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finley/src/FinleyDomain.h
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1 
2 /*****************************************************************************
3 *
4 * Copyright (c) 2003-2020 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 2014-2017 by Centre for Geoscience Computing (GeoComp)
14 * Development from 2019 by School of Earth and Environmental Sciences
15 **
16 *****************************************************************************/
17 
18 #ifndef __FINLEY_DOMAIN_H__
19 #define __FINLEY_DOMAIN_H__
20 
21 /****************************************************************************
22 
23  Finley: Domain
24 
25  A mesh is built from nodes and elements which describe the domain, surface,
26  and point sources (the latter are needed to establish links with other
27  codes, in particular particle codes). The nodes are stored in a NodeFile
28  and elements in ElementFiles. Finley domains have four ElementFiles
29  containing the elements, surface, contact and point sources, respectively.
30  Notice that the surface elements do not necessarily cover the entire
31  surface of the domain.
32 
33  The element type is fixed by the reference element, see ReferenceElement.h.
34  The numbering of the nodes starts with 0.
35 
36  Important: it is assumed that every node appears in at least one element or
37  surface element and that any node used in an element, surface element or as
38  a point is specified in the NodeFile, see also resolveNodeIds.
39 
40  In some cases it is useful to refer to a mesh entirely built from
41  order 1 (=linear) elements. The linear version of the mesh can be
42  accessed by referring to the first few nodes of each element
43  (thanks to the way the nodes are ordered). As the numbering of
44  these nodes is not continuous a relabeling vector is introduced
45  in the NodeFile. This feature is not fully implemented yet.
46 
47  All nodes and elements are tagged. The tag allows to group nodes and
48  elements. A typical application is to mark surface elements on a
49  certain portion of the domain with the same tag. All these surface
50  elements can then be assigned the same value e.g. for the pressure.
51 
52  The spatial dimensionality is determined by the type of elements
53  used and can be queried using getDim(). Notice that the element type
54  also determines the type of surface elements to be used.
55 
56 *****************************************************************************/
57 
58 #include "system_dep.h"
59 
60 #include <finley/Finley.h>
61 #include <finley/ElementFile.h>
62 #include <finley/NodeFile.h>
63 #include <finley/Util.h>
64 
65 #include <escript/AbstractContinuousDomain.h>
66 #include <escript/FunctionSpace.h>
67 #include <escript/FunctionSpaceFactory.h>
68 
69 #ifdef ESYS_HAVE_PASO
70 #include <paso/SystemMatrixPattern.h>
71 #endif
72 #ifdef ESYS_HAVE_TRILINOS
73 #include <trilinoswrap/types.h>
74 #endif
75 
76 #include <map>
77 #include <string>
78 #include <vector>
79 
80 namespace finley {
81 
82 typedef std::map<std::string, int> TagMap;
83 
85  SMT_PASO = 1<<8,
86  SMT_TRILINOS = 1<<10,
87  SMT_COMPLEX = 1<<16,
88  SMT_UNROLL = 1<<17
89 };
90 
97 {
98 public:
104  static escript::Domain_ptr load(const std::string& filename);
105 
118  static escript::Domain_ptr read(escript::JMPI mpiInfo,
119  const std::string& fileName,
120  int integrationOrder = -1,
121  int reducedIntegrationOrder = -1,
122  bool optimize = false);
123 
138  const std::string& filename,
139  int numDim, int integrationOrder = -1,
140  int reducedIntegrationOrder = -1,
141  bool optimize = false,
142  bool useMacroElements = false);
143 
161  static escript::Domain_ptr createRec4(dim_t NE0, dim_t NE1,
162  double L0, double L1,
163  bool periodic0, bool periodic1, int order,
164  int reducedOrder, bool useElementsOnFace,
165  bool optimize, escript::JMPI jmpi);
166 
187  static escript::Domain_ptr createRec8(dim_t NE0, dim_t NE1,
188  double l0, double l1,
189  bool periodic0, bool periodic1, int order,
190  int reducedOrder, bool useElementsOnFace,
191  bool useFullElementOrder,
192  bool useMacroElements, bool optimize,
193  escript::JMPI jmpi);
194 
215  static escript::Domain_ptr createHex8(dim_t NE0, dim_t NE1, dim_t NE2,
216  double l0, double l1, double l2,
217  bool periodic0, bool periodic1, bool periodic2,
218  int order, int reducedOrder,
219  bool useElementsOnFace,
220  bool optimize, escript::JMPI jmpi);
221 
244  static escript::Domain_ptr createHex20(dim_t NE0, dim_t NE1, dim_t NE2,
245  double l0, double l1, double l2,
246  bool periodic0, bool periodic1, bool periodic2,
247  int order, int reducedOrder,
248  bool useElementsOnFace,
249  bool useFullElementOrder,
250  bool useMacroElements, bool optimize,
251  escript::JMPI jmpi);
252 
261  FinleyDomain(const std::string& name, int numDim, escript::JMPI jmpi);
262 
267  FinleyDomain(const FinleyDomain& in);
268 
273  ~FinleyDomain();
274 
280  void addDiracPoints(const std::vector<double>& points,
281  const std::vector<int>& tags);
282 
287  NodeFile* getNodes() const { return m_nodes; }
288 
293  void setElements(ElementFile* elements);
294 
299  ElementFile* getElements() const { return m_elements; }
300 
305  void setFaceElements(ElementFile* elements);
306 
311  ElementFile* getFaceElements() const { return m_faceElements; }
312 
317  void setContactElements(ElementFile* elements);
318 
323  ElementFile* getContactElements() const { return m_contactElements; }
324 
329  void setPoints(ElementFile* elements);
330 
335  ElementFile* getPoints() const { return m_points; }
336 
341  virtual escript::JMPI getMPI() const { return m_mpiInfo; }
342 
347  virtual int getMPISize() const { return m_mpiInfo->size; }
348 
353  virtual int getMPIRank() const { return m_mpiInfo->rank; }
354 
359  virtual void MPIBarrier() const;
360 
365  virtual bool onMasterProcessor() const { return getMPIRank() == 0; }
366 
367  MPI_Comm getMPIComm() const { return m_mpiInfo->comm; }
368 
375  void write(const std::string& fileName) const;
376 
381  void Print_Mesh_Info(bool full=false) const;
382 
388  void dump(const std::string& fileName) const;
389 
396  int getTagFromSampleNo(int functionSpaceType, index_t sampleNo) const;
397 
403  const index_t* borrowSampleReferenceIDs(int functionSpaceType) const;
404 
410  virtual bool isValidFunctionSpaceType(int functionSpaceType) const;
411 
416  virtual std::string getDescription() const;
417 
422  virtual std::string functionSpaceTypeAsString(int functionSpaceType) const;
423 
428  void setFunctionSpaceTypeNames();
429 
434  virtual int getContinuousFunctionCode() const;
435 
440  virtual int getReducedContinuousFunctionCode() const;
441 
446  virtual int getFunctionCode() const;
447 
452  virtual int getReducedFunctionCode() const;
453 
458  virtual int getFunctionOnBoundaryCode() const;
459 
464  virtual int getReducedFunctionOnBoundaryCode() const;
465 
470  virtual int getFunctionOnContactZeroCode() const;
471 
476  virtual int getReducedFunctionOnContactZeroCode() const;
477 
482  virtual int getFunctionOnContactOneCode() const;
483 
488  virtual int getReducedFunctionOnContactOneCode() const;
489 
494  virtual int getSolutionCode() const;
495 
500  virtual int getReducedSolutionCode() const;
501 
506  virtual int getDiracDeltaFunctionsCode() const;
507 
511  typedef std::map<int, std::string> FunctionSpaceNamesMapType;
512 
516  virtual int getDim() const { return m_nodes->numDim; }
517 
524  virtual StatusType getStatus() const;
525 
530  virtual dim_t getNumDataPointsGlobal() const;
531 
537  virtual std::pair<int,dim_t> getDataShape(int functionSpaceCode) const;
538 
544  virtual void setToX(escript::Data& arg) const;
545 
552  virtual void setTagMap(const std::string& name, int tag);
553 
559  virtual int getTag(const std::string& name) const;
560 
566  virtual bool isValidTagName(const std::string& name) const;
567 
572  virtual std::string showTagNames() const;
573 
578  virtual void setNewX(const escript::Data& arg);
579 
584  virtual void interpolateOnDomain(escript::Data& target,
585  const escript::Data& source) const;
586 
587  virtual bool probeInterpolationOnDomain(int functionSpaceType_source,
588  int functionSpaceType_target) const;
589 
590  virtual signed char preferredInterpolationOnDomain(int functionSpaceType_source, int functionSpaceType_target) const;
591 
596  bool commonFunctionSpace(const std::vector<int>& fs, int& resultcode) const;
597 
602  virtual void interpolateAcross(escript::Data& target, const escript::Data& source) const;
603 
607  virtual bool probeInterpolationAcross(int functionSpaceType_source,
608  const escript::AbstractDomain& targetDomain,
609  int functionSpaceType_target) const;
610 
616  virtual void setToNormal(escript::Data& out) const;
617 
623  virtual void setToSize(escript::Data& out) const;
624 
630  virtual void setToGradient(escript::Data& grad, const escript::Data& arg) const;
631 
637  virtual void setToIntegrals(std::vector<escript::DataTypes::real_t>& integrals,
638  const escript::Data& arg) const;
639  virtual void setToIntegrals(std::vector<escript::DataTypes::cplx_t>& integrals,
640  const escript::Data& arg) const;
641 
650  virtual int getSystemMatrixTypeId(const boost::python::object& options) const;
651 
661  virtual int getTransportTypeId(int solver, int preconditioner, int package,
662  bool symmetry) const;
663 
669  virtual bool isCellOriented(int functionSpaceCode) const;
670 
671  virtual bool ownSample(int fsCode, index_t id) const;
672 
677  virtual void addPDEToSystem(
679  const escript::Data& A, const escript::Data& B,
680  const escript::Data& C, const escript::Data& D,
681  const escript::Data& X, const escript::Data& Y,
682  const escript::Data& d, const escript::Data& y,
683  const escript::Data& d_contact,
684  const escript::Data& y_contact,
685  const escript::Data& d_dirac,
686  const escript::Data& y_dirac) const;
687 
692  virtual void addPDEToLumpedSystem(escript::Data& mat,
693  const escript::Data& D,
694  const escript::Data& d,
695  const escript::Data& d_dirac,
696  bool useHRZ) const;
697 
702  virtual void addPDEToRHS(escript::Data& rhs, const escript::Data& X,
703  const escript::Data& Y, const escript::Data& y,
704  const escript::Data& y_contact,
705  const escript::Data& y_dirac) const;
706 
711  virtual void addPDEToTransportProblem(
713  escript::Data& source, const escript::Data& M,
714  const escript::Data& A, const escript::Data& B,
715  const escript::Data& C, const escript::Data& D,
716  const escript::Data& X, const escript::Data& Y,
717  const escript::Data& d, const escript::Data& y,
718  const escript::Data& d_contact,
719  const escript::Data& y_contact,
720  const escript::Data& d_dirac,
721  const escript::Data& y_dirac) const;
722 
727  escript::ASM_ptr newSystemMatrix(
728  int row_blocksize,
729  const escript::FunctionSpace& row_functionspace,
730  int column_blocksize,
731  const escript::FunctionSpace& column_functionspace,
732  int type) const;
733 
738  escript::ATP_ptr newTransportProblem(int blocksize,
739  const escript::FunctionSpace& functionspace,
740  int type) const;
741 
745  virtual escript::Data getX() const;
746 
747 #ifdef ESYS_HAVE_BOOST_NUMPY
748 
751  virtual boost::python::numpy::ndarray getNumpyX() const;
752 
756  virtual boost::python::numpy::ndarray getConnectivityInfo() const;
757 #endif
758 
762  virtual int getVTKElementType() const;
763 
768  virtual escript::Data getNormal() const;
769 
773  virtual escript::Data getSize() const;
774 
778  virtual bool operator==(const escript::AbstractDomain& other) const;
779  virtual bool operator!=(const escript::AbstractDomain& other) const;
780 
785  virtual void setTags(int functionSpaceType, int newTag,
786  const escript::Data& mask) const;
787 
793  virtual int getNumberOfTagsInUse(int functionSpaceCode) const;
794 
795  virtual const int* borrowListOfTagsInUse(int functionSpaceCode) const;
796 
801  virtual bool canTag(int functionSpaceCode) const;
802 
806  virtual int getApproximationOrder(int functionSpaceCode) const;
807 
808  virtual bool supportsContactElements() const { return true; }
809 
810  virtual escript::Data randomFill(const escript::DataTypes::ShapeType& shape,
811  const escript::FunctionSpace& what, long seed,
812  const boost::python::tuple& filter) const;
813 
818  const TagMap& getTagMap() const { return m_tagMap; }
819 
820  void createMappings(const IndexVector& dofDistribution,
821  const IndexVector& nodeDistribution);
822 
823 #ifdef ESYS_HAVE_PASO
824  paso::SystemMatrixPattern_ptr getPasoPattern(bool reducedRowOrder,
826  bool reducedColOrder) const;
827 #endif
828 
829 #ifdef ESYS_HAVE_TRILINOS
830  esys_trilinos::const_TrilinosGraph_ptr getTrilinosGraph(bool reducedOrder) const;
832 #endif
833 
834  void glueFaces(double safetyFactor, double tolerance, bool optimize);
835 
836  void joinFaces(double safetyFactor, double tolerance, bool optimize);
837 
840  static FinleyDomain* merge(const std::vector<const FinleyDomain*>& meshes);
841 
842 private:
843  void prepare(bool optimize);
844 
845  void setOrders();
846 
854  void resolveNodeIds();
855 
858  void relabelElementNodes(const IndexVector& newNode, index_t offset);
859 
860  template<typename Scalar>
861  void setToIntegralsWorker(std::vector<Scalar>& integrals,
862  const escript::Data& arg) const;
863 
864 #ifdef ESYS_HAVE_PASO
865  paso::SystemMatrixPattern_ptr makePasoPattern(bool reducedRowOrder,
866  bool reducedColOrder) const;
867 #endif
868 #ifdef ESYS_HAVE_TRILINOS
869  esys_trilinos::GraphType* createTrilinosGraph(bool reducedOrder) const;
870 #endif
871  void createColoring(const IndexVector& dofMap);
872  void distributeByRankOfDOF(const IndexVector& distribution);
873  void markNodes(std::vector<short>& mask, index_t offset, bool useLinear) const;
874  void optimizeDOFDistribution(IndexVector& distribution);
875  void optimizeDOFLabeling(const IndexVector& distribution);
876  void optimizeElementOrdering();
877  void findMatchingFaces(double safetyFactor, double tolerance, int* numPairs,
878  int* elem0, int* elem1, int* matchingNodes) const;
879  void updateTagList();
880  void printElementInfo(const ElementFile* e, const std::string& title,
881  const std::string& defaultType, bool full) const;
882 
883  void writeElementInfo(std::ostream& stream, const ElementFile* e,
884  const std::string& defaultType) const;
885 
889  std::string m_name;
906 #ifdef ESYS_HAVE_PASO
907  // pointer to the sparse matrix patterns
908  mutable paso::SystemMatrixPattern_ptr FullFullPattern;
909  mutable paso::SystemMatrixPattern_ptr FullReducedPattern;
910  mutable paso::SystemMatrixPattern_ptr ReducedFullPattern;
911  mutable paso::SystemMatrixPattern_ptr ReducedReducedPattern;
912 #endif
913 #ifdef ESYS_HAVE_TRILINOS
914  mutable esys_trilinos::TrilinosGraph_ptr m_fullGraph;
915  mutable esys_trilinos::TrilinosGraph_ptr m_reducedGraph;
916 #endif
917 
919 };
920 
921 } // end of namespace
922 
923 #endif // __FINLEY_DOMAIN_H__
924 
finley::FinleyDomain::optimizeDOFLabeling
void optimizeDOFLabeling(const IndexVector &distribution)
optimizes the labeling of the DOFs on each processor
Definition: finley/src/FinleyDomain.cpp:2903
finley::FinleyDomain::getNumDataPointsGlobal
virtual dim_t getNumDataPointsGlobal() const
Return the number of data points summed across all MPI processes.
Definition: finley/src/FinleyDomain.cpp:1048
finley::NodeFile::updateTagList
void updateTagList()
Definition: finley/src/NodeFile.h:326
finley::FinleyDomain::setContactElements
void setContactElements(ElementFile *elements)
replaces the contact element file by elements
Definition: finley/src/FinleyDomain.cpp:134
dudley::DudleyDomain::getFaceElements
ElementFile * getFaceElements() const
returns a pointer to this domain's face element file
Definition: DudleyDomain.h:202
finley::brick_driver
Domain_ptr brick_driver(const bp::list &args)
Definition: finley/src/DomainFactory.cpp:1105
escript::SolverOptions
SolverOptions
Definition: SolverOptions.h:82
MPI_Status
int MPI_Status
Definition: EsysMPI.h:47
escript::SolverBuddy
Definition: SolverOptions.h:161
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:2782
escript::Data::isComplex
bool isComplex() const
True if components of this data are stored as complex.
Definition: Data.cpp:1160
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:1172
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:1646
escript::FunctionSpace::getSize
escript::Data getSize() const
Returns the sample size (e.g. the diameter of elements, radius of particles).
Definition: FunctionSpace.cpp:295
FinleyDomain.h
finley::FinleyDomain
FinleyDomain implements the AbstractContinuousDomain interface for the Finley library.
Definition: finley/src/FinleyDomain.h:97
finley::FinleyDomain::relabelElementNodes
void relabelElementNodes(const IndexVector &newNode, index_t offset)
Definition: finley/src/FinleyDomain.cpp:203
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:34
finley::SMT_COMPLEX
@ SMT_COMPLEX
Definition: finley/src/FinleyDomain.h:87
finley::FaceElements
@ FaceElements
Definition: Finley.h:68
finley::NodeFile::globalReducedNodesIndex
index_t * globalReducedNodesIndex
Definition: finley/src/NodeFile.h:181
escript::DataTypes::real_t
double real_t
type of all real-valued scalars in escript
Definition: DataTypes.h:52
finley::FinleyDomain::approximationOrder
int approximationOrder
Definition: finley/src/FinleyDomain.h:890
REGISTER_ESCRIPT_EXCEPTION_TRANSLATORS
#define REGISTER_ESCRIPT_EXCEPTION_TRANSLATORS
Definition: ExceptionTranslators.h:27
finley::FinleyDomain::m_mpiInfo
escript::JMPI m_mpiInfo
MPI information.
Definition: finley/src/FinleyDomain.h:887
getTag
int getTag(unsigned char sourcex, unsigned char sourcey, unsigned char sourcez, unsigned char targetx, unsigned char targety, unsigned char targetz)
Definition: blocktools.cpp:413
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:932
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:507
escript::reducedContinuousFunction
FunctionSpace reducedContinuousFunction(const AbstractDomain &domain)
Return a continuous with reduced order FunctionSpace (overlapped node values on reduced element order...
Definition: FunctionSpaceFactory.cpp:37
finley::FinleyDomain::setToIntegrals
virtual void setToIntegrals(std::vector< escript::DataTypes::cplx_t > &integrals, const escript::Data &arg) const
finley::Rec9
@ Rec9
Definition: ReferenceElements.h:52
weipa::FinleyDomain::~FinleyDomain
virtual ~FinleyDomain()
Definition: weipa/src/FinleyDomain.cpp:79
finley::FinleyDomain::m_tagMap
TagMap m_tagMap
the tag map mapping names to tag keys
Definition: finley/src/FinleyDomain.h:905
FINLEY_REDUCED_FACE_ELEMENTS
#define FINLEY_REDUCED_FACE_ELEMENTS
Definition: Finley.h:57
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:2583
finley::FinleyDomain::updateTagList
void updateTagList()
regenerates list of tags in use for node file and element files
Definition: finley/src/FinleyDomain.cpp:3084
finley::NodeFile::createDenseDOFLabeling
dim_t createDenseDOFLabeling()
Definition: finley/src/NodeFile.cpp:525
finley::FinleyDomain::getSolutionCode
virtual int getSolutionCode() const
Return a Solution code.
Definition: finley/src/FinleyDomain.cpp:1030
paso::SystemMatrix
this class holds a (distributed) stiffness matrix
Definition: SystemMatrix.h:50
finley::FinleyDomain::borrowListOfTagsInUse
virtual const int * borrowListOfTagsInUse(int functionSpaceCode) const
Definition: finley/src/FinleyDomain.cpp:2685
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:34
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:105
finley::NodeFile::globalDegreesOfFreedom
index_t * globalDegreesOfFreedom
Definition: finley/src/NodeFile.h:173
weipa::FinleyDomain::removeGhostZones
virtual void removeGhostZones(int ownIndex)
Removes 'ghost' elements and nodes.
Definition: weipa/src/FinleyDomain.cpp:488
escript::SO_METHOD_DIRECT
@ SO_METHOD_DIRECT
Definition: SolverOptions.h:102
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:2374
FINLEY_REDUCED_ELEMENTS
#define FINLEY_REDUCED_ELEMENTS
Definition: Finley.h:56
finley::FinleyDomain::borrowSampleReferenceIDs
const index_t * borrowSampleReferenceIDs(int functionSpaceType) const
Return the reference number of the given sample number.
Definition: finley/src/FinleyDomain.cpp:2502
finley::FinleyDomain::getFunctionOnContactZeroCode
virtual int getFunctionOnContactZeroCode() const
Return a FunctionOnContactZero code.
Definition: finley/src/FinleyDomain.cpp:1010
dudley::readGmsh
Domain_ptr readGmsh(const string &fileName, int numDim, int, int, bool optimize)
reads a gmsh mesh file
Definition: dudley/src/DomainFactory.cpp:681
finley::NodeFile::getNumReducedNodes
dim_t getNumReducedNodes() const
returns the number of reduced order FEM nodes (on this rank)
Definition: finley/src/NodeFile.h:261
FINLEY_REDUCED_CONTACT_ELEMENTS_1
#define FINLEY_REDUCED_CONTACT_ELEMENTS_1
Definition: Finley.h:58
finley::FinleyDomain::getReducedFunctionOnContactOneCode
virtual int getReducedFunctionOnContactOneCode() const
Return a FunctionOnContactOne code with reduced integration order.
Definition: finley/src/FinleyDomain.cpp:1025
weipa::FinleyDomain::getElementsForFunctionSpace
virtual ElementData_ptr getElementsForFunctionSpace(int fsCode) const
Returns the element data for given function space code.
Definition: weipa/src/FinleyDomain.cpp:253
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:2289
finley::const_ReferenceElementSet_ptr
boost::shared_ptr< const ReferenceElementSet > const_ReferenceElementSet_ptr
Definition: ReferenceElementSets.h:80
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:2731
weipa::FinleyDomain::faces
FinleyElements_ptr faces
Definition: weipa/src/FinleyDomain.h:73
finley::NodeFile::assignMPIRankToDOFs
void assignMPIRankToDOFs(std::vector< int > &mpiRankOfDOF, const IndexVector &distribution)
Definition: finley/src/NodeFile.cpp:438
weipa::FinleyDomain::getMeshNames
virtual StringVec getMeshNames() const
Returns the names of all meshes within this domain.
Definition: weipa/src/FinleyDomain.cpp:334
finley::NodeFile::Tag
int * Tag
Tag[i] is the tag of node i.
Definition: finley/src/NodeFile.h:166
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:2307
weipa::VisItControl::initialized
bool initialized
Definition: VisItControl.cpp:38
finley::ReducedContactElementsOne
@ ReducedContactElementsOne
Definition: Finley.h:74
escript::SolverBuddy::getPackage
SolverOptions getPackage() const
Definition: SolverOptions.cpp:513
finley::NodeFile::getFirstNode
index_t getFirstNode() const
Definition: finley/src/NodeFile.h:216
weipa::FinleyDomain::nodes
FinleyNodes_ptr nodes
Definition: weipa/src/FinleyDomain.h:71
finley::Tet10
@ Tet10
Definition: ReferenceElements.h:56
escript::continuousFunction
FunctionSpace continuousFunction(const AbstractDomain &domain)
Create function space objects.
Definition: FunctionSpaceFactory.cpp:31
finley::ElementFile::Tag
int * Tag
Tag[i] is the tag of element i.
Definition: finley/src/ElementFile.h:129
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:372
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:2543
escript::NotImplementedError
An exception class for features which are not (yet) implemented.
Definition: EsysException.h:90
finley::FinleyException
Definition: FinleyException.h:27
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:1139
FINLEY_NODES
#define FINLEY_NODES
Definition: Finley.h:48
finley::Tet10Macro
@ Tet10Macro
Definition: ReferenceElements.h:116
dudley::DudleyDomain::getElements
ElementFile * getElements() const
returns a pointer to this domain's element file
Definition: DudleyDomain.h:190
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:470
finley::NodeFile::nodesDistribution
escript::Distribution_ptr nodesDistribution
MPI distribution of nodes.
Definition: finley/src/NodeFile.h:186
finley::FinleyDomain::integrationOrder
int integrationOrder
Definition: finley/src/FinleyDomain.h:892
escript::DataTypes::DataVectorAlt< real_t >
escript::SolverBuddy::getSolverMethod
SolverOptions getSolverMethod() const
Definition: SolverOptions.cpp:441
escript::randomFillArray
void randomFillArray(long seed, double *array, size_t n)
Definition: Random.cpp:79
finley::FinleyDomain::m_faceElements
ElementFile * m_faceElements
the table of face elements
Definition: finley/src/FinleyDomain.h:899
escript::AbstractDomain::StatusType
int StatusType
Definition: AbstractDomain.h:53
paso::SystemMatrixPattern_ptr
boost::shared_ptr< SystemMatrixPattern > SystemMatrixPattern_ptr
Definition: SystemMatrixPattern.h:40
finley::NodeFile::reducedNodesId
index_t * reducedNodesId
Definition: finley/src/NodeFile.h:203
finley::NodeFile::globalReducedDOFIndex
index_t * globalReducedDOFIndex
Definition: finley/src/NodeFile.h:178
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:2145
finley::FinleyDomain::showTagNames
virtual std::string showTagNames() const
Returns all tag names in a single string sperated by commas.
Definition: finley/src/FinleyDomain.cpp:2641
paso::TransportProblem::borrowTransportMatrix
SystemMatrix_ptr< double > borrowTransportMatrix() const
Definition: Transport.h:65
MATRIX_FORMAT_COMPLEX
#define MATRIX_FORMAT_COMPLEX
Definition: Paso.h:66
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:249
DUDLEY_NODES
#define DUDLEY_NODES
Definition: Dudley.h:42
finley::const_ReferenceElement_ptr
boost::shared_ptr< const ReferenceElement > const_ReferenceElement_ptr
Definition: ReferenceElements.h:216
finley::FinleyDomain::getMPISize
virtual int getMPISize() const
returns the number of processors used for this domain
Definition: finley/src/FinleyDomain.h:347
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:2654
escript::Domain_ptr
boost::shared_ptr< AbstractDomain > Domain_ptr
Definition: AbstractDomain.h:41
escript::AbstractTransportProblem
Give a short description of what AbstractTransportProblem does.
Definition: AbstractTransportProblem.h:45
finley::ReducedNodes
@ ReducedNodes
Definition: Finley.h:65
escript::SO_PRECONDITIONER_ILUT
@ SO_PRECONDITIONER_ILUT
Definition: SolverOptions.h:122
finley::FinleyDomain::getSize
virtual escript::Data getSize() const
returns the element size
Definition: finley/src/FinleyDomain.cpp:2497
escript::SolverBuddy::isComplex
bool isComplex() const
Definition: SolverOptions.cpp:679
finley::ElementFile::setTags
void setTags(const int newTag, const escript::Data &mask)
Definition: finley/src/ElementFile.cpp:216
finley::FinleyDomain::getApproximationOrder
virtual int getApproximationOrder(int functionSpaceCode) const
returns the approximation order used for a function space functionSpaceCode
Definition: finley/src/FinleyDomain.cpp:2755
finley::ElementFile::Nodes
index_t * Nodes
Definition: finley/src/ElementFile.h:144
escript::FunctionSpace
Definition: FunctionSpace.h:36
finley::ElementFile::getNodeRange
std::pair< index_t, index_t > getNodeRange() const
Definition: finley/src/ElementFile.h:174
finley::FinleyDomain::m_nodes
NodeFile * m_nodes
the table of the nodes
Definition: finley/src/FinleyDomain.h:895
finley::Points
@ Points
Definition: Finley.h:70
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:330
finley::SystemMatrixType
SystemMatrixType
Definition: finley/src/FinleyDomain.h:84
finley::FinleyDomain::resolveNodeIds
void resolveNodeIds()
Definition: finley/src/FinleyDomain.cpp:2984
escript::Data::getFunctionSpace
const FunctionSpace & getFunctionSpace() const
Return the function space.
Definition: Data.h:463
FINLEY_REDUCED_DEGREES_OF_FREEDOM
#define FINLEY_REDUCED_DEGREES_OF_FREEDOM
Definition: Finley.h:54
finley::NodeFile::getNumReducedDegreesOfFreedom
dim_t getNumReducedDegreesOfFreedom() const
returns the number of reduced order degrees of freedom (on this rank)
Definition: finley/src/NodeFile.h:271
weipa::DataVar_ptr
boost::shared_ptr< DataVar > DataVar_ptr
Definition: weipa.h:65
weipa
Definition: DataVar.cpp:51
finley::FinleyDomain::getElements
ElementFile * getElements() const
returns a pointer to this domain's element file
Definition: finley/src/FinleyDomain.h:299
speckley::probeInterpolationAcross
bool probeInterpolationAcross(int fsType_source, const escript::AbstractDomain &domain, int fsType_target, int dim)
Definition: CrossDomainCoupler.cpp:32
finley::Rec9Macro
@ Rec9Macro
Definition: ReferenceElements.h:115
finley::FinleyDomain::getDiracDeltaFunctionsCode
virtual int getDiracDeltaFunctionsCode() const
Return a DiracDeltaFunctions code.
Definition: finley/src/FinleyDomain.cpp:1040
escript::FunctionSpace::getDomain
const_Domain_ptr getDomain() const
Returns the function space domain.
Definition: FunctionSpace.cpp:103
MPI_INT
#define MPI_INT
Definition: EsysMPI.h:48
escript::DataTypes::index_t_max
index_t index_t_max()
Returns the maximum finite value for the index_t type.
Definition: DataTypes.h:81
finley::Hex27
@ Hex27
Definition: ReferenceElements.h:60
weipa::VisItControl::initialize
bool initialize(const std::string &simFile, const std::string &comment)
Definition: VisItControl.cpp:178
paso::SystemMatrix_ptr
boost::shared_ptr< SystemMatrix< T > > SystemMatrix_ptr
Definition: SystemMatrix.h:42
finley::FinleyDomain::getDescription
virtual std::string getDescription() const
Return a description for this domain.
Definition: finley/src/FinleyDomain.cpp:927
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:1820
finley::SMT_UNROLL
@ SMT_UNROLL
Definition: finley/src/FinleyDomain.h:88
MPI_MAX
#define MPI_MAX
Definition: EsysMPI.h:56
weipa::FinleyDomain::siloPath
std::string siloPath
Definition: weipa/src/FinleyDomain.h:75
finley::FinleyDomain::m_points
ElementFile * m_points
the table of points (treated as elements of dimension 0)
Definition: finley/src/FinleyDomain.h:903
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:1210
finley::NodeFile::getNumNodes
dim_t getNumNodes() const
returns the number of FEM nodes (on this rank)
Definition: finley/src/NodeFile.h:256
finley::FinleyDomain::getReducedFunctionOnContactZeroCode
virtual int getReducedFunctionOnContactZeroCode() const
Return a FunctionOnContactZero code with reduced integration order.
Definition: finley/src/FinleyDomain.cpp:1015
weipa::FinleyDomain::contacts
FinleyElements_ptr contacts
Definition: weipa/src/FinleyDomain.h:74
weipa::ZONE_CENTERED
@ ZONE_CENTERED
Definition: DomainChunk.h:33
finley::NodeFile::createNodeMappings
void createNodeMappings(const IndexVector &indexReducedNodes, const IndexVector &dofDistribution, const IndexVector &nodeDistribution)
Definition: finley/src/NodeFile.cpp:1004
finley::FinleyDomain::getReducedFunctionCode
virtual int getReducedFunctionCode() const
Return a function with reduced integration order FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:995
escript::FunctionSpace::getNormal
escript::Data getNormal() const
Returns the surface normal field.
Definition: FunctionSpace.cpp:286
finley::NodeFile::Coordinates
double * Coordinates
Coordinates[INDEX2(k,i,numDim)] is the k-th coordinate of node i.
Definition: finley/src/NodeFile.h:175
finley::FinleyDomain::getReducedFunctionOnBoundaryCode
virtual int getReducedFunctionOnBoundaryCode() const
Return a function on boundary with reduced integration order FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:1005
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:2283
finley::ElementFile::numElements
dim_t numElements
number of elements
Definition: finley/src/ElementFile.h:122
finley::FinleyDomain::getFunctionCode
virtual int getFunctionCode() const
Return a function FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:990
finley::ElementFile::Owner
int * Owner
Owner[i] contains the rank that owns element i.
Definition: finley/src/ElementFile.h:132
escript::Data
Data represents a collection of datapoints.
Definition: Data.h:64
paso::TransportProblem_ptr
boost::shared_ptr< TransportProblem > TransportProblem_ptr
Definition: Transport.h:32
paso::util::l2
double l2(dim_t n, const double *x, escript::JMPI mpiinfo)
returns the global L2 norm of x
Definition: PasoUtil.cpp:501
finley::NodeFile::getLastNode
index_t getLastNode() const
Definition: finley/src/NodeFile.h:221
weipa::FinleyElements_ptr
boost::shared_ptr< FinleyElements > FinleyElements_ptr
Definition: FinleyElements.h:64
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:2750
finley::FinleyDomain::getFunctionOnBoundaryCode
virtual int getFunctionOnBoundaryCode() const
Return a function on boundary FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:1000
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:42
finley::FinleyDomain::Print_Mesh_Info
void Print_Mesh_Info(bool full=false) const
Definition: finley/src/Mesh_write.cpp:148
escript::FunctionSpace::getX
escript::Data getX() const
Returns the spatial locations of the data points.
Definition: FunctionSpace.cpp:229
escript::DataTypes::dim_t
index_t dim_t
Definition: DataTypes.h:66
escript::DataTypes::ShapeType
std::vector< int > ShapeType
The shape of a single datapoint.
Definition: DataTypes.h:44
weipa::FinleyDomain::initFromFile
virtual bool initFromFile(const std::string &filename)
Reads the domain from a dump file.
Definition: weipa/src/FinleyDomain.cpp:184
finley::ContactElementsZero
@ ContactElementsZero
Definition: Finley.h:71
escript::JMPI
boost::shared_ptr< JMPI_ > JMPI
Definition: EsysMPI.h:74
FINLEY_FACE_ELEMENTS
#define FINLEY_FACE_ELEMENTS
Definition: Finley.h:50
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:1999
finley::ReducedDegreesOfFreedom
@ ReducedDegreesOfFreedom
Definition: Finley.h:63
escript::ATP_ptr
boost::shared_ptr< AbstractTransportProblem > ATP_ptr
Definition: AbstractTransportProblem.h:161
escript::AbstractSystemMatrix
Base class for escript system matrices.
Definition: AbstractSystemMatrix.h:44
finley::FinleyDomain::getFaceElements
ElementFile * getFaceElements() const
returns a pointer to this domain's face element file
Definition: finley/src/FinleyDomain.h:311
weipa::FinleyDomain::cells
FinleyElements_ptr cells
Definition: weipa/src/FinleyDomain.h:72
finley::DegreesOfFreedom
@ DegreesOfFreedom
Definition: Finley.h:62
finley::NodeFile::borrowGlobalNodesIndex
const index_t * borrowGlobalNodesIndex() const
Definition: finley/src/NodeFile.h:231
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:1057
finley::NodeFile::createDenseReducedLabeling
dim_t createDenseReducedLabeling(const std::vector< short > &reducedMask, bool useNodes)
Definition: finley/src/NodeFile.cpp:702
finley::Tri6Macro
@ Tri6Macro
Definition: ReferenceElements.h:114
finley::FinleyDomain::createColoring
void createColoring(const IndexVector &dofMap)
tries to reduce the number of colours for all element files
Definition: finley/src/FinleyDomain.cpp:3066
finley::Hex27Macro
@ Hex27Macro
Definition: ReferenceElements.h:117
IndexList.h
finley::FinleyDomain::setToIntegralsWorker
void setToIntegralsWorker(std::vector< Scalar > &integrals, const escript::Data &arg) const
Definition: finley/src/FinleyDomain.cpp:1712
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:1251
weipa::ElementData_ptr
boost::shared_ptr< ElementData > ElementData_ptr
Definition: weipa.h:67
FINLEY_DEGREES_OF_FREEDOM
#define FINLEY_DEGREES_OF_FREEDOM
Definition: Finley.h:47
finley::ElementFile::Color
index_t * Color
Definition: finley/src/ElementFile.h:150
finley::FinleyDomain::m_name
std::string m_name
domain description
Definition: finley/src/FinleyDomain.h:889
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:1754
finley::FinleyDomain::getNodes
NodeFile * getNodes() const
returns a pointer to this domain's node file
Definition: finley/src/FinleyDomain.h:287
weipa::FinleyElements::getReducedElements
virtual ElementData_ptr getReducedElements() const
Returns the reduced elements.
Definition: FinleyElements.h:155
weipa::NODE_CENTERED
@ NODE_CENTERED
Definition: DomainChunk.h:32
finley::readGmsh_driver
Domain_ptr readGmsh_driver(const bp::list &args)
Definition: finley/src/DomainFactory.cpp:985
finley::FinleyDomain::getDim
virtual int getDim() const
returns the dimensionality of this domain
Definition: finley/src/FinleyDomain.h:516
paso::TransportProblem::borrowMassMatrix
SystemMatrix_ptr< double > borrowMassMatrix() const
Definition: Transport.h:70
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:1665
finley::FinleyDomain::optimizeElementOrdering
void optimizeElementOrdering()
redistributes elements to minimize communication during assemblage
Definition: finley/src/FinleyDomain.cpp:3075
FINLEY_ELEMENTS
#define FINLEY_ELEMENTS
Definition: Finley.h:49
finley::FinleyDomain::reducedApproximationOrder
int reducedApproximationOrder
Definition: finley/src/FinleyDomain.h:891
finley::NodeFile::Id
index_t * Id
Id[i] is the unique ID number of FEM node i.
Definition: finley/src/NodeFile.h:164
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:2024
finley::FinleyDomain::getFunctionOnContactOneCode
virtual int getFunctionOnContactOneCode() const
Return a FunctionOnContactOne code.
Definition: finley/src/FinleyDomain.cpp:1020
DUDLEY_REDUCED_ELEMENTS
#define DUDLEY_REDUCED_ELEMENTS
Definition: Dudley.h:46
finley::ElementFile::Id
index_t * Id
Definition: finley/src/ElementFile.h:126
weipa::FinleyDomain::FinleyDomain
FinleyDomain()
Definition: weipa/src/FinleyDomain.cpp:58
finley::NodeFile::createDenseNodeLabeling
dim_t createDenseNodeLabeling(IndexVector &nodeDistribution, const IndexVector &dofDistribution)
Definition: finley/src/NodeFile.cpp:588
finley::ReferenceElementInfo
this struct holds the definition of the reference element
Definition: ReferenceElements.h:123
finley::FinleyDomain::FunctionSpaceNamesMapType
std::map< int, std::string > FunctionSpaceNamesMapType
Definition: finley/src/FinleyDomain.h:511
finley::FinleyDomain::FinleyDomain
FinleyDomain(const std::string &name, int numDim, escript::JMPI jmpi)
Constructor for FinleyDomain.
Definition: finley/src/FinleyDomain.cpp:73
finley::FinleyDomain::getReducedContinuousFunctionCode
virtual int getReducedContinuousFunctionCode() const
Return a continuous on reduced order nodes FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:985
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:1186
dudley::DudleyDomain::getNodes
NodeFile * getNodes() const
returns a pointer to this domain's node file
Definition: DudleyDomain.h:178
finley::NodeFile::status
int status
Definition: finley/src/NodeFile.h:209
weipa::FinleyDomain::cleanup
void cleanup()
Definition: weipa/src/FinleyDomain.cpp:87
finley::NodeFile::setCoordinates
void setCoordinates(const escript::Data &newX)
copies the array newX into this->coordinates
Definition: finley/src/NodeFile.cpp:242
finley::FinleyDomain::m_functionSpaceTypeNames
static FunctionSpaceNamesMapType m_functionSpaceTypeNames
Definition: finley/src/FinleyDomain.h:918
escript::SO_PRECONDITIONER_AMG
@ SO_PRECONDITIONER_AMG
Definition: SolverOptions.h:119
DUDLEY_ELEMENTS
#define DUDLEY_ELEMENTS
Definition: Dudley.h:43
finley::joinFaces
Domain_ptr joinFaces(const bp::list &meshList, double safetyFactor, double tolerance, bool optimize)
Definition: finley/src/DomainFactory.cpp:1300
finley::FinleyDomain::reducedIntegrationOrder
int reducedIntegrationOrder
Definition: finley/src/FinleyDomain.h:893
finley::FinleyDomain::operator!=
virtual bool operator!=(const escript::AbstractDomain &other) const
Return true if given domains are not equal.
Definition: finley/src/FinleyDomain.cpp:2302
paso::TransportProblem
Definition: Transport.h:38
finley::SMT_TRILINOS
@ SMT_TRILINOS
Definition: finley/src/FinleyDomain.h:86
paso::TransportProblem::getTypeId
static int getTypeId(int solver, int preconditioner, int package, bool symmetry, const escript::JMPI &mpi_info)
Definition: Transport.h:95
finley::FinleyDomain::getTagMap
const TagMap & getTagMap() const
returns a reference to the tag name->value map
Definition: finley/src/FinleyDomain.h:818
finley::Assemble_getSize
void Assemble_getSize(const NodeFile *nodes, const ElementFile *elements, escript::Data &size)
Definition: finley/src/Assemble_getSize.cpp:33
finley::SMT_PASO
@ SMT_PASO
Definition: finley/src/FinleyDomain.h:85
escript::SolverBuddy::isSymmetric
bool isSymmetric() const
Definition: SolverOptions.cpp:689
DUDLEY_REDUCED_FACE_ELEMENTS
#define DUDLEY_REDUCED_FACE_ELEMENTS
Definition: Dudley.h:47
paso::SystemMatrix::getSystemMatrixTypeId
static int getSystemMatrixTypeId(int solver, int preconditioner, int package, bool is_complex, bool symmetry, const escript::JMPI &mpi_info)
Definition: SystemMatrix.h:504
finley::ReducedFaceElements
@ ReducedFaceElements
Definition: Finley.h:69
finley::FinleyDomain::m_contactElements
ElementFile * m_contactElements
the table of contact elements
Definition: finley/src/FinleyDomain.h:901
finley::FinleyDomain::getMPI
virtual escript::JMPI getMPI() const
returns a reference to the MPI information wrapper for this domain
Definition: finley/src/FinleyDomain.h:341
escript::SolverBuddy::getPreconditioner
SolverOptions getPreconditioner() const
Definition: SolverOptions.cpp:358
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:2272
finley::FinleyDomain::getContactElements
ElementFile * getContactElements() const
returns a pointer to this domain's contact element file
Definition: finley/src/FinleyDomain.h:323
finley::Tri6
@ Tri6
Definition: ReferenceElements.h:47
escript::load
Data load(const std::string fileName, const AbstractDomain &domain)
reads Data on domain from file in netCDF format
Definition: DataFactory.cpp:708
weipa::FinleyDomain::getElementsByName
virtual ElementData_ptr getElementsByName(const std::string &name) const
Returns element data with given name.
Definition: weipa/src/FinleyDomain.cpp:433
MPI_MIN
#define MPI_MIN
Definition: EsysMPI.h:55
escript::isDirectSolver
bool isDirectSolver(const SolverOptions &method)
returns true if the passed solver method refers to a direct solver type
Definition: SolverOptions.h:145
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:1689
finley::FinleyDomain::getNormal
virtual escript::Data getNormal() const
returns boundary normals at the quadrature point on the face elements
Definition: finley/src/FinleyDomain.cpp:2492
finley::FinleyDomain::onMasterProcessor
virtual bool onMasterProcessor() const
returns true if on MPI processor 0, else false
Definition: finley/src/FinleyDomain.h:365
finley::NodeFile::degreesOfFreedomDistribution
escript::Distribution_ptr degreesOfFreedomDistribution
Definition: finley/src/NodeFile.h:188
finley::FinleyDomain::getContinuousFunctionCode
virtual int getContinuousFunctionCode() const
Return a continuous FunctionSpace code.
Definition: finley/src/FinleyDomain.cpp:980
finley::FinleyDomain::ownSample
virtual bool ownSample(int fsCode, index_t id) const
Definition: finley/src/FinleyDomain.cpp:1871
finley::NodeFile::getDOFRange
std::pair< index_t, index_t > getDOFRange() const
Definition: finley/src/NodeFile.cpp:215
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:564
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:37
escript::RuntimeErrorTranslator
void RuntimeErrorTranslator(const EsysException &e)
Function which translates an EsysException into a python RuntimeError.
Definition: ExceptionTranslators.cpp:37
escript::DataTypes::index_t
int index_t
type for array/matrix indices used both globally and on each rank
Definition: DataTypes.h:61
finley::FinleyDomain::load
static escript::Domain_ptr load(const std::string &filename)
recovers domain from a dump file
Definition: finley/src/DomainFactory.cpp:491
finley::Line3Macro
@ Line3Macro
Definition: ReferenceElements.h:113
finley::NodeFile::getGlobalNumNodes
dim_t getGlobalNumNodes() const
Definition: finley/src/NodeFile.h:226
finley::glueFaces
Domain_ptr glueFaces(const bp::list &meshList, double safetyFactor, double tolerance, bool optimize)
Definition: finley/src/DomainFactory.cpp:1288
finley::FinleyDomain::setElements
void setElements(ElementFile *elements)
replaces the element file by elements
Definition: finley/src/FinleyDomain.cpp:122
finley::NodeFile
Definition: finley/src/NodeFile.h:42
finley::FinleyDomain::getPoints
ElementFile * getPoints() const
returns a pointer to this domain's point (nodal) element file
Definition: finley/src/FinleyDomain.h:335
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:2636
escript::DataTypes::DataVectorAlt::size
size_type size() const
Return the number of elements in this DataVectorAlt.
Definition: DataVectorAlt.h:215
finley::FinleyDomain::getMPIRank
virtual int getMPIRank() const
returns the number MPI rank of this processor
Definition: finley/src/FinleyDomain.h:353
finley::ElementFile::markNodes
void markNodes(std::vector< short > &mask, int offset, bool useLinear)
Definition: finley/src/ElementFile.cpp:305
finley::NodeFile::reducedDegreesOfFreedomId
index_t * reducedDegreesOfFreedomId
Definition: finley/src/NodeFile.h:205
finley::FinleyDomain::newTransportProblem
escript::ATP_ptr newTransportProblem(int blocksize, const escript::FunctionSpace &functionspace, int type) const
creates a TransportProblem
Definition: finley/src/FinleyDomain.cpp:1967
finley::Nodes
@ Nodes
Definition: Finley.h:64
weipa::FinleyDomain::initialized
bool initialized
Definition: weipa/src/FinleyDomain.h:70
weipa::NodeData_ptr
boost::shared_ptr< NodeData > NodeData_ptr
Definition: weipa.h:69
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:86
FINLEY_REDUCED_CONTACT_ELEMENTS_2
#define FINLEY_REDUCED_CONTACT_ELEMENTS_2
Definition: Finley.h:59
escript::SO_DEFAULT
@ SO_DEFAULT
Definition: SolverOptions.h:83
finley::FinleyDomain::setOrders
void setOrders()
Definition: finley/src/FinleyDomain.cpp:146
weipa::StringVec
std::vector< std::string > StringVec
Definition: weipa.h:61
finley::FinleyDomain::setPoints
void setPoints(ElementFile *elements)
replaces the point element file by elements
Definition: finley/src/FinleyDomain.cpp:140
BOOST_PYTHON_MODULE
BOOST_PYTHON_MODULE(finleycpp)
Definition: finleycpp.cpp:32
escript::FunctionSpace::getTypeCode
int getTypeCode() const
Returns the function space type code.
Definition: FunctionSpace.cpp:95
finley::NodeFile::globalNodesIndex
index_t * globalNodesIndex
assigns each local node a global unique ID in a dense labeling
Definition: finley/src/NodeFile.h:183
finley::ReducedElements
@ ReducedElements
Definition: Finley.h:67
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:89
FinleyException.h
dudley::DudleyDomain
DudleyDomain implements the AbstractContinuousDomain interface for the Dudley library.
Definition: DudleyDomain.h:88
escript::function
FunctionSpace function(const AbstractDomain &domain)
Return a function FunctionSpace.
Definition: FunctionSpaceFactory.cpp:43
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:125
finley::ElementFile::tagsInUse
std::vector< int > tagsInUse
array of tags which are actually used
Definition: finley/src/ElementFile.h:135
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:1897
paso::M
static dim_t M
Definition: SparseMatrix_saveHB.cpp:37
finley::ElementFile
Definition: finley/src/ElementFile.h:63
finley::FinleyDomain::distributeByRankOfDOF
void distributeByRankOfDOF(const IndexVector &distribution)
Definition: finley/src/FinleyDomain.cpp:2853
weipa::FinleyDomain::getVarNames
virtual StringVec getVarNames() const
Returns the names of all 'special' domain variables.
Definition: weipa/src/FinleyDomain.cpp:352
escript::functionOnBoundary
FunctionSpace functionOnBoundary(const AbstractDomain &domain)
Return a function on boundary FunctionSpace.
Definition: FunctionSpaceFactory.cpp:55
finley::FinleyDomain::createMappings
void createMappings(const IndexVector &dofDistribution, const IndexVector &nodeDistribution)
Definition: finley/src/FinleyDomain.cpp:185
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:367
MPI_Comm
int MPI_Comm
Definition: EsysMPI.h:44
finley::FinleyDomain::optimizeDOFDistribution
void optimizeDOFDistribution(IndexVector &distribution)
Definition: finley/src/Mesh_optimizeDOFDistribution.cpp:66
FINLEY_REDUCED_NODES
#define FINLEY_REDUCED_NODES
Definition: Finley.h:55
FINLEY_DLL_API
#define FINLEY_DLL_API
Definition: finley/src/system_dep.h:29
paso::Pattern_ptr
boost::shared_ptr< Pattern > Pattern_ptr
Definition: Pattern.h:39
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:2620
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:33
weipa::FinleyDomain::getNodes
virtual NodeData_ptr getNodes() const
Returns a pointer to the full nodes.
Definition: weipa/src/FinleyDomain.h:63
finley::NodeFile::getNumDegreesOfFreedom
dim_t getNumDegreesOfFreedom() const
returns the number of degrees of freedom (on this rank)
Definition: finley/src/NodeFile.h:266
finley::FinleyDomain::getTag
virtual int getTag(const std::string &name) const
Return the tag key for tag name.
Definition: finley/src/FinleyDomain.cpp:2625
finley::TagMap
std::map< std::string, int > TagMap
Definition: finley/src/FinleyDomain.h:82
escript::AbstractDomain
Base class for all escript domains.
Definition: AbstractDomain.h:51
weipa::FinleyNodes
Stores and manipulates finley mesh nodes.
Definition: FinleyNodes.h:52
weipa::FinleyDomain::getMeshByName
virtual NodeData_ptr getMeshByName(const std::string &name) const
Returns the node mesh with given name.
Definition: weipa/src/FinleyDomain.cpp:455
weipa::FinleyNodes_ptr
boost::shared_ptr< FinleyNodes > FinleyNodes_ptr
Definition: FinleyNodes.h:43
finley::FinleyDomain::setFaceElements
void setFaceElements(ElementFile *elements)
replaces the face element file by elements
Definition: finley/src/FinleyDomain.cpp:128
finley::NodeFile::degreesOfFreedomId
index_t * degreesOfFreedomId
Definition: finley/src/NodeFile.h:204
weipa::FinleyDomain::getMeshForFunctionSpace
virtual NodeData_ptr getMeshForFunctionSpace(int fsCode) const
Returns the node mesh for given function space code.
Definition: weipa/src/FinleyDomain.cpp:236
escript::IndexList
Definition: escriptcore/src/IndexList.h:29
finley::ElementFile::referenceElementSet
const_ReferenceElementSet_ptr referenceElementSet
the reference element to be used
Definition: finley/src/ElementFile.h:120
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:5837
finley::ContactElementsOne
@ ContactElementsOne
Definition: Finley.h:73
escript::SO_PACKAGE_TRILINOS
@ SO_PACKAGE_TRILINOS
Definition: SolverOptions.h:92
escript::ASM_ptr
boost::shared_ptr< AbstractSystemMatrix > ASM_ptr
Definition: AbstractSystemMatrix.h:33
finley::NodeFile::gather_global
void gather_global(const index_t *index, const NodeFile *in)
Definition: finley/src/NodeFile.cpp:329
system_dep.h
escript::DataTypes::cplx_t
std::complex< real_t > cplx_t
complex data type
Definition: DataTypes.h:55
finley::rectangle_driver
Domain_ptr rectangle_driver(const bp::list &args)
Definition: finley/src/DomainFactory.cpp:1207
ReferenceElements.h
weipa::Centering
Centering
Definition: DomainChunk.h:31
finley::NodeFile::tagsInUse
std::vector< int > tagsInUse
vector of tags which are actually used
Definition: finley/src/NodeFile.h:168
finley::ElementFile::optimizeOrdering
void optimizeOrdering()
reorders the elements so that they are stored close to the nodes
Definition: finley/src/ElementFile.cpp:174
finley::ElementFile::updateTagList
void updateTagList()
Definition: finley/src/ElementFile.h:179
escript::Data::expand
void expand()
Whatever the current Data type make this into a DataExpanded.
Definition: Data.cpp:1180
weipa::IntVec
std::vector< int > IntVec
Definition: weipa.h:60
weipa::FinleyElements
Stores and manipulates one type of finley mesh elements (cells, faces or contacts).
Definition: FinleyElements.h:77
finley::ReducedContactElementsZero
@ ReducedContactElementsZero
Definition: Finley.h:72
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:88
finley
A suite of factory methods for creating various finley domains.
Definition: finley/src/Assemble.h:32
finley::NodeFile::setTags
void setTags(int newTag, const escript::Data &mask)
set tags to newTag where mask > 0
Definition: finley/src/NodeFile.cpp:267
finley::NodeFile::numDim
int numDim
number of spatial dimensions
Definition: finley/src/NodeFile.h:162
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:79
finley::FinleyDomain::supportsContactElements
virtual bool supportsContactElements() const
Definition: finley/src/FinleyDomain.h:808
finley::util::packMask
std::vector< index_t > packMask(const std::vector< short > &mask)
Definition: finley/src/Util.cpp:332
finley::FinleyDomain::setFunctionSpaceTypeNames
void setFunctionSpaceTypeNames()
Build the table of function space type names.
Definition: finley/src/FinleyDomain.cpp:950
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:127
finley::FinleyDomain::getVTKElementType
virtual int getVTKElementType() const
returns the VTK element type
Definition: finley/src/FinleyDomain.cpp:2435
escript::ValueError
An exception class that signals an invalid argument value.
Definition: EsysException.h:100
DUDLEY_FACE_ELEMENTS
#define DUDLEY_FACE_ELEMENTS
Definition: Dudley.h:44
finley::FinleyDomain::prepare
void prepare(bool optimize)
prepares the mesh for further use
Definition: finley/src/FinleyDomain.cpp:2796
finley::FinleyDomain::MPIBarrier
virtual void MPIBarrier() const
If compiled for MPI then execute an MPI_Barrier, else do nothing.
Definition: finley/src/FinleyDomain.cpp:115
finley::FinleyDomain::m_elements
ElementFile * m_elements
the table of the elements
Definition: finley/src/FinleyDomain.h:897
weipa::DataVar
A class that provides functionality to read an escript data object from a dump file or an escript::Da...
Definition: DataVar.h:37
finley::FinleyDomain::setNewX
virtual void setNewX(const escript::Data &arg)
assigns new location to the domain
Definition: finley/src/FinleyDomain.cpp:1858
finley::Elements
@ Elements
Definition: Finley.h:66
escript::AbstractContinuousDomain
AbstractContinuousDomain, base class for continuous domains.
Definition: AbstractContinuousDomain.h:47
finley::FinleyDomain::getX
virtual escript::Data getX() const
returns locations in the FEM nodes
Definition: finley/src/FinleyDomain.cpp:2386
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:943
FINLEY_CONTACT_ELEMENTS_2
#define FINLEY_CONTACT_ELEMENTS_2
Definition: Finley.h:53
weipa::FinleyDomain::initFromEscript
virtual bool initFromEscript(const escript::AbstractDomain *domain)
Initialises the domain using an escript domain instance.
Definition: weipa/src/FinleyDomain.cpp:99
finley::FinleyDomain::getReducedSolutionCode
virtual int getReducedSolutionCode() const
Return a ReducedSolution code.
Definition: finley/src/FinleyDomain.cpp:1035
Assemble.h
finley::FinleyDomain::markNodes
void markNodes(std::vector< short > &mask, index_t offset, bool useLinear) const
Definition: finley/src/FinleyDomain.cpp:194
finley::readMesh_driver
Domain_ptr readMesh_driver(const bp::list &args)
Definition: finley/src/DomainFactory.cpp:904
FINLEY_CONTACT_ELEMENTS_1
#define FINLEY_CONTACT_ELEMENTS_1
Definition: Finley.h:52
finley::meshMerge
Domain_ptr meshMerge(const bp::list &meshList)
Definition: finley/src/DomainFactory.cpp:1272
escript::DataTypes::IndexVector
std::vector< index_t > IndexVector
Definition: DataTypes.h:64
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:219
finley::ElementFile::numNodes
int numNodes
number of nodes per element
Definition: finley/src/ElementFile.h:138
finley::ReferenceElementInfo::Name
const char * Name
the name in text form e.g. "Line1", "Rec12", ...
Definition: ReferenceElements.h:127
finley::FinleyDomain::~FinleyDomain
~FinleyDomain()
Destructor for FinleyDomain.
Definition: finley/src/FinleyDomain.cpp:106
weipa::FinleyDomain
Represents a full Finley or Dudley domain including nodes and elements.
Definition: weipa/src/FinleyDomain.h:43