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/******************************************************* |
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* |
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* Copyright (c) 2003-2009 by University of Queensland |
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* Earth Systems Science Computational Center (ESSCC) |
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* http://www.uq.edu.au/esscc |
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* |
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* Primary Business: Queensland, Australia |
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* Licensed under the Open Software License version 3.0 |
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* http://www.opensource.org/licenses/osl-3.0.php |
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* |
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*******************************************************/ |
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|
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#if !defined finley_MeshAdapter_20040526_H |
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#define finley_MeshAdapter_20040526_H |
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#include "system_dep.h" |
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|
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extern "C" { |
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#include "../Mesh.h" |
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#include "../Finley.h" |
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#include "../Assemble.h" |
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#include "paso/SystemMatrix.h" |
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#include "paso/SolverFCT.h" |
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#include "paso/Paso_MPI.h" |
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} |
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|
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#include "FinleyError.h" |
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#include "FinleyAdapterException.h" |
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|
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#include "SystemMatrixAdapter.h" |
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#include "TransportProblemAdapter.h" |
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#include "escript/AbstractContinuousDomain.h" |
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#include "escript/FunctionSpace.h" |
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#include "escript/FunctionSpaceFactory.h" |
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|
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#include <boost/shared_ptr.hpp> |
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#include <boost/python/dict.hpp> |
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#include <boost/python/extract.hpp> |
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|
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#include <map> |
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#include <vector> |
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#include <string> |
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#include <sstream> |
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|
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// |
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// forward declarations |
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class Data; |
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|
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//using namespace escript; |
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|
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namespace finley { |
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|
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struct null_deleter |
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{ |
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void operator()(void const *ptr) const |
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{ |
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} |
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}; |
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|
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|
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/** |
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\brief |
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MeshAdapter implements the AbstractContinuousDomain |
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interface for the Finley library. |
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|
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Description: |
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MeshAdapter implements the AbstractContinuousDomain |
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interface for the Finley library. |
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*/ |
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|
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class MeshAdapter : public escript::AbstractContinuousDomain { |
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|
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public: |
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|
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// |
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// Codes for function space types supported |
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static const int DegreesOfFreedom; |
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static const int ReducedDegreesOfFreedom; |
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static const int Nodes; |
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static const int ReducedNodes; |
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static const int Elements; |
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static const int ReducedElements; |
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static const int FaceElements; |
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static const int ReducedFaceElements; |
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static const int Points; |
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static const int ContactElementsZero; |
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static const int ReducedContactElementsZero; |
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static const int ContactElementsOne; |
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static const int ReducedContactElementsOne; |
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|
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/** |
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\brief |
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Constructor for MeshAdapter |
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|
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Description: |
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Constructor for MeshAdapter. The pointer passed to MeshAdapter |
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is deleted using a call to Finley_Mesh_free in the |
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MeshAdapter destructor. |
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|
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Throws: |
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May throw an exception derived from EsysException |
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|
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\param finleyMesh Input - A pointer to the externally constructed |
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finley mesh.The pointer passed to MeshAdapter |
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is deleted using a call to |
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Finley_Mesh_free in the MeshAdapter |
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destructor. |
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*/ |
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FINLEY_DLL_API |
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MeshAdapter(Finley_Mesh* finleyMesh=0); |
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|
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/** |
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\brief |
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Copy constructor. |
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*/ |
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FINLEY_DLL_API |
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MeshAdapter(const MeshAdapter& in); |
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|
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/** |
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\brief |
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Destructor for MeshAdapter. As specified in the constructor |
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this calls Finley_Mesh_free for the pointer given to the |
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constructor. |
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*/ |
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FINLEY_DLL_API |
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~MeshAdapter(); |
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|
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/** |
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\brief |
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return the number of processors used for this domain |
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*/ |
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FINLEY_DLL_API |
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virtual int getMPISize() const; |
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/** |
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\brief |
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return the number MPI rank of this processor |
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*/ |
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|
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FINLEY_DLL_API |
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virtual int getMPIRank() const; |
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|
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/** |
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\brief |
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If compiled for MPI then execute an MPI_Barrier, else do nothing |
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*/ |
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|
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FINLEY_DLL_API |
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virtual void MPIBarrier() const; |
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|
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/** |
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\brief |
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Return true if on MPI processor 0, else false |
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*/ |
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|
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FINLEY_DLL_API |
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virtual bool onMasterProcessor() const; |
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|
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FINLEY_DLL_API |
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#ifdef PASO_MPI |
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MPI_Comm |
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#else |
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unsigned int |
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#endif |
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getMPIComm() const; |
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|
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/** |
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\brief |
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return this as an AbstractContinuousDomain. |
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*/ |
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inline const AbstractContinuousDomain& asAbstractContinuousDomain() const |
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{ |
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return *(static_cast<const AbstractContinuousDomain*>(this)); |
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} |
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|
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/** |
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\brief |
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return this as an AbstractDomain. |
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*/ |
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inline const AbstractDomain& asAbstractDomain() const |
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{ |
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return *(static_cast<const AbstractDomain*>(this)); |
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} |
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|
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/** |
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\brief |
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Write the current mesh to a file with the given name. |
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\param fileName Input - The name of the file to write to. |
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*/ |
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FINLEY_DLL_API |
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void write(const std::string& fileName) const; |
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|
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/** |
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\brief |
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\param full |
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*/ |
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FINLEY_DLL_API |
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void Print_Mesh_Info(const bool full=false) const; |
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|
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/** |
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\brief |
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dumps the mesh to a file with the given name. |
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\param fileName Input - The name of the file |
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*/ |
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FINLEY_DLL_API |
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void dump(const std::string& fileName) const; |
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|
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/** |
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\brief |
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return the pointer to the underlying finley mesh structure |
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*/ |
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FINLEY_DLL_API |
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Finley_Mesh* getFinley_Mesh() const; |
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|
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/** |
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\brief |
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Return the tag key for the given sample number. |
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\param functionSpaceType Input - The function space type. |
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\param sampleNo Input - The sample number. |
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*/ |
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FINLEY_DLL_API |
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int getTagFromSampleNo(int functionSpaceType, int sampleNo) const; |
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|
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/** |
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\brief |
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Return the reference number of the given sample number. |
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\param functionSpaceType Input - The function space type. |
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*/ |
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FINLEY_DLL_API |
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const int* borrowSampleReferenceIDs(int functionSpaceType) const; |
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|
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/** |
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\brief |
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Returns true if the given integer is a valid function space type |
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for this domain. |
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*/ |
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FINLEY_DLL_API |
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virtual bool isValidFunctionSpaceType(int functionSpaceType) const; |
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|
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/** |
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\brief |
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Return a description for this domain |
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*/ |
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FINLEY_DLL_API |
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virtual std::string getDescription() const; |
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|
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/** |
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\brief |
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Return a description for the given function space type code |
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*/ |
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FINLEY_DLL_API |
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virtual std::string functionSpaceTypeAsString(int functionSpaceType) const; |
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|
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/** |
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\brief |
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Build the table of function space type names |
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*/ |
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FINLEY_DLL_API |
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void setFunctionSpaceTypeNames(); |
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|
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/** |
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\brief |
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Return a continuous FunctionSpace code |
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*/ |
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FINLEY_DLL_API |
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virtual int getContinuousFunctionCode() const; |
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|
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/** |
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\brief |
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Return a continuous on reduced order nodes FunctionSpace code |
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*/ |
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FINLEY_DLL_API |
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virtual int getReducedContinuousFunctionCode() const; |
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|
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/** |
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\brief |
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Return a function FunctionSpace code |
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*/ |
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FINLEY_DLL_API |
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virtual int getFunctionCode() const; |
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|
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/** |
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\brief |
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Return a function with reduced integration order FunctionSpace code |
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*/ |
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FINLEY_DLL_API |
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virtual int getReducedFunctionCode() const; |
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|
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/** |
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\brief |
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Return a function on boundary FunctionSpace code |
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*/ |
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FINLEY_DLL_API |
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virtual int getFunctionOnBoundaryCode() const; |
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|
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/** |
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\brief |
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Return a function on boundary with reduced integration order FunctionSpace code |
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*/ |
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FINLEY_DLL_API |
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virtual int getReducedFunctionOnBoundaryCode() const; |
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|
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/** |
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\brief |
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Return a FunctionOnContactZero code |
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*/ |
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FINLEY_DLL_API |
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virtual int getFunctionOnContactZeroCode() const; |
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|
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/** |
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\brief |
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Return a FunctionOnContactZero code with reduced integration order |
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*/ |
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FINLEY_DLL_API |
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virtual int getReducedFunctionOnContactZeroCode() const; |
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|
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/** |
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\brief |
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Return a FunctionOnContactOne code |
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*/ |
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FINLEY_DLL_API |
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virtual int getFunctionOnContactOneCode() const; |
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|
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/** |
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\brief |
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Return a FunctionOnContactOne code with reduced integration order |
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*/ |
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FINLEY_DLL_API |
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virtual int getReducedFunctionOnContactOneCode() const; |
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|
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/** |
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\brief |
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Return a Solution code |
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*/ |
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FINLEY_DLL_API |
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virtual int getSolutionCode() const; |
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|
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/** |
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\brief |
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Return a ReducedSolution code |
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*/ |
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FINLEY_DLL_API |
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virtual int getReducedSolutionCode() const; |
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|
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/** |
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\brief |
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Return a DiracDeltaFunction code |
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*/ |
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FINLEY_DLL_API |
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virtual int getDiracDeltaFunctionCode() const; |
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|
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/** |
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5B |
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\brief |
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*/ |
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typedef std::map<int, std::string> FunctionSpaceNamesMapType; |
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|
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/** |
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\brief |
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*/ |
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FINLEY_DLL_API |
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virtual int getDim() const; |
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|
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/** |
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\brief |
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Returns a status indicator of the domain. The status identifier should be unique over |
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the live time if the object but may be updated if changes to the domain happen, e.g. |
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modifications to its geometry. |
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|
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This has to be implemented by the actual Domain adapter. |
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*/ |
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FINLEY_DLL_API |
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virtual StatusType getStatus() const; |
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|
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|
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/** |
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\brief |
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Return the number of data points summed across all MPI processes |
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*/ |
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FINLEY_DLL_API |
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virtual int getNumDataPointsGlobal() const; |
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|
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/** |
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\brief |
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Return the number of data points per sample, and the number of samples as a pair. |
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\param functionSpaceCode Input - |
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*/ |
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FINLEY_DLL_API |
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virtual std::pair<int,int> getDataShape(int functionSpaceCode) const; |
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|
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/** |
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\brief |
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copies the location of data points into arg. The domain of arg has to match this. |
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has to be implemented by the actual Domain adapter. |
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*/ |
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FINLEY_DLL_API |
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virtual void setToX(escript::Data& arg) const; |
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|
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/** |
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\brief |
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sets a map from a clear tag name to a tag key |
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\param name Input - tag name. |
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\param tag Input - tag key. |
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*/ |
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FINLEY_DLL_API |
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virtual void setTagMap(const std::string& name, int tag); |
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|
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/** |
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\brief |
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Return the tag key for tag name. |
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\param name Input - tag name |
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*/ |
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FINLEY_DLL_API |
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virtual int getTag(const std::string& name) const; |
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|
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/** |
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\brief |
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Returns true if name is a defined tage name. |
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\param name Input - tag name to be checked. |
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*/ |
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FINLEY_DLL_API |
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virtual bool isValidTagName(const std::string& name) const; |
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|
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/** |
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\brief |
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Returns all tag names in a single string sperated by commas |
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*/ |
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FINLEY_DLL_API |
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virtual std::string showTagNames() const; |
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|
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/** |
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\brief |
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assigns new location to the domain |
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*/ |
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FINLEY_DLL_API |
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virtual void setNewX(const escript::Data& arg); |
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|
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/** |
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\brief |
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interpolates data given on source onto target where source and target have to be given on the same domain. |
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*/ |
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FINLEY_DLL_API |
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virtual void interpolateOnDomain(escript::Data& target,const escript::Data& source) const; |
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|
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|
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FINLEY_DLL_API |
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virtual bool probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const; |
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|
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/** |
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\brief given a vector of FunctionSpace typecodes, pass back a code which then can all be interpolated to. |
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\return true is result is valid, false if not |
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*/ |
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FINLEY_DLL_API |
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bool |
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commonFunctionSpace(const std::vector<int>& fs, int& resultcode) const; |
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|
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/** |
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\brief |
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interpolates data given on source onto target where source and target are given on different domains. |
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has to be implemented by the actual Domain adapter. |
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*/ |
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FINLEY_DLL_API |
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virtual void interpolateACross(escript::Data& target, const escript::Data& source) const; |
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|
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/** |
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\brief determines whether interpolation from source to target is possible. |
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Must be implemented by the actual Domain adapter |
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*/ |
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FINLEY_DLL_API |
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virtual bool probeInterpolationACross(int functionSpaceType_source,const escript::AbstractDomain& targetDomain, int functionSpaceType_target) const; |
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|
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/** |
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\brief |
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copies the surface normals at data points into out. The actual function space to be considered |
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is defined by out. out has to be defined on this. |
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*/ |
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FINLEY_DLL_API |
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virtual void setToNormal(escript::Data& out) const; |
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|
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/** |
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\brief |
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copies the size of samples into out. The actual function space to be considered |
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is defined by out. out has to be defined on this. |
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*/ |
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FINLEY_DLL_API |
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virtual void setToSize(escript::Data& out) const; |
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|
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/** |
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\brief |
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copies the gradient of arg into grad. The actual function space to be considered |
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for the gradient is defined by grad. arg and grad have to be defined on this. |
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*/ |
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FINLEY_DLL_API |
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virtual void setToGradient(escript::Data& grad,const escript::Data& arg) const; |
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|
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/** |
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\brief |
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copies the integrals of the function defined by arg into integrals. |
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arg has to be defined on this. |
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*/ |
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FINLEY_DLL_API |
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virtual void setToIntegrals(std::vector<double>& integrals,const escript::Data& arg) const; |
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|
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/** |
| 505 |
\brief |
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return the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package, perconditioner, |
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and symmetric matrix is used. |
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\param solver |
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\param preconditioner |
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\param package |
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\param symmetry |
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*/ |
| 513 |
FINLEY_DLL_API |
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virtual int getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const; |
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|
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/** |
| 517 |
\brief |
| 518 |
return the identifier of the transport problem type to be used when a particular solver, perconditioner, package |
| 519 |
and symmetric matrix is used. |
| 520 |
\param solver |
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\param preconditioner |
| 522 |
\param package |
| 523 |
\param symmetry |
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*/ |
| 525 |
FINLEY_DLL_API |
| 526 |
virtual int getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const; |
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|
| 528 |
/** |
| 529 |
\brief |
| 530 |
returns true if data on this domain and a function space of type functionSpaceCode has to |
| 531 |
considered as cell centered data. |
| 532 |
*/ |
| 533 |
FINLEY_DLL_API |
| 534 |
virtual bool isCellOriented(int functionSpaceCode) const; |
| 535 |
|
| 536 |
/** |
| 537 |
\brief |
| 538 |
Saves a dictonary of Data objects to an OpenDX input file. The keywords are used as identifier |
| 539 |
|
| 540 |
This has to be implemented by the actual Domain adapter. |
| 541 |
*/ |
| 542 |
FINLEY_DLL_API |
| 543 |
virtual void saveDX(const std::string& filename,const boost::python::dict& arg) const; |
| 544 |
|
| 545 |
|
| 546 |
/** |
| 547 |
\brief |
| 548 |
Saves a dictonary of Data objects to an VTK XML input file. The keywords are used as identifier |
| 549 |
|
| 550 |
This has to be implemented by the actual Domain adapter. |
| 551 |
*/ |
| 552 |
FINLEY_DLL_API |
| 553 |
virtual void saveVTK(const std::string& filename,const boost::python::dict& arg, const std::string& metadata, const std::string& metadata_schema) const; |
| 554 |
|
| 555 |
/** |
| 556 |
\brief |
| 557 |
returns the function space representation of the type functionSpaceCode on this domain |
| 558 |
as a vtkObject. |
| 559 |
*/ |
| 560 |
// vtkObject createVtkObject(int functionSpaceCode) const; |
| 561 |
|
| 562 |
/** |
| 563 |
\brief |
| 564 |
adds a PDE onto the stiffness matrix mat and a rhs |
| 565 |
*/ |
| 566 |
FINLEY_DLL_API |
| 567 |
virtual void addPDEToSystem( |
| 568 |
SystemMatrixAdapter& mat, escript::Data& rhs, |
| 569 |
const escript::Data& A, const escript::Data& B, const escript::Data& C, |
| 570 |
const escript::Data& D, const escript::Data& X, const escript::Data& Y, |
| 571 |
const escript::Data& d, const escript::Data& y, |
| 572 |
const escript::Data& d_contact, const escript::Data& y_contact) const; |
| 573 |
/** |
| 574 |
\brief |
| 575 |
adds a PDE onto the lumped stiffness matrix matrix |
| 576 |
*/ |
| 577 |
FINLEY_DLL_API |
| 578 |
virtual void addPDEToLumpedSystem( |
| 579 |
escript::Data& mat, |
| 580 |
const escript::Data& D, |
| 581 |
const escript::Data& d) const; |
| 582 |
|
| 583 |
/** |
| 584 |
\brief |
| 585 |
adds a PDE onto the stiffness matrix mat and a rhs |
| 586 |
*/ |
| 587 |
FINLEY_DLL_API |
| 588 |
virtual void addPDEToRHS(escript::Data& rhs, |
| 589 |
const escript::Data& X, const escript::Data& Y, |
| 590 |
const escript::Data& y, const escript::Data& y_contact) const; |
| 591 |
/** |
| 592 |
\brief |
| 593 |
adds a PDE onto a transport problem |
| 594 |
*/ |
| 595 |
|
| 596 |
FINLEY_DLL_API |
| 597 |
virtual void addPDEToTransportProblem( |
| 598 |
TransportProblemAdapter& tp, escript::Data& source, |
| 599 |
const escript::Data& M, |
| 600 |
const escript::Data& A, const escript::Data& B, const escript::Data& C,const escript::Data& D, |
| 601 |
const escript::Data& X,const escript::Data& Y, |
| 602 |
const escript::Data& d, const escript::Data& y, |
| 603 |
const escript::Data& d_contact,const escript::Data& y_contact) const; |
| 604 |
|
| 605 |
|
| 606 |
/** |
| 607 |
\brief |
| 608 |
creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros: |
| 609 |
*/ |
| 610 |
FINLEY_DLL_API |
| 611 |
SystemMatrixAdapter newSystemMatrix( |
| 612 |
const int row_blocksize, |
| 613 |
const escript::FunctionSpace& row_functionspace, |
| 614 |
const int column_blocksize, |
| 615 |
const escript::FunctionSpace& column_functionspace, |
| 616 |
const int type) const; |
| 617 |
/** |
| 618 |
\brief |
| 619 |
creates a TransportProblemAdapter |
| 620 |
|
| 621 |
*/ |
| 622 |
|
| 623 |
FINLEY_DLL_API |
| 624 |
TransportProblemAdapter newTransportProblem( |
| 625 |
const double theta, |
| 626 |
const int blocksize, |
| 627 |
const escript::FunctionSpace& functionspace, |
| 628 |
const int type) const; |
| 629 |
|
| 630 |
/** |
| 631 |
\brief returns locations in the FEM nodes |
| 632 |
*/ |
| 633 |
FINLEY_DLL_API |
| 634 |
virtual escript::Data getX() const; |
| 635 |
|
| 636 |
/** |
| 637 |
\brief return boundary normals at the quadrature point on the face elements |
| 638 |
*/ |
| 639 |
FINLEY_DLL_API |
| 640 |
virtual escript::Data getNormal() const; |
| 641 |
|
| 642 |
/** |
| 643 |
\brief returns the element size |
| 644 |
*/ |
| 645 |
FINLEY_DLL_API |
| 646 |
virtual escript::Data getSize() const; |
| 647 |
|
| 648 |
/** |
| 649 |
\brief comparison operators |
| 650 |
*/ |
| 651 |
FINLEY_DLL_API |
| 652 |
virtual bool operator==(const escript::AbstractDomain& other) const; |
| 653 |
FINLEY_DLL_API |
| 654 |
virtual bool operator!=(const escript::AbstractDomain& other) const; |
| 655 |
|
| 656 |
/** |
| 657 |
\brief assigns new tag newTag to all samples of functionspace with a positive |
| 658 |
value of mask for any its sample point. |
| 659 |
|
| 660 |
*/ |
| 661 |
FINLEY_DLL_API |
| 662 |
virtual void setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const; |
| 663 |
|
| 664 |
/** |
| 665 |
\brief |
| 666 |
return the number of tags in use and a pointer to an array with the number of tags in use |
| 667 |
*/ |
| 668 |
FINLEY_DLL_API |
| 669 |
virtual int getNumberOfTagsInUse(int functionSpaceCode) const; |
| 670 |
|
| 671 |
FINLEY_DLL_API |
| 672 |
virtual const int* borrowListOfTagsInUse(int functionSpaceCode) const; |
| 673 |
|
| 674 |
|
| 675 |
/** |
| 676 |
\brief Checks if this domain allows tags for the specified functionSpaceCode. |
| 677 |
*/ |
| 678 |
FINLEY_DLL_API |
| 679 |
virtual |
| 680 |
bool canTag(int functionSpaceCode) const; |
| 681 |
|
| 682 |
|
| 683 |
protected: |
| 684 |
|
| 685 |
private: |
| 686 |
void extractArgsFromDict(const boost::python::dict& arg, int& numData, |
| 687 |
char**& names, escriptDataC*& data, |
| 688 |
escriptDataC**& dataPtr) const; |
| 689 |
|
| 690 |
// |
| 691 |
// pointer to the externally created finley mesh |
| 692 |
boost::shared_ptr<Finley_Mesh> m_finleyMesh; |
| 693 |
|
| 694 |
static FunctionSpaceNamesMapType m_functionSpaceTypeNames; |
| 695 |
|
| 696 |
}; |
| 697 |
|
| 698 |
} // end of namespace |
| 699 |
|
| 700 |
#endif |
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