/[escript]/trunk/finley/src/CPPAdapter/MeshAdapter.h
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revision 782 by bcumming, Tue Jul 18 00:47:47 2006 UTC revision 2640 by jfenwick, Mon Aug 31 06:22:10 2009 UTC
# Line 1  Line 1 
1  // $Id$  
2  /*  /*******************************************************
3   ************************************************************  *
4   *          Copyright 2006 by ACcESS MNRF                   *  * Copyright (c) 2003-2009 by University of Queensland
5   *                                                          *  * Earth Systems Science Computational Center (ESSCC)
6   *              http://www.access.edu.au                    *  * http://www.uq.edu.au/esscc
7   *       Primary Business: Queensland, Australia            *  *
8   *  Licensed under the Open Software License version 3.0    *  * Primary Business: Queensland, Australia
9   *     http://www.opensource.org/licenses/osl-3.0.php       *  * Licensed under the Open Software License version 3.0
10   *                                                          *  * http://www.opensource.org/licenses/osl-3.0.php
11   ************************************************************  *
12  */  *******************************************************/
13                                                                              
14    
15  #if !defined finley_MeshAdapter_20040526_H  #if !defined finley_MeshAdapter_20040526_H
16  #define finley_MeshAdapter_20040526_H  #define finley_MeshAdapter_20040526_H
17  #include "system_dep.h"  #include "system_dep.h"
# Line 20  extern "C" { Line 21  extern "C" {
21  #include "../Finley.h"  #include "../Finley.h"
22  #include "../Assemble.h"  #include "../Assemble.h"
23  #include "paso/SystemMatrix.h"  #include "paso/SystemMatrix.h"
24    #include "paso/SolverFCT.h"
25    #include "paso/Paso_MPI.h"
26  }  }
27    
28  #include "FinleyError.h"  #include "FinleyError.h"
29  #include "FinleyAdapterException.h"  #include "FinleyAdapterException.h"
30    
31  #include "SystemMatrixAdapter.h"  #include "SystemMatrixAdapter.h"
32    #include "TransportProblemAdapter.h"
33  #include "escript/AbstractContinuousDomain.h"  #include "escript/AbstractContinuousDomain.h"
34  #include "escript/FunctionSpace.h"  #include "escript/FunctionSpace.h"
35  #include "escript/FunctionSpaceFactory.h"  #include "escript/FunctionSpaceFactory.h"
# Line 74  class MeshAdapter : public escript::Abst Line 78  class MeshAdapter : public escript::Abst
78    static const int DegreesOfFreedom;    static const int DegreesOfFreedom;
79    static const int ReducedDegreesOfFreedom;    static const int ReducedDegreesOfFreedom;
80    static const int Nodes;    static const int Nodes;
81      static const int ReducedNodes;
82    static const int Elements;    static const int Elements;
83      static const int ReducedElements;
84    static const int FaceElements;    static const int FaceElements;
85      static const int ReducedFaceElements;
86    static const int Points;    static const int Points;
87    static const int ContactElementsZero;    static const int ContactElementsZero;
88      static const int ReducedContactElementsZero;
89    static const int ContactElementsOne;    static const int ContactElementsOne;
90      static const int ReducedContactElementsOne;
91    
92    /**    /**
93       \brief       \brief
# Line 86  class MeshAdapter : public escript::Abst Line 95  class MeshAdapter : public escript::Abst
95    
96       Description:       Description:
97       Constructor for MeshAdapter. The pointer passed to MeshAdapter       Constructor for MeshAdapter. The pointer passed to MeshAdapter
98       is deleted using a call to Finley_Mesh_deallocate in the       is deleted using a call to Finley_Mesh_free in the
99       MeshAdapter destructor.       MeshAdapter destructor.
100    
101       Throws:       Throws:
# Line 95  class MeshAdapter : public escript::Abst Line 104  class MeshAdapter : public escript::Abst
104       \param finleyMesh Input - A pointer to the externally constructed       \param finleyMesh Input - A pointer to the externally constructed
105                                 finley mesh.The pointer passed to MeshAdapter                                 finley mesh.The pointer passed to MeshAdapter
106                                 is deleted using a call to                                 is deleted using a call to
107                                 Finley_Mesh_deallocate in the MeshAdapter                                 Finley_Mesh_free in the MeshAdapter
108                                 destructor.                                 destructor.
109    */    */
110    FINLEY_DLL_API    FINLEY_DLL_API
# Line 111  class MeshAdapter : public escript::Abst Line 120  class MeshAdapter : public escript::Abst
120    /**    /**
121       \brief       \brief
122       Destructor for MeshAdapter. As specified in the constructor       Destructor for MeshAdapter. As specified in the constructor
123       this calls Finley_Mesh_deallocate for the pointer given to the       this calls Finley_Mesh_free for the pointer given to the
124       constructor.       constructor.
125    */    */
126    FINLEY_DLL_API    FINLEY_DLL_API
# Line 119  class MeshAdapter : public escript::Abst Line 128  class MeshAdapter : public escript::Abst
128    
129    /**    /**
130       \brief       \brief
131         return the number of processors used for this domain
132      */
133      FINLEY_DLL_API
134      virtual int getMPISize() const;
135      /**
136         \brief
137         return the number MPI rank of this processor
138      */
139    
140      FINLEY_DLL_API
141      virtual int getMPIRank() const;
142    
143      /**
144         \brief
145         If compiled for MPI then execute an MPI_Barrier, else do nothing
146      */
147    
148      FINLEY_DLL_API
149      virtual void MPIBarrier() const;
150    
151      /**
152         \brief
153         Return true if on MPI processor 0, else false
154      */
155    
156      FINLEY_DLL_API
157      virtual bool onMasterProcessor() const;
158    
159      FINLEY_DLL_API
160    #ifdef PASO_MPI
161      MPI_Comm
162    #else
163      unsigned int
164    #endif
165      getMPIComm() const;
166    
167      /**
168         \brief
169       return this as an AbstractContinuousDomain.       return this as an AbstractContinuousDomain.
170    */    */
171    inline const AbstractContinuousDomain& asAbstractContinuousDomain() const    inline const AbstractContinuousDomain& asAbstractContinuousDomain() const
# Line 145  class MeshAdapter : public escript::Abst Line 192  class MeshAdapter : public escript::Abst
192    
193    /**    /**
194       \brief       \brief
195         \param full
196      */
197      FINLEY_DLL_API
198      void Print_Mesh_Info(const bool full=false) const;
199    
200      /**
201         \brief
202         dumps the mesh to a file with the given name.
203         \param fileName Input - The name of the file
204      */
205      FINLEY_DLL_API
206      void dump(const std::string& fileName) const;
207    
208      /**
209         \brief
210       return the pointer to the underlying finley mesh structure       return the pointer to the underlying finley mesh structure
211    */    */
212    FINLEY_DLL_API    FINLEY_DLL_API
# Line 163  class MeshAdapter : public escript::Abst Line 225  class MeshAdapter : public escript::Abst
225       \brief       \brief
226       Return the reference number of  the given sample number.       Return the reference number of  the given sample number.
227       \param functionSpaceType Input - The function space type.       \param functionSpaceType Input - The function space type.
      \param sampleNo Input - The sample number.  
228    */    */
229    FINLEY_DLL_API    FINLEY_DLL_API
230    int getReferenceNoFromSampleNo(int functionSpaceType, int sampleNo) const;    const int* borrowSampleReferenceIDs(int functionSpaceType) const;
231    
232    /**    /**
233       \brief       \brief
# Line 206  class MeshAdapter : public escript::Abst Line 267  class MeshAdapter : public escript::Abst
267    
268    /**    /**
269       \brief       \brief
270       Return a functon FunctionSpace code       Return a continuous on reduced order nodes FunctionSpace code
271      */
272      FINLEY_DLL_API
273      virtual int getReducedContinuousFunctionCode() const;
274    
275      /**
276         \brief
277         Return a function FunctionSpace code
278    */    */
279    FINLEY_DLL_API    FINLEY_DLL_API
280    virtual int getFunctionCode() const;    virtual int getFunctionCode() const;
281    
282    /**    /**
283       \brief       \brief
284         Return a function with reduced integration order FunctionSpace code
285      */
286      FINLEY_DLL_API
287      virtual int getReducedFunctionCode() const;
288    
289      /**
290         \brief
291       Return a function on boundary FunctionSpace code       Return a function on boundary FunctionSpace code
292    */    */
293    FINLEY_DLL_API    FINLEY_DLL_API
# Line 220  class MeshAdapter : public escript::Abst Line 295  class MeshAdapter : public escript::Abst
295    
296    /**    /**
297       \brief       \brief
298         Return a function on boundary with reduced integration order FunctionSpace code
299      */
300      FINLEY_DLL_API
301      virtual int getReducedFunctionOnBoundaryCode() const;
302    
303      /**
304         \brief
305       Return a FunctionOnContactZero code       Return a FunctionOnContactZero code
306    */    */
307    FINLEY_DLL_API    FINLEY_DLL_API
# Line 227  class MeshAdapter : public escript::Abst Line 309  class MeshAdapter : public escript::Abst
309    
310    /**    /**
311       \brief       \brief
312         Return a FunctionOnContactZero code  with reduced integration order
313      */
314      FINLEY_DLL_API
315      virtual int getReducedFunctionOnContactZeroCode() const;
316    
317      /**
318         \brief
319       Return a FunctionOnContactOne code       Return a FunctionOnContactOne code
320    */    */
321    FINLEY_DLL_API    FINLEY_DLL_API
# Line 234  class MeshAdapter : public escript::Abst Line 323  class MeshAdapter : public escript::Abst
323    
324    /**    /**
325       \brief       \brief
326         Return a FunctionOnContactOne code  with reduced integration order
327      */
328      FINLEY_DLL_API
329      virtual int getReducedFunctionOnContactOneCode() const;
330    
331      /**
332         \brief
333       Return a Solution code       Return a Solution code
334    */    */
335    FINLEY_DLL_API    FINLEY_DLL_API
# Line 267  class MeshAdapter : public escript::Abst Line 363  class MeshAdapter : public escript::Abst
363    
364    /**    /**
365       \brief       \brief
366          Returns a status indicator of the domain. The status identifier should be unique over
367          the live time if the object but may be updated if changes to the domain happen, e.g.
368          modifications to its geometry.
369    
370         This has to be implemented by the actual Domain adapter.
371      */
372      FINLEY_DLL_API
373      virtual StatusType getStatus() const;
374    
375    
376      /**
377         \brief
378         Return the number of data points summed across all MPI processes
379      */
380      FINLEY_DLL_API
381      virtual int getNumDataPointsGlobal() const;
382    
383      /**
384         \brief
385       Return the number of data points per sample, and the number of samples as a pair.       Return the number of data points per sample, and the number of samples as a pair.
386       \param functionSpaceCode Input -       \param functionSpaceCode Input -
387    */    */
# Line 283  class MeshAdapter : public escript::Abst Line 398  class MeshAdapter : public escript::Abst
398    
399    /**    /**
400       \brief       \brief
401         sets a map from a clear tag name to a tag key
402         \param name Input - tag name.
403         \param tag Input - tag key.
404      */
405      FINLEY_DLL_API
406      virtual void setTagMap(const std::string& name,  int tag);
407    
408      /**
409         \brief
410         Return the tag key for tag name.
411         \param name Input - tag name
412      */
413      FINLEY_DLL_API
414      virtual int getTag(const std::string& name) const;
415    
416      /**
417         \brief
418         Returns true if name is a defined tage name.
419         \param name Input - tag name to be checked.
420      */
421      FINLEY_DLL_API
422      virtual bool isValidTagName(const std::string& name) const;
423    
424      /**
425         \brief
426         Returns all tag names in a single string sperated by commas
427      */
428      FINLEY_DLL_API
429      virtual std::string showTagNames() const;
430    
431      /**
432         \brief
433       assigns new location to the domain       assigns new location to the domain
434    */    */
435    FINLEY_DLL_API    FINLEY_DLL_API
# Line 294  class MeshAdapter : public escript::Abst Line 441  class MeshAdapter : public escript::Abst
441    */    */
442    FINLEY_DLL_API    FINLEY_DLL_API
443    virtual void interpolateOnDomain(escript::Data& target,const escript::Data& source) const;    virtual void interpolateOnDomain(escript::Data& target,const escript::Data& source) const;
444    
445    
446    FINLEY_DLL_API    FINLEY_DLL_API
447    virtual bool probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const;    virtual bool probeInterpolationOnDomain(int functionSpaceType_source,int functionSpaceType_target) const;
448    
449    /**    /**
450        \brief given a vector of FunctionSpace typecodes, pass back a code which then can all be interpolated to.
451        \return true is result is valid, false if not
452      */
453      FINLEY_DLL_API
454      bool
455      commonFunctionSpace(const std::vector<int>& fs, int& resultcode) const;
456    
457      /**
458       \brief       \brief
459       interpolates data given on source onto target where source and target are given on different domains.       interpolates data given on source onto target where source and target are given on different domains.
460       has to be implemented by the actual Domain adapter.       has to be implemented by the actual Domain adapter.
461    */    */
462    FINLEY_DLL_API    FINLEY_DLL_API
463    virtual void interpolateACross(escript::Data& target, const escript::Data& source) const;    virtual void interpolateACross(escript::Data& target, const escript::Data& source) const;
464    
465      /**
466      \brief determines whether interpolation from source to target is possible.
467      Must be implemented by the actual Domain adapter
468      */
469    FINLEY_DLL_API    FINLEY_DLL_API
470    virtual bool probeInterpolationACross(int functionSpaceType_source,const AbstractDomain& targetDomain, int functionSpaceType_target) const;    virtual bool probeInterpolationACross(int functionSpaceType_source,const escript::AbstractDomain& targetDomain, int functionSpaceType_target) const;
471    
472    /**    /**
473       \brief       \brief
# Line 341  class MeshAdapter : public escript::Abst Line 503  class MeshAdapter : public escript::Abst
503    
504    /**    /**
505       \brief       \brief
506       return the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package       return the identifier of the matrix type to be used for the global stiffness matrix when a particular solver, package, perconditioner,
507       and symmetric matrix is used.       and symmetric matrix is used.
508       \param solver       \param solver
509         \param preconditioner
510         \param package
511       \param symmetry       \param symmetry
512    */    */
513    FINLEY_DLL_API    FINLEY_DLL_API
514    virtual int getSystemMatrixTypeId(const int solver, const int package, const bool symmetry) const;    virtual int getSystemMatrixTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const;
515    
516      /**
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
521         \param preconditioner
522         \param package
523         \param symmetry
524      */
525      FINLEY_DLL_API
526      virtual int getTransportTypeId(const int solver, const int preconditioner, const int package, const bool symmetry) const;
527    
528    /**    /**
529       \brief       \brief
# Line 374  class MeshAdapter : public escript::Abst Line 550  class MeshAdapter : public escript::Abst
550       This has to be implemented by the actual Domain adapter.       This has to be implemented by the actual Domain adapter.
551    */    */
552    FINLEY_DLL_API    FINLEY_DLL_API
553    virtual void saveVTK(const std::string& filename,const boost::python::dict& arg) const;    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       \brief
# Line 394  class MeshAdapter : public escript::Abst Line 570  class MeshAdapter : public escript::Abst
570                       const escript::Data& D, const escript::Data& X, const escript::Data& Y,                       const escript::Data& D, const escript::Data& X, const escript::Data& Y,
571                       const escript::Data& d, const escript::Data& y,                       const escript::Data& d, const escript::Data& y,
572                       const escript::Data& d_contact, const escript::Data& y_contact) const;                       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       \brief
# Line 403  class MeshAdapter : public escript::Abst Line 588  class MeshAdapter : public escript::Abst
588    virtual void addPDEToRHS(escript::Data& rhs,    virtual void addPDEToRHS(escript::Data& rhs,
589                       const escript::Data& X, const escript::Data& Y,                       const escript::Data& X, const escript::Data& Y,
590                       const escript::Data& y, const escript::Data& y_contact) const;                       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       \brief
608      creates a SystemMatrixAdapter stiffness matrix an initializes it with zeros:      creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros:
609    */    */
610    FINLEY_DLL_API    FINLEY_DLL_API
611    SystemMatrixAdapter newSystemMatrix(    SystemMatrixAdapter newSystemMatrix(
# Line 415  class MeshAdapter : public escript::Abst Line 614  class MeshAdapter : public escript::Abst
614                        const int column_blocksize,                        const int column_blocksize,
615                        const escript::FunctionSpace& column_functionspace,                        const escript::FunctionSpace& column_functionspace,
616                        const int type) const;                        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       \brief returns locations in the FEM nodes
# Line 438  class MeshAdapter : public escript::Abst Line 649  class MeshAdapter : public escript::Abst
649       \brief comparison operators       \brief comparison operators
650    */    */
651    FINLEY_DLL_API    FINLEY_DLL_API
652    virtual bool operator==(const AbstractDomain& other) const;    virtual bool operator==(const escript::AbstractDomain& other) const;
653    FINLEY_DLL_API    FINLEY_DLL_API
654    virtual bool operator!=(const AbstractDomain& other) const;    virtual bool operator!=(const escript::AbstractDomain& other) const;
655    
656    /**    /**
657       \brief assigns new tag newTag to all samples of functionspace with a positive       \brief assigns new tag newTag to all samples of functionspace with a positive
# Line 450  class MeshAdapter : public escript::Abst Line 661  class MeshAdapter : public escript::Abst
661    FINLEY_DLL_API    FINLEY_DLL_API
662    virtual void setTags(const int functionSpaceType, const int newTag, const escript::Data& mask) const;    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:   protected:
684    
685   private:   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    // pointer to the externally created finley mesh

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