Definition: SolverOptions.h:122
finley::FinleyDomain::getTransportTypeId
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,...
Definition: finley/src/FinleyDomain.cpp:2359
FINLEY_REDUCED_ELEMENTS
#define FINLEY_REDUCED_ELEMENTS
Definition: Finley.h:68
finley::FinleyDomain::glueFaces
void glueFaces(double safetyFactor, double tolerance, bool optimize)
Definition: Mesh_glueFaces.cpp:47
finley::FinleyDomain::borrowSampleReferenceIDs
const index_t * borrowSampleReferenceIDs(int functionSpaceType) const
Return the reference number of the given sample number.
Definition: finley/src/FinleyDomain.cpp:2386
finley::FinleyDomain::getFunctionOnContactZeroCode
virtual int getFunctionOnContactZeroCode() const
Return a FunctionOnContactZero code.
Definition: finley/src/FinleyDomain.cpp:1008
finley::NodeFile::getNumReducedNodes
dim_t getNumReducedNodes() const
returns the number of reduced order FEM nodes (on this rank)
Definition: finley/src/NodeFile.h:259
FINLEY_REDUCED_CONTACT_ELEMENTS_1
#define FINLEY_REDUCED_CONTACT_ELEMENTS_1
Definition: Finley.h:70
finley::FinleyDomain::getReducedFunctionOnContactOneCode
virtual int getReducedFunctionOnContactOneCode() const
Return a FunctionOnContactOne code with reduced integration order.
Definition: finley/src/FinleyDomain.cpp:1023
weipa::FinleyDomain::getElementsForFunctionSpace
virtual ElementData_ptr getElementsForFunctionSpace(int fsCode) const
Returns the element data for given function space code.
Definition: weipa/src/FinleyDomain.cpp:251
finley::FinleyDomain::setToIntegrals
virtual void setToIntegrals(std::vector< escript::DataTypes::real_t > &integrals, const escript::Data &arg) const
copies the integrals of the function defined by arg into integrals. arg has to be defined on this.
finley::FinleyDomain::operator==
virtual bool operator==(const escript::AbstractDomain &other) const
comparison operators
Definition: finley/src/FinleyDomain.cpp:2281
finley::FinleyDomain::canTag
virtual bool canTag(int functionSpaceCode) const
Checks if this domain allows tags for the specified functionSpace code.
Definition: finley/src/FinleyDomain.cpp:2615
weipa::FinleyDomain::faces
FinleyElements_ptr faces
Definition: weipa/src/FinleyDomain.h:71
finley::NodeFile::assignMPIRankToDOFs
void assignMPIRankToDOFs(std::vector< int > &mpiRankOfDOF, const IndexVector &distribution)
Definition: finley/src/NodeFile.cpp:448
weipa::FinleyDomain::getMeshNames
virtual StringVec getMeshNames() const
Returns the names of all meshes within this domain.
Definition: weipa/src/FinleyDomain.cpp:332
finley::NodeFile::Tag
int * Tag
Tag[i] is the tag of node i.
Definition: finley/src/NodeFile.h:164
finley::FinleyDomain::getSystemMatrixTypeId
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...
Definition: finley/src/FinleyDomain.cpp:2299
weipa::VisItControl::initialized
bool initialized
Definition: VisItControl.cpp:60
finley::ReducedContactElementsOne
Definition: Finley.h:86
escript::SolverBuddy::getPackage
SolverOptions getPackage() const
Definition: SolverOptions.cpp:487
finley::NodeFile::getFirstNode
index_t getFirstNode() const
Definition: finley/src/NodeFile.h:214
weipa::FinleyDomain::nodes
FinleyNodes_ptr nodes
Definition: weipa/src/FinleyDomain.h:69
finley::Tet10
Definition: ReferenceElements.h:51
escript::continuousFunction
FunctionSpace continuousFunction(const AbstractDomain &domain)
Create function space objects.
Definition: FunctionSpaceFactory.cpp:41
finley::ElementFile::Tag
int * Tag
Tag[i] is the tag of element i.
Definition: finley/src/ElementFile.h:139
weipa::FinleyDomain::getDataVarByName
virtual DataVar_ptr getDataVarByName(const std::string &name) const
Creates and returns a variable with domain data.
Definition: weipa/src/FinleyDomain.cpp:370
finley::FinleyDomain::getTagFromSampleNo
int getTagFromSampleNo(int functionSpaceType, index_t sampleNo) const
Return the tag key for the given sample number.
Definition: finley/src/FinleyDomain.cpp:2427
escript::NotImplementedError
An exception class for features which are not (yet) implemented.
Definition: EsysException.h:89
finley::FinleyException
Definition: FinleyException.h:36
finley::FinleyDomain::addPDEToSystem
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
Definition: finley/src/FinleyDomain.cpp:1137
FINLEY_NODES
#define FINLEY_NODES
Definition: Finley.h:60
finley::Tet10Macro
Definition: ReferenceElements.h:111
dudley::DudleyDomain::getElements
ElementFile * getElements() const
returns a pointer to this domain's element file
Definition: DudleyDomain.h:222
weipa::FinleyDomain::reorderGhostZones
virtual void reorderGhostZones(int ownIndex)
Reorders elements so that 'ghost' elements (i.e. those that do not belong to ownIndex) appear last.
Definition: weipa/src/FinleyDomain.cpp:468
finley::NodeFile::nodesDistribution
escript::Distribution_ptr nodesDistribution
MPI distribution of nodes.
Definition: finley/src/NodeFile.h:184
paso::SystemMatrix_ptr
boost::shared_ptr< SystemMatrix > SystemMatrix_ptr
Definition: SystemMatrix.h:51
finley::FinleyDomain::integrationOrder
int integrationOrder
Definition: finley/src/FinleyDomain.h:916
paso::TransportProblem::borrowMassMatrix
SystemMatrix_ptr borrowMassMatrix() const
Definition: Transport.h:68
escript::DataTypes::DataVectorAlt< real_t >
escript::SolverBuddy::getSolverMethod
SolverOptions getSolverMethod() const
Definition: SolverOptions.cpp:424
escript::randomFillArray
void randomFillArray(long seed, double *array, size_t n)
Definition: Random.cpp:73
finley::FinleyDomain::m_faceElements
ElementFile * m_faceElements
the table of face elements
Definition: finley/src/FinleyDomain.h:923
escript::AbstractDomain::StatusType
int StatusType
Definition: AbstractDomain.h:59
paso::SystemMatrixPattern_ptr
boost::shared_ptr< SystemMatrixPattern > SystemMatrixPattern_ptr
Definition: SystemMatrixPattern.h:50
finley::NodeFile::reducedNodesId
index_t * reducedNodesId
Definition: finley/src/NodeFile.h:201
finley::NodeFile::globalReducedDOFIndex
index_t * globalReducedDOFIndex
Definition: finley/src/NodeFile.h:176
finley::FinleyDomain::probeInterpolationOnDomain
virtual bool probeInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const
True if interpolation is possible from source to target.
Definition: finley/src/FinleyDomain.cpp:2137
finley::FinleyDomain::showTagNames
virtual std::string showTagNames() const
Returns all tag names in a single string sperated by commas.
Definition: finley/src/FinleyDomain.cpp:2525
finley::ElementFile::createColoring
void createColoring(const IndexVector &dofMap)
Tries to reduce the number of colours used to colour the elements.
Definition: finley/src/ElementFile.cpp:259
DUDLEY_NODES
#define DUDLEY_NODES
Definition: Dudley.h:52
finley::FinleyDomain::getMPISize
virtual int getMPISize() const
returns the number of processors used for this domain
Definition: finley/src/FinleyDomain.h:388
finley::ElementFile::relabelNodes
void relabelNodes(const IndexVector &newNode, index_t offset)
finley::FinleyDomain::getNumberOfTagsInUse
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
Definition: finley/src/FinleyDomain.cpp:2538
escript::Domain_ptr
boost::shared_ptr< AbstractDomain > Domain_ptr
Definition: AbstractDomain.h:47
escript::AbstractTransportProblem
Give a short description of what AbstractTransportProblem does.
Definition: AbstractTransportProblem.h:54
finley::ReducedNodes
Definition: Finley.h:77
finley::FinleyDomain::readGmsh
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.
Definition: finley/src/Mesh_readGmsh.cpp:1538
escript::SO_PRECONDITIONER_ILUT
Definition: SolverOptions.h:142
finley::FinleyDomain::getSize
virtual escript::Data getSize() const
returns the element size
Definition: finley/src/FinleyDomain.cpp:2381
escript::SolverBuddy::isComplex
bool isComplex() const
Definition: SolverOptions.cpp:653
finley::ElementFile::setTags
void setTags(const int newTag, const escript::Data &mask)
Definition: finley/src/ElementFile.cpp:226
finley::FinleyDomain::getApproximationOrder
virtual int getApproximationOrder(int functionSpaceCode) const
returns the approximation order used for a function space functionSpaceCode
Definition: finley/src/FinleyDomain.cpp:2639
finley::ElementFile::Nodes
index_t * Nodes
Definition: finley/src/ElementFile.h:154
escript::FunctionSpace
Definition: FunctionSpace.h:45
finley::FinleyDomain::createHex20
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.
Definition: Mesh_hex20.cpp:36
finley::ElementFile::getNodeRange
std::pair< index_t, index_t > getNodeRange() const
Definition: finley/src/ElementFile.h:184
finley::FinleyDomain::m_nodes
NodeFile * m_nodes
the table of the nodes
Definition: finley/src/FinleyDomain.h:919
finley::Points
Definition: Finley.h:82
finley::ElementFile::distributeByRankOfDOF
void distributeByRankOfDOF(const std::vector< int > &mpiRankOfDOF, index_t *nodesId)
redistributes the elements including overlap by rank
Definition: finley/src/ElementFile.cpp:340
finley::SystemMatrixType
SystemMatrixType
Definition: finley/src/FinleyDomain.h:125
finley::FinleyDomain::resolveNodeIds
void resolveNodeIds()
Definition: finley/src/FinleyDomain.cpp:2868
escript::Data::getFunctionSpace
const FunctionSpace & getFunctionSpace() const
Return the function space.
Definition: Data.h:461
FINLEY_REDUCED_DEGREES_OF_FREEDOM
#define FINLEY_REDUCED_DEGREES_OF_FREEDOM
Definition: Finley.h:66
finley::NodeFile::getNumReducedDegreesOfFreedom
dim_t getNumReducedDegreesOfFreedom() const
returns the number of reduced order degrees of freedom (on this rank)
Definition: finley/src/NodeFile.h:269
weipa::DataVar_ptr
boost::shared_ptr< DataVar > DataVar_ptr
Definition: weipa.h:63
weipa
Definition: DataVar.cpp:49
finley::FinleyDomain::getElements
ElementFile * getElements() const
returns a pointer to this domain's element file
Definition: finley/src/FinleyDomain.h:340
finley::Rec9Macro
Definition: ReferenceElements.h:110
finley::FinleyDomain::getDiracDeltaFunctionsCode
virtual int getDiracDeltaFunctionsCode() const
Return a DiracDeltaFunctions code.
Definition: finley/src/FinleyDomain.cpp:1038
escript::FunctionSpace::getDomain
const_Domain_ptr getDomain() const
Returns the function space domain.
Definition: FunctionSpace.cpp:101
MPI_INT
#define MPI_INT
Definition: EsysMPI.h:44
escript::DataTypes::index_t_max
index_t index_t_max()
Returns the maximum finite value for the index_t type.
Definition: DataTypes.h:102
finley::Hex27
Definition: ReferenceElements.h:55
finley::FinleyDomain::getDescription
virtual std::string getDescription() const
Return a description for this domain.
Definition: finley/src/FinleyDomain.cpp:925
finley::FinleyDomain::findMatchingFaces
void findMatchingFaces(double safetyFactor, double tolerance, int *numPairs, int *elem0, int *elem1, int *matchingNodes) const
Definition: Mesh_findMatchingFaces.cpp:84
finley::FinleyDomain::setToSize
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....
Definition: finley/src/FinleyDomain.cpp:1819
finley::SMT_UNROLL
Definition: finley/src/FinleyDomain.h:129
MPI_MAX
#define MPI_MAX
Definition: EsysMPI.h:52
weipa::FinleyDomain::siloPath
std::string siloPath
Definition: weipa/src/FinleyDomain.h:73
finley::FinleyDomain::m_points
ElementFile * m_points
the table of points (treated as elements of dimension 0)
Definition: finley/src/FinleyDomain.h:927
finley::FinleyDomain::addPDEToTransportProblem
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
Definition: finley/src/FinleyDomain.cpp:1208
finley::NodeFile::getNumNodes
dim_t getNumNodes() const
returns the number of FEM nodes (on this rank)
Definition: finley/src/NodeFile.h:254
finley::FinleyDomain::getReducedFunctionOnContactZeroCode
virtual int getReducedFunctionOnContactZeroCode() const
Return a FunctionOnContactZero code with reduced integration order.
Definition: finley/src/FinleyDomain.cpp:1013
weipa::FinleyDomain::contacts
FinleyElements_ptr contacts
Definition: weipa/src/FinleyDomain.h:72
weipa::ZONE_CENTERED
Definition: DomainChunk.h:31
finley::NodeFile::createNodeMappings
void createNodeMappings(const IndexVector &indexReducedNodes, const IndexVector &dofDistribution, const IndexVector &nodeDistribution)
Definition: finley/src/NodeFile.cpp:1014
finley::FinleyDomain::getReducedFunctionCode
virtual int getReducedFunctionCode() const
Return a function with reduced integration order FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:993
escript::FunctionSpace::getNormal
escript::Data getNormal() const
Returns the surface normal field.
Definition: FunctionSpace.cpp:236
finley::NodeFile::Coordinates
double * Coordinates
Coordinates[INDEX2(k,i,numDim)] is the k-th coordinate of node i.
Definition: finley/src/NodeFile.h:173
finley::FinleyDomain::getReducedFunctionOnBoundaryCode
virtual int getReducedFunctionOnBoundaryCode() const
Return a function on boundary with reduced integration order FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:1003
finley::FinleyDomain::probeInterpolationAcross
virtual bool probeInterpolationAcross(int functionSpaceType_source, const escript::AbstractDomain &targetDomain, int functionSpaceType_target) const
determines whether interpolation from source to target is possible.
Definition: finley/src/FinleyDomain.cpp:2275
finley::ElementFile::numElements
dim_t numElements
number of elements
Definition: finley/src/ElementFile.h:132
finley::FinleyDomain::getFunctionCode
virtual int getFunctionCode() const
Return a function FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:988
finley::ElementFile::Owner
int * Owner
Owner[i] contains the rank that owns element i.
Definition: finley/src/ElementFile.h:142
escript::Data
Data represents a collection of datapoints.
Definition: Data.h:62
paso::TransportProblem_ptr
boost::shared_ptr< TransportProblem > TransportProblem_ptr
Definition: Transport.h:30
paso::util::l2
double l2(dim_t n, const double *x, escript::JMPI mpiinfo)
returns the global L2 norm of x
Definition: PasoUtil.cpp:524
paso::TransportProblem::borrowTransportMatrix
SystemMatrix_ptr borrowTransportMatrix() const
Definition: Transport.h:63
finley::NodeFile::getLastNode
index_t getLastNode() const
Definition: finley/src/NodeFile.h:219
weipa::FinleyElements_ptr
boost::shared_ptr< FinleyElements > FinleyElements_ptr
Definition: FinleyElements.h:62
finley::FinleyDomain::getStatus
virtual StatusType getStatus() const
Returns a status indicator of the domain. The status identifier should be unique over the live time i...
Definition: finley/src/FinleyDomain.cpp:2634
finley::FinleyDomain::getFunctionOnBoundaryCode
virtual int getFunctionOnBoundaryCode() const
Return a function on boundary FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:998
escript::AbstractSystemMatrix::getPtr
ASM_ptr getPtr()
Returns smart pointer which is managing this object. If one does not exist yet it creates one.
Definition: AbstractSystemMatrix.cpp:52
finley::FinleyDomain::Print_Mesh_Info
void Print_Mesh_Info(bool full=false) const
Definition: finley/src/Mesh_write.cpp:146
escript::FunctionSpace::getX
escript::Data getX() const
Returns the spatial locations of the data points.
Definition: FunctionSpace.cpp:227
escript::DataTypes::dim_t
index_t dim_t
Definition: DataTypes.h:87
escript::DataTypes::ShapeType
std::vector< int > ShapeType
The shape of a single datapoint.
Definition: DataTypes.h:65
weipa::FinleyDomain::initFromFile
virtual bool initFromFile(const std::string &filename)
Reads the domain from a dump file.
Definition: weipa/src/FinleyDomain.cpp:182
finley::ContactElementsZero
Definition: Finley.h:83
escript::JMPI
boost::shared_ptr< JMPI_ > JMPI
Definition: EsysMPI.h:70
FINLEY_FACE_ELEMENTS
#define FINLEY_FACE_ELEMENTS
Definition: Finley.h:62
finley::FinleyDomain::isCellOriented
virtual bool isCellOriented(int functionSpaceCode) const
returns true if data on this domain and a function space of type functionSpaceCode has to considered ...
Definition: finley/src/FinleyDomain.cpp:1991
finley::ReducedDegreesOfFreedom
Definition: Finley.h:75
escript::ATP_ptr
boost::shared_ptr< AbstractTransportProblem > ATP_ptr
Definition: AbstractTransportProblem.h:171
escript::AbstractSystemMatrix
Base class for escript system matrices.
Definition: AbstractSystemMatrix.h:53
finley::FinleyDomain::getFaceElements
ElementFile * getFaceElements() const
returns a pointer to this domain's face element file
Definition: finley/src/FinleyDomain.h:352
weipa::FinleyDomain::cells
FinleyElements_ptr cells
Definition: weipa/src/FinleyDomain.h:70
finley::DegreesOfFreedom
Definition: Finley.h:74
finley::NodeFile::borrowGlobalNodesIndex
const index_t * borrowGlobalNodesIndex() const
Definition: finley/src/NodeFile.h:229
finley::FinleyDomain::getDataShape
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.
Definition: finley/src/FinleyDomain.cpp:1055
finley::NodeFile::createDenseReducedLabeling
dim_t createDenseReducedLabeling(const std::vector< short > &reducedMask, bool useNodes)
Definition: finley/src/NodeFile.cpp:712
finley::Tri6Macro
Definition: ReferenceElements.h:109
finley::FinleyDomain::createColoring
void createColoring(const IndexVector &dofMap)
tries to reduce the number of colours for all element files
Definition: finley/src/FinleyDomain.cpp:2950
finley::Hex27Macro
Definition: ReferenceElements.h:112
IndexList.h
finley::FinleyDomain::setToIntegralsWorker
void setToIntegralsWorker(std::vector< Scalar > &integrals, const escript::Data &arg) const
Definition: finley/src/FinleyDomain.cpp:1710
finley::FinleyDomain::addDiracPoints
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 creat...
Definition: Mesh_addPoints.cpp:46
finley::FinleyDomain::interpolateOnDomain
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 do...
Definition: finley/src/FinleyDomain.cpp:1249
weipa::ElementData_ptr
boost::shared_ptr< ElementData > ElementData_ptr
Definition: weipa.h:65
FINLEY_DEGREES_OF_FREEDOM
#define FINLEY_DEGREES_OF_FREEDOM
Definition: Finley.h:59
finley::ElementFile::Color
index_t * Color
Definition: finley/src/ElementFile.h:160
finley::FinleyDomain::m_name
std::string m_name
domain description
Definition: finley/src/FinleyDomain.h:913
finley::FinleyDomain::setToGradient
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 ...
Definition: finley/src/FinleyDomain.cpp:1753
finley::FinleyDomain::getNodes
NodeFile * getNodes() const
returns a pointer to this domain's node file
Definition: finley/src/FinleyDomain.h:328
weipa::NODE_CENTERED
Definition: DomainChunk.h:30
finley::readGmsh_driver
Domain_ptr readGmsh_driver(const bp::list &args)
Definition: finley/src/DomainFactory.cpp:983
finley::FinleyDomain::getDim
virtual int getDim() const
returns the dimensionality of this domain
Definition: finley/src/FinleyDomain.h:557
finley::FinleyDomain::setToNormal
virtual void setToNormal(escript::Data &out) const
copies the surface normals at data points into out. The actual function space to be considered is def...
Definition: finley/src/FinleyDomain.cpp:1663
finley::FinleyDomain::optimizeElementOrdering
void optimizeElementOrdering()
redistributes elements to minimize communication during assemblage
Definition: finley/src/FinleyDomain.cpp:2959
FINLEY_ELEMENTS
#define FINLEY_ELEMENTS
Definition: Finley.h:61
finley::FinleyDomain::reducedApproximationOrder
int reducedApproximationOrder
Definition: finley/src/FinleyDomain.h:915
finley::NodeFile::Id
index_t * Id
Id[i] is the unique ID number of FEM node i.
Definition: finley/src/NodeFile.h:162
finley::FinleyDomain::commonFunctionSpace
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.
Definition: finley/src/FinleyDomain.cpp:2016
finley::FinleyDomain::getFunctionOnContactOneCode
virtual int getFunctionOnContactOneCode() const
Return a FunctionOnContactOne code.
Definition: finley/src/FinleyDomain.cpp:1018
DUDLEY_REDUCED_ELEMENTS
#define DUDLEY_REDUCED_ELEMENTS
Definition: Dudley.h:56
finley::ElementFile::Id
index_t * Id
Definition: finley/src/ElementFile.h:136
weipa::FinleyDomain::FinleyDomain
FinleyDomain()
Definition: weipa/src/FinleyDomain.cpp:56
finley::NodeFile::createDenseNodeLabeling
dim_t createDenseNodeLabeling(IndexVector &nodeDistribution, const IndexVector &dofDistribution)
Definition: finley/src/NodeFile.cpp:598
finley::FinleyDomain::FunctionSpaceNamesMapType
std::map< int, std::string > FunctionSpaceNamesMapType
Definition: finley/src/FinleyDomain.h:552
finley::FinleyDomain::FinleyDomain
FinleyDomain(const std::string &name, int numDim, escript::JMPI jmpi)
Constructor for FinleyDomain.
Definition: finley/src/FinleyDomain.cpp:71
finley::FinleyDomain::getReducedContinuousFunctionCode
virtual int getReducedContinuousFunctionCode() const
Return a continuous on reduced order nodes FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:983
finley::FinleyDomain::addPDEToRHS
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
Definition: finley/src/FinleyDomain.cpp:1184
dudley::DudleyDomain::getNodes
NodeFile * getNodes() const
returns a pointer to this domain's node file
Definition: DudleyDomain.h:210
finley::NodeFile::status
int status
Definition: finley/src/NodeFile.h:207
weipa::FinleyDomain::cleanup
void cleanup()
Definition: weipa/src/FinleyDomain.cpp:85
finley::NodeFile::setCoordinates
void setCoordinates(const escript::Data &newX)
copies the array newX into this->coordinates
Definition: finley/src/NodeFile.cpp:252
finley::FinleyDomain::m_functionSpaceTypeNames
static FunctionSpaceNamesMapType m_functionSpaceTypeNames
Definition: finley/src/FinleyDomain.h:942
escript::SO_PRECONDITIONER_AMG
Definition: SolverOptions.h:139
DUDLEY_ELEMENTS
#define DUDLEY_ELEMENTS
Definition: Dudley.h:53
finley::joinFaces
Domain_ptr joinFaces(const bp::list &meshList, double safetyFactor, double tolerance, bool optimize)
Definition: finley/src/DomainFactory.cpp:1298
finley::FinleyDomain::reducedIntegrationOrder
int reducedIntegrationOrder
Definition: finley/src/FinleyDomain.h:917
finley::FinleyDomain::operator!=
virtual bool operator!=(const escript::AbstractDomain &other) const
Return true if given domains are not equal.
Definition: finley/src/FinleyDomain.cpp:2294
paso::TransportProblem
Definition: Transport.h:34
finley::SMT_TRILINOS
Definition: finley/src/FinleyDomain.h:127
paso::TransportProblem::getTypeId
static int getTypeId(int solver, int preconditioner, int package, bool symmetry, const escript::JMPI &mpi_info)
Definition: Transport.h:93
finley::FinleyDomain::getTagMap
const TagMap & getTagMap() const
returns a reference to the tag name->value map
Definition: finley/src/FinleyDomain.h:842
finley::Assemble_getSize
void Assemble_getSize(const NodeFile *nodes, const ElementFile *elements, escript::Data &size)
Definition: finley/src/Assemble_getSize.cpp:46
finley::SMT_PASO
Definition: finley/src/FinleyDomain.h:126
escript::SolverBuddy::isSymmetric
bool isSymmetric() const
Definition: SolverOptions.cpp:663
DUDLEY_REDUCED_FACE_ELEMENTS
#define DUDLEY_REDUCED_FACE_ELEMENTS
Definition: Dudley.h:57
finley::ReducedFaceElements
Definition: Finley.h:81
finley::FinleyDomain::m_contactElements
ElementFile * m_contactElements
the table of contact elements
Definition: finley/src/FinleyDomain.h:925
finley::FinleyDomain::getMPI
virtual escript::JMPI getMPI() const
returns a reference to the MPI information wrapper for this domain
Definition: finley/src/FinleyDomain.h:382
escript::SolverBuddy::getPreconditioner
SolverOptions getPreconditioner() const
Definition: SolverOptions.cpp:355
finley::FinleyDomain::preferredInterpolationOnDomain
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,...
Definition: finley/src/FinleyDomain.cpp:2264
finley::FinleyDomain::getContactElements
ElementFile * getContactElements() const
returns a pointer to this domain's contact element file
Definition: finley/src/FinleyDomain.h:364
finley::Tri6
Definition: ReferenceElements.h:42
weipa::FinleyDomain::getElementsByName
virtual ElementData_ptr getElementsByName(const std::string &name) const
Returns element data with given name.
Definition: weipa/src/FinleyDomain.cpp:431
MPI_MIN
#define MPI_MIN
Definition: EsysMPI.h:51
escript::isDirectSolver
bool isDirectSolver(const SolverOptions &method)
returns true if the passed solver method refers to a direct solver type
Definition: SolverOptions.h:153
finley::FinleyDomain::interpolateAcross
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.
Definition: finley/src/FinleyDomain.cpp:1687
finley::FinleyDomain::getNormal
virtual escript::Data getNormal() const
returns boundary normals at the quadrature point on the face elements
Definition: finley/src/FinleyDomain.cpp:2376
finley::FinleyDomain::read
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.
Definition: finley/src/Mesh_read.cpp:151
finley::FinleyDomain::onMasterProcessor
virtual bool onMasterProcessor() const
returns true if on MPI processor 0, else false
Definition: finley/src/FinleyDomain.h:406
finley::NodeFile::degreesOfFreedomDistribution
escript::Distribution_ptr degreesOfFreedomDistribution
Definition: finley/src/NodeFile.h:186
finley::FinleyDomain::getContinuousFunctionCode
virtual int getContinuousFunctionCode() const
Return a continuous FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:978
finley::FinleyDomain::ownSample
virtual bool ownSample(int fsCode, index_t id) const
Definition: finley/src/FinleyDomain.cpp:1870
finley::NodeFile::getDOFRange
std::pair< index_t, index_t > getDOFRange() const
Definition: finley/src/NodeFile.cpp:225
finley::FinleyDomain::dump
void dump(const std::string &fileName) const
dumps the mesh to a file with the given name.
Definition: finley/src/FinleyDomain.cpp:562
finley::Assemble_LumpedSystem
void Assemble_LumpedSystem(const NodeFile *nodes, const ElementFile *elements, escript::Data &lumpedMat, const escript::Data &D, bool useHRZ)
Definition: finley/src/Assemble_LumpedSystem.cpp:52
escript::RuntimeErrorTranslator
void RuntimeErrorTranslator(const EsysException &e)
Function which translates an EsysException into a python RuntimeError.
Definition: ExceptionTranslators.cpp:47
escript::DataTypes::index_t
int index_t
type for array/matrix indices used both globally and on each rank
Definition: DataTypes.h:82
finley::FinleyDomain::load
static escript::Domain_ptr load(const std::string &filename)
recovers domain from a dump file
Definition: finley/src/DomainFactory.cpp:489
finley::Line3Macro
Definition: ReferenceElements.h:108
finley::NodeFile::getGlobalNumNodes
dim_t getGlobalNumNodes() const
Definition: finley/src/NodeFile.h:224
finley::glueFaces
Domain_ptr glueFaces(const bp::list &meshList, double safetyFactor, double tolerance, bool optimize)
Definition: finley/src/DomainFactory.cpp:1286
finley::FinleyDomain::setElements
void setElements(ElementFile *elements)
replaces the element file by elements
Definition: finley/src/FinleyDomain.cpp:120
finley::NodeFile
Definition: finley/src/NodeFile.h:39
finley::FinleyDomain::getPoints
ElementFile * getPoints() const
returns a pointer to this domain's point (nodal) element file
Definition: finley/src/FinleyDomain.h:376
finley::FinleyDomain::isValidTagName
virtual bool isValidTagName(const std::string &name) const
Returns true if name is a defined tag name.
Definition: finley/src/FinleyDomain.cpp:2520
finley::FinleyDomain::getMPIRank
virtual int getMPIRank() const
returns the number MPI rank of this processor
Definition: finley/src/FinleyDomain.h:394
finley::ElementFile::markNodes
void markNodes(std::vector< short > &mask, int offset, bool useLinear)
Definition: finley/src/ElementFile.cpp:315
finley::NodeFile::reducedDegreesOfFreedomId
index_t * reducedDegreesOfFreedomId
Definition: finley/src/NodeFile.h:203
finley::FinleyDomain::newTransportProblem
escript::ATP_ptr newTransportProblem(int blocksize, const escript::FunctionSpace &functionspace, int type) const
creates a TransportProblem
Definition: finley/src/FinleyDomain.cpp:1959
finley::Nodes
Definition: Finley.h:76
weipa::FinleyDomain::initialized
bool initialized
Definition: weipa/src/FinleyDomain.h:68
weipa::NodeData_ptr
boost::shared_ptr< NodeData > NodeData_ptr
Definition: weipa.h:67
finley::Assemble_PDE
void Assemble_PDE(const NodeFile *nodes, const ElementFile *elements, escript::ASM_ptr S, escript::Data &F, const escript::Data &A, const escript::Data &B, const escript::Data &C, const escript::Data &D, const escript::Data &X, const escript::Data &Y)
Definition: finley/src/Assemble_PDE.cpp:122
FINLEY_REDUCED_CONTACT_ELEMENTS_2
#define FINLEY_REDUCED_CONTACT_ELEMENTS_2
Definition: Finley.h:71
escript::SO_DEFAULT
Definition: SolverOptions.h:104
finley::FinleyDomain::setOrders
void setOrders()
Definition: finley/src/FinleyDomain.cpp:144
weipa::StringVec
std::vector< std::string > StringVec
Definition: weipa.h:59
finley::FinleyDomain::setPoints
void setPoints(ElementFile *elements)
replaces the point element file by elements
Definition: finley/src/FinleyDomain.cpp:138
BOOST_PYTHON_MODULE
BOOST_PYTHON_MODULE(finleycpp)
Definition: finleycpp.cpp:30
escript::FunctionSpace::getTypeCode
int getTypeCode() const
Returns the function space type code.
Definition: FunctionSpace.cpp:93
finley::NodeFile::globalNodesIndex
index_t * globalNodesIndex
assigns each local node a global unique ID in a dense labeling
Definition: finley/src/NodeFile.h:181
finley::ReducedElements
Definition: Finley.h:79
finley::IndexList_insertElementsWithRowRangeNoMainDiagonal
void IndexList_insertElementsWithRowRangeNoMainDiagonal(IndexList *index_list, index_t firstRow, index_t lastRow, ElementFile *elements, index_t *row_map, index_t *col_map)
Definition: finley/src/IndexList.cpp:101
FinleyException.h
dudley::DudleyDomain
DudleyDomain implements the AbstractContinuousDomain interface for the Dudley library.
Definition: DudleyDomain.h:119
escript::function
FunctionSpace function(const AbstractDomain &domain)
Return a function FunctionSpace.
Definition: FunctionSpaceFactory.cpp:53
escript::Vector
Data Vector(double value, const FunctionSpace &what, bool expanded)
Return a Data object containing vector data-points. ie: rank 1 data-points.
Definition: DataFactory.cpp:96
finley::ElementFile::tagsInUse
std::vector< int > tagsInUse
array of tags which are actually used
Definition: finley/src/ElementFile.h:145
finley::FinleyDomain::newSystemMatrix
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
Definition: finley/src/FinleyDomain.cpp:1896
paso::M
static dim_t M
Definition: SparseMatrix_saveHB.cpp:48
finley::ElementFile
Definition: finley/src/ElementFile.h:72
FinleyDomain.h
finley::FinleyDomain::distributeByRankOfDOF
void distributeByRankOfDOF(const IndexVector &distribution)
Definition: finley/src/FinleyDomain.cpp:2737
weipa::FinleyDomain::getVarNames
virtual StringVec getVarNames() const
Returns the names of all 'special' domain variables.
Definition: weipa/src/FinleyDomain.cpp:350
escript::functionOnBoundary
FunctionSpace functionOnBoundary(const AbstractDomain &domain)
Return a function on boundary FunctionSpace.
Definition: FunctionSpaceFactory.cpp:65
finley::FinleyDomain::createMappings
void createMappings(const IndexVector &dofDistribution, const IndexVector &nodeDistribution)
Definition: finley/src/FinleyDomain.cpp:183
finley::FinleyDomain::getMPIComm
MPI_Comm getMPIComm() const
get the communicator for this domain. Returns an integer on non-MPI builds Routine must be implemente...
Definition: finley/src/FinleyDomain.h:408
MPI_Comm
int MPI_Comm
Definition: EsysMPI.h:40
finley::FinleyDomain::optimizeDOFDistribution
void optimizeDOFDistribution(IndexVector &distribution)
Definition: finley/src/Mesh_optimizeDOFDistribution.cpp:76
FINLEY_REDUCED_NODES
#define FINLEY_REDUCED_NODES
Definition: Finley.h:67
paso::Pattern_ptr
boost::shared_ptr< Pattern > Pattern_ptr
Definition: Pattern.h:48
finley::FinleyDomain::setTagMap
virtual void setTagMap(const std::string &name, int tag)
sets a map from a clear tag name to a tag key
Definition: finley/src/FinleyDomain.cpp:2504
finley::Assemble_getNormal
void Assemble_getNormal(const NodeFile *nodes, const ElementFile *elements, escript::Data &normals)
calculates the normal vector at quadrature points on face elements
Definition: finley/src/Assemble_getNormal.cpp:46
weipa::FinleyDomain::getNodes
virtual NodeData_ptr getNodes() const
Returns a pointer to the full nodes.
Definition: weipa/src/FinleyDomain.h:61
finley::NodeFile::getNumDegreesOfFreedom
dim_t getNumDegreesOfFreedom() const
returns the number of degrees of freedom (on this rank)
Definition: finley/src/NodeFile.h:264
finley::FinleyDomain::getTag
virtual int getTag(const std::string &name) const
Return the tag key for tag name.
Definition: finley/src/FinleyDomain.cpp:2509
finley::TagMap
std::map< std::string, int > TagMap
Definition: finley/src/FinleyDomain.h:123
escript::AbstractDomain
Base class for all escript domains.
Definition: AbstractDomain.h:56
finley::FinleyDomain::printElementInfo
void printElementInfo(const ElementFile *e, const std::string &title, const std::string &defaultType, bool full) const
Definition: finley/src/Mesh_write.cpp:51
weipa::FinleyNodes
Stores and manipulates finley mesh nodes.
Definition: FinleyNodes.h:49
weipa::FinleyDomain::getMeshByName
virtual NodeData_ptr getMeshByName(const std::string &name) const
Returns the node mesh with given name.
Definition: weipa/src/FinleyDomain.cpp:453
weipa::FinleyNodes_ptr
boost::shared_ptr< FinleyNodes > FinleyNodes_ptr
Definition: FinleyNodes.h:41
paso::SystemMatrix::getSystemMatrixTypeId
static int getSystemMatrixTypeId(int solver, int preconditioner, int package, bool symmetry, const escript::JMPI &mpi_info)
Definition: SystemMatrix.cpp:543
finley::FinleyDomain::setFaceElements
void setFaceElements(ElementFile *elements)
replaces the face element file by elements
Definition: finley/src/FinleyDomain.cpp:126
finley::NodeFile::degreesOfFreedomId
index_t * degreesOfFreedomId
Definition: finley/src/NodeFile.h:202
weipa::FinleyDomain::getMeshForFunctionSpace
virtual NodeData_ptr getMeshForFunctionSpace(int fsCode) const
Returns the node mesh for given function space code.
Definition: weipa/src/FinleyDomain.cpp:234
escript::IndexList
Definition: escriptcore/src/IndexList.h:27
finley::ElementFile::referenceElementSet
const_ReferenceElementSet_ptr referenceElementSet
the reference element to be used
Definition: finley/src/ElementFile.h:130
escript::Data::getExpandedVectorReference
DataTypes::RealVectorType & getExpandedVectorReference(DataTypes::real_t dummy=0)
Ensures that the Data is expanded and returns its underlying vector Does not check for exclusive writ...
Definition: Data.cpp:5844
finley::ContactElementsOne
Definition: Finley.h:85
escript::SO_PACKAGE_TRILINOS
Definition: SolverOptions.h:113
escript::ASM_ptr
boost::shared_ptr< AbstractSystemMatrix > ASM_ptr
Definition: AbstractSystemMatrix.h:43
finley::NodeFile::gather_global
void gather_global(const index_t *index, const NodeFile *in)
Definition: finley/src/NodeFile.cpp:339
escript::DataTypes::cplx_t
std::complex< real_t > cplx_t
complex data type
Definition: DataTypes.h:76
finley::rectangle_driver
Domain_ptr rectangle_driver(const bp::list &args)
Definition: finley/src/DomainFactory.cpp:1205
weipa::Centering
Centering
Definition: DomainChunk.h:29
finley::NodeFile::tagsInUse
std::vector< int > tagsInUse
vector of tags which are actually used
Definition: finley/src/NodeFile.h:166
finley::ElementFile::optimizeOrdering
void optimizeOrdering()
reorders the elements so that they are stored close to the nodes
Definition: finley/src/ElementFile.cpp:184
finley::ElementFile::updateTagList
void updateTagList()
Definition: finley/src/ElementFile.h:189
escript::Data::expand
void expand()
Whatever the current Data type make this into a DataExpanded.
Definition: Data.cpp:1183
weipa::IntVec
std::vector< int > IntVec
Definition: weipa.h:58
weipa::FinleyElements
Stores and manipulates one type of finley mesh elements (cells, faces or contacts).
Definition: FinleyElements.h:74
finley::ReducedContactElementsZero
Definition: Finley.h:84
finley::FinleyDomain::write
void write(const std::string &fileName) const
writes the current mesh to a file with the given name in the fly file format.
Definition: finley/src/Mesh_write.cpp:86
finley
A suite of factory methods for creating various finley domains.
Definition: finley/src/Assemble.h:31
finley::NodeFile::setTags
void setTags(int newTag, const escript::Data &mask)
set tags to newTag where mask > 0
Definition: finley/src/NodeFile.cpp:277
finley::NodeFile::numDim
int numDim
number of spatial dimensions
Definition: finley/src/NodeFile.h:160
ESYS_ASSERT
#define ESYS_ASSERT(a, b)
EsysAssert is a MACRO that will throw an exception if the boolean condition specified is false.
Definition: Assert.h:77
finley::FinleyDomain::supportsContactElements
virtual bool supportsContactElements() const
Definition: finley/src/FinleyDomain.h:832
finley::util::packMask
std::vector< index_t > packMask(const std::vector< short > &mask)
Definition: finley/src/Util.cpp:354
finley::FinleyDomain::setFunctionSpaceTypeNames
void setFunctionSpaceTypeNames()
Build the table of function space type names.
Definition: finley/src/FinleyDomain.cpp:948
finley::NodeFile::allocTable
void allocTable(dim_t numNodes)
allocates the node table within this node file to hold numNodes nodes.
Definition: finley/src/NodeFile.cpp:137
escript::ValueError
An exception class that signals an invalid argument value.
Definition: EsysException.h:99
DUDLEY_FACE_ELEMENTS
#define DUDLEY_FACE_ELEMENTS
Definition: Dudley.h:54
finley::FinleyDomain::prepare
void prepare(bool optimize)
prepares the mesh for further use
Definition: finley/src/FinleyDomain.cpp:2680
finley::FinleyDomain::MPIBarrier
virtual void MPIBarrier() const
If compiled for MPI then execute an MPI_Barrier, else do nothing.
Definition: finley/src/FinleyDomain.cpp:113
finley::FinleyDomain::m_elements
ElementFile * m_elements
the table of the elements
Definition: finley/src/FinleyDomain.h:921
weipa::DataVar
A class that provides functionality to read an escript data object from a dump file or an escript::Da...
Definition: DataVar.h:34
finley::FinleyDomain::setNewX
virtual void setNewX(const escript::Data &arg)
assigns new location to the domain
Definition: finley/src/FinleyDomain.cpp:1857
finley::Elements
Definition: Finley.h:78
escript::AbstractContinuousDomain
AbstractContinuousDomain, base class for continuous domains.
Definition: AbstractContinuousDomain.h:56
finley::FinleyDomain::getX
virtual escript::Data getX() const
returns locations in the FEM nodes
Definition: finley/src/FinleyDomain.cpp:2371
finley::FinleyDomain::isValidFunctionSpaceType
virtual bool isValidFunctionSpaceType(int functionSpaceType) const
Returns true if the given integer is a valid function space type for this domain.
Definition: finley/src/FinleyDomain.cpp:941
FINLEY_CONTACT_ELEMENTS_2
#define FINLEY_CONTACT_ELEMENTS_2
Definition: Finley.h:65
weipa::FinleyDomain::initFromEscript
virtual bool initFromEscript(const escript::AbstractDomain *domain)
Initialises the domain using an escript domain instance.
Definition: weipa/src/FinleyDomain.cpp:97
finley::FinleyDomain::getReducedSolutionCode
virtual int getReducedSolutionCode() const
Return a ReducedSolution code.
Definition: finley/src/FinleyDomain.cpp:1033
Assemble.h
finley::FinleyDomain::createHex8
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.
Definition: Mesh_hex8.cpp:37
finley::FinleyDomain::markNodes
void markNodes(std::vector< short > &mask, index_t offset, bool useLinear) const
Definition: finley/src/FinleyDomain.cpp:192
finley::readMesh_driver
Domain_ptr readMesh_driver(const bp::list &args)
Definition: finley/src/DomainFactory.cpp:902
FINLEY_CONTACT_ELEMENTS_1
#define FINLEY_CONTACT_ELEMENTS_1
Definition: Finley.h:64
finley::meshMerge
Domain_ptr meshMerge(const bp::list &meshList)
Definition: finley/src/DomainFactory.cpp:1270
finley::FinleyDomain::merge
static FinleyDomain * merge(const std::vector< const FinleyDomain * > &meshes)
Definition: Mesh_merge.cpp:23
escript::DataTypes::IndexVector
std::vector< index_t > IndexVector
Definition: DataTypes.h:85
weipa::FinleyDomain::getCenteringForFunctionSpace
virtual Centering getCenteringForFunctionSpace(int fsCode) const
Returns whether data on given function space is node or cell centered.
Definition: weipa/src/FinleyDomain.cpp:217
finley::ElementFile::numNodes
int numNodes
number of nodes per element
Definition: finley/src/ElementFile.h:148
finley::FinleyDomain::~FinleyDomain
~FinleyDomain()
Destructor for FinleyDomain.
Definition: finley/src/FinleyDomain.cpp:104
finley::FinleyDomain::writeElementInfo
void writeElementInfo(std::ostream &stream, const ElementFile *e, const std::string &defaultType) const
Definition: finley/src/Mesh_write.cpp:32
weipa::FinleyDomain
Represents a full Finley or Dudley domain including nodes and elements.
Definition: weipa/src/FinleyDomain.h:40
finley::FinleyDomain::createRec4
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,...
Definition: Mesh_rec4.cpp:24